Assessing the impact of varietal resistance and planting dates on pest spectrum in chickpea

The cotton bollworm Helicoverpa armigera [Hübner (1808)] is one of the most widely spread pest which limits the chickpea production, while the beet armyworm, Spodoptera exigua (Hübner, 1808) has emerged as a serious pest in recent years, in southern India and parasitic wasp Campoletis chlorideae Uchida, 1968 is an important larval parasitoid which naturally manages both pests under field condition. Insecticides adoption leads to development of resistance in pod borer. In view of climate change scenario, the focus of the present studies was the identification of climate resilient cultivars of chickpea for pod borers and the results reveled, that there were significant variations in the level of eggs and larval population among the genotypes. Across seasons, the crop sown in October recorded the maximum number of eggs. ‘ICC 3137’ had the highest number of H. armigera eggs (11.6) across seasons. ‘JG 11’, (6.3) in 2012 and’ ICCV 10’ (3.6) in 2013 recorded the lowest number of H. armigera eggs. During 2014-15, the maximum(80.7) H. armigera larval incidence was observed in October sown crop and the lowest (21.1) in January crop. The number of S. exigua larvae were substantially higher in the December crop. For all seasons, the highest number of C. chlorideae were found in October crop. Across seasons, multiple regression analysis for both pest had a strong interaction with weather patterns

Effect of varied weather parameters and different sowing dates on the incidence of insect pest in chickpea

It is important to identify genotypes with resistance varied sowing windows. Therefore, evaluated a five diverse genotypes for resistance to H. armigera for three years over four sowing window. More number of eggs were observed in 2012 than in 2013 and 2014. Highest numbers of eggs were recorded in the crop sown in October in cumulative three seasons. Among the genotypes tested, ICC 3137 had the highest number of H. armigera eggs (11.6) across the seasons. The lowest number of H. armigera eggs was observed on JG 11 (6.3) in 2012, on ICCV 10 (3.6) in 2013. The H. armigera larvae were highest in October sown crop (80.7) and lowest in the January sown crop (21.1) in 2014-15. The larval incidence decreased from October to December but increased in the January. Greater numbers of cocoons were recorded in the December sown crop (3.4) in 2012-13.However highest number of cocoons were recorded on ICC 3137 (2.5) and lowest on KAK 2 (1.6). The maximum temperature and minimum temperature shows a significant negative and positive correlation with H. armigera larvae population for October and November sown crop. Multiple regression analysis of the H. armigera, S. exigua eggs and larval population showed a significant interaction with weather parameters during all cropping seasons. The coefficient of multiple determinations (R2) was varied per cent during across different seasons for H. armigera, S. exigua populatio

Climate change effects on pest spectrum and incidence in grain legumes

Global warming and climate change will influence activity, diversity, distribution and population dynamics of insect pests including the grain legumes. Several insect pests damage grain legume crops, of which the pod borer, Helicoverpa armigera; spotted pod borer, Maruca vitrata; spiny pod borer, Etiella zinckenella; pod fly, Melanagromyza obtusa; aphid, Aphis craccivora; defoliators, Spodoptera litura and S. exigua; thrips, Megaleurothrips usitatus and Caliothrips indicus and the bruchid, Callasobruchus chinensis cause extensive losses in grain legumes. The incidence and extent of losses due to these pests varies across seasons, locations, and cropping systems. The pest spectrum on grain legumes will change considerably due to impending global warming and climate change. The geographical distribution of some of the pests might extend to temperate regions in Europe and America, while the outbreaks of some other pests will become more frequent. Several outbreaks of pod borer, H. armigera and spotted pod borer, M. vitrata have been recorded on grain legumes in India, which at times have resulted in complete crop loss. The scale insect, Ceroplastodes cajani in pigeonpea and beet armyworm, Spodoptera exigua, mealy bug, Ferrisia virgata, and white fly, Bemisia tabaci in chickpea have emerged as new pests; while leaf miner, Porphyrosela neodoxa, mealy bugs, Drepanococcus cajani, and Coccidohystrix insolita are some of the emerging pest problems in pigeonpea in India. In addition, there will be greater genotype x environment interactions for expression of resistance to insect pests, and this warrants a greater effort for identification of diverse sources of resistance and need for integrated pest management packages that will be effective under global warming and climate change

Structural analysis of the regulatory GAF domains of cGMP phosphodiesterase elucidates the allosteric communication pathway

Regulation of photoreceptor phosphodiesterase (PDE6) activity is responsible for the speed, sensitivity, and recovery of the photoresponse during visual signaling in vertebrate photoreceptor cells. It is hypothesized that the physiological differences in the light responsiveness of rods and cones may result in part from differences in the structure and regulation of the distinct isoforms of rod and cone PDE6. Although rod and cone PDE6 catalytic subunits share a similar domain organization consisting of tandem GAF domains (GAFa and GAFb) and a catalytic domain, cone PDE6 is a homodimer whereas the rod PDE6 catalytic dimer is composed of two homologous catalytic subunits. Here we provide the x-ray crystal structure of cone GAFab regulatory domain solved at 3.3 Å resolution in conjunction with chemical cross-linking and mass spectrometric analysis of conformational changes to GAFab induced upon binding of cGMP and the PDE6 inhibitory γ-subunit (Pγ). Ligand-induced changes in cross-linked residues implicate the α4-helix of GAFa (close to the cGMP binding site) and the β1/β2 loop of GAFb as key motifs that have been previously proposed to communicate with the catalytic domains of PDE6. Molecular dynamics (MD) simulations of cone GAFab revealed asymmetry in the two GAFab subunits forming the homodimer and allosteric perturbations on cGMP binding. Cross-linking of Pγ to GAFab in conjunction with solution NMR spectroscopy of isotopically labeled Pγ identified the central polycationic region of Pγ interacting with the GAFb domain. These results provide a mechanistic basis for developing allosteric activators of PDE6 with therapeutic implications for halting the progression of certain retinal degenerative diseases

Молекулярный фенотип клеток крови, ассоциированный с прогрессированием трижды негативного рака молочной железы

Introduction. triple negative breast cancer is an aggressive clinical phenotype characterized by poor prognosis. immune system plays an important role in the development, treatment response, and progression of solid tumor. The search for immune-related markers associated with the prediction of treatment efficacy and disease prognosis, and based on the use of high-resolution molecular techniques, is a promising area of research, the results of which can be translated into clinical practice. Case description. The molecular profile of blood mononuclear cells in a 48-year-old female patient with histologically proven triple negative breast cancer (estrogen Receptor – 0; progesteron Receptor – 0; Her2/neu – 0; gata-3 – 0, androgen Receptor – 0 and Ki67 – 70 %) was described. The patient did not response to neoadjuvant chemotherapy with 4 cycles of paclitaxel + carboplatin followed by 2 cycles of adriamycin + cyclophosphamide. The patient underwent surgery. disease progression (pelvic bone metastases) occurred 2 months after surgery. The features of blood lymphocytes and monocytes associated with a lack of response to neoadjuvant chemotherapy and disease progression were described.Conclusion. This clinical case demonstrates that sequencing of peripheral blood mononuclear cells can be used as a method for identifying predictive markers of therapy efficacy and developing personalized treatments for patients with triple negative breast cancer.Актуальность. Трижды негативный подтип рака молочной железы характеризуется агрессивным течением и неблагоприятным прогнозом. Компоненты иммунной системы как непосредственные участники патогенеза играют роль в развитии, ответе на терапию и прогрессировании этой нозологии. Поиск маркеров иммунных клеток, ассоциированных с предсказанием эффективности лечения и прогнозом заболевания, основанный на применении молекулярных методов высокого разрешения, является перспективным направлением поискового исследования, результаты которого можно транслировать в клиническую практику. Описание клинического случая. Представлен первый опыт описания молекулярного профиля мононуклеарных клеток крови пациентки с трижды негативным раком молочной железы. Опухоль: инвазивная карцинома неспецифического типа с экспрессией: estrogen Receptor – 0; progesteron Receptor – 0; Her2/neu – 0; gata-3 – 0, androgen Receptor – 0, Ki67 – 70 % опухолевых клеток. Отмечено отсутствие ответа на неоадъювантную химиотерапию по схеме: 4 цикла «паклитаксел + + карбоплатин», с последующими 2 курсами АС (адриамицин + циклофосфан). Пациентке проведено оперативное лечение, через 2 мес после которого выявлены метастазы в кости таза. У пациентки описаны особенности лимфоцитов и моноцитов крови, которые могут быть ассоциированы с отсутствием ответа на неоадъювантную химиотерапию и прогрессированием заболевания.Заключение. Представленное клиническое наблюдение показывает, что метод секвенирования мононуклеарных клеток периферической крови можно использовать в качестве поискового для обнаружения предиктивных маркеров эффективности терапии и создания персонифицированной системы лечения пациенток с трижды негативным раком молочной железы

Coevolution of insulin-like growth factors, insulin and their receptors and binding proteins in new world monkeys

Previous work has shown that the evolution of both insulin-like growth factor 1 (IGF1) and insulin shows an episode of accelerated change on the branch leading to New World monkeys (NWM). Here the possibility that this is accompanied by a corresponding episode of accelerated evolution of IGF1 receptor (IGF1R), insulin receptor (IR) and/or IGF binding proteins (IGFBPs) was investigated. Analysis of receptor sequences from a range of primates and some non-primate mammals showed that accelerated evolution did indeed occur on this branch in the case of IGF1R and IR, but not for the similar insulin receptor-related receptor (IRRR) which does not bind insulin or IGF1. Marked accelerated evolution on this branch was also seen for some IGFBPs, but not the mannose 6-phosphate/IGF2 receptor or epidermal growth factor receptor. The rate of evolution slowed before divergence of the lineages leading to the NWM for which sequences are available (Callithrix and Saimiri). For the IGF1R and IR the accelerated evolution was most marked for the extracellular domains (ectodomains). Application of the branch-sites method showed dN/dS ratios significantly greater than 1.0 for both receptor ectodomains and for IGFBP1, and allowed identification of residues likely to have been subject to selection. These residues were concentrated in the N-terminal half of the IGF1R ectodomain but the C-terminal half of the IR ectodomain, which could have implications for the formation of hybrid receptors. Overall the results suggest that adaptive coevolution of IGF1, insulin and their receptors and some IGFBPs occurred during the evolution of NWM. For the most part, the residues that change on this branch could not be associated with specific functional aspects (ligand binding, receptor dimerization, glycosylation) and the physiological significance of this coevolution remains to be established

Reference Gene Selection for Quantitative Real-time PCR Normalization in Quercus suber

The use of reverse transcription quantitative PCR technology to assess gene expression levels requires an accurate normalization of data in order to avoid misinterpretation of experimental results and erroneous analyses. Despite being the focus of several transcriptomics projects, oaks, and particularly cork oak (Quercus suber), have not been investigated regarding the identification of reference genes suitable for the normalization of real-time quantitative PCR data. In this study, ten candidate reference genes (Act, CACs, EF-1α, GAPDH, His3, PsaH, Sand, PP2A, ß-Tub and Ubq) were evaluated to determine the most stable internal reference for quantitative PCR normalization in cork oak. The transcript abundance of these genes was analysed in several tissues of cork oak, including leaves, reproduction cork, and periderm from branches at different developmental stages (1-, 2-, and 3-year old) or collected in different dates (active growth period versus dormancy). The three statistical methods (geNorm, NormFinder, and CV method) used in the evaluation of the most suitable combination of reference genes identified Act and CACs as the most stable candidates when all the samples were analysed together, while ß-Tub and PsaH showed the lowest expression stability. However, when different tissues, developmental stages, and collection dates were analysed separately, the reference genes exhibited some variation in their expression levels. In this study, and for the first time, we have identified and validated reference genes in cork oak that can be used for quantification of target gene expression in different tissues and experimental conditions and will be useful as a starting point for gene expression studies in other oaks

Substrate binding and translocation of the serotonin transporter studied by docking and molecular dynamics simulations

The serotonin (5-HT) transporter (SERT) plays an important role in the termination of 5-HT-mediated neurotransmission by transporting 5-HT away from the synaptic cleft and into the presynaptic neuron. In addition, SERT is the main target for antidepressant drugs, including the selective serotonin reuptake inhibitors (SSRIs). The three-dimensional (3D) structure of SERT has not yet been determined, and little is known about the molecular mechanisms of substrate binding and transport, though such information is very important for the development of new antidepressant drugs. In this study, a homology model of SERT was constructed based on the 3D structure of a prokaryotic homologous leucine transporter (LeuT) (PDB id: 2A65). Eleven tryptamine derivates (including 5-HT) and the SSRI (S)-citalopram were docked into the putative substrate binding site, and two possible binding modes of the ligands were found. To study the conformational effect that ligand binding may have on SERT, two SERT–5-HT and two SERT–(S)-citalopram complexes, as well as the SERT apo structure, were embedded in POPC lipid bilayers and comparative molecular dynamics (MD) simulations were performed. Our results show that 5-HT in the SERT–5-HTB complex induced larger conformational changes in the cytoplasmic parts of the transmembrane helices of SERT than any of the other ligands. Based on these results, we suggest that the formation and breakage of ionic interactions with amino acids in transmembrane helices 6 and 8 and intracellular loop 1 may be of importance for substrate translocation

Exploring the Conformational Transitions of Biomolecular Systems Using a Simple Two-State Anisotropic Network Model

Biomolecular conformational transitions are essential to biological functions. Most experimental methods report on the long-lived functional states of biomolecules, but information about the transition pathways between these stable states is generally scarce. Such transitions involve short-lived conformational states that are difficult to detect experimentally. For this reason, computational methods are needed to produce plausible hypothetical transition pathways that can then be probed experimentally. Here we propose a simple and computationally efficient method, called ANMPathway, for constructing a physically reasonable pathway between two endpoints of a conformational transition. We adopt a coarse-grained representation of the protein and construct a two-state potential by combining two elastic network models (ENMs) representative of the experimental structures resolved for the endpoints. The two-state potential has a cusp hypersurface in the configuration space where the energies from both the ENMs are equal. We first search for the minimum energy structure on the cusp hypersurface and then treat it as the transition state. The continuous pathway is subsequently constructed by following the steepest descent energy minimization trajectories starting from the transition state on each side of the cusp hypersurface. Application to several systems of broad biological interest such as adenylate kinase, ATP-driven calcium pump SERCA, leucine transporter and glutamate transporter shows that ANMPathway yields results in good agreement with those from other similar methods and with data obtained from all-atom molecular dynamics simulations, in support of the utility of this simple and efficient approach. Notably the method provides experimentally testable predictions, including the formation of non-native contacts during the transition which we were able to detect in two of the systems we studied. An open-access web server has been created to deliver ANMPathway results. © 2014 Das et al