Commit faea1e38 authored by mk11g11's avatar mk11g11
Browse files

added 4 first chapters, 3 reviewed

parent 15feabbe
# Introduction {#intro}
nocite: |
@chen1997, @araujo1988, @couturier1990, @cooper1991, @lee1967, @brown1936, @mishina1986, @zirger2003, @mongeon2011, @lewis1987, @treinin1998, @richmond1999, @boulin2008, @touroutine2005,
Background and introduction chapter
\ No newline at end of file
# General introduction {#generalintro}
## Chemical treatment in agriculture
Insecticides are compounds utilised in agriculture, medicine, industry and private households to protect crops, life-stock and human health from pest infestation. Their identity evaluated over the years to improve the effectiveness and reduce the undesirable effects on human health and the environment.
Until late 1800s organic, natural compounds contained within the plant or animal matter were utilised [@agarwal2006]. For example, tobacco plant containing nicotine was applied in France to protect pear orchards against bug lice, whereas *Chrysanthemum* plants containing pyrethrum were used against worms and insects in America and Europe. These treatment were however suitable only for small scale agricultural treatment.
Arsenic compounds were the earliest synthetic insecticides. Although their history dates back to 5th century [@kerkut1985], they did not gain popularity until the 19th century. Aceto-arsenite Paris Green was used in controlling Colorado potato beetles and mosquitoes @cullen2008; @peryea1998], whereas lead arsenate was an effective insecticide for apple and cherry orchards [@peryea1998]. Although effective against pests, these substances are toxic to humans [@nelson1973; @gibb2010; @argos2010].
In the last century, several synthetic compounds became available, including dichlorodiphenyltrichloroethane (DDT), and members of the carbamate, organophosphate and pyrethroid class of compounds. DTT was one of the most popular insecticides in the 1900s, with the peak annual use of over 85 000 tonnes in the U.S. alone [@phsa2002]. DDT's potent insecticidal activity was discovered 60 years after its synthesis in 1874, by the Swiss chemist Paul Hermann Muller, who was later awarded a Nobel prize in Medicine “for his discovery of the high efficiency of DDT as a contact poison against several arthropods.” [@nobel2019]. DTT became commercially available in the 1940s in Europe and the U.S., and it was used to suppress potato beatles, mosquitoes, fleas and lice. Since 1970s, the use of DDT has been progressively phased out due to its propensity to bio-accumulate in the adipose tissues of animals resulting in the environmental persistence [@EUEPA1975].
Diminishing popularity of DDT, created a market space for organophosphates, carbamates and pyrothroids (Table \@ref(tab:insecticidegroups)). By the 1990s, the respective market share of members of these three classes of insecticides was: 43 %, 15 % and 16 % [@jeschke2011]. The main issue associated with the use of organophosphates and carbamates is their ability to cause serious human poisonings, some of which can lead to death [@king2015]. The lack of selectivity combined with increasing resistance [@bass2014] instigated new management strategies aimed to combat these negative effects. In the 1990s research activities concentrated on finding new insecticides which have greater selectivity and better environmental and toxicological profiles.
```{r insecticidegroups, echo=FALSE, warning = FALSE, message=FALSE}
insecticide_groups <- data.frame(
Class = c("Organophosphates", "Carbamates", "Pyrethroids"),
Marketed = c("1930s-current", "1951-current", "1949s-current"),
Sales = c("3.42 bn", "1.19 bn", "1.169 bn"),
Chemicals = c("Parathion, malathion, azinphosmethyl", "Aldicarb, carbamyl, carbofuran", "Allethrin, Cypermethrin"))
insecticide_groups %>%
kable("latex", align = "l", booktabs = TRUE, escape = F,
caption = 'Synthesis insecticides insectides') %>%
kable_styling(position = "center", full_width = FALSE, latex_options = "hold_position") %>%
add_footnote("Sales as of 2008, according to Jeschke et al. 2011",
threeparttable = T)
## Neonicotinoids
### Synthesis
In 1970s, the scientists of Shell Development Company Biological Research Centre in California identified alpha- DBPN (2-(dibromonitromethyl)-3-(methylpyridine)), first synthesised by Prof. Henry Feuer [@feuer1986]. This lead compound showed low insecticidal activity against aphid and house fly [@tomizawa2003; @tomizawa2005]. Structural alterations of DBPN resulted in production of nithiazine (Figure \@ref(fig:neonics-structure-label)). Nithiazine showed improved insecticidal activity and was particularly effective as a new housefly repellent [@kollmeyer1999]. Further replacement of the thiazine ring by chloropyridinylmethyl (CPM) group, addition of the imidazolidine or its acyclic counterpart, and retention of the nitromethylene group resulted in generation of more potent compounds, one of which, nitenpyram, exhibited particularly high efficacy. Regrettably, both nithiazine and nitenpyram are not useful in fields, as they substantially absorb in the sunlight, resulting in their degradation and loss of activity against pests. The latter however is successfully used in veterinary medicine as an external parasite treatment for cats and dogs.
To solve the issue of photo-instability, nitromethylene group was replaced by nitroguanidine and cyanoamidine [@kagabu1995]. These chemical moieties have absorbance spectra at much shorter wavelengths hence do not degrade upon exposure to sunlight. Further alterations, such as replacement of imidazolidine by thiazolidine or oxadiazinane, and/or chloropyridinylmethyl by chlorothiazole or tetrahydrofuran (THF) did not hinder insecticidal activity [@yamamoto1999]. As a result of these modifications, all 6 currently used neonicotinoids were synthesised. They are grouped according to their pharmacophore into N-nitroguanidines, nitromethylenes and N-cyanoamidines (Figure \@ref(fig:neonics-structure-label)). Generally compounds with acyclic- guanidine or amidine and with nitromethylene are more efficacious against moth- and butterfly- pests than those with cyclic counterparts or nitroimine respectively [@ihara2006], nevertheless all are commonly used in agriculture. Imidacloprid, currently the most widely used neonicotinoid, was synthesised in 1970 in Bayer Agrochemical Japan and introduced to the EU market in 1991. Its trade names include Confidor, Admire and Advantage. Together with thiacloprid (Calypso), imidacloprid is marketed by Bayer CropScience. Thiamethoxam (Actara) is produced by Syngenta, Clothianidin (Poncho, Dantosu, Dantop) and Nitenpyram (Capstar) by Sumitomo Chemical, acetamiprid (Mospilan) by Certis, whereas dinotefuran (Starkle) by Mitsui Chemicals company. Last neonicotinoid (dinotefuran) was launched in the EU in 2008.
Research into novel neonicotinoids continues [@shao2013]. In the last decade, several novel insecticides have been characterised and approved for use in the EU. Sulfoxafrol [@zhu2011; @eu2019a] and flupyradifurone [@nauen2015; @eu2019b] have been classified as representatives of new chemical classes, namely sulfoximines and butenolides. However, due to their mode of action and similar biochemical properties, some argue that they are in fact neonicotinoids [@pan2019] whereas their mis-classification has been deliberate to avoid association with neonicotinoids.
(ref:neonics-structure) **Development and chemical structures of synthetic insecticides neonicotinoids.** Systematic modification of the lead and prototype compounds led to the discovery of seven neonicotinoids currently used in agriculture and animal health. They are classified according to the pharmacophore moiety into N-nitroguanidines, N-cyanoamidines and nitromethylenes.
```{r neonics-structure-label, fig.cap="(ref:neonics-structure)", fig.scap='Development and chemical structures of synthetic insecticides neonicotinoids.',fig.align='center', out.height = '60%', echo = FALSE}
### Economical status ###{#economicalstatus}
The use of neonicotinoids in agriculture has been increasing steadily since the market launch in the early 1990s. By 2008, they became major players in the agriculture [@jeschke2011], replacing organophosphates and carbamates [@jeschke2011]. Continual increase in popularity of neonicotinoids is reflected in the total usage data. In Great Britain, the yearly use of neonicotinoids increased by over 10-fold from 10 tonnes/year in 1996 to over 105 tonnes/year in 2016 [@fera2019]. Similar trends are observed in the U.S. [@usgs2019], Sweden and Japan [@simon-delso2015]. Continual increase in usage coincides with the raise in their economical impact. In 2008, the estimated global market value of neonicotinoids was 1.5 bn dollars [@jeschke2011]. This increased to 3.1 bn dollars in 2012 [@bass2015].
The raising usage and monetary value of neonicotinoids is a reflection of their many advantages.
<!-- Important in the pest managment, used in over 120 coutries on 140 crop types [@jeschke2011]. -->
## Physicochemical properties ##{#physchem}
One of the major benefits of neonicotinoids are their beneficial physical and chemical property profiles (Table \@ref(tab:properties)), therefore are stable in the environment and can be applied by a diversity of methods. Due to relatively high water solubility, they act as systemic insecticides [@westwood1998]. This means that once applied on crops, neonicotinoids dissolve in the available water and can be taken up by the developing roots or leaves. Upon plant entry, they are then distributed to all parts of the plant [@haas2006], providing protection against herbivorous pests. This systemic property of neonicotinoids means they can be used as a seed coating, reducing the required frequency of application. Indeed, seed dressing is the most commonly used method, accounting for 60 % of all neonicotinoids applications worldwide [@jeschke2011] and particularly popular to protect potatoes, oilseed rape, cereal, sunflower and sugar beet. In addition, neonicotinoids half-life in soil is from several weeks to years [@cox1997; @sarkar2001; @gupta2007), hence seed-dressing creates a continual source for re-uptake by plants. They are also suitable for ground treatment and are used as soil drenching for the protection of citrus trees and vines, granules for amenity grassland and ornament flowers and as a trunk-injection to protect trees against herbivores. Low vapor pressure and low Henry’s Law constant of neonicotinoids means they are not volatile, therefore can be applied as spray. This method is used in garden for flowers and vegetables and in agriculture on soft fruits and greenhouse crops. Low lipophilicity, indicated by octanol/water partition coefficient value (log Pow), suggest they do not bio-accumulate in the adipose tissues [@turaga2016]. However, moderate water solubility combined with low lipophilicity means they may have a potential to accumulate in water.
Although structurally related nicotine has similar properties, it is not appropriate for the agricultural use due to low toxicity to insects [@nauen1996].
```{r properties, echo=FALSE, warning = FALSE, message=FALSE}
properties <- data.frame(
Compound = c("Nitenpyram", "Clothianidin", "Thiacloprid"),
log = c("-0.64 (1)", "0.70 (1)", "1.26 (1)"),
pKa = c("3.1 and 11.5", "11.09 (5)", "NA (5)"),
Water = c("590 000 (3)", "340 (3)", "184 (3)"),
Henry = c("4 x 10\\textsuperscript{-13} (5)", "3 x 10\\textsuperscript{-11} (5)", "5 x 10\\textsuperscript{-10} (5)" ),
Water = c("NA (3)", "56.4 (3)", "28.0 (3)"))
properties %>%
mutate_all(linebreak) %>%
kable("latex", align = "l", booktabs = TRUE, escape = F,
col.names = linebreak(c("Compound", "log Pow\npH=7.4\n24 $^\\circ$C", "pKa at\n20 $^\\circ$C", "Water solubility\nmg / L\n20 $^\\circ$C\npH=7", "Henry's law\nPa x m$^3$ x mol$^-1$\n20 $^\\circ$C", "Water sediment \nDT50 (days)")),
caption = 'Physichochemical properties of neonicotinoids',
) %>%
kable_styling(position = "center", full_width = FALSE, latex_options = "hold_position") %>%
add_footnote("log Pow = octanol/water partitioning, DT50 = half-life for degradation, 1 = Jeschke and Nauen 2008, 2 = Sangster 1997, 3 = Bonmatin et al., 2015, 4 = Maeda et al., 1978, 5 = Pesticide Properties Database (PPDB), 2019",
threeparttable = T)
### Highly potent against insect pests ###{#potentpests}
<!-- look at this paper to see the symptoms of imi exposure on insects -->
<!-- @sone1994 -->
Neonicotinoids are highly potent against insect pests, as measured in the acute toxicity assays. During those assays, animals were dosed orally, systemically or topically with various concentrations of drugs. The number of dead animals was scored to derive the LC50/LD50 (the concentration/dose of a compound that kills 50 % of the population). The lower the LC(D)50, the greater the potency of a compound.
Neonicotinoids are effective against a wide range of piercing-sucking pests such as cotton and peach aphids (**Aphis gossypii** and *Myzus persicae*) [@nauen1996; @mota-sanchez2006; @bass2011], domestic (*Malus domestica*) and may-flies (*Epeorus longimanus*) [@tomizawa2000; @alexander2007] as well as planthoppers (*Nilaparvata lugens*) [@zewen2003]. Their IC50 is in generally the region of 2 $\mu$M. Although all neonicotinoids are highly effective against insect pests, their potency depends on the chemical structure. The rank order of insecticidal potency on the cotton aphid **A. gossypii** and the Colorado potato beetle, *Leptinotarsa decemlineata* was clothianidin > nitenpyram = thiacloprid, suggesting nitroguanidines are generally more potent than nitromethylenes and cyanoamidines [@shi2011; @mota-sanchez2006].
The potency also depends on the route of exposure. LC50s are lower upon systemic or oral administration in comparison to the topical exposure [@alexander2007]. Imidacloprid injected into the abdomen of American cockroaches *Periplaneta americana*, killed 50 % of animals at 1 nM [@ihara2006]. Concentrations of 285.49 nM and 1.83 $\mu$M were required to observe the same effect upon oral or contact exposure, respectively in the peach aphid *Myzus persicae* [@nauen1996]. Effective doses obtained from oral and topical studies are most relevant, since these are the two main routes of exposure of pests in the agriculture.
The LC(D)50 values of neonicotinoids are at least 6-fold higher than those of structurally related nicotine, highlighting the superiority of neonicotinoids as pest controlling agents.
```{r tox-all-animal-labels, echo=FALSE, warning = FALSE, message = FALSE}
footnotea <- "References (Ref) 16: Shi et al. 2011, 1: Nauen et al. 1996, 2: Mota-Sanchez et al. 2006, 3: Bass et al. 2011, 4: Zewen et al. 2003, 5: reported in Tomizawa et al. 2000, 6: Alexander et al. 2007, 7: De Cant and Barrett 2010, 8: Luo et al. 1999, 9: De Cant and Barrett 2010, 10: Wang et al. 2012, 11: Wang et al. 2015, 13: = Dong et al. 2017, 14: Cresswell 2011, 15: = Godfray et al. 2015"
toxic <-data.frame (
Drug = c("Thia", "Clo", "Nit", "Imi", "Imi", "Nic", "Nic", "Imi", "Thtx","Imi", "Thtx","Nic", "Dino", "Thia", "Imi", "Nit", "Thia", "Clo", "Ace", "Imi", "Thia", "Nic", "Imi", "Imi", "Imi", "Imi", "Imi", "Clo", "Thx", "Clo", "Clo", "Clo", "Clo", "Clo", "Clo", "Imi", "Imi", "Clo", "Clo", "Clo", "Imi", "Acet", "Nit", "Clo", "Thia", "Thia"),
Species = c("A. gossypii", "A. gossypii", "A. gossypii", "M.persicae", "M.persicae", "M.persicae", "M.persicae", "M.persicae", "M.persicae","M.persicae", "M.persicae", "L. decemlineata", "L. decemlineata", "L. decemlineata", "L. decemlineata", "L. decemlineata", "L. decemlineata", "L. decemlineata", "L. decemlineata", "N.lugens","M. domestica", "M. domestica", "E. longimanus", "E. longimanus", "A. mellifera", "A. mellifera", "A. mellifera","A. mellifera","A. mellifera", "Bobwhite quail", "Bobwhite quail", "Mallard duck", "Mouse", "O. mykiss", "L. macrochirus", " E. fetida", "E. fetida", "E. fetida", " E. fetida", " E. fetida", " E. fetida", " E. fetida", " E. fetida", " E. fetida", " E. fetida", "M. incognita"),
Taxon = c("Insect", "Insect", "Insect", "Insect", "Insect", "Insect", "Insect", "Insect", "Insect", "Insect", "Insect", "Insect", "Insect", "Insect", "Insect","Insect", "Insect", "Insect", "Insect", "Insect", "Insect", "Insect", "Insect", "Insect", "Insect", "Insect", "insect", "Insect", "Insect", "Bird", "Bird", "Bird", "Mammal", "Fish", "Fish", "Earth worm", "Earth worm","Earth worm", "Earth worm", "Earth worm", "Earth worm", "Earth worm", "Earth worm", "Earth worm", "Earth worm", "Nematode"),
LD50 = c("-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "0.35 ng/mg", "0.05 ng/mg", "6.8 ng/beetle", "0.34 ng/beetle", "0.20 ng/beetle", "0.18 ng/mg", "0.15 ng/mg", "0.14 ng/mg", "0.82 ng/mg", "3 ng/mg", ">50 ng/mg", "-", "-", "-", "0.81 ng/mg", "0.81 ng/mg", "0.44 ng/mg", "0.24 ng/mg", ">200 mg/kg (acute)", ">5040 mg/kg (5 days)", ">5230 mg/kg (5 days)", "389-465 mg/kg", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-"),
LC50 = c("9.35 $\\mu$M", "7.29 $\\mu$M", "9.12 $\\mu$M", "1.83 $\\mu$M", "285.49 nM", "1.85 mM", "27.74 mM", "3.87 $\\mu$M", "2.19 $\\mu$M", "257.52 nM", "1.64 mg/L", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "82.13 nM (24 hrs)", "2.54 nM (96 hrs)", "6.88 $\\mu$M", "-", "-","-","-","-", "-", "-", "-", "424.51 $\\mu$M", "468.60 $\\mu$M", "4.81 $\\mu$M (24 hours)", "2.74 $\\mu$M (48 hours)", "62.08 $\\mu$M (14 days)", "24.24 $\\mu$M (7 days)", "24.27 $\\mu$M (14 days)", "11.93 $\\mu$M (14 days)", "12.08 $\\mu$M (14 days)", "26.75 $\\mu$M (14 days)", "3.72 $\\mu$M (14 days)", "10.60 $\\mu$M (14 days)", "143. 24 $\\mu$M (6 hours)"),
Bioassay = c("Topical", "Topical", "Topical", "Topical", "Oral", "Topical", "Oral", "Topical", "Topical", "Topical", "Topical", "Topical", "Topical", "Topical", "Topical", "Topical", "Topical", "Topical", "Topical", "Topical", "?", "?", "Topical", "Topical", "Oral", "Oral", "Topical", "Topical", "Topical", "Oral","Oral", "Oral", "Oral", "?", "?", "Topical", "Topical", "Topical", "Topical", "Topical", "Topical", "Topical", "Topical", "Topical", "Topical", "Topical"),
Ref = c("16", "16", "16", "1", "1", "1", "1", "3", "3", "3", "3", "2", "2", "2", "2", "2", "2", "2", "2", "4", "5", "5", "6", "6", "14", "14", "15", "15", "15", "7", "7", "7", "7", "7", "7", "8", "8", "9", "10", "10", "11", "11", "11", "11", "12", "13"))
toxic %>%
kable("latex", align = "l", escape = F, booktabs = TRUE, longtable = TRUE,
caption = 'Toxicity of nicotine and neonicotinoids') %>%
kable_styling(font_size=10, position = "center", full_width = FALSE, latex_options = c( "hold_position", "repeat_header")) %>%
footnote(general = footnotea,
threeparttable = TRUE)
```{r tox, echo=FALSE, warning = FALSE, message = FALSE}
# toxic <-data.frame (
# Drug = c("Thia", "Clo", "Nit", "Thia", "Clo", "Nit", "Nic"),
# Species = c("Aphis gossypii", "Aphis gossypii", "Aphis gossypii", "Aphis gossypii", "L. decemlineata", "L. decemlineata", "L. decemlineata"),
# Taxon = c("Insect", "Insect", "Insect", "Insect","Insect", "Insect", "Insect"),
# LD50 = c("", "", "", "0.18 ng/mg", "0.15 ng/mg", "0.20 ng/mg", "0.35 ng/mg"),
# LC50 = c("9.35 $\\mu$M", "7.29 $\\mu$M", "9.12 $\\mu$M", "", "", "", ""),
# Bioassay = c("Topical", "Topical", "Topical", "Topical", "Topical", "Topical", "Topical"),
# Ref = c( "Mota-Sanchez et al. 2006", "Mota-Sanchez et al. 2006", "Mota-Sanchez et al. 2006"))
# toxic %>%
# kable("latex", align = "l", escape = F, booktabs = TRUE, longtable = TRUE,
# caption = 'Toxicity of nicotine and neonicotinoids') %>%
# kable_styling(font_size=10, position = "center", full_width = FALSE, latex_options = c( "hold_position", "repeat_header"))
# to calculate the ng/mg cocroach divided by 175, bee by 100
### Selectively toxic to insect pests. ###{#seltox}
One of the key determinants of success of agrochemical compounds is their ability to selectively target insects over non-target species. Neonicotinoids are generally effective at ~ 2 $\mu$M concentrations against piercing-sucking pest infestations, whereas their LD50s is in the region of 0.2 - 0.3 ng/mg of body weight [@mota-sanchez2006; @zewen2003; @tomizawa2000; @alexander2007]. The LC(D)50 values for non-target species is at least 2 times higher. Honeybees (*Apis mellifera*) are among the most susceptible non-targets, with the average LC50 and LD50 values for imidacloprid of 7.04 $\mu$M and 4.5 ng per mg of body weight, respectively [@cresswell2011]. Some studies report high potency of neonicotinoids on earth worms, with the LC50 as low as 2.74 $\mu$M on redworm *Eisenia fetida* (*E. fetida*) [@luo1999]. Fish and birds are hundred fold less susceptible [@decant2010], whereas mammals are the least susceptible with LD50 doses higher than 130 mg/kg of body weight [@decant2010; @legocki2008]. This differential susceptibility between target and non-target species, in expected to enable an environmental release of neonicotinoids at concentrations which will exterminate pests without killing the non-targets. Indeed, field realistic concentrations of neonicotinoids are higher than those causing lethality of the most susceptible species (i.e. worms and honey bee).
Concentrations of neonicotinoids in nectar, wax and pollen was been investigated. Generally, the highest concentrations are found in the former [@goulson2013]. @cresswell2011 determined that the imidacloprid is present in most commonly bee-consumed nectar at 2.3 - 20 $\mu$M. He also estimated that the average realistic amount of imidacloprid in a nectar load is 0.024-0.3 ng. This is higher than the reported honeybee LC50 and LD50 values of 7.04 $\mu$M and 4.5 ng, respectively [@@cresswell2011].
The concentration of neonicotinoids in soils with several years of history of treatment by seed coating were also investigated. Samples were collected 10 months after sowing [@botias2015] just before [@jones2014; @schaafsma2016] or after planting [@perre2015]. The average reported concentrations of neonicotinoids in the centre of the field are in the region of 20 $\mu$M, which is higher than the concentrations effective against earth worms and nematodes; the LC50 against the most susceptible species is 2.74 $\mu$M [@luo1999].
<!-- [@botias2015] -->
<!-- Selected 5 oilseed or wheat fields treated for at least three previous years with neonicotinoids. Soil samples were collected 10 months after sowing. The presence of neonicotinoids was detected using spectrometry. oilseed rape cropland : mean 3.46 ng / g of tmx, 13.28 clo, imc 3.03, thc 0.04 ng / g. -->
<!-- Margin : tmx 0.72 ng / g, clo 6.57, imc 1.92, thc $\le$ 0.01 and this is not significantly differen t from the margins of the wheat fields. -->
<!-- Based on laboratory conditions, half life of neonicotinoids is highly variable ranging from 8 days for nitenpyram to almost 7000 for clothianidin [reviewed in @bonmatin2015]. Several field studies were conducted to estimate dissipation time of neonicotinoids. @schaafsma2016 collected 18 Canadian and pre-planting soil samples over 2 successive years. These samples originated from variable-crop fields which had been treated for at least 4 successive years. Concentration of clothianidin and thiacloprid was measured in year 1 samples and averaged at 19.22 $\mu$M. Based on the history of crops planted and insecticide recharge regime, the degradation half-life (TD50) of clothianidin was estimated at 0.4 years 9 (146 days). It was also concluded that clothianidin and thiacloprid residues would accumulate for 3-4 years and plateau at ~ 23 $\mu$M in agricultural fields with one-year insecticide application routine. Using similar approach, @schaafsma2016 also estimated the DT50 of imidacloprid at 208 days. -->
<!-- Based on these data the average total neonicotinoid concentration is in the region of 20 $\mu$M. Therefore, average concentrations of neonicotinoids in the field are lower than doses causing worm lethality. However, higher concentrations of neonicotinoids may be experienced, particularly during the sowing period. -->
<!-- It is also probable that the concentration of neonicotinods is higher near the coated seed. The coating typically contains from 0.17 - 1 mg of the active ingredient [@goulson2013]. Up to 98 % of the active ingredient leaches into the environment [@goulson2014]. Therefore upper concentrations of environmental doses may have sublethal effect on soil inhabiting worms and nematodes. -->
### Sub-lethal effects of neonicotinoids on non-target species ###{#sublethal}
#### Insect pollinators
Although field realistic neonicotinoids are not expected to kill bees, a substantial body of evidence from lab- and field- based experiments suggest that they can impair on the cognitive function and reproduction of these biological pollinators.
##### Reduced olfactory learning and memory
Bees are social insects, living in colonies where a clear division of labor exists. Worker bees account for ~ 90 % of the entire colony. These non-reproductive females are responsible for finding, collecting and transporting nectar or pollen from the flowering plants to the hive. Their ability to process, learn and memorise sensory cues is crucial for the survival and overall success of the entire hive.
The ability of bees to olfactory learn can be measured with Proboscis Extension Reflex (PER) paradigm. PER conditioning is a process by which an insect learns to extend its tongue (proboscis) in response to olfactory stimuli, typically evoked by the sugar solution contacting the antenna [@takeda1961]. Alternatively, their olfactory learning capability can be measured by scoring various aspects of foraging behaviour. Laboratory and semi-field studies show that many aspects of worker bees' behaviour is impaired by neonicotinoids.
Bees exposed to 93 nM of imidacloprid in the sugar solution showed reduced ability to olfactory learn, as showed by the PER [@decourtye2004]. Imidacloprid also compromised foraging activity of honeybees [@decourtye2004; @gill2012] and bumblebees. 4- week exposure of early-developmental stages to imidacloprid at 23 nM in pollen reduced the foraging efficiency and duration [@gill2012]. Neonicotinoids also reduce the number of bees returning to hives. Increased home failure were noted in honeybees exposed to a single dose of thiamethoxam at 1.35 ng [@henry2012] and in bumblebees fed diet containing imidacloprid at 23 nM and 3 nM for 2 weeks [@feltham2014].
<!-- #### Learning and memory -->
<!-- Honeybees exposed to a , reduced Reducing homing rates were also noted in a study conducted by @schneider2012, where bees were exposed to clothianidin, thiamethoxam and imidacloprid at doses ranging from 0.05 ng/bee to 6 ng/bee. -->
<!-- <!-- Reduced response in conditioning assay was noted in honey bees treated with imidacloprid at 10 and 100 nM chronically (4 days), which were then allowed to recover for three days [@williamson2013]. --> -->
##### Impaired Reproduction
The reproduction of bees is performed by a single member of the colony - the queen. She lays fertilised and unfertilised eggs into cells of the comb. These eggs develop into larva, pupa and adult male drones and female workers.
Neonicotinoids negatively impact on various aspects of bees' fecundity. 14-days exposure of bumblebees to imidacloprid at 2, 4 and 23 nM, increased number of empty pupal cells [@whitehorn2012]. Imidacloprid has been shown to reduce the total size of treated colonies, reduce the brood production [@laycock2012] and the number of born queens [@whitehorn2012] and workers [@gill2012] of bumblebees. Exposure of drones to thiamethoxam at 15.5 nM and clothianidin at 6 nM led to shortening of life-spam and hindered sperm vitality and quantity [@straub2016].
Negative impact of neonicotinoids is also seen in the field-studies. Bumblebees foraging on oilseed rape coated with clothianidin, exhibited decreased queen production, colony growth and reduced bumblebee density [@rundlof2015]. More recently, international field studies confirmed negative effects of neonicotinoids on overwinter success and reproduction of honey and wild bees [@woodcock2017].
Insect pollinators play an important ecological, economical and evolutionary role. They pollinate wild plants [@kwak1998], food crops [@klein2007] and promote plant sexual reproduction [@gervasi2017]. The emerging evidence of the negative impact of neonicotinoids on bees and honeybees, restricted their use in Europe in 2013 [@eucomission2013] and is likely to lead to a complete ban of neonicotinoids in the future [@efsa2018].
#### soil worms
To investigate the effects of neonicotinoids on soil dwellers, worms were exposed to various concentrations of drugs in solution, or in artificial soils. The concentrations effective against various behaviours and parameters such as fecundity, body weight, locomotion, sensory processing and burrowing were noted.
Clothianidin and thiacloprid at concentrations $\ge$ than 1.2 $\mu$M and the EC50 of 5.1 $\mu$M and 3.4 $\mu$M, respectively reduced the reproductive potential of redworm *E. fetida*, as measured by the cocoon production [@gomez-eyles2009]. Neonicotinoids showed a negative impact on the reproduction of other species, including *Lumbricus rubellus* (*L. rubellus*) [@baylay2012], *Dendrobaena octaedra* (*D. octaedra*) [@kreutzweiser2008] and *Eisenia andrei* [@alves2013]. Reduction of body weight of *E. fetida* and *D. octaedra* were observed after 14-day treatment with imidacloprid at 27.08 and 54.75 $\mu$M [@kreutzweiser2008]. Imidacloprid at 488.85 nM to 7.82 $\mu$M increased avoidance of *E. andrei* [@alves2013], whereas at 782 nM it reduced the *A. caliginosa* burrowing depth and length [@dittbrenner2011]. Burrowing of *L. terrestris* was also impacted, but at higher imidacloprid concentrations [@dittbrenner2011]. Neonicotinoids also induce a sublethal effect on the the free-living nematode *C. elegans*. Thiacloprid and imidacloprid have an effect on the reproduction of *C. elegans* with EC50 of 1.14 nM and 2.09 mM, respectively [@gomez-eyles2009]. Thiacloprid at 37 nM has an effect on chemosensing, whereas at 18 $\mu$M it impairs motility of this free living nematode [@hopewell2017]. Impaired motility of *C. elegans* in response to $\ge$ 120 $\mu$M imidacloprid was also recorded [@mugova2018]. Taken together, neonicotinoids have sublethal effects on earth worms and soil nematodes at concentrations as low as nM.
Most of the doses effective against worms are higher than the average doses of neonicotinoids in the field. However, the presence of clothianidin, imidacloprid and thiamethoxam has been detected at lower than average levels, such as 80.10 nM for imidacloprid, 23.01 nM for imidacloprid and 68.56 nM for thiamethoxam [@jones2014]. This suggests that the environmentally relevant concentrations of neonicotinoids may negatively impact on the the well-being of soil dwellers.
<!-- Data regarding toxicity of neonicotinoids on soil worms and nematodes focuses on earthworm *Eisenia fetida* (*E. fetida*, redworm). The toxicity is assessed either following treatment in solution or in the artificial soils. In solution, the LC50 of imidacloprid after 24 hour exposure is 62.08 $\mu$M [@luo1999]. This increases to 24.24 $\mu$M after 48 hour exposure [@luo1999]. Clothianidin is less potent; its LC50 after 14 days is 24.27 $\mu$M [@decant2010]. -->
#### Birds
Evidence suggests that environmental relevant concentrations of neonicotinoids may have negative effects on birds [@hallmann2014]. In particular, granivorous and insectivorous vertebrates may be at risk, should they consume neonicotinoid-contaminated seeds and/or insects [@goulson2013]. Environmental neonicotinoids may impair migratory ability [@eng2017] and negatively impact on the growth and reproduction [@sanchez-bayo2016] of birds.
The environmental ecotoxicity of neonicotinoids highlights the importance of selective toxicity of agrochemical compounds in successful pest management programmes. The development of new insecticides, effective against pest and not beneficial insects or other species requires a detailed knowledge of their mode of action.
## Neonicotinoids act on the cholinergic neurotransmission as a nicotine mimic
<!-- ### Nicotinic acetylcholine receptors -->
<!-- Name Cys-loop was devoted because all members contain a disulphide bond between cystines separated by a highly conserved sequence of 13 amino acids. Cys-loop receptors also share a common topology (Figure \@ref(fig:nachr-topology-label)): five receptor subunits arranged around the central pore. The five subunits can be the same, or different and form homo- or hetero-pentamers. -->
<!-- (ref:nachr-topology) **Topology of cys-loop receptors.** A single subunit of the cys-loop receptor consists of 4 transmembrane subunits (M1 - M4) and a conserved disulphide bridge in the N-terminal extracellular domain. 5 subunits come together to form a functional receptor (b). Receptors can be formed from either 5 identical (c) or from a combination of different subunits (d). -->
<!-- ```{r nachr-topology-label, fig.cap="(ref:nachr-topology)", echo=FALSE, fig.scap= 'Topology of cys-loop receptors.', fig.align='center', out.height = '80%', echo=FALSE} -->
<!-- knitr::include_graphics("fig/general_intro/png/nAChR_topology_3.png") -->
<!-- ``` -->
### nAChR structure ###{structure}
nAChRs are members of the pentameric ligand-gated ion channels which are found in a diversity of species from bacteria to human. They are the representatives of the Cys-loop superfamily of channels which also include $\gamma$ -aminobutyric acid type A (GABA) receptors, 5-hydroxytryptamine type-3 receptors (5-HT3), and glycine receptors. Structural studies of the nAChRs from the muscle of the electric fish **Torpedo** (Figure \@ref(structure-nachr-label)a) shed light on the the stechiometry, the shape and the size of Cys-loop receptors.
The identity of the NMJ nAChR was first investigated using indirect, biochemical approaches. Membrane bound NMJ receptors were isolated by in-situ cross-linking with a radiolabelled antagonist and a subsequent purification. SDS-resolved fragments pattern suggesting the pentameric nature of these receptors [@hucho1986; @schiebler1980] of the total size 270 000 kDa composed of 4 different subunits namely $\alpha$, $\beta$, $\delta$ and $\gamma$ arranged into a pentamer. The SDS-PAGE pattern and the analysis of nAChR complexes purified with the use of non-denaturing buffer led to a suggestion that the stechiometry is: $\alpha1$, $\beta1$, $\delta$, $\alpha1$, $\gamma$ (clockwise) [@reynolds1978]. Heterologous expression in Xenopus oocytes confirmed that 4 subunits are needed to achieve expression. In the absence of any other one of the subunits, the responses to acetylcholine were either absent or greatly reduced, therefore 4 subunits are required for the normal function of this protein [@mishina1984].
The stechiometry and structural details of muscle type nAChRs were confirmed by more direct structural approaches: cryo- and electron-microscopy. The receptor protein is in the shape of an elongated, 125 Å funnel [@unwin1993; @toyoshima1990]. It consists of large, extending to the synaptic space [@toyoshima1990] N-terminal ligand binding domain [@sigel1992], the membrane spanning pore-domain [@eisele1993], intracellular MA helix [@toyoshima1990; @unwin1993], and C-terminus positioned extracellularly. Constituting nAChR subunits are arranged pseudosymmetrically, around the central ion conduction pore [@brisson1985]. The subunit composition of the neuromuscular nAChR follows the strict order of $\alpha1$, $\beta1$, $\delta$, $\alpha1$, $\gamma$ (clockwise). Each subunit of the nAChR contains 4 transmembrane helices [@noda1982; @noda1983] named M1, M2, M3 and M4, as moving from N- to C- terminus. M1, M3 and M4 are exposed to the plasma membrane [@blanton1994], shielding M2, pore-forming helices [@imoto1986; @hucho1986] from the hydrophobic environment of the bilayer. As the outer helices progress from the outer to the inner leaflet of the membrane, they tilt inwards [@miyazawa2003], narrowing down the width of the channel. M2 on the other hand, bends roughly in the middle of the bilayer [@unwin1995], where it forms the most restricted part of the ion conductivity pathway. There are hydrophobic interactions between the outer helices, which stabilise the outer wall of the receptor and hence limit the conformational changes adopted by the inner helix. In contrast there are no extensive bonds between the inner and outer helices [@miyazawa2003]. As lining pore structures, the inner helix and flanking sequences contain molecular determinants for ion selectivity, permeability, the rate of conductance and gating. These were investigated by pharmacological, biochemical and electrophysiological approaches. [@imoto1988; @imoto1991; @konno1991] investigated the function of several rings of anionic and neutral amino acids with side chains facing towards each other in the centre of the pore. The so called intermediate ring (constituting of αE241 and equivalent) and the adjacent to $\alpha$ E241 in helical configuration central ring, (formed by $\alpha$ L244 and equivalent) form a narrow constriction of the ion pore, hence have the strongest effect on the conductance rate [@imoto1991; @imoto1988]. In addition, the negatively charged side chains of intermediate ring are crucial for ion selectivity [@konno1991]. The gating of the channel is governed by conserved leucine residues, slightly towards the extracellular side from the centre of the bilayer with side chains projecting inwards [@unwin1995], hence occluding the passage for ions.
(ref:structure-nachr) **Structural features of the nicotinic acetylcholine receptor.** Torpedo nAChR is a transmembrane protein, made up of 5 subunits (colour-coded), arranged around the ion conductivity pore. Each subunit consists of extracellular ligand-binding, transmembrane and intracellular domain (a) (PBD code:2BG9). Extracellular domain of a single subunit consists of 10 $\beta$-strands and N-terminal $\alpha$-helix. It contains a disulphide bridge between Cys192 and Cys193 (highlighted in yellow) (b). Fully formed receptors have five ligand binding pockets formed by the contributions from the neighboring subunits (A-B, B-C, C-D, D-E and E-A), named the principle and the adjacent components, respectively. Top view of the molluscan AChBP (PDB:1I9B) with amino acids forming the agonist binding site in ball and stick representation (c). Images generated with the UCSF Chimera software.
```{r structure-nachr-label, fig.cap="(ref:structure-nachr)", fig.scap='Structural features of the nicotinic acetylcholine receptor.', fig.align='center', echo=FALSE}
Determination of the crystal structure of the molluscan acetylcholine binding protein [@brejc2001] (Figure \@ref (fig:binding-pocket-label)b and c)) provided a platform to study the ligand binding domain of nAChRs. Acetylcholine binding protein (AChBP) is a soluble protein, secreted by snail glial cells into the cholinergic synapses to bind released ACh and modulate neurotransmission [@sixma2003]. It shares 24 % sequence identity with mammalian $\alpha7$ homopentameric receptor. It is has similar structure to the extracellular domain of the nAChRs mammalian $\alpha1$ [@dellisanti2007] and $alpha7$ [@li2011]. It is a homopentamer with N-terminal helix and 10 $\beta$sheets. It also shares similar pharmacological properties to this receptor. AChBP binds to classical nAChR agonist and antagonists: nicotine, acetylcholine and $\alpha$-bungarotoxin [@smit2001]. Therefore AChBP is considered a good model for the nAChR ligand-binding domain structural studies. The structures of AChBP inactive [@brejc2001], bound to agonist and antagonist [@celie2004; @hansen2005], chimera $\alpha1$ [@dellisanti2007] and $\alpha7$ are known [@li2011]. The common structural features of the ligand binding site emerge from all available data. Here data from Ls will be discussed.
<!-- (it unlike Ac, all aromatic residues in Ls are conserved). -->
### Binding site
The nicotinic acetylcholine receptor binding pocket is formed on the interface of the adjacent subunits [@brejc2001; @middleton1991; @blount1989] (Figure \@ref(fig:binding-pocket-label)). In case of the neuromuscular heteropentameric receptors, it constitutes of $\alpha$ and non-$\alpha$ subunit contributions, whereas in homopentameric or $\alpha$ heteropentameric receptors it is made up of neighboring subunits. The principal, $\alpha$-subunit site subsides amino acid side chains originating from discontinuous loops A (loop $\beta4$-$\beta5$), B (loop $\beta7$-$\beta8$) and C (loop $\beta9$-$\beta10$), whereas the complementary (non-$\alpha$) subunit contributes amino acid side chains originated from loop D (loop $\beta2$-$\beta3$), E (loop $\beta5$-$\beta6$) and F (loop $\beta8$-$\beta9$). Specific residues involved in the formation of the ligand binding pocket were depicted by the molluscan AChBP (Figure \@ref(fig:binding-pocket-label)). Amino acids of the principal component are: Tyr93, Trp147, Tyr188 and Tyr195, whereas non-$\alpha$ component contributes Trp53, Gln55, Arg104, Val106, Leu112 and Met114, Tyr164.
(ref:binding-pocket) **The ligand binding domain of acetylcholine binding protein.** Agonist binds to the loops situated in the adjecent subunits of the nAChR. In muscle type receptor, there are 2 binding sites, and thee are 5 in homopentameric receptor, such as mammalian $\alpha7$ (a). The ligand binding pocket of the AChBP (PDB:1I9B) is formed from loops of the neighboring subunit (b). Principal and complementary subunits contributed amino acids from loops A, B, C and D, E, F, respectively (c). Crystal structure of the AChBP generated with the USCF Chimera software.
```{r binding-pocket-label, fig.cap="(ref:binding-pocket)", fig.scap='The ligand binding domain of acetylcholine binding protein.', fig.align='center', echo = FALSE}
### Pharmacophore
Crystal structure of the AChBP bound to acetylcholine, carbamylcholine, nicotine [@celie2004] and its analogue epibatidine [@hansen2005] provided some general features of the nAChR binding pocket. More recently, structures of mammalian receptors: $\alpha9$ [@zouridakis2014] bound to methyllycaconitine, $\alpha2$ extracellular domain bound to epibatidine [@kouvatsos2016] and $\alpha4\beta2$ receptor bound to nicotine [@morales-perez2016] have been obtained. These, together with the AChBP structures provide details of how structurally varied agonists bind to nAChRs.
Agonist are buried on the interface of the neighboring subunits. They are stabilised in the binding pocket 5 conserved aromatic residues from A, B and C loops of the principal site (known as the aromatic box) engulf the cationic nitrogen of bound agonist. There are two major and conserved features: caption - $\pi$ interaction and hydrogen bond.
Cation -$\pi$ interactions are formed between the cationic nitrogen and aromatic side chain of tryptophan in loop B (143 in AChBP) of the principal side of the binding pocket. Whereas hydrogen bond is formed between the bond acceptor and amino acids of the complementary side of the binding pocket via water molecule [@celie2004; @olsen2014]. In ACh and nicotine bound to AChBP structures, water bridges to the oxygen of the carbonyl group of Leu112 and amide group of Met114 in loop E [@olsen2014; @celie2004].
Choline is an agonist lacking the hydrogen bond acceptor, which is likely contributing to its lower efficacy and affinity. Heterologously expressed $\alpha7$ are activated with choline with the EC50 between 0.4 and 1.6 mM, whereas the EC50 of nicotine is between 49 and 113 $\mu$M [@wonnacott2007]. Radiolabelled studies report up to 500 times lower binding affinity of choline in comparison to nicotine [@wonnacott2007].
Cation-$\pi$ interactions and a hydrogen bond are the staple features of the ligand-receptor interactions, however there are also some less conserved characteristics. For example, in AChBP-nicotine structures, there is a hydrogen bond between cationic nitrogen of the agonist and the carbonyl of TrpB in the principal site of the receptor [@celie2004]. Similarly, in human $\alpha2$ structures a hydrogen bond between the cationic nitrogen of apibatidine and carbonyl of TrpB or Tyr in loop A is formed [@kouvatsos2016]. In contrast, cationic nitrogen of ACh forms cation-pi with Trp53 in loop D of AChBP and $\alpha2\beta2$ proteins [@morales-perez2016; @olsen2014].
(ref:pharmacophore) **Nicotinic acetylcholine receptor agonist pharmacophore.** Agonists of the nAChRs contain hydrogen bond acceptor (red) and cationic nitrogen (blue). Interactions with the receptor based on the crystal structure of the AChBP and nicotine (PB:1UW6) b. Chemical structures generated in ChemDraw. b taken from @blum2010. Cation-$\pi$ interactions between protonated nitrogen of tertiary amine and indole of TrpB.
```{r pharmacophore-label, fig.cap="(ref:pharmacophore)", fig.scap='Nicotinic acetylcholine receptor agonist pharmacophore.', fig.align='center', echo=FALSE}
### Neonicotinoid-pharmacophore
Structure of AChBP proved to be valuable in determining structural elements which may account for neonicotinoids’ selectivity @ihara2008; @talley2008 derived crystal structures of the great pond snail (Lymnaea stagnalis, Ls) and California sea slug (Aplysia californica, Ac) AChBP complexed with bound neonicotinoids (imidacloprid, clothianidin, thiacloprid), and non-selective nAChR ligands- nicotinoids (nicotine, epibatidine and desmotroimidacloprid). Comparison of these structures revealed differences in binding modes between nicotinoids and neonicotinoids described below (see Appendix \@ref(fig:pharacophore-seq-label) for sequence alignment), which allowed for predictions of the binding interactions between neonicotinoids and insect receptors (Figure \@ref(fig:imi-binding-label)). The positioning of the pyridine ring of neonicotinoids and nicotinoids is virtually identical. In imidacloprid bound structure, nitrogen forms hydrogen bond with the amide group of Met114 and carbonyl group of Leu102 of loop E, via water molecule. The presence of water molecule, position of the nitrogen and similar interactions are also seen in nicotinic-bound structures [@celie2004; @ihara2008; @talley2008). In addition, chlorine atom of imidacloprid, thiacloprid as well as epibatidine makes van der Waals interactions with oxygen of Ile106 and oxygen of Met116 of AChBP.
One of the main features of nAChR-bound nicotine is the presence of the cation-$\pi$ interactions between the cationic nitrogen of the pyrrolidine ring and TrpB. In imidacloprid bound structures, the ring stacks with aromatic residues Tyr185 and Tyr188 of loop C. These stacking interactions result in the formation of CH-$\pi$ interactions between the methyline bridge (CH2-CH2) of imidacloprid and TrpB. The 5-member ring of imidacloprid stacks with evolutionary conserved tyrosine residue (Tyr188 of Ac and Tyr 185 of Ls), which is also seen in epidibine, but not in nicotine. All residues described so far are conserved in other agonist-bound nAChR structures, therefore do not account for neonicotinoids-selectivity.
The differences come to light when one begins to dissect the interactions between imidacloprid ring substituents and the AChBP. Partially positive nitro group (NO2) bridges to glutamine of loop D (Gln55 in Ls and Glu 57 in As) via hydrogen bond. It is interesting that in some nAChR subunits, such as chicken $\alpha2$, honeybee $\alpha6$, $\alpha7$, $\beta1$ and $\beta2$, glutamine corresponds to basic residue (lysine/arginine). Basic residues electrostatically attract nitro group, possibly forming a hydrogen bond, which in turn would strengthen the stacking and aromatic CH/$\pi$ hydrogen bond interactions between the ring and the protein. In contrast, other subunits contain either acidic or polar amino acids in the exact position, repulsing or forming no electrostatic interactions with imidacloprid. Thus it has been proposed that the basic residue in loop D interacting with the nitro group of the imidazole ring is important in confirming neonicotinoid selectivity in insect nAChR subunits. This is supported by the genetic studies. Loop D arginine to threonine mutation naturally occurring in $\beta1$ subunit of peach aphid *Myzus persicae*, and cotton aphid *Aphis gossypii* [@hirata2015; @hirata2017; @bass2011] gives rise to neonicotinoid resistance. Additionally, @shimomura2002 showed that mutation of glutamine in loop D of human $\alpha7$ to basic residue, markedly increases sensitivity of the $\alpha7$ homopentamer to nitro-containing neonicotinoids, whereas mutation of loop D threonine to acidic residues in chicken $\alpha4\beta2$ and hybrid chicken/Drosophila $\alpha2\beta2$ receptor had an opposite effect [@shimomura2006]. Interestingly, described mutations did not influence the efficacy to nicotinoids, suggesting this interaction is specific to neonicotinoids.
The basic residue of loop D, which may account for the selectivity of neonicotinoids to insect receptors, originates from the complementary site of the binding pocket, suggesting the complementary binding site is more important than the principal binding site in determination of the neonicotinoid selectivity. This supports the ideas that selectivity of nAChR agents is determined by the complementary subunit amino acids [@marotta2014]. Swapping of $\beta$ subunits in heteromeric receptor diminished cytisine activity on the receptor [@harpsoe2013] which became responsive to cytisine at sub-$\mu$M concentrations by a mutation in a single amino acid in the complementary binding pocket [@marotta2014]. The variation in this binding pocket residues gives rise to ligand binding specifities and pharmacological differences between various compounds and receptors. So for example, conserved Trp in loop D is essential for the high affinity binding of $\alpha$-Bgtx to Ac AChBP [@hansen2004].
Basic residue in loop D is not the only feature determining the affinity of neonicotinoids to insect nAChRs. Amino acids in the principal site may also play a role. Studies on Drosophila/chicken $\alpha2\beta2$ hybrid and chicken $\alpha2\beta4$ receptors showed that the presence of nonpolar proline in YXCC motif of loop C enhances affinity, whereas mutation of proline to glutamate markedly reduces affinity of neonicotinoids to these receptors [@shimomura2005]. The importance of C-loop regions was also demonstrated by @meng2015 who showed that chimera receptors are deferentially sensitive to imidacloprid at least partly due to the difference in loop C region, equivalent to Ls184-191. Genetic analysis of imidacloprid-resistant strain of Nilaparvata lugens identified Y151S mutation in loop B of $\alpha1$ and $\alpha3$ [@liu2005]. This residue corresponds to LsAChBP H145 of the loop B, suggesting loop B may be also important.
(ref:imi-binding) **The predicted interactions between imidacloprid and insect nAChR.** Electrostatic interactions between the nitro group of imidazole ring of imidacloprid and basic residue of Loop D strengthens the interactions between neonicotinoids and nAChRs. Imidazole ring forms stacking interactions with Tryptophan of loop B. Its position is also stabilised by the Tyrosines of loops A and C. Carbonyl group of TrpB can form alternative interaction with imidacloprid. Image taken and modified from @matsuda2005.
```{r imi-binding-label, fig.cap="(ref:imi-binding)", fig.scap= "The predicted interactions between imidacloprid and insect nAChR", fig.align='center', echo=FALSE}
### Cholinergic neurotransmission
<!-- Upon arrival of an electrical signal at the presynpatic terminal, acetylcholine is released into the synaptic cleft. It then binds to nicotinic acetylcholine receptors (nAChRs) expressed at the post-synpatic membrane. Binding of acetylcholine results in depolarisation and excitation of the post-synaptic neurons, or muscle contraction at the neuromusclular junction (NMJ) [@hille1978]. Acetylcholine can also act on other class of receptors, the metabotropic cholinergic G-protein coupled receptor, which are involved in the modulatation of neurotransmission release. The acetylcholine-evoked signal is terminated mainly by synaptic enzyme cholinesterase which hydrolyses acetylcholine to choline and acetate [@fukuto1990], but also by choline uptake to the presynaptic cell by Na^+^-choline transporter. -->
Cholinergic neurotransmission is the process of signal propagation between neurons as well as neurons and muscle cells mediated by a neurotransmitter acetylcholine (ACh) (Figure \@ref(fig:cholineric-synapse-label)) [@williamson2009], via nAChRs. The function and properties of these receptors were studied using mammalian and amphibian muscle preparations.
In 1930s, @brown1936; @bacq1937 demonstrated that the application of acetylcholine, as well as nicotine and choline to the isolated mammalian muscle leads to sustained contraction, as showed by the increase in the muscle tension. The muscle contraction was associated with an increase in the frequency of the action potential firings [@brown1936] and the depolarisation of the end-plate [@katz1957]. Acetylcholine-evoked responses could be inhibited by pre-incubation with several compounds, including snake venom proteins, $\alpha$-bungarotoxin [@chang1963].
Prolonged exposure to high concentration of agonist has a secondary effects on the muscle: desensitisation [@katz1957]. Desensitisation is a post-contraction period, after the removal of the agonist, at which the muscle is relaxed and a subsequent contraction cannot be elicited [@thesleft1955]. Recovery from desensitisation typically lasts few seconds after the agonist removal [@bouzat2008], however the duration varies depending on the receptor, the compound [@briggs1998] and its concentration [@gerzanich1994]. Full recovery may not occur or may be slower if the receptor are exposed to the large doses of agonist for a prolonged time [@katz1957].
Biochemical, electrophysiological, genetic and pharmacological approaches were utilised to identify the role of nAChRs in neurotransmission. nAChRs were solubilised and purified from the electric organ of the *Torpedo* and reconstituted into liposomes [@anholt1982]. In the presence of acetylcholine and other agonists, the ionic current was elicited, confirming nAChR is an ion channel [@anholt1982]. Acetylcholine evoked activation ans desensitisation of nAChRs, which correspond to the effects in the muscle, provided evidence that nAChRs mediate fast synaptic transmission at the cholinergic synapse.
Kinetic properties of nAChRs were studies with the patch clamp technique. Patch clamp is a technique which enables for the resolution of agonist-evoked responses at a single receptor level [@colquhoun1981; @colquhoun1985]. In response to acetylcholine the channel switches between active and inactive form, with the active form interrupted by the short-lived channel closing bursts. Temporal characterisation revealed the average duration of each event. The receptor remains opened for 1.4 ms; this is interrupted by channel closing bursts of 20 $\mu$s which occur at a frequency of 1.9 closures/opening burst. The mean period between the successive channel openings is 342 ms. Further experiments provided the showed that channel opening is not an all or nothing event. Instead, a channel exhibits multiple conductance states, one on which it is fully opened, named a full conductance state (i.e. the active form), and one in which the channel is partially opened, named the sub-conductance state [@colquhoun1985]. The fine structure of full conductance states (or opening bursts) and sub-conductance states varies depending on the agonist used and a receptor protein [@colquhoun1985; @nagata1996; @nagata1998].
(ref:cholineric-synapse) **Chemical transmission at the cholinergic synapse.** Upon excitation of the presynaptic neuron (1), synaptic vesicles fuse with the membrane, releasing neurotransmitter (2). Neurotransmitter binds to the ligand-gated ion channel (LGIC) expressed on the post-synaptic membrane (3) leading to opening of ion channels and a flux of ions down their electrochemical gradient (4). This leads to either excitation or inhibition of the post-synaptic neuron (5). The signal is terminated by the action of cholinesterase which cleaves the ACh into choline and acetic acid. Choline is then transported back into the synapse and used to make more ACh.
```{r cholineric-synapse-label, fig.cap="(ref:cholineric-synapse)", echo=FALSE, fig.scap= 'Chemical transmission at the cholinergic synapse.', fig.align='center', out.height = '60%', echo=FALSE}
<!-- This phenomenon is due to the distinct conformation of nAChRs, at in which they are not capable of ion conduction [@nemecz2016]. -->
<!-- In the continual presence of agonist, the membrane potential gradually repolarises until it reaches the resting state, hovewer the next depolarisation will not occur, until the agonist are washed off and the receptor recovers from desensitisation [@katz1957]. -->
<!-- Development of molecular cloning technique enabled for expression and kinetic characterisation of nAChRs. In 1985, @mishina1984 generated DNA constructs containing cDNA sequences encoding for the muscle type nAChR. These sequences were injected into the *Xenopus oocytes* [@mishina1984]. Upon application of acetylcholine, a current was recorded, suggesting successful cell surface expression. Single channel recordings revealed that in the presence of agonist, nAChR channel switches between active and inactive form. The active form comprises short-lived channel closing and opening [@mishina1986] and longer pauses in-between the receptor twitching. In addition, channel opening does not seem to be an all or nothing event. Instead, a channel exhibits multiple conductance states, one on which it is fully opened, named a full conductance state, and on in which the channel is partially opened, names sub-conductance state [@nagata1996; @nagata1998]. -->
<!-- Intracellulal recordings have shown that this is not due to the muscle cell itself, but rather the insensiticity of membrane receptors [@thesleft1955]. -->
<!-- $\alpha$-bungarotoxin ($\alpha$-bgtx), is a 74-amino acid long, 8 kDa proteins isolated from the venom of a snake *Bungarus multicinctus*. It binds with high affinity to the NMJ post-synaptic membranes [@lee1967] and blocks synaptic responses evoked by acetylcholine and other agonists [@chang1963] by blocking the access of an agoinist to the nAChR binging site [@@mishina1984]. -->
## Biological relevance of the cholinergic neurotransmission
Acetylcholine is the main neurotransmitter in the nervous system of insects [@florey1963]. Its action is mediated predominately by nAChRs, which are the main cholinergic receptor type in their central nervous system [@breer1987]. The presence of nAChR in various brain regions has been detected using biochemical and electrophysiological techniques on neuronal preparations extracted from the Fruit fly *Drosophila melanogaster*, honey bee *Apis mellifera* and American cocroach *Periplaneia americana*. nAChRs have been found to be expressed in the regions associated with learning, formation of memory and the sensory processing [@heisenberg1998], namely the muschroom bodies [@kreissl1989; @gu2006; @oleskevich1999]. They are also present in the insect ganglia, which connects the brain to the peripheral nervous system. In particular, they were identified in the abdominal, thoracic and the terminal ganglia [@sattelle1981; @bai1992], which are involved in the movement of wings, abdomen and legs, as well as the regulation of the anal and reproductive muscles [@smarandache-wellmann2016]. In contrast to mammals and invertebrates (Table \@ref(chlinergic-nts)), insects do not express nAChRs at the neuromuscular junction.
### Biological role of nAChRs in insects
Insect nAChRs are widely expressed in the insect nervous system, where they mediate fast synaptic transmission. Their involvement in the regulation of diverse biological processes is evident from toxicity studies during which insects were exposed to nAChR agonists.
Nicotine is a naturally occurring alkaloid found in the *Solanaceae* family of plants, including tobacco [@steppuhn2004]. It is effective against plant insect pests [@david1953], and used in organic farming in form of tobacco tea [@isman2006]. Exposure of insects to lethal dose of nicotine results in symptoms characteristic for the nervous system intoxication [@chadwick1947] and include increased locomotory activity, followed by convulsions, twitching and eventual death [@carlile2006].
### Neonicotinoids target nAChRs ### {#neonicstarget}
#### Electrophysiological evidence
The effects of neonicotinoids on the neuronal transmission was investigated on insect neuronal preparations which express high levels of nAChRs (Section \@ref()).
@sone1994 investigated the effects of imidacloprid on the neuronal activity at the thoracic ganglia of male adult American cockroaches, *Periplaneta americana* using extracurricular recordings. This method allows for a record of changes in spontaneous neuronal activity in response to mechanical or pharmacological interventions. At a very low concentration of 1 nM, imidacloprid induced a sustained for over 2 minutes increase in the rate of neuronal firing. At concentrations ranging from 10 nM to 100 $\mu$M, the following sequence of events was noted: an increase of the rate of spontaneous action potentials of neurons followed by a gradual decline, leading to a complete block of neuronal activity [@sone1994]. Imidacloprid had the same effect on various insect preparations including thoracic ganglion of the Leptinotarsa decemlineata [@tan2008] and on the abdominal ganglion of *Periplaneta americana* [@buchingham1997]. The same observations were made for other neonicotinoids [@thany2009; @schroeder1984]. This provided evidence that neonicotinoids stimulate the nervous system of insects. This conclusion was supported by the behavioural observation, whereby the neonicotinoid intoxication mirrors intoxication seen with cholinergic agents (Section . In response to imidacloprid, insects become hyper excited as evident by excessive pacing. They then collapse and exhibit diminishing uncoordinated leg and abdomen movement until eventual death [@sone1994; @elbart1997; @suchail2001]. Sub-lethal doses (i.e. < 4 nM) have distinct effect, such as an inhibition of feeding leading to starvation [@nauen1995; @elbart1997].
@sattelle1989 used isolated cocroach neuronal preparation to record post-synaptic intracellular currents in response to neonicotinoid prototype 2(nitromethylene) tetrahydro-1, 3-thiazine (NMTHT). NMTHT depolarised the post-synaptic unpaired median neurons and the cell body of motor neurons of the abdominal ganglion. Agriculturally relevant neonicotinoids had the same effect on the post-synaptic membrane of the isolated cocroach thoracic ganglia [@tan2007; @thany2009] potato beetle isolated neurons [@tan2008], and on cultured cocroach [@ihara2006], honeybee [@palmer2013] and fruit fly [@brown2006] neurons. These data provide evidence that neonicotinoids act directly on the post-synaptic neuron in both target and non-target insects.
Pharmacological characterisation of neonicotinoids-induced currents provided further evidence for their mode of action. The inward current elicited by neonicotinoids were dose-dependent, whereby the higher the concentration, the grater the depolarisation. EC50 values (concentrations at which the half of the maximum current was observed) are in the region of 1 - 5 $\mu$M [@thany2009; @tan2007]. Such low values indicate highly potent action of neonicotinoids on insects, in agreement with toxicological data (Section \@ref(otentpests)). Neonicotinoid-induced currents were reminiscent of those induced by acetylcholine and nicotine, and were prevented by the application of nAChRs antagonists ($\alpha$-bungarotoxin, methyllycaconitine, mecamylamine or d-tubocurarine) not by muscarinic receptor antagonists (atropine, pirenzepine), suggesting neonicotinoid-induced currents are due to the activation of nicotinic receptors.
#### Biochemical evidence
@tomizawa1996 developed neonicotinoid agarose affinity column to isolate proteins with high binding affinity to neonicotinoids. Using Drosophila and Musca head membrane preparations, he identified three nAChR subunits as potential neonicotinoid-targets.
##### Ligand binding studies
The binding affinity of imidacloprid to nAChRs expressed in insect membrane homogenates was assessed in the saturation ligand binding studies.
In the saturation binding experiment, various concentration of the labelled ligand is added to the preparation and the concentration of the ligand at the equilibrium is determined. This is then used to derive the binding constant (as a measure of dissociation constant, Kd). Here, it was used to define the binding strength of neonicoinoids to insect nAChRs (Table \@ref(tab:bindignrecombinant)).
Imidacloprid and thiamethoxam bind with high affinity to proteins in the whole membrane preparations of the domestic fly and aphids with the Kd in the low nM range [@liu1993; @wellmann2004; @liu2005]. Interestingly, two binding affinities have been derived from the imidacloprid study in the brown planthopper and pea aphid [@wellmann2004; @taillebois2014] suggesting there are two binding sites in these animals.
The binding affinity of neonicotinoids-related compounds was compared to the insecticidal activity; the correlative relationship between the two was found [@kagabu2002; @liu2005], providing further evidence that neonicotinoids act by targeting nAChRs.
```{r potencyintact, echo=FALSE, warning = FALSE, message=FALSE}
potencyintact <- data.frame(
Compound = c("Imidacloprid", "Imidacloprid", "Imidacloprid", "Imidacloprid", "", "Imidacloprid", "", "Thiamethoxam"),
Species = c("Musca domestica", "Aphis craccivora", "Myzus persicae", "Nilaparvata lugens", "", "Acyrthosiphon pisum", "", "Myzus persicae"),
Common = c("domestic fly", "cowpea aphid", "green peach aphid", "brown plantohopper", "", "pea aphid", "", "green peach aphid"),
Kd = c("1.2", "12.3", "4.1", "<0.01", "1.5", "0.008", "0.002", "15.4"),
References = c("Liu et al. 1993", "Wellmann et al. 2004", "", "Liu et al. 2005", "", "Taillebois et al. 2014", "", "Wellmann et al. 2004"))
potencyintact %>%
mutate_all(linebreak) %>%
kable("latex", align = "l", booktabs = TRUE, escape = F,
col.names = linebreak(c("Compound", "Species", "Common\nname", "Kd\n(nM)", "References")),
caption = 'Binding affinity of neonicotinoids') %>%
kable_styling(position = "left", full_width = FALSE, latex_options = "hold_position") %>%
add_footnote(notation = "none", "Binding affinity measured in the whole membrane or head membrane (Musca domestica experiment)",
threeparttable = T)
In addition to the saturation studies, the competitive ligand binding studies were carried out. In the the competitive ligand binding studies, biological preparation is incubated with radiolabelled ligand. The ability of various concentrations of unlabeled ligand is measured to define its equilibrium inhibition constant (Ki). This method informs both on the affinity and on the interactions between ligands.
Various concentrations of neonicotinoid prototype isothiaocynate were incubated with the homogenate of fruit fly *Drosophila melanogaster* and a homogenate of the abdominal nerve cords of *Periplaneta americana* before the exposure to radiolabelled nAChR antagonist $\alpha$-bgtx [@gepner1978]. Isothiaocynate inhibited binding of $\alpha$-bgtx in the concentration dependent manner [@gepner1978], suggesting the two compounds share the binding site. Similarly, imidacloprid has been shown to displace $\alpha$-bgtx from brain membrane preparations from honey bee *Apis mellifera* [@tomizawa1992; @tomizawa1993], *Drosophila melanogaster* [@zhang2004], house fly *Musca domestica* and isolated cockroach nerve cords [@bai1991].
#### Genetic evidence
Resistance to neonicotinoids arises from mutations in nAChR subunits. Field isolates of peach aphid *Myzus persicae* [@bass2011], the cotton aphid *Aphis gossypii* [@hirata2015; @hirata2017] and the Colorado potato beetle *Leptinotarsa decemlineata* [@szendrei2012], as well as lab-isolates of brown planthopper, *Nilaparvata lugens* [@liu2005], fruit fly *Drosophila melanogaster* [@perry2008] with decreased sensitivity to neonicotinoids have been identified. Behavioral analysis shows that their sensitivity is up to 1500-fold lower in comparison to the reference strains, as shown by the shift in LD50. Analysis of the coding genome of the resistant strains identified mutations in nAChR subunit coding sequence [@bass2011; @perry2008; @hirata2015].
### Mode of action of neonicotinoids
Neonicotinoids can have diverse mode of action. The currents produced by neonicotinoids and ACh on cultured or isolated insect neuronal preparation were compared. Neonicotinoids evoking current lower than that evoked by ACh were classed as partial agonists, those eliciting similar response were classed as true agonists, whereas those more efficacious than ACh, super-agonists. Thiacloprid and imidacloprid are partial agonists, nitenpyram, clothianidin, acetamiprid and dinotefuran are true agonists, whereas thiamethoxam has no effect on the isolated American cockroach thoracic ganglion neurons [@tan2007]. This differs from the mode of action of neonicotinoids on cultured terminal abdominal ganglion neurons of this insect. Currents produced by all neonicotinoids tested was lower than that evoked by ACh [@ihara2006], suggesting they are all partial agonists on these cells. The mode of action of neonicotinoids on the fruit fly [@brown2006] and honey bee neurons [@palmer2013] differs still, implying the presence of distinct nAChRs in different insect species and neuronal preparations.
<!-- cultured Drosophila CNS cholinergic neurons, whereas imidacloprid is a partial agonist there . -->
<!-- Clothianidin and imidacloprid are partial and full, agonist, respectively on the isolated Kenyon cells of the honeybee . In addition imidacloprid, and imidacloprid but not other neonicotinoids tested blocked ACh-induced action on the American cockroach neurons [@ihara2006] and isolated honeybee neurons [@palmer2013], suggesting antagonistic capabilities of these compounds. -->
<!-- Single channel recordings provided mechanistic details of the mode of action of these compounds. Super-agonists have been shown to increased the frequency of larger conductance state openings [@jones2007a], whereas partial agonists increase the activity of the sub- conductance state of nAChRs [@nagata1996; @nagata1998]. -->
<!-- Note that neonicotinoids cause depolarizing block by desensitising receptors [@palmer2012]. -->
<!-- In cultured honeybee mushroom bodies, imidacloprid acts at nM concentrations [@palmer2013]. In the bee Kenyon cells, the EC50 of imidacloprid was 25 $\mu$M [@deglise2002], whereas on the antenna lobe cells 0.87 $\mu$M [@nauen2001]. Similarly, the EC50 of imidacloprid on isolated cockroach neurons [@tan2007; @ihara2006] and in Drosophila CNS neurons [@brown2006] were in a single digit $\mu$M range. -->
<!-- Neonicotinoids are less potent on vertebrate receptors. EC50 of clothianidin and imidacloprid on heterologously expressed human $\alpha7$ nAChRs is 0.74 mM and 0.73 mM, respectively [@cartereau2018]. Whereas the EC50 of imidacloprid on heterogouslty expressed chicken $\alpha7$ is 357 $\mu$M [@ihara2003]. Other vertebral receptors may be more susceptible. Two-digit $\mu$M imidacloprid doses were needed to activate nAChRs in mammalian neurons [@bal2010; @nagata1998], and the EC50 of this compound on cells containing native mammalian $alpha4\beta2$ nAChRs is 70 $\mu$M [@tomizawa2000a]. Higher EC50 of neonicotinoids on vertebrate receptors suggests neonicotinoids bind preferentially to the insect nAChR. This supports the toxicological data demonstrating increased toxicity of neonicotinoids on insects versus vertebrate species (Section \@ref(nontargeteffect)). -->
<!-- In addition, nAChR-like current was evoked in Xenopus oocytes transfected with membrane preparations of pea aphid *Acyrthosiphon pisum* in response to clothianidin, acetylcholine and nicotine [@crespin2016]. -->
<!-- nAChRs are expressed pre-, post- synaptically at the cell body, as determined mainly with electrophysiological approaches, whereby upon application of classical agonists (Section \@ref(pharma-generalintro)), nAChR-like currents were elicited from various parts of neuronal preparations. The agonist-induced currents were blocked with nAChR antagonists. The presence of nAChRs in the Fruit fly *Drosophila melanogaster* (refereed to as Drosophila, in short) Kenyon cells was shown by recording spontaneous and nicotine or acetylcholine-evoked post-synaptic currents of neurons. These responses were blocked by selective nAChR antagonists $\alpha$-Bgtx [@gu2006]. nAChR are also expressed in the postsynapatic neurons of the honeybee mushroom bodies based on the antibody staining against the nAChR as well as staining with labelled $\alpha$-Bgtx [@kreissl1989]. In addition, mushroom bodies produced a nAChR-like current in response to nicotine and ACh, and it was blocked by $\alpha$-Bgtx [@oleskevich1999]. In cocroach, cell bodies in the thoracic ganglion depolarised in the presence of nicotine and was blocked by selective antagonist mecamylamine [@bai1992]. -->
```{r chlinergic-nts, echo=FALSE, warning = FALSE, message=FALSE}
footnote1 <- "NT = neurotransmitter, NMJ = neuromuscular junction"
footnote2 <- "References: 1 = Chen and Patrick 1997, 2 = Araujo et al. 1988, 3 = Couturier et al. 1990; Cooper et al. 1991, 4 = Lee et al. 1967; 5 = Brown et al. 1936, 6 = Mishina et al. 1986, 7 = Zirger et al. 2003, 8 = Mongeon et al. 2011, 9 = Lewis et al. 1987, 10 = Treinin et al. 1998, 11 = Richmond and Jorgensen 1999; 12 = Boulin et al. 2008, 13 = Touroutine et al. 2005, 14 = McKay et al. 2004"
cholnts <- data.frame(
Species = c("Mouse", "D. melanogaster", "D. rerio", "C. elegans", "A. mellifera"),
Localisation = c("Nervous system\nNMJ", "Nervous system", "Nervous system\nNMJ", "Nervous system\nNMJ", "Nervous system"),
Function = c("NT release modulation\nMuscle contraction", "Major NT", "NT release modulator\nMuscle contraction", "Major NT\nMuscle contraction", "Major NT"),
Major = c("$\\alpha4\\beta2$ and $\\alpha7$\n$\\alpha1\\beta1\\epsilon\\delta$", "?", "$\\alpha4\\beta2$ and $\\alpha7$\n$\\alpha1\\beta1\\epsilon\\delta$", "DES-2/DEG-3\nL-type, N-type and EAT-2 containing", "?"),
Ref = c("1-3\n4-6", "in-text", "7\n8", "9, 10\n11-14", "in-text"))
cholnts %>%
mutate_all(linebreak) %>%
kable("latex", align = "l", booktabs = TRUE, escape = F,
col.names = linebreak(c("Species", "Localisation", "Function", "Major\nreceptor", "Ref")),
caption = 'Cholinergic neurotransmission',
) %>%
kable_styling(position = "center", full_width = FALSE, latex_options = "hold_position") %>%
add_footnote(notation = "none", c(footnote1, footnote2),
threeparttable = T)
### nAChR subunits in insects ###{expressionfail}
nAChR are assemblies of 5 different or identical receptor subunits (Section \@ref(structure)). Each subunit is encoded by a separate gene and is classified as either $\alpha$ or non-$\alpha$, depending on the primary amino acid sequence, whereby $\alpha$ subunits contain a disulphide bond formed between the adjacent cysteines in the ligand binding domain (Figure \@ref(fig:structure-nachr-label)). Genome sequencing projects enabled identification of nAChR subunit families in several insect species. Fruit fly and model organism *Drosophila melanogaster* has 10 subunits, 7 of which are $\alpha$ ($\alpha1-7$) and 3 are $\beta$ ($\beta1-3$) [@adams2000a; @sattelle2005]. There are 11 subunits in the beneficial insect honeybee *A. mellifera* ($\alpha1-9$, $\beta1-2$) [@jones2006a; @consortium2006], 12 subunits in the pest red flour beetle *Tribolium castaneum* ($\alpha1-11$,, $\beta1$) [@consortium2008] and 7 in the Pea Aphid, *Acyrthosiphon pisum* ($\alpha1-6$, $\beta1-2$) [@yi-peng2013; @Consortium2010]. With the aid of molecular cloning techniques, equivalent subunits have been identified in many other insects, including cat flea *Ctenocephalides felis* [@bass2006] and green peach aphid *Myzus persicae* [@huang2000]. Amino acid sequence alignment of equivalent subunits revealed that they are highly conserved, with sequence identity typically greater than 60 % [@jones2010].
Insect nAChR gene families are among the least diverse when compared to other animal phyla. Mammals express 17 subunits: $\alpha1-10$, $\beta1-4$, $\delta$, $\gamma$ and $\epsilon$ [@millar2009] and there are 29 subunits in the representative of the phylum *Nematoda, C. elegans* [@jones2007b].
### RIC-3 improves recombinant nAChR assembly ###{ric3insect}
<!-- There are different receptor types in insects. -->
<!-- -->
To identify which subunits assemble to form functional receptors, recombinant expression techniques were used.
Recombinant expression is a technique receptor stoichiometry and function can be studied in a heterologous system. cDNA is injected into the Xenopus oocytes, or used to transfect insect or mammalian cell line. Using internal cellular machinery, it is transcribed, translated and processed to the surface of the cell. Should a protein form, cell-surface expression can be detected using biochemical approaches (such as ligand binding studies), whereas function studied by means of electrical recordings. These approaches were utilised to identify the major receptor assemblies in mammals, nematode and fish (Table \@ref(tab:chlinergic-nts)).
<!-- To determine which insect nAChR subunits come together to form a functional receptor, various nAChR subunits were injected into the expression systems (*Xenopus oocytes* or cell lines) to determine whether cell surface expression and receptor function can be obtained. -->
To determine which insect subunits form functional nAChRs, @lansdell2012 transfected cultured insect cells with over 70 *Drosophila melanogaster* nAChR subunit cDNAs either singularly or in combinations. No cell surface was achieved, as shown by the radiolabelled ligand binding studies. Difficulties in expression of *Drosophila melanogaster* were also encountered in Xenopus oocytes [@lansdell2012] and mammalian cell lines [@lansdell1997]. The attempts to express receptors from other species were also largely unsuccessful. No ligand binding and/or agonist evoked currents were detected from cells transfected with genes encoding for the brown planthopper *Nilaparvata lugens* [@liu2005; @liu2009; @yixi2009], cat flea *Ctenocephalides felis* [@bass2006], aphid *Myzus persicae* nAChR subunits [@huang2000] and brown dog tick *Rhipicephalus sanguineus* [@lees2014]. Homomeric Locust *Schistocerca gregaria* $\alpha1$ [@marshall1990], *Myzus Persicae* $\alpha1$ and *Myzus Persicae* $\alpha2$ [@sgard1998] produced receptors with nAChR-like pharmacological and electrophysiological characteristics, however the channel-generated currents were of low amplitude, and the expression inconsistent.
Difficulties in recombinant receptor expression highlight the complexity of receptor formation (Figure \@ref(fig:turnover-label)). Assembly and oligomerisation are critical steps in the receptor maturation. These steps require a number of ER and Golgi resident chaperons. RIC-3 (resistant to inhibitors of cholinesterase-3) is an evolutionary conserved, ER-residing [@roncarati2006; @alexander2010] transmembrane protein [@wang2009]. The role of RIC-3 in receptor expression was first described using *C. elegans* and human receptors (Section \@ref(ric-3nacho) and \@ref(ric-3celegans)). More recently, its role in receptor folding and maturation of insect nAChRs has been demonstrated. Co-expression of Dm$\alpha2$-containing and Dm$\alpha5$/$\alpha7$ receptors with RIC-3 improved [@lansdell2008], and in some instances enabled expression in otherwise non-permissible systems [@lansdell2012]. Up to 3.5-fold increase in specific binding of radiolabelled antagonist was noted in insect cells co-transfected with RIC-3, suggesting the presence of greater number of folded receptors on the cell surface [@lansdell2008]. Expressed receptors have been also shown to be functional. In Xenopus oocytes, ionic currents were detected in response to acetylcholine in cells co-expressing RIC-3 [@lansdell2012].
RIC-3 enabled identification of potential nAChR in insects: homomeric $\alpha5$ and $\alpha7$ and heteromeric $\alpha5$/$\alpha7$. The identity of other insect receptors is unknown.
(ref:turnover) **Nicotinic acetylcholine receptor turnover.** Synthesised nAChR subunit peptides undergo folding and oligomerisation in the ER. Correctly folded receptors are transported into the Golgi (1). Misfolded subunits and misassembled receptors are retained in the ER and eventually degraded (2). Receptors transported to the Golgi undergo maturation to be shipped to the plasma membrane (4). Receptors in the plasma membrane are eventually degraded or recycled. Receptors are first packed into the endosome (4) and transported to the lysosome or proteosome for degradation (5) or re-inserted into the plasma membrane (6).
```{r turnover-label, fig.cap="(ref:turnover)", fig.scap= 'Nicotinic acetylcholine receptor turnover.', fig.align='center', echo=FALSE}
### Insect sensitivity to neonicotinoids in recombinant systems
Difficulties in expression of recombinant insect nAChRs (Section \@ref(expressionfail)) hiders their pharmacological analysis and identification of receptors sensitive to neonicotinoids. Insect-mammal hybrid receptors served as a platform to investigate the potency and affinity of neonicotinoids.
#### High affinity of neonicotinoids to insect-chimera receptors
Mammalian $\alpha4$/$\beta2$ receptor expresses well in Xenopus oocytes [@cooper1991] and cell lines [@lansdell2000] and it has low affinity to imidacloprid (Kd >1000 $\mu$M) [@lansdell2000]. $\beta2$ from rat and chicken has been shown to enable recombinant expression of several insect $\alpha$ subunits in cell lines. Chimera of rat $\beta2$ and $\alpha$ subunits from the fruit fly *Drosophila melanogaster* [@lansdell2000], aphid *Myzus Persicae* [@huang1999], planthopper *Nilaparvata lugens* [@liu2009], cat flea *Ctenocephalides felis* [@bass2006] and sheep blowfly *Lucilia cuprina* [@dederer2011] have been generated. It needs to be noted that the potency of neonicotinoids on these receptors is unknown due to the lack of reported data, suggesting these receptors are not functional. However, their pharmacological profiles have been determined using saturation ligand binding studies [@hulme2010] (Table \@ref(tab:bindignrecombinant)).
The affinity of neonicotinoids to insect-chimera rectors varies, depending on the identity of the $\alpha$ subunit. Imidacloprid did not bind to Mp$\alpha1$/rat$\beta2$ receptor, whereas its Ki at Mp$\alpha2$ and Mp$\alpha3$-containing receptor was 3 and 2.8 nM, respectively [@huang1999]. Four to five fold-difference between the most and least susceptible *Drosophila melanogaster* and *Ctenocephalides felis* receptor assemblies were also identified [@lansdell2000; @bass2006]
Imidacloprid exhibits the highest affinity against target pest *Myzus Persicae* with the lowest reported Ki of 2.8 nM on $\alpha3$/$\beta2$ receptor [@huang1999]. It binds less tightly to the non-target insect, the fruit fly nAChRs; the Kd values range from 8.4 to 34.9 nM [@lansdell2000], suggesting it is selectively toxic to pest insects.
```{r bindignrecombinant, echo=FALSE, warning = FALSE, message=FALSE}
footnotez <- ("Receptors were expressed in insect S2 cell line")
footnotey <- ("Rn = Rattus norvegicus (rat), Dm = *Drosophila melanogaster (fruit fly), Mp = Myzus persicae (aphid), Nl = Nilaparvata lugens (planthopper), Cf = Ctenocephalides felis (cat flea)), N/B = no binding,")
bindingrecombinant <- data.frame(
Receptor = c("Rn$\\alpha4\\beta2$", "Dm$\\alpha1$/Rn$\\beta2$", "Dm$\\alpha2$/Rn$\\beta2$", "Dm$\\alpha3$/Rn$\\beta2$", "Mp$\\alpha1$/Rn$\\beta2$", "Mp$\\alpha2$/Rn$\\beta2$", "Mp$\\alpha3$/Rn$\\beta2$", "Mp$\\alpha4$/Rn$\\beta2$", "Nl$\\alpha1$/Rn$\\beta2$", "Cf$\\alpha1$/Dm$\\alpha2$/Rn$\\beta2$", "Cf$\\alpha3$/Dm$\\alpha2$/Rn$\\beta2$"),
Kd= c(">1000", "34.9", "20", "8.4", "N/B", "3", "2.8", "N/B", "24.3", "141", "28.7"),
References = c("Lansdell and Millar, 2000", "", "", "", "Huang et al., 1999", "", "", "", "Liu et al., 2005", "Bass et al. 2006", ""))
bindingrecombinant %>%
mutate_all(linebreak) %>%
kable("latex", align = "c", booktabs = TRUE, escape = F,
col.names = linebreak(c("Receptor", "Kd\n(nM)", "Rerefence")),
caption = 'Binding affinity of imidacloprid to recombinant insect-hybrid receptors') %>%
kable_styling(position = "center", full_width = FALSE, latex_options = "hold_position") %>%
add_footnote(notation = "none", c(footnotez, footnotey),
threeparttable = T)
#### High potency of neonicotinoids on insect-hybrid receptors
The potency of neonicotinoids on insect-mammal hybrid nAChRs have been determined using electrophysiological techniques. $\alpha$ nAChR subunit from the fruit fly, the cat flea and the planthopper were co-expressed with rat or mouse $\beta2$. The responses of the formed channel were recorded in the presence of various neonicotinoids: cyanoamidines clothianidin and imidacloprid, nitroguanidines thiacloprid and acetamiprid and nitromethylene nitenpyram.
Upward (depolarising) current was recorded from cells expressing insect-hybrid nAchRs in responses to all tested neonicotinoids. This response was dose-dependent. The potency of neonicotinoids varied, as indicated by the EC50 value, between 0.04 and 45.8 $\mu$M, however it is generally in the region of 1 $\mu$M.
The rank order of potency of cyanoamidines, nitroguanidine and nitromethylene differs, depending on the receptor identity. For example, in imidacloprid and clothianidin are the most potent on the fruit fly $\alpha1$ containing receptors [@dederer2011], whereas planthopper $\alpha3\alpha8$ hybrid, thiacloprid is the most efficacious [@yixi2009]. Nitenpyram has consistently the highest EC50.
```{r potencyrecombinant, echo=FALSE, warning = FALSE, message=FALSE}
footnotew <- ("Receptors were expressed in Xenopus oocytes")
footnotex <- ("Rn = Rattus norvegicus (rat), Gg = Gallus gallus (chicken), Dm = *Drosophila melanogaster (fruit fly), Nl = Nilaparvata lugens (planthopper), Cf = Ctenocephalides felis (cat flea)), Lc = Lucilia cuprina (sheep blowfly)")
potencyrecombinant <- data.frame(
Receptor = c("Nl$\\alpha1$/Rn$\\beta2$", "Nl$\\alpha2$/Rn$\\beta2$", "Nl$\\alpha3$/Rn$\\beta2$", "Nl$\\alpha3\\alpha8$/Rn$\\beta2$", "", "", "", "Dm$\\alpha1$/Gg$\\beta2$", "", "", "", "Dm$\\alpha2$/Gg$\\beta2$", "", "", "", "Cf$\\alpha1$/Gg$\\beta2$", "", "", "", "Cf$\\alpha2$/Gg$\\beta2$", "", "", "", "Cf$\\alpha4$/Gg$\\beta2$", "", "", ""),
Compound = c("Imidacloprid", "Imidacloprid", "Imidaclorprid", "Imidacloprid", "Clothianidin", "Thiacloprid", "Nitenpyram", "Imidacloprid", "Clothianidin", "Acetamiprid", "Nitenpyram", "Imidacloprid", "Clothianidin", "Acetamiprid", "Nitenpyram", "Imidacloprid", "Clothianidin", "Acetamiprid", "Nitenpyram", "Imidacloprid", "Clothianidin", "Acetamiprid", "Nitenpyram", "Imidacloprid", "Clothianidin", "Acetamiprid", "Nitenpyram"),
EC50 = c("61", "870", "350", "3.2", "5.1", "2.8", "5.6", "0.04", "0.34", "0.23", "0.4", "0.84", "5.4", "2", "35.4", "0.02", "0.15", "0.11", "0.63", "1.31", "1.65", "2.63", "24.4", "13.8", "21.3", "9.4", "45.8"),
References = c("Liu et al. 2009", "", "", "Yixi et al. 2009", "", "", "", "Dederer et al. 2011", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", ""))
potencyrecombinant %>%
mutate_all(linebreak) %>%
kable("latex", align = "c", booktabs = TRUE, escape = F,
col.names = linebreak(c("Receptor", "Compound", "EC50\n($\\mu$M)", "Rerefence")),
caption = 'The potency of neonicotinoids on recombinantly expressed insect hybrid nAChRs.') %>%
kable_styling(position = "center", full_width = FALSE, latex_options = "hold_position") %>%
add_footnote(notation = "none", c(footnotew, footnotex),
threeparttable = T)
Based on the expression of several potential assemblies have been identified.
Subunits with various degree of sensitivity to neonicotinoids, suggesting some and not all receptors confer neonicotinoid sensitivity.
<!-- clothiandidin on the abdominal ganglion [@thany2009] and imidacloprid on the Colorado potato beetle (CPB), . -->
<!-- Imi IC5 0 = 0.4 mM EC50 = 18.3 nM these vaues are from @tan2007. note he also look at the resistant strain -->
<!-- single-electrode voltage clamp @tan2007 (intracellular) depolarisation and see for comparison of activity between all neonics -->
<!-- @thany2009 also did patch clamp inward current -->
<!-- @ihara2006 whole cell patch clamp inward current -->
<!-- Mannitol-gap recordings - must read this was used @buchingham1997, @tan2007 - extracellular recording schematic in tan2007 -->
<!-- The process starts in the nucleus where nAChR gene is transcribed into the mRNA. mRNA contains specific signal sequence which allows for nucleus exit and targeting to the endoplasmic reticulum (ER). Upon arrival at the ER membrane, the co-translational synthesis of receptor subunit occurs, starting from the N-terminus. The protein is inserted into the ER membrane, the signal sequence is cleaved off, and the N-glycosylation chain is attached to the glycosylation recognition sequence [@blount1990]. In addition, the initial folding and oligomerisation occurs. Upon completion of protein synthesis, post-translation events are taking place which include disulphide bridge formation [@blount1990] and further folding and oligomerisation. There are two models describing the process of subunit assembly based of mammalian muscle receptors. First assumes that fully folded subunit forms dimers, and then assembly into pentameric assemblies [@gu1991]. Second theory describes that trimers are formed before the remainder subunits are added to form a pentamer [@green1993]. -->
<!-- The process of subunit assembly is complex and probably regulated by a set of rules, such as the control over the subunits expression in the cell [@missias1996] and the primary structure of receptor subunits. In particular sequences within N-terminal (extracellular ligand binding domain) [@sumikawa1992; @sumikawa1994; @kreienkamp1995] but also regions within the TM domain [@wang1996a] and C-terminus [@eertmoed1999]. During receptor assembly, these sequences become buried within the folding protein and the receptor can be transported to the cell surface. Should a protein misfold, the sequences become exposed and the protein retained in the ER. -->
<!-- Therefore, the process of receptor biogenesis is complex and highly regulated. Should a protein misfold or misoligomerise, it is sent for degradation [@brodsky1999] mediated by the ER-associated system [@hampton2002]. In contrast, properly folded and oligomerised receptors are targeted to appropriate cellular localisation. Neuronal receptors are sent to the synapse, those in muscle cells are targeted to the NMJ during synaptogenesis, where they can perform their important function in signal propagation. The process of receptor turnover is demostarted in Figure \@ref(fig:turnover-label). -->
<!-- Receptor assembly and -->
<!-- The role of RIC-3 (resistant to inhibitors of cholinesterase-3) protein in an ER residing proteinin receptor maturation was first identified by @@halevi2002, who demonstrated that . Heterogous expression of *C. elegans* however, upon co-expression of RIC-3 proteins, both receptor current and ligand binding were detected [@holevi2002]. -->
<!-- The stoichiometry of these receptors in unknown, however there are some potential assemblies. For example Drosophila receptors contain $\alpha4\beta3$, $\alpha1\alpha2\beta2$ and $\beta1\beta2$ subunits [@chamaon2002], based on the immunoprecipitation using antibodies against various receptor subunit types. Using a similar approach, it was shown that *Nilaparvata lugens* $\alpha1$, $\alpha2$ and $\beta1$, as well as $\alpha3$, $\alpha8$ and $\beta1$ co-assembly. -->
<!-- These neuronal effects are reflected in the behavioural data [@sone1994]. Upon exposure to toxic dose of neonicotinoids, insects udergo convulsions, uncoordinated movement, tremors as well as feeding inhibition, eventual paralysis and death [@suchail2001; @boiteau1997; @alexander2007]. -->
<!-- "connections between afferents sensory neurons with interneurons or with motoneurons in several insects such as the cockroach" -->
### Recombinant receptors
Recombinant insect nAChR are notoriously difficult to express. Several interventions have been tested including expression of hybrid receptor in which insect subunits have been co-expressed with mammalian ones. It need to be noted that this method has several limitations. First, hybrid receptors are not biologically relevant, thus conclusions from these studies should be drawn with caution. Second, some some of the expressed receptors may be folded, but not functional. Lastly, this method enabled expression of only a handful of receptors, thus most remained uncharacterised. This hinders their pharmacological characterisation and identification of subunits important in conferring the agricultural role of neonicotinoids. Heterologous expression of nAChR from insects and other species would allow for the characterisation of the interactions of these proteins with neonicotinoids to better define their mode of action and selective toxicity. Development of the platform in which the heterologous expression of insect nAChRs could be achieved, would open the door to screening of novel insecticides, to combat emerging and spreading neonicotinoid-resistance (Section \@ref(resistancegenintro)). In addition, by expressing nAChRs from pest and other species identification of compounds with no adverse effects on beneficial insects and other biologically important species may be achieved. Model organism *C. elegans* is a system in which the mode of action and the selective toxicity can be studied.
## Overview of *C. elegans*
*C. elegans* is a transparent non-parasitic nematode, inhabiting temperate soil environments. This worm was first described as a new species in 1900 [@maupas1900] and named *Caenorhabditis elegans* Greek *caeno* meaning recent, *rhabditis* meaning rod-like and Latin *elegans* meaning elegant. The natural isolate of this species was extracted from the compost heap in Bristol by Sydney Brenner in 1960's and named N2. Since, *C. elegans* has become a valued lab tool and a model organism due to ethical, economical and biological reasons. In contrast to vertebral organisms, *C. elegans* is not protected under most animal research legislation. The cost of use is low, due to the cost of purchase (~$6/strain), maintenance, fast life cycle and high fertility of these animals. *C. elegans* has also is also the first multicellular organism to have the whole genome sequenced [@consortium1998] and the neuronal network has been mapped [@white1986]. It has an advantage over other model organisms in that its nervous system is relatively simple and it is amenable to genetic manipulations.
## General biology ##{#genbiology}
*C. elegans* exists as a male and hermaphrodite, with the latter sex being the more prevalent one. In the lab, 99.9 % of worms are hermaphrodites, which self-fertilize their eggs. *C. elegans* has a fast life-cycle (, which is temperature-dependent. At 15^o^C, it takes 5.5 days from egg-fertilization to the development of a worm into an adult. This process is shortened to 3.5 and 2.5 days at 20 and 25 deg;C, respectively (Figure \@ref(fig:life-cycle-label)). At 20 degrees, hermaphrodite lay eggs 2.5 hours after the fertilisation. 8 hours later the embryo hatches as a larvae in the first stage of its development (L1). In the presence of food, larvae develops into an adult through three further developmental stages, namely L2, L3 and L4. The transition between each larval stage is marked by a process of maulting, during which the old cuticle is shed and replaced by a new one. In the absence of food, developing L2 and L3 worms enter the dauer stage. The worms can remain arrested at this low metabolic activity state for up to several weeks, and will develop into adults, should the food re-appear. Hermaphrodites remain fertile for the first three days of their adulthood. Their eggs can be fertilised internally with the sperm produced by the hermaphrodite, or, if there are males available, by mating. Unmated worm can lay up to 350 eggs, whereas mated over a 1000 eggs. Figure \@ref(fig:life-cycle-label) illustrated the full *C. elegans* life cycle.
(ref:life-cycle) **The life cycle of *C. elegans*.** *C. elegans* develops into an adult through 4 larval stages L1- L4. These stages are separated by molts associated with shedding of an old and exposure of a new cuticle. Adults emerge can lay over a 1000 eggs a day which hatch within several hours. Dauer stage is a metabolic compromised worm stage entered in the absence of food. Upon re-appearance of food, worms develop into L4 and adults normally. Figure taken from
```{r life-cycle-label, fig.cap="(ref:life-cycle)", fig.scap='The life cycle of \\textit{C. elegans}.', fig.align='center', echo=FALSE}
### Nervous system
A great advantage of *C. elegans* is that the entire nervous system has been mapped [@white1986], using electron microscopy of serial worm cross sections. A hermaphrodite has a total of 302 neurons present in the ventral nerve cord, the pharynx, the circumpharangeal ring and the tail. These neurons are assigned to 118 classes based on morphology and positioning. There are 39 sensory neurons, 27 motor neurons and 52 interneurons. Pharyngeal nervous system consists of 20 neurons belonging to 14 types.
### Behaviour as an analytical tool ###{#analytical_behaviour}
Over half of the century of *C. elegans* research developed a great depth of understanding of many of their simple and more sophisticated behaviors. These behaviors can be can be scored and quantified to inform on the effects of compounds or genetic alterations on worms.
#### Pharyngeal pumping
An example of a well defined worm behavior is pharyngeal pumping. Pharyngeal pumping is the feeding behavior of the worm mediated by the pharynx. Successive and timed contraction-relaxation cycles of this muscular organ results in the capture, misceration and passage of the food particles down the alimentary track.
Pharyngeal pumping can be easily scored by counting the number of pharyngeal pumps over time to determine the effects of compounds or genetic alteration on the function of the pharynx. In addition, pharyngeal cellular assays can be performed which offer not only a greater temporal resolution of the activity of the pharynx, but also an analysis of the function of distinct anatomical features of the pharynx.
EPG (electropharyngeogram) is an extracellular electrical recording from the pharynx of the worm. It arises as a result of the flow of ions out of the worm's mouth, due to the changes in the membrane potential of the pharyngeal muscle. A single pharyngeal pump gives rise a series of electrical transients collectively called an EPG. These electrical transients are temporally defined and represents activities of distinct anatomical feature of the phayngeal muscle, namely the corpus, isthmus and the teminal bulb [@raizen1994; @franks2006].
#### Locomotion ####{#locomotionbehaviour}
*C. elegans* exhibits distinct locomotory behavior in liquid and on solid medium. Whilst in liquid it flexes back and forth in the middle of the body. On solid medium, it performs S shaped, crawling movement. The direction of this movement is mostly forward and achieved due to the friction between the substrate and the body [@niebur1993]. By counting the number of bends in the unit of time in the presence and absence of treatment, the effects on locomotory behaviour can be measured.
#### Egg laying ####{#egglayingbehaviour}
*C. elegans* reproduces mainly by self-fertilisation of hermaphrodites or less frequently by mating with males. Hermaphrodite is sexually ready to be fertilized from young adult, the eggs are stored in the uterus and laid in defined spacio-temporal fashion. Typically, 5 eggs are laid at the time in approximately 20 minute intervals [@waggoner1998]. The number of egg laid in the unit of time can be counted and used to inform on the effects of treatment on the reproductive ability of the worm.
### Mode of action studies
*C. elegans* is amenable to genetic manipulations. There is a range of genetic techiques available to generate mutant strains, in which the expression of a certain protein is greatly reduced or eliminated [@boulin2012]. Using these techniques, hundreds of mutant strains have been generated. These strains have been deposited and are available for purchase from the Caenorhabditis Genetics Center (CGC). Behaviour analysis of mutant strains allows for the identification of proteins important in the regulation of many aspects of worm behaviour; an approach used for the mode of action studies.