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Introduction. Early-onset neonatal sepsis is a major cause of morbidness and death in newborn children. Its timely diagnosis is usually a challenge in developing countries like India. Aim. To study the efficacy of C-reactive protein (CRP), micro-ESR, and gastric aspirate for polymorphs in the diagnosis of early-onset neonatal sepsis. Materials and Methods. This study included sixty term and preterm children, inborn and referred cases. The children who presented before day seven of life with clinical suspicion of sepsis or who were at high risk of developing sepsis were included. These were further investigated. Significant values for screening tests were taken asC−reactive protein>0.6 mg/dl, micro-ESR—after 1 hour, fall in the column of blood in capillary tube was measured, and result was taken as mm fall in 1 hr, and gastric aspirate forpolymorphs>5 polymorphs/HPF. Sepsis screen positive result was 2 or more positive tests. The statistical evaluation was done using Fisher, and ANOVA tests using SPSS 20.0 version. Results. Sixty children were included in the study with forty as the referred ones. Most of them had tachypnea (45%). CRP showed high sensitivity, whereas micro-ESR and gastric aspirate for polymorphs showed high specificity. Conclusions. Neonatal sepsis screening is required for the detection of infection as the blood culture report may not be positive in all the cases, and even if positive, the result takes few hours. CRP showed high sensitivity, whereas micro-ESR and gastric aspirate for polymorphs showed high specificity independently as well as when combined.

The wild Malus germplasm is considered as a gene reservoir for various biotic and abiotic stresses tolerance/resistance genes, including important novel horticultural traits. The dwarf vigour is considered an important trait in Malus for promoting high-density plantations and enhancing productivity. Thus, an indigenous and exotic wild Malus species collected in the apple field gene bank were evaluated for their dwarfing potential, based on the diverse traits like stomatal features, photosynthetic pigments and anatomical structures. Among different parameters, inter-nodal length, root bark percentage, palisade: spongy tissue thickness ratio, xylem: phloem ratio, wood: bark ratio, vessel diameter of stem cross-section and photosynthetic pigments exhibited significant variation between dwarf and vigorous Malus species. The indigenous Himalayan crabapple—Malus baccata (L.) Borkh. (Rohru) showed the shortest inter-nodal length (23.82 ± 1.08 mm), low root bark percentage (69.30 ± 0.37), low xylem: phloem ratio (0.43 ± 0.01), low wood: bark ratio (0.49 ± 0.07), smaller xylem vessel diameter (9.67 ± 0.40 µm), and higher palisade: spongy tissue thickness ratio (1.25 ± 0.04) than the vigorous counterparts. These parameters were comparatively at par with the known dwarfing rootstock M.9. The foliar photosynthetic pigments content was significantly higher in M. baccata (Rohru) compared to other studied Malus species. Furthermore, stomatal density showed much dependence on the size of stomata, specifically its length rather than the vigour of Malus genotypes. The study revealed that Malus baccata (Rohru) had several dwarfing attributes which were comparable to the dwarfing rootstock M.9 and thus could serve as an important genetic resource for the development of indigenous dwarfing rootstock.

Purpose The importance of nutraceuticals and functional foods has been a topic of interest in nutrition research for many years. This review aims to summarize the findings on the nutritive value and health benefits of chia, as well as its use as a food fortificant. Design/methodology/approach Published literature on the nutritive value and therapeutic properties of chia has been reviewed. Findings Chia, an ancient grain, belongs to the mint family (Lamiaceae) and was cultivated in Mexico and Guatemala by the Mayas and Aztecs of a pre-Columbian era. In addition to being gluten-free, chia seeds are concentrated source of omega-3 fatty acids (mainly α-linolenic acid), fiber (insoluble) and polyphenolic compounds (myricetin, quercetin, kaempferol, chlorogenic and caffeic acids), which were found to be comparatively higher than many other grains, cereals and oily seeds. Chia supplementation has potential to lower incidence of cardiovascular disease, obesity, hypertension, cancer, diabetes, pruritus and celiac disease. Because of its nutraceutical and physiochemical properties, chia has been widely used as a whole seed, flour, seed mucilage, gel and oil for developing various enriched food products, such as bread, pasta, cakes, cookies, chips, cheese, yoghurt, meat, fish and poultry. Originality/value With advancement in nutrition research, chia would have a great future perspective as feed, food and medicine. However, further research is needed to validate the potential therapeutic effect of chia supplementation on human health.

Plants nutrients are necessary in increasing production and productivity of crops and healthy food for the world’s ever increasing population. Today, soil management strategies are mainly dependent on inorganic chemical-based fertilizers, which cause a serious threat to human health and the environment. Bio-fertilizer has been identified as an alternative for increasing soil fertility and crop production in sustainable farming. The exploitation of beneficial microbes as bio-fertilizers has become of paramount importance in agricultural sector due to their potential role in food safety and sustainable crop production. Bio-fertilizer can be an important component of integrated nutrients management. Microorganisms that are commonly used as bio-fertilizer components include; nitrogen fixers (N-fixer), potassium and phosphorus solubilizers, growth promoting rhizobacteria (PGPRs), endo and ecto mycorrhizal fungi, cyanobacteria and other useful microscopic organisms. The use of bio-fertilizers leads to improved nutrients and water uptake, plant growth and plant tolerance to abiotic and biotic factors. In wheat, non-symbiotic spp. like Azotobacter and streptomyces may be used as a potential source of plant growth promoter and also can reduce chemical fertilizer up to 25% with compromising yield. Thus, these potential biological fertilizers would play a key role in productivity and sustainability of soil and also in protecting the environment as eco-friendly and cost effective inputs for the farmers. This review will overview the importance of biofertilizers with different sources of chemical fertilizers in wheat.

SUMMARYAnimals with complex nervous systems demand sleep for memory consolidation and synaptic remodeling. Here we show that though theCaenorhabditis elegansnervous system has a limited number of neurons, sleep is necessary for both processes. In addition, it is unclear in any system if sleep collaborates with experience to alter synapses between specific neurons and whether this ultimately affects behavior.C. elegansneurons have defined connections and well-described contributions to behavior. We show that spaced odor-training and post-training sleep induce long-term memory. Memory consolidation, but not acquisition, requires a pair of interneurons, the AIYs, which play a role in odor-seeking behavior. In worms that consolidate memory, both sleep and odor conditioning are required to diminish inhibitory synaptic connections between the AWC chemosensory neurons and the AIYs. Thus, we demonstrate in a living organism that sleep is required for events immediately after training that drive memory consolidation and alter synaptic structures.

Chickpea (Cicer arietinum L.) is second largest grown legumes worldwide contributing 75% of total pulse production. It is a cool season legume crop and grown in tropical and subtropical areas. Due to drastic climatic changes, chickpea suffers from many biotic (blight and wilt) and abiotic (salinity, drought, cold) stresses that directly impact the growth and yield. In our study, we predicted and annotated the genes related to biotic and abiotic stresses. Total 20162 ESTs for salinity, 34346 for drought and 191 for cold stress were downloaded. For biotic stresses, viz., wilt and blight disease, 7866 and 56 ESTs were collected, respectively from public domain. All these ESTs were assembled into contigs and blast against protein non-redundant database. Each blast results were mapped to get the corresponding GO terms. Total 1631, 3133 and 13 contigs for salinity, drought and cold stress showed 1333, 2693 and 7 GO terms respectively, while 1144 contigs for Fusarium wilt and 6 contigs for Ascochyta blight disease showed 955 and 4 GO terms. These GO terms describe biological process, molecular function and cellular components of corresponding stresses. Remaining 298 (salinity), 440 (drought), 6 (cold), 189 (wilt) and 2 (blight) contigs were mapped to reference genome and further used for annotation using gene prediction methods and promoter analysis. This study provide insight to novel gene related to abiotic and biotic stress mechanism that can be further analyzed in molecular biology studies for breeding programs.

Introduction: Acute graft-vs.-host disease (aGVHD) remains a major diagnostic and clinical problem in patients after allogenic hematopoietic stem cell transplant (HSCT). Finding biomarkers that play a role in aGVHD not only helps in predicting and diagnosing aGVHD, but might help in developing prophylaxis and therapeutic approaches. Using Next Generation Sequencing (NGS) and targeted RNA sequencing along with a machine learning approach to predict, we investigated the potential of discovering new biomarkers that can predict aGVHD. Methods: RNA extracted from bone marrow aspiration samples collected around day 90 post HSCT from 46 patients were sequenced using 1408 targeted genes. cDNA was first generated, then adapters were ligated. The coding regions of the expressed genes were captured from this library using sequence-specific probes to create the final library. Sequencing was performed using an Illumina NextSeq 550 platform. Ten million reads per sample in a single run were required. Read length was 2 × 150 bp. Expression profile was generated using Cufflinks. A machine learning system is developed to predict the GVHD cases and to discover the relevant genes. A subset of genes relevant to GVHD is automatically selected for the classification system, based on a k-fold cross-validation procedure (with k=10). For an individual gene, a Naïve Bayesian classifier was constructed on the training of k-1 subsets and tested on the other testing subset. To eliminate the underflow problem commonly associated with the standard Naïve Bayesian classifiers, we applied Geometric Mean Naïve Bayesian (GMNB) as the classifier to predict GVHD. The processes of gene selection and GVHD classification are applied iteratively to obtain an optimal classification system and a subset of genes relevant to GVHD. Results: The analyzed bone marrow samples included patients transplanted for aplastic anemia (#1), acute lymphoblastic leukemia (#9), acute myeloid leukemia (#16), mixed phenotype acute leukemia (#1), myelodysplastic syndrome (#10), chronic myelomonocytic leukemia (#5), and myeloproliferative neoplasm (#4). Of the 46 patients, 30 (65%) had a diagnosis of aGVHD (grade 2-4). The GMNB modified Bayesian model selected 7 genes as top classifiers. These top classifier genes included Class II Major Histocompatibility gene (CIITA), B-cell markers genes (CD19 and CD22), early T-cell related gene (TCL1A), hematopoietic-specific transcription factor (IKZF3), a gene involved in protein-protein interaction, and a gene involved in DNA helicase nucleotide excision repair (ERCC3). When these 7 genes were used in GMNB-modified classifier with 10-fold cross validation to predict aGVHD, the model classified 28 of the 30 positive cases accurately and 14 of the 16 negative cases accurately. The sensitivity was 93% (95% CI, 76%-99%). The specificity was 87.5% (95% CI: 60%-97%). The positive predictive value (PPV) was 93% (95% CI: 76%-99%) and the negative predictive value (NPV) was 87.5% (95% CI: 60%-98%). Conclusion: While most biomarker discovery has been focused on inflammatory cytokines, chemokines, and their receptors, our data suggest that hematopoietic proliferation and transcription regulators in bone marrow might provide important information for the diagnosis and prediction of aGVHD. This data suggests that biomarkers related to B-cell, T-cell, and MHC play a role in aGVHD at the bone marrow level. These findings also suggest that targeting these biomarkers in the bone marrow might be a realistic approach for prophylaxis and treatment that needs to be explored. Although further validation is needed, this study suggests that targeted RNA sequencing by NGS combined with machine learning algorithm can be a practical and cost-effective approach for the diagnosis and prediction of aGVHD. Figure 1 Figure 1. Disclosures Pecora: Genetic testing cooperative: Other: equity investor; Genetic testing cooperative: Membership on an entity's Board of Directors or advisory committees. Goy: Rosewell Park: Consultancy; Elsevier's Practice Update Oncology, Intellisphere, LLC(Targeted Oncology): Consultancy; Acerta: Consultancy, Research Funding; Genentech/Hoffman la Roche: Research Funding; Vincerx pharma: Membership on an entity's Board of Directors or advisory committees; Physicians' Education Resource: Consultancy, Other: Meeting/travel support; Vincerx: Honoraria, Membership on an entity's Board of Directors or advisory committees; AstraZeneca: Honoraria, Membership on an entity's Board of Directors or advisory committees, Research Funding; Xcenda: Consultancy; Janssen: Membership on an entity's Board of Directors or advisory committees; AstraZeneca: Membership on an entity's Board of Directors or advisory committees; Gilead: Membership on an entity's Board of Directors or advisory committees; Janssen: Consultancy, Honoraria, Membership on an entity's Board of Directors or advisory committees, Research Funding; Kite, a Gilead Company: Consultancy, Honoraria, Membership on an entity's Board of Directors or advisory committees, Research Funding; OncLive Peer Exchange: Honoraria; Xcenda: Consultancy, Honoraria; AbbVie/Pharmacyclics: Membership on an entity's Board of Directors or advisory committees; COTA (Cancer Outcome Tracking Analysis): Current holder of stock options in a privately-held company, Membership on an entity's Board of Directors or advisory committees, Other: Leadership role; Elsevier PracticeUpdate: Oncology: Consultancy, Honoraria; Infinity/Verastem: Research Funding; Kite Pharma: Membership on an entity's Board of Directors or advisory committees; Bristol Meyers Squibb: Membership on an entity's Board of Directors or advisory committees; MorphoSys: Honoraria, Other; Genomic Testing Cooperative: Current holder of stock options in a privately-held company, Membership on an entity's Board of Directors or advisory committees, Other: Leadership role; Celgene: Consultancy, Honoraria, Research Funding; Novartis: Consultancy, Honoraria; Hoffman la Roche: Consultancy; Michael J Hennessey Associates INC: Consultancy; LLC(Targeted Oncology): Consultancy; Medscape: Consultancy; Bristol Meyers Squibb: Consultancy, Honoraria, Membership on an entity's Board of Directors or advisory committees; AbbVie/Pharmacyclics: Consultancy, Honoraria, Membership on an entity's Board of Directors or advisory committees, Research Funding; Incyte: Honoraria; Constellation: Research Funding; Janssen: Research Funding; Karyopharm: Research Funding; Phamacyclics: Research Funding; Hackensack Meridian Health, Regional Cancer Care Associates/OMI: Current Employment. Rowley: ReAlta Life Sciences: Consultancy.

Tomato (Solanum lycopersicum) is one of the major vegetable plant and a model system for fruit development. Its global importance is due to its lycopene pigment which has anti-oxidative and anti-cancerous properties. Though > 1.5 M biotic stress associated ESTs of tomato are available but cumulative analysis to predict genes is warranted. Availability of whole genome de novo assembly can advantageously be used to map them over different chromosome. Further, available 0.14 M catalogued markers can be used to introgress specific desirable genes in varietal improvement program. We report here 57 novel genes associated with biotic stress of tomato along with 50 genes having physical location over different chromosomes. We also report 52 cis-regulating elements and 69 putative miRNAs which are involved in regulation of these biotic stresses associated genes. These putative candidate genes associated with biotic stress can be used in molecular breeding in the endeavor of tomato productivity along with its sustainable germplasm management.

The rising demand for popcorn necessitates improving the popping quality with higher yield of popcorn cultivars. Towards this direction several Quantitative Traits Loci (QTLs) for popping traits have been identified. However, identification of accurate and consistent QTLs across different genetic backgrounds and environments is necessary to effectively utilize the identified QTLs in marker-assisted breeding. In the current study, 99 QTLs related to popping traits reported in 8 different studies were assembled and projected on the reference map "Genetic 2005" using BioMercator v4.2 to identify metaQTLs with consistent QTLs. Total ten metaQTLs were identified on chromosome 1 (7 metaQTLs) and 6 (3 metaQTLs) with physical distance ranging between 0.43 and 12.75 Mb, respectively. Four identified metaQTLs, viz., mQTL1_1, mQTL1_5, mQTL1_7 and mQTL6_2 harboured 5–8 QTL clusters with moderately high R2 value. The clustered QTLs were from two or more experiments. Based on the expression pattern in endosperm and pericarp tissues, a total of 229 genes were selected. Nineteen of these genes are involved in carbohydrate metabolism. Of the 19 genes specifically involved in carbohydrate metabolism, 11 of them were in these regions, implying the importance of these clustered QTLs. MetaQTL1_1 at bin location 1.01 coincided with the reported QTLs related to various agronomic traits like stalk diameter, tassel length, leaf area and plant height. The identified metaQTLs can be further explored for fine mapping and candidate gene identification, which can be validated by loss or gain of function. Identified metaQTLs can be used for introgression of popping traits towards enhancing the popping ability.

Background: Neonatal septicemia is a major cause of morbidity and mortality in the neonates. It presented a diagnostic challenge in the resource poor setting of most of the developing countries of world.Methods: This prospective observational study included all term and preterm babies inborn and outborn referred cases. We included neonates less than 7 days of age with clinical suspicion of sepsis. Significant values for screening tests were taken as total leucocyte count (TLC) of >25,000/0.6 mg/dl and gastric aspirate polymorphs>5 per HPF. Sepsis screen was considered positive for two or more positive tests. Blood culture was used as the gold standard. The statistical analysis was done using SPSS 22.0 version.Results: A total number of 60 subjects were included in the study with 45 (75%) as outborn neonates. Most of them presented with tachypnea followed by difficulty in feeding and lethargy. Significant p values were observed using CRP and gastric aspirate polymorphs as independent sepsis screening markers and when combined together (p

Inadequate and nutritionally unbalanced supply of forage results in low productivity of livestock. There is an urgent need of burgeoning forage supply by amalgamating organic and inorganic components in integrated manner.Thereupon, the present investigation was carried out to evaluate the potential of liquid microbial inoculants on growth and yield of forage cowpea.The field experiments were conducted during kharif season (2018) at Punjab Agricultural University, Regional Research Station, Bathinda and Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab respectively. The experiment was laid out in randomized complete block design with a total of eleven treatment combinations of liquid microbial inoculants (Burkholderia seminalis, Burkholderia sp. and Bradyrhizobium sp.) with 75% and 100% RDF and replicated thrice. Results indicated that the treatment T10 (75% RDF + Burkholderia sp. + Burkholderia seminalis) significantly p less then0.05 enhanced vine length (210.47 and 205.33 cm), leaf length (11.77 and 11.53), leaf breadth (8.97 and 9.14 cm) and dry matter yield (40.13 and 38.18 q/ha) at Ludhiana and Bathinda respectively. Moreover, the percentage increase in green fodder yield (q/ha) with T10 treatment over T1 (control) was 13.21% at Ludhiana and 12.50% at Bathinda. Accordingly, it can be concluded that liquid microbial inoculants could play a predominant role in integrated nutrient management of forage cowpea for enhanced productivity.

Even though cultivated rice is highly sensitive to salinity, significant variability exists in the primary and secondary gene-pool of rice with respect to traits of salinity tolerance. Breeding salinity tolerance rice varieties is imperative due to climate change and increasing rice demand for global population. A meta-analysis of plethora of genomic data and published literature available on various genes/factors associated with response to rice salinity and tolerance can be used to enlist selected candidates genes affecting salinity. Such genes can be utilized to identify potential candidate salinity resistance genes from donor rice genotypes and facilitate their transfer to high yielding varieties of rice through marker-assisted breeding. This approach has tremendous advantage over transgenic approach as no bio-safety or regulatory issues are involved in exploiting the variability. Meta-analyses were performed on three datasets viz., rice microarray data of 166 series comprising of 2586 samples, 1228 published research literature in the last one and half decades and RNA-Seq data of 454 and Illumina from Sequence Retrieval Archive (SRA) at NCBI. Among microarray dataset, six salinity related series were finally selected and multi experiment analysis revealed 2289 differentially expressed genes belonging to 44 gene families. Out of these, 13 families viz., AP2-EREBP, AUX/IAA, bZIP, C2H2, bHLH, C3H, HB, HSF, MYB, MYB-related, NAC, Tify and WRKY were selected. Applying various parameters on the published literature data, 13 genes were selected, of which five were common to the different microarray datasets. From RNA-Seq data, total of 751 differentially expressed genes were obtained from 21 gene families, out of which 11 genes were common with those obtained from microarray data and five genes, viz., AP2-EREBP/DREB, MYB, HSF, bZIP and NAC were common to all the three data sets. Based on the results obtained, a total of 31 meta-analyzed genes have been selected and recommended for use in genetic improvement programs aimed at salinity resistance in rice. The meta-analysis of microarray, RNA-Seq and published literature has been successfully used to select 31 best salinity tolerance associated genes which can be exploited by candidate gene approach for targeted introgression through marker assisted breeding. This approach has multi-fold advantages, as it obviates statutory and ecological issues. Such endeavors are more warranted for combating the key abiotic stresses like salinity, whose effects are increasing due to a changing climate.

The study of the seed storage behavior and cryopreservation of embryonic axes was attempted in Citrus jambhiri genotypes using air desiccation-freezing, vitrification, and encapsulation-dehydration methods. Seeds of this species revealed nonorthodox seed storage behavior with moderate seed longevity and sensitivity to desiccation and freezing. Successful cryopreservation was achieved with all three methods using embryonic axes; however, the recovery growth percentage significantly differed among these methods. Cryopreservation was efficient for the embryonic axes desiccated to 13%-15% moisture content. Freezing of embryonic axes at this moisture content in liquid nitrogen showed a good recovery rate of 40%-50%. In the vitrification method, embryonic axes subjected to PVS2 treatment for 40 min had the highest recovery rate of 25% after cryopreservation. In the encapsulation-dehydration method, encapsulated axes precultured on 0.5 M sucrose medium followed by 6 h of desiccation had the highest recovery growth of 30%-60% after cryopreservation. Out of the three methods employed, the encapsulation-dehydration method gave the best recovery values for embryonic axes. High regeneration values of embryos in comparison to embryonic axes prompted us to undertake large-scale cryobanking of C. jambhiri using embryos (seeds without seed coats) and more than 100 accessions of C. jambhiri have been cryostored in the national cryobank. This would further serve the purpose of conserving nucellar embryos with zygotic embryos.

The dairy industry is a major concern of present era, because it generates a large amount of wastewater. Treatment of the dairy wastewater has a great significance because treated water may be used for irrigation and industrial processes. The present research focused on the evaluation of Vermifiltration process using padding media (garden waste) and filter bed material to treat dairy wastewater at different hydraulic loading rates. Vermifilter constituted the Eisenia fetida species of earthworm for the treatment of dairy effluent to achieve the critical quality of the treated wastewater. In this Vermifiltration, three hydraulic loading rates of 1.5, 2 and 2.5 m3/m2/d were applied to get optimize results from treatment of dairy wastewater through Vermifiltration process. Performance of the vermifilter was determined by analyzing the parameters such as pH, BOD (Biological Oxygen Demand), COD (Chemical Oxygen Demand), TSS (Total Suspended Solids), TP (Total phosphorus) and the optimum efficiency was observed in the case of hydraulic loading rate 1.5 m3/m2/d. For this hydraulic loading rate, the removal efficiency of BOD, COD, TSS and TP were observed to be 95.76%, 90.56%, 80.24% and 88.76% respectively. Furthermore, the vermicompost resulting from the vermifiltration was found to be very rich in nitrates and phosphates and treated effluent can be used for irrigation purpose.

Identification of a small core germplasm set representing the available genetic diversity is essential for its proper evaluation and subsequent utilization in rice improvement programmes. For constituting a small diverse mini-core panel of Indian rice germplasm, a representative set of 6912 accessions drawn based on their geographic origin from the whole rice germplasm collection available in the National Gene Bank was genotyped using 36 microsatellite markers. Automated fragment analysis of amplicons yielded a total of 435 alleles, with an average 12.4 and range of 3–29 alleles per locus. Polymorphism information content (PIC) ranged from 0.08 (RGNMS190) to 0.86 (RM552) with an average of 0.528. Based on genotyping data, a mini-core consisting of 98 genotypes was identified. Ninety-four per cent of the alleles present in the core set were present in the mini-core. The identified small but diverse panel will be useful for further intensive trait-specific evaluation and utilization in allele mining.

Pummelo is a natural non hybrid mono-embryonic and sub-tropical fruit species with vast morphological variability. Morphological characterization of 46 accessions collected from different parts of India on the basis of 42 phenotypic characters including leaf, fruit and seed characters is presented in the paper. Pair-wise similarity analysis revealed moderate to significant variation in the 46 accessions of pummel accessions. Pairwise similarity among the pummelo accessions ranged from 0.31 to 0.66 with an average of 0.48 based on morphometric data. Maximum similarity (0.66) was observed between accessions number of PS-1 and PS-3. Based on Euclidean distance divided these accessions into five main clusters out of which, Cluster I proved the largest cluster comprising of 14 accessions while cluster II consisted of seven accessions and cluster III with ten accessions. Cluster IV was smallest one with only two accessions, while cluster V consisted of 13 accessions. Principal component analysis based on 42 morphological characters showed significant variation among all the accessions. The least variation was observed in qualitative characters, while the quantitative characters significantly differed. The two dimensional (2-D) plot generated from PCA showed three groups which were found to be more or less similar to the clustering pattern of the UPGMA dendrogram. The PCA identified traits were most significant that were responsible for grouping of certain genotypes into specific cluster and hence, revealed some aspects of interrelation among genotypes that were not discernable by the UPGMA analysis. The analysis gave 36 principal components out of which first ten principal components contributed 69.52% of the total variability. The results derived from this study indicated significant level of variability present within the pummelo group in India, which can be used as important source of genetic diversity and for future breeding programmes.

Hepatitis C virus (HCV) is a major cause of global morbidity, causing chronic liver injury that can progress to cirrhosis and hepatocellular carcinoma. The liver is a large and complex organ containing multiple cell types, including hepatocytes, sinusoidal endothelial cells (LSEC), Kupffer cells, and biliary epithelial cells. Hepatocytes are the major reservoir supporting HCV replication; however, the role of nonparenchymal cells in the viral lifecycle remains largely unexplored. LSEC secrete factors that promote HCV infection and transcript analysis identified bone morphogenetic protein 4 (BMP4) as a candidate endothelial-expressed proviral molecule. Recombinant BMP4 increased HCV replication and neutralization of BMP4 abrogated the proviral activity of LSEC-conditioned media. Importantly, BMP4 expression was negatively regulated by vascular endothelial growth factor A (VEGF-A) by way of a VEGF receptor-2 (VEGFR-2) primed activation of p38 MAPK. Consistent with our in vitro observations, we demonstrate that in normal liver VEGFR-2 is activated and BMP4 expression is suppressed. In contrast, in chronic liver disease including HCV infection where there is marked endothelial cell proliferation, we observed reduced endothelial cell VEGFR-2 activation and a concomitant increase in BMP4 expression. Conclusion: These studies identify a role for LSEC and BMP4 in HCV infection and highlight BMP4 as a new therapeutic target for treating individuals with liver disease. (Hepatology 2014;59:375–384)

The present study was aimed to assess urban-rural disparity in the physical activity pattern of government school children of Punjab (India). A survey was conducted on 1050 children (11–17 years) randomly selected from urban and rural government schools to collect information on their physical activity pattern (school sports, leisure time physical activity/LTPA and mode of commuting to school) and sedentary behaviour (screen time). The study revealed no urban-rural disparity in mean time spent by school children in LTPA (5.1 h wk−1 each) and screen activities (9.8 for urban vs. 9.5 h wk−1 for rural subjects). Urban school children were spending (p≤ 0.05) more time (7.5 h wk−1) in school sports, than rural school children (6.6 h wk−1). The percentage of active commuters was more from rural schools (92%) as compared to urban schools (85%). Overall the children were spending on an average 6.9, 5.1 and 9.6 h wk−1 in school sports, LTPA and screen activities, respectively. Based on AAP and WHO levels, children from government schools of Punjab did not possess sedentary behaviour as they had adequate physical activity level, low screen time and were mostly active commuters.

The N-end rule pathway is conserved from bacteria to man and determines the half-life of a protein based on its N-terminal amino acid. In Escherichia coli, model substrates bearing an N-degron are recognised by ClpS and degraded by ClpAP in an ATP-dependent manner. Here, we report the isolation of 23 ClpS-interacting proteins from E. coli. Our data show that at least one of these interacting proteins--putrescine aminotransferase (PATase)--is post-translationally modified to generate a primary N-degron. Remarkably, the N-terminal modification of PATase is generated by a new specificity of leucyl/phenylalanyl-tRNA-protein transferase (LFTR), in which various combinations of primary destabilising residues (Leu and Phe) are attached to the N-terminal Met. This modification (of PATase), by LFTR, is essential not only for its recognition by ClpS, but also determines the stability of the protein in vivo. Thus, the N-end rule pathway, through the ClpAPS-mediated turnover of PATase may have an important function in putrescine homeostasis. In addition, we have identified a new element within the N-degron, which is required for substrate delivery to ClpA.

Protein degradation in the cytosol of Escherichia coli is carried out by a variety of different proteolytic machines, including ClpAP. The ClpA component is a hexameric AAA+ (ATPase associated with various cellular activities) chaperone that utilizes the energy of ATP to control substrate recognition and unfolding. The precise role of the N-domains of ClpA in this process, however, remains elusive. Here, we have analysed the role of five highly conserved basic residues in the N-domain of ClpA by monitoring the binding, unfolding and degradation of several different substrates, including short unstructured peptides, tagged and untagged proteins. Interestingly, mutation of three of these basic residues within the N-domain of ClpA (H94, R86 and R100) did not alter substrate degradation. In contrast mutation of two conserved arginine residues (R90 and R131), flanking a putative peptide-binding groove within the N-domain of ClpA, specifically compromised the ability of ClpA to unfold and degrade selected substrates but did not prevent substrate recognition, ClpS-mediated substrate delivery or ClpP binding. In contrast, a highly conserved tyrosine residue lining the central pore of the ClpA hexamer was essential for the degradation of all substrate types analysed, including both folded and unstructured proteins. Taken together, these data suggest that ClpA utilizes two structural elements, one in the N-domain and the other in the pore of the hexamer, both of which are required for efficient unfolding of some protein substrates.

TRAF2 is a component of TNF superfamily signalling complexes and plays an essential role in the regulation and homeostasis of immune cells. TRAF2 deficient mice die around birth, therefore its role in adult tissues is not well-explored. Furthermore, the role of the TRAF2 RING is controversial. It has been claimed that the atypical TRAF2 RING cannot function as a ubiquitin E3 ligase but counterclaimed that TRAF2 RING requires a co-factor, sphingosine-1-phosphate, that is generated by the enzyme sphingosine kinase 1, to function as an E3 ligase. Keratinocyte-specific deletion of Traf2, but not Sphk1 deficiency, disrupted TNF mediated NF-kappa B and MAP kinase signalling and caused epidermal hyperplasia and psoriatic skin inflammation. This inflammation was driven by TNF, cell death, non-canonical NF-kB and the adaptive immune system, and might therefore represent a clinically relevant model of psoriasis. TRAF2 therefore has essential tissue specific functions that do not overlap with those of Sphk1. Refereed/Peer-reviewed

BACKGROUND: During organogenesis the embryo is highly sensitive to oxidative stress. We hypothesize that oxidative stress and activation of a redox-sensitive transcription factor, activator protein-1 (AP-1), are early indicators of embryonic stress in response to a teratogenic insult. 5-Bromo-2′-deoxyuridine (BrdU) was chosen as a model teratogen to test this hypothesis; BrdU is a thymidine analog that is incorporated into replicating DNA. METHODS: Timed pregnant CD1 mice were given vehicle or BrdU (400, 600, 800, or 1000 mg of BrdU/kg of body weight) on gestation day 9 (GD 9). Oxidative stress, assessed as the ratio of glutathione disulfide (GSSG) to reduced glutathione (GSH), and AP-1 DNA binding activity (c-Fos- and c-Jun-dependent DNA binding) were measured in the maternal livers and embryos 0.5, 3, and 6 hr after treatment. External and skeletal malformations were assessed on GD 18. N-acetylcysteine, a glutathione precursor, was coadministered with BrdU to further explore the relationship between teratogenicity and redox homeostasis. RESULTS: BrdU exposure produced a dose-dependent increase in skeletal malformations, which included polydactyly, and delayed ossification of the sternebrae and vertebrae. Exposure to teratogenic doses of BrdU depleted GSH concentrations and increased oxidative stress, as assessed by the GSSG:GSH ratio, in both maternal livers and embryos. While c-Jun DNA binding activity in embryos was not affected, c-Fos DNA binding activity was elevated significantly 3 hr after BrdU exposure. Coadministration of N-acetylcysteine decreased the skeletal malformations and AP-1 DNA binding activity induced by BrdU. CONCLUSIONS: BrdU exposure induced an embryonic stress response manifested as an increase in oxidative stress and AP-1 DNA binding activity; these data support the hypothesis that disturbances in redox homeostasis mediate the response of the conceptus to a teratogenic insult. Birth Defects Research (Part A), 2006. © 2006 Wiley-Liss, Inc.

Biotic stress is a major cause of heavy loss in grape productivity. In order to develop biotic stress-resistant grape varieties, the key defense genes along with its pathway have to be deciphered. In angiosperm plants, lipase-like protein phytoalexin deficient 4 (PAD4) is well known to be essential for systemic resistance against biotic stress. PAD4 functions together with its interacting partner protein enhanced disease susceptibility 1 (EDS1) to promote salicylic acid (SA)-dependent and SA-independent defense pathway. Existence and structure of key protein of systemic resistance EDS1 and PAD4 are not known in grapes. Before SA pathway studies are taken in grape, molecular evidence of EDS1: PAD4 complex is to be established. To establish this, EDS1 protein sequence was retrieved from NCBI and homologous PAD4 protein was generated using Arabidopsis thaliana as template and conserved domains were confirmed. In this study, computational methods were used to model EDS1 and PAD4 and simulated the interactions of EDS1 and PAD4. Since no structural details of the proteins were available, homology modeling was employed to construct three-dimensional structures. Further, molecular dynamic simulations were performed to study the dynamic behavior of the EDS1 and PAD4. The modeled proteins were validated and subjected to molecular docking analysis. Molecular evidence of stable complex of EDS1:PAD4 in grape supporting SA defense pathway in response to biotic stress is reported in this study. If SA defense pathway genes are explored, then markers of genes involved can play pivotal role in grape variety development especially against biotic stress leading to higher productivity.

West Nile Virus (WNV) first arrived in Ontario, Canada in 2001 and has since spread throughout most of the province, causing disease in humans. The provincial government established a province-wide surveillance program to monitor WNV transmission throughout the 36 regional health units. Here we have acquired records of WNV human and mosquito surveillance from 2002 to 2013 to describe seasonal and geographic trends in WNV activity in southern Ontario. Additionally, we obtained climate data from seven municipalities to investigate how temperature and precipitation affect WNV transmission dynamics. We identified a strong quadratic relationship between the number of confirmed human cases and positive Culex mosquito pools recorded at the end of each year (R2 = 0.9783, p < 0.001). Using Spearman rank correlation tests, we identified that the minimum infection rate of Culex pipiens/restuans pools are the strongest predictor of human cases at a 1 week lag period. We also identified positive correlations between minimum infection rates, temperature, vector abundance, and cumulative precipitation. Global Moran's I index indicates strong positive autocorrelation and clustering of positive Culex pool counts in southern Ontario. Local indicators of spatial association tests revealed a total of 44 high-high and 1 high-low trap locations (n = 680). In the current work we have identified when and where hot spots of WNV activity have occurred in southern Ontario. The municipalities surrounding the western shore of the Lake Ontario and Windsor-Essex County have the largest records of positive mosquitoes and human cases. We identified that positive mosquitoes are a strong indicator of human cases to follow in the coming weeks. An epidemic action threshold of cumulative positive Culex pools was established, allowing Ontario public health officials to predict an epidemic at epidemiological week 34 (rho = 0.90, p < 0.001). These data have the potential to contribute to more efficient larvicide programs and awareness campaigns for the public.

Necroptosis is considered to be complementary to the classical caspase-dependent programmed cell death pathway, apoptosis. The pseudokinase Mixed Lineage Kinase Domain-Like (MLKL) is an essential effector protein in the necroptotic cell death pathway downstream of the protein kinase Receptor Interacting Protein Kinase-3 (RIPK3). How MLKL causes cell death is unclear, however RIPK3–mediated phosphorylation of the activation loop in MLKL trips a molecular switch to induce necroptotic cell death. Here, we show that the MLKL pseudokinase domain acts as a latch to restrain the N-terminal four-helix bundle (4HB) domain and that unleashing this domain results in formation of a high-molecular-weight, membrane-localized complex and cell death. Using alanine-scanning mutagenesis, we identified two clusters of residues on opposing faces of the 4HB domain that were required for the 4HB domain to kill cells. The integrity of one cluster was essential for membrane localization, whereas MLKL mutations in the other cluster did not prevent membrane translocation but prevented killing; this demonstrates that membrane localization is necessary, but insufficient, to induce cell death. Finally, we identified a small molecule that binds the nucleotide binding site within the MLKL pseudokinase domain and retards MLKL translocation to membranes, thereby preventing necroptosis. This inhibitor provides a novel tool to investigate necroptosis and demonstrates the feasibility of using small molecules to target the nucleotide binding site of pseudokinases to modulate signal transduction.

Mutations in Bloom helicase (BLM) lead to Bloom Syndrome (BS). BS is characterized by multiple clinical manifestations including predisposition to a wide spectrum of cancers. Studies have revealed the mechanism of BLM recruitment after stalled replication and its role during the repair of DNA damage. We now provide evidence that BLM undergoes K48-linked ubiquitylation and subsequent degradation during mitosis due to the E3 ligase, Fbw7α. Fbw7α carries out its function after GSK3β- and CDK2/cyclin A2-dependent phosphorylation events on Thr171 and Ser175 of BLM which lies within a well-defined phosphodegron, a sequence which is conserved in all primates. Phosphorylation on BLM Thr171 and Ser175 depends on prior phosphorylation at Thr182 by Chk1/Chk2. Thr182 phosphorylation not only controls BLM ubiquitylation and degradation during mitosis but is also a determinant for its localization on the ultrafine bridges. Consequently lack of Thr182 phosphorylation leads to multiple manifestations of chromosomal instability including increased levels of DNA damage, lagging chromatin, micronuclei formation, breaks and quadriradials. Hence Thr182 phosphorylation on BLM has two functions-it regulates BLM turnover during mitosis and also helps to maintain the chromosomal stability.

In Escherichia coli, the ClpAP protease, together with the adaptor protein ClpS, is responsible for the degradation of proteins bearing an amino-terminal destabilizing amino acid (N-degron). Here, we determined the three-dimensional structures of ClpS in complex with three peptides, each having a different destabilizing residue--Leu, Phe or Trp--at its N terminus. All peptides, regardless of the identity of their N-terminal residue, are bound in a surface pocket on ClpS in a stereo-specific manner. Several highly conserved residues in this binding pocket interact directly with the backbone of the N-degron peptide and hence are crucial for the binding of all N-degrons. By contrast, two hydrophobic residues define the volume of the binding pocket and influence the specificity of ClpS. Taken together, our data suggest that ClpS has been optimized for the binding and delivery of N-degrons containing an N-terminal Phe or Leu.

The rice root-knot nematode, Meloidogyne graminicola is one of the major pest of the rice-wheat cropping system, and is responsible for considerable yield reductions. Resistance against M. graminicola in rice could be most valuable in alleviating this problem. In the present study, 64 rice cvs./landraces were evaluated for resistance against rice root-knot nematode on the basis of root-knot index. Our study showed a large variation in susceptibility and sensitivity to M. graminicola infection among the rice cvs./landraces examined. Out of the total 64 rice cvs., seven (Abhishek, Khaja, Super Sugandhamati, Kishori Dehraduni, Gaudeshwari, Tuniaslet, Chima Kamin) had less than 10 galls/plant and of these, Abhishek exhibited a strong resistance response with least number of galls (2 galls/plant) and necrotic browning of roots. The nematode females in the roots of cv. Abhishek were smaller in size compared to those on the highly susceptible cv. Bangla Patni. The histopathological studies showed that the giant cells collapsed and degenerated before the J2s developed into adults. The resistant trait exhibiting rice cultivar, Abhishek, holds promise for resistance breeding and also for identifying resistance gene/s against M. graminicola.

The availability of zinc in the autoclaved black-gram diet was better as compared to germinated, fermented and raw black-gram diets and this may be due to more destruction of phytate.