Junker: an intergenic explorer for bacterial genomes

In the past few decades, scientists from all over the world have taken a keen interest in novel functional units such as small regulatory RNAs, small open reading frames, pseudogenes, transposons, integrase binding attB/attP sites, repeat elements within the bacterial intergenic regions (IGRs) and in the analysis of those "junk" regions for genomic complexity. Here we have developed a web server, named Junker, to facilitate the in-depth analysis of IGRs for examining their length distribution, four-quadrant plots, GC percentage and repeat details. Upon selection of a particular bacterial genome, the physical genome map is displayed as a multiple loci with options to view any loci of interest in detail. In addition, an IGR statistics module has been created and implemented in the web server to analyze the length distribution of the IGRs and to understand the disordered grouping of IGRs across the genome by generating the four-quadrant plots. The proposed web server is freely available at the URL http://pranag.physics.iisc.ernet.in/junker/.     

Novel small RNA-encoding genes in the intergenic regions of Bacillus subtilis

Small, non-coding RNAs (ncRNAs) perform diverse functions in a variety of organisms, but few ncRNAs have been identified in Bacillus subtilis. To search the B. subtilis genome for genes encoding ncRNAs, we focused on 123 intergenic regions (IGRs) over 500 bp in length and analyzed expression from these regions. Seven IGRs termed bsrC, bsrD, bsrE, bsrF, bsrG, bsrH and bsrI expressed RNAs smaller than 380 nt. All small RNAs except BsrD RNA were expressed in transformed Escherichia coli cells harboring a plasmid with PCR-amplified IGRs of B. subtilis, indicating that their own promoters independently express small RNAs. Under the non-stressed condition, depletion of the genes for the small RNAs did not affect growth. Although their functions are unknown, gene expression profiles at several time points showed that most of the genes except for bsrD were expressed during the vegetative phase (4-6 h), but undetectable during the stationary phase (8 h). Mapping the 5' ends of the 6 small RNAs revealed that the genes for BsrE, BsrF, BsrG, BsrH, and BsrI RNAs are preceded by a recognition site for RNA polymerase sigma factor sigma(A). These small RNAs might lack an SD sequence and exert their actions as ncRNAs.     

The use of insect growth regulators - implications for ipm with citrus in southern africa as an example

IGRs have been widely promoted as being ideal IPM compatible pesticides. A number of IGRs have been used extensively on citrus in southern Africa providing excellent control of some target pests. However, field experience has indicated that this has had considerable direct and indirect detrimental effects on IPM. Bioassays confirmed that some of the IGRs used are highly detrimental to certain coccinellid and hymenopteran biocontrol agents of economic importance. Field experience and bioassays have indicated extreme persistence and widespread contamination resulting from agricultural use of some of these products. This presents a serious obstacle to maximisation of biocontrol in IPM and the success of future biocontrol projects using IGR-sensitive species. It also gives rise to concern about potential environmental contamination. In conclusion the use of IGRs should not be considered advantageous to IPM without careful investigation of their potential non-target effects in the particular agro-ecosystem and appropriate consideration for non-target effects in the surrounding environment.     

Genomic and Phylogenetic Analysis of the Human CD1 and HLA Class I Multicopy Genes

The human CD1 proteins belong to a lipid-glycolipid antigen-presenting gene family and are related in structure and function to the MHC class I molecules. Previous mapping and DNA hybridization studies have shown that five linked genes located within a cluster on human chromosome 1q22-23 encode the CD1 protein family. We have analyzed the complete genomic sequence of the human CD1 gene cluster and found that the five active genes are distributed over 175,600 nucleotides and separated by four expanded intervening genomic regions (IGRs) ranging in length between 20 and 68 kb. The IGRs are composed mostly of retroelements including five full-length L1 PA sequences and various pseudogenes. Some L1 sequences have acted as receptors for other subtypes or families of retroelements. Alu molecular clocks that have evolved during primate history are found distributed within the HLA class I duplicated segments (duplicons) but not within the duplicons of CD1. Phylogeny of the alpha3 domain of the class I-like superfamily of proteins shows that the CD1 cluster is well separated from HLA class I by a number of superfamily members including MIC (PERB11), HFE, Zn-alpha2-GP, FcRn, and MR1. Phylogenetically, the human CD1 sequences are interspersed by CD1 sequences from other mammalian species, whereas the human HLA class I sequences cluster together and are separated from the other mammalian sequences. Genomic and phylogenetic analyses support the view that the human CD1 gene copies were duplicated prior to the evolution of primates and the bulk of the HLA class I genes found in humans. In contrast to the HLA class I genomic structure, the human CD1 duplicons are smaller in size, they lack Alu clocks, and they are interrupted by IGRs at least 4 to 14 times longer than the CD1 genes themselves. The IGRs seem to have been created as "buffer zones" to protect the CD1 genes from disruption by transposable elements.     

Control of mushroom sciarid fly Lycoriella ingenua populations with insect growth regulators applied by soil drench

Mushroom sciarid fly Lycoriella ingenua (Dufour, 1839) comb. nov., is one of the most common fly pests affecting the cultivation of Agaricus bisporus (Lange) Imbach in Turkey. In this study, eight insect growth regulators (IGRs)--diflubenzuron, flufenoxuron, lufenuron, methoprene, novaluron, pyriproxyfen, teflubenzuron, and triflumuron-were tested for their potential to control L. ingenua populations in two successive growing periods. Treatments were targeted at larvae as soil drenches; treatment efficacy was evaluated by assessing adult emergence and larval damage. These products were compared with a control treated with water (negative control) and a conventional chemical insecticide (chlorpyrifos ethyl) (positive control). Treatments with the IGRs caused significant reductions in emerging adult numbers and sporophore damage rates compared with the water-treated control over the two growing periods. Of the IGRs tested, novaluron, diflubenzuron, and teflubenzuron had significantly lower numbers of emerging adults than the rest of the IGRs and chlorpyrifos ethyl-treated control in both periods. Treatments with teflubenzuron, pyriproxyfen, novaluron, and diflubenzuron resulted in significantly lower sporophore damage rates than all other treatments. Compared with negative control, there were no significant yield reductions due to applications of selected IGRs. The results suggest that all the IGRs tested can be used as alternatives to conventional pesticides in controlling L. ingenua populations on mushroom.     

两种昆虫生长调节剂对嗜虫书虱的致死作用

系统测定了灭幼宝（Pyriproxyfen)和烯虫酯（Methoprene) 2种昆虫生长调节剂对储藏物主要害虫嗜虫书虱（Liposcelis entomophila)的生物活性。采用饲料混药法,针对不同浓度的灭幼宝和烯虫酯分别对嗜虫书虱若虫的致死作用,对若虫发育历期,成虫繁殖力和卵孵化率的影响设置不同处理和重复。结果表明,灭幼宝对嗜虫书虱若虫的致死作用非常明显,其效果比烯虫酯好;不同浓度的灭幼宝使若虫的发育历期明显延长; 灭幼宝和烯虫酯对嗜虫书虱的成虫无杀伤作用,但对成虫的产卵量有明显的抑制作用,两者的作用浓度却相差5倍。灭幼宝对卵的孵化率影响更大,因而具有更显著的杀卵效果。     

昆虫生长调节剂的毒理机制与抗药性研究进展

昆虫生长调节剂是通过干扰昆虫正常生长发育,致使昆虫个体死亡或活动能力下降,从而导致种群灭绝的一类特异性杀虫剂。本文对3类重要的昆虫生长调节剂（保幼激素类似物、几丁质合成抑制剂和蜕皮激素类似物）的毒理作用机制以及害虫对其抗药性的研究进展进行了综述,叙述了害虫对该类药剂的抗药性发展情况,并对其抗药性机理进行了探讨。目前研究表明,害虫对该类药剂的主要抗性机理是解毒代谢酶增强和表皮穿透率降低。     

New lead discovery of insect growth regulators based on the scaffold hopping strategy

Insect growth regulators (IGRs), which can interrupt or inhibit pest life cycles, are low-toxicity pesticides widely used in integrated pest management (IPM). Ecdysone analogues and chitinase inhibitors are familiar IGRs that have attracted considerable attention because of their unique modes of action and low toxicity to non-target organisms. To find new and highly effective candidate IGRs with novel mechanisms, D-08 (N-(4-(tert-butyl)phenyl)-2-phenyl-2,4,5,6,7,8-hexahydrocyclohepta[c]pyrazole-5-carboxamide) was chosen as a lead compound, and a series of novel heptacyclic pyrazolamide derivatives were designed and synthesized using the scaffold hopping strategy. The bioassay showed that III-27 (N-(2-methylphenethyl)-1-phenyl-1,4,5,6,7,8-hexahydrocyclohepta[c]pyrazole-5-carboxamide) had excellent activity against Plutella xylostella. Protein verification and molecular docking indicated that III-27 could act on both the ecdysone receptor (EcR) and Ostrinia furnacalis chitinase (Of ChtI) and is a promising new lead IGRs. The interaction mechanism of III-27 with EcR and Of ChtI was then studied by molecular docking. These results provide important guidance for the study of new dual-target IGRs.     

Survey of insect growth regulator (IGR) resistance in house flies (Musca domestica L.) from southwestern Turkey

Insect growth regulators (IGRs) are currently the fastest‐growing class of insecticides, and in Turkey these products represent a new approach to pest control. In recent years, several IGRs were also registered for the control of the house fly, Musca domestica L. (Diptera: Muscidae), in Turkey. A field survey was conducted in the summers of 2006 and 2007 to evaluate resistance to some agriculturally and medically used IGRs on house flies from livestock farms and garbage dumps in the greenhouse production areas (Merkez, Kumluca, Manavgat, and Serik) of Antalya province (Southwestern Turkey). The results of larval feeding assay with technical diflubenzuron, methoprene, novaluron, pyripoxyfen, and triflumuron indicate that low levels (RF<10‐fold) of resistance to the IGRs exist in the house fly populations from Antalya province. Exceptions, however, were two populations, Guzoren and Toptas, from the Kumluca area which showed moderate resistance to diflubenzuron with 11.8‐fold in 2006 and 13.2‐fold in 2007, respectively. We found substantial variation in susceptibility of field‐collected house fly populations from year to year and from product to product. We generally observed an increase in resistance at many localities sampled from 2006 to 2007. The implications of these results to the future use of IGRs for house fly control are discussed. It will be critically important to continue monitoring efforts so that appropriate steps can be taken if resistance levels start to increase.     

The role of insect growth regulators in arthropod control

Insect growth regulators (IGRs) represent a relatively new category of insect control agents aimed mainly at covering the need for safer compounds and overcoming the development o f resistance to 'classical' insecticides. The various types of IGR are reviewed here by Jean-Francois Graf and their mechanism of action, their practical application and their respective advantages and limitations are discussed. A comprehensive assessment is made of current and future prospects for IGRs in insect and ectoparasite control.     

3D-QSAR based optimization of insect neuropeptide allatostatin analogs

Allatostatins (AST) are neuropeptides originally described as inhibitors of juvenile hormone (JH) synthesis in insects. Consequently, they have been considered as potential lead compounds for the discovery of new insect growth regulators (IGRs). In the present work, receptor-based three-dimensional quantitative structure-activity relationship (3D-QSAR) was studied with 48 AST analogs, and a general approach for novel potent bioactive AST analogs is proposed. Hence, six novel AST analogs were designed and synthesized. Bioassays indicated that the majority novel analogs exhibited potent JH inhibitory activity, especially analog A6 (IC₅₀: 3.79?nmol/L), which can be used as lead compound to develop new IGRs.     

Improved Conservation of Natural Enemies with Selective Management Systems for Bemisia tabaci (Homoptera: Aleyrodidae) in Cotton

A large-scale study was conducted in 1996 to evaluate and demonstrate strategies for pest management of Bemisia tabaci (Gennadius) in cotton involving different insecticide regimes, application methods, and action thresholds. Here we examined the effects of the various management systems on the abundance and activity of native natural enemies. Population densities of 18 out of 20 taxa of arthropod predators were significantly higher in regimes initiated with the insect growth regulators (IGRs) buprofezin (chitin inhibitor) or pyriproxyfen (juvenile hormone analog) compared with a regime dependent on a rotation of conventional, broad-spectrum insecticides. There were no differences in predator density between the two IGR regimes, and generally no effects due to application method or action threshold level. Predator to prey ratios were significantly higher in regimes utilizing the two IGRs compared with the conventional regime, but were unaffected by application method or threshold level. Rates of parasitism by Eretmocerus eremicus Rose and Zolnerowich and Encarsia meritoria Gahan were higher in the IGR regimes compared with the conventional regime, but were unaffected by insecticide application method, or the action threshold used to initiate applications of the IGRs. Results demonstrate the selective action of these two IGRs and suggest that their use may enhance opportunities for conservation biological control in cotton systems affected by B. tabaci, especially relative to conventional insecticide alternatives.     

In silico and bio assay of juvenile hormone analogs as an insect growth regulator against Galleria mellonella (wax moth) – Part I

Juvenile hormone (JH) analogs are nowadays in use to control harmful pests. In order to develop new bioactive molecules as potential pesticides, we have incorporated different active structural features like sulfonamide, aromatic rings, amide group, and amino acid moiety to the base structure. We have screened a series of designed novel JH analogs against JH receptor protein (jhbpGm-2RCK) of Galleria mellonella in comparison to commercial insect growth regulators (IGRs) – Pyriproxyfen (T₁) and Fenoxycarb (T₂). All analogs exhibit the binding energy profile comparable to commercial IGRs. Based upon these results, a series of sulfonamide-based JHAs (T₃–T₈) as IGRs have been synthesized and characterized. Further, the efficacy of synthesized analogs (T₃–T₈) and commercial IGRs (Pyriproxyfen and Fenoxycarb) has been assessed against fourth instars larvae of G. mellonella under the laboratory conditions. LC₅₀ values of all the analogs (T₁–T₈) against the fourth instars larvae were 9.99, 10.12, 24.76, 30.73, 38.45, 34.15, 34.14, 19.48 ppm and the LC₉₀ 153.27, 131.69, 112.15, 191.46, 427.02, 167.13, 217.10, 172.00 ppm, respectively. Among these analogs, N-(1-isopropyl-2-oxo-3-aza-3-N-ethyl-pentanyl)-p-toluene sulfonamide (T₈) and N-(1-isopropyl-2-oxo-3-aza-3-N-ethyl-pentanyl) benzene sulfonamide (T₇) exhibited the good pest larval mortality at different exposure periods (in hours) and different concentrations (in ppm) in comparison to in use IGRs- T₁ and T₂. Bio assay results are supported by docking at higher concentration. The present investigation clearly exhibits that analog T₈ could serve as a potential IGR in comparison to in use IGRs (T₁ and T₂). The results are promising and provide new array of synthetic chemicals that may be utilized as IGRs.     

Genomics and variation of ionotropic glutamate receptors: implications for neuroplasticity

Summary. We used two approaches to identify sequence variants in ionotropic glutamate receptor (IGR) genes: high-throughput screening and resequencing techniques, and information mining of public (e.g. dbSNP, ENSEMBL) and private (i.e. Celera Discovery System) sequence databases. Each of the 16 known IGRs is represented in these databases, their positions on a canonical physical map are established. Comparisons of mouse, rat, and human sequences revealed substantial conservation among these genes, which are located on different chromosomes but found within syntenic groups of genes. The IGRs are members of a phylogenetically ancient gene family, sharing similarities with glutamate-like receptors in plants. Parsimony analysis of amino acid sequences groups the IGRs into three distinct clades based on ligand-binding specificity and structural features, such as the channel pore and membrane spanning domains. A collection of 38 variants with amino acid changes was obtained by combining screening, resequencing, and informatics approaches for several of the IGR genes. This represents only a fraction of the sequence variation across these genes, but in fact these may constitute a large fraction of the common polymorphisms at these genes and these polymorphisms are a starting point for understanding the role of these variants in function.Genetically influenced human neurobehavioral phenotypes are likely to be linked to IGR genetic variants. Because ionotropic glutamate receptor activation leads to calcium entry, which is fundamental in brain development and in forms of synaptic plasticity essential for learning and memory and is essential for neuronal survival, it is likely that sequence variants in IGR genes may have profound functional roles in neuronal activation and survival mechanisms.     

Insecticide and acaricide molecules and/or combinations to prevent pet infestation by ectoparasites

External antiparasitic drugs used in cats and dogs have evolved in terms of active ingredients but also regarding formulations. Old chemical groups have been supplanted by phenylpyrazoles, neonicotinoids, oxadiazines, spinosyns or others which are entering the veterinary market. In addition to insecticides-acaricides, insect and mite growth inhibitors (IGRs) have emerged. These IGRs are used in animals or in the environment, either alone or in combination with insecticides-acaricides. The notion of antiparasitic treatment has evolved to the concept of prevention of ectoparasite infestation but also of transmitted diseases through the introduction of formulations providing long-lasting activity. At the same time, ease-of-use has been improved with the development of spot-on formulations. Progress has also been achieved through the development of antiparasitic drugs providing control of both external and internal parasites.     

Population Development and Reproduction of Fungus- and Bacterium Feeding Nematodes in the Presence of Insect Growth Regulators

The insect growth regulators (IGRs), diflubenzuron and BAY SIR 8514, at 300 and 1,000 ppm a.i. in potato dextrose agar (PDA) inhibited the radial growth of the fungus Rhizoctonia solani host of Aphelenchus avenae. The IGRs had no effect on the growth of the bacterium Pseudomonas pseudoalcaligenes host of Acrobeloides nanus and Diplogaster iheritieri. At 59 ppm a.i., neither IGR inhibited the population development of A. nanus and D. iheritieri on P. pseudoalcaligenes; however, diflubenzuron stimulated the population development of D. iheritieri. At 300 ppm, both IGRs inhibited the population development of A. nanus and D. iheritieri; however, BAY SIR 8514 was more effective than diflubenzuron except on A. nanus L₄''s. At 300 ppm, only BAY SIR 8514 affected the population development of A. avenae, except the L₄''s. At 1,000 ppm, both IGRs inhibited development, except diflubenzuron for L₂ and L₃''s. Again, BAY SIR 8514 was more effective than diflubenzuron. With single females of A. nanus and D. iheritieri, both IGRs at 300 ppm reduced egg laying, inhibited embryonation, and slowed larval development.