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Subcellular localization prediction of the proteome is one of major goals of large-scale genome or proteome sequencing projects to define the gene functions that could be possible with the help of computational modeling techniques. Previously, different methods have been developed for this purpose using multi-label classification system and achieved a high level of accuracy. However, during the validation of our blind dataset of plant vacuole proteins, we observed that they have poor performance with accuracy value range from ~1.3% to 48.5%. The results showed that the previously developed methods are not very accurate for the plant vacuole protein prediction and thus emphasize the need to develop a more accurate and reliable algorithm. In this study, we have developed various compositions as well as PSSM-based models and achieved a high accuracy than previously developed methods. We have shown that our best model achieved ~63% accuracy on blind dataset, which is far better than currently available tools. Furthermore, we have implemented our best models in the form of GUI-based free software called ‘VacPred’ which is compatible with both Linux and Window platform. This software is freely available for download at www.deepaklab.com/vacpred.

Developing herbicide-tolerant wheat varieties is highly desirable for effective weed management and improved crop yield. The enzyme acetolactate synthase (ALS) is the target enzyme for the sulfonylurea class of herbicides. The structural analysis of mutable sites in ALS is crucial for the generation of herbicide-resistant crops. Previous studies indicated that mutant lines of Triticum aestivum ALS (TaALS) with amino acid substitutions at P174, G631, and G632 residues provided resistance to sulfonylurea herbicide, nicosulfuron. The present study aimed to provide structural insights into mutable residues causing sulfonylurea herbicide resistance to TaALS enzyme through in-silico molecular docking and simulation approaches. The molecular docking analysis suggested a single point mutation at TaALS-P174S, its double mutant conformations (TaALS-G632S/P174S and TaALS-G631D/G632S) and associated triple mutant conformation (TaALS-G631D/G632S/P174S) to have the lowest binding affinity with nicosulfuron than the wild-type conformation of TaALS. Furthermore, the molecular dynamic simulation study confirms the weakest and more stable binding of the triple mutant conformation with nicosulfuron. Our computational study identifies a triple mutant conformation (TaALS-G631D/G632S/P174S) to be more effective in developing sulfonylurea herbicide-resistant wheat crops.

GRAS genes belong to the plant-specific transcription factors (TF’s) family that are known to be involved in plant growth and development. In this study, we have identified 37 genes from the bottle gourd genome that encodes for GRAS TF’s. Except for the SCLA, we were able to identify at least one gene from each of the 17 subfamilies. Gene structure and chromosomal analysis showed that maximum seven genes are present on Chr7 followed by six genes on Chr1. The subcellular location analysis revealed that most of the genes were localized in the nucleus, except for a few in chloroplast and mitochondria. Additionally, we have identified one tandem gene duplication event on Chr7 and three major motifs that were present in all the GRAS genes. Furthermore, the protein–protein interaction prediction and gene expression analysis showed five candidate hub-genes interact with various other genes and thus probably control the expression of interacting partners in different plant tissues. Overall, this study provides a comprehensive analysis of GRAS transcription factors in bottle gourd genome which could be further extended to other vegetable crops.

The striatum serves an important role in motor control, and neurons in this area encode the body’s initiation, cessation, and speed of locomotion. However, it remains unclear whether the same neurons also encode the step-by-step rhythmic motor patterns of individual limbs that characterize gait. By combining high-speed video tracking, electrophysiology, and optogenetic tagging, we found that a sizable population of both D1 and D2 receptor expressing medium spiny projection neurons (MSNs) were phase-locked to the gait cycle of individual limbs in mice. Healthy animals showed balanced limb phase-locking between D1 and D2 MSNs, while dopamine depletion led to stronger phase-locking in D2 MSNs. These findings indicate that striatal neurons represent gait on a single-limb and step basis, and suggest that elevated limb phase-locking of D2 MSNs may underlie some of the gait impairments associated with dopamine loss.

Sugarcane ( Saccharum spp.)is an economically useful crop grown globally for sugar, ethanol and biofuel production. The crop is vulnerable to fungus Colletotrichum falcatum known to cause red rot disease. The pathogen hydrolyses stalk parenchyma cells where sucrose is accumulated resulting in upto 75% losses in sugar recovery. In this study, transgenic sugarcane having resistance against red rot was developed by introducing Trichoderma spp. endochitinase following Agrobacterium mediated transformation. The transgene introduction and expression in genetically modified plants were verified through qRT-PCR revealing upto 6-fold enhancement in endochitinase expression than non-transgenic plants. Hyperspectral Imaging of transgenic plants displayed altered leaf reflectance spectra and vegetative indices that were positively correlated with ransgene expression. The bioassay with virulent pathotypes of C . falcatum CF08 and CF13 known for epiphytotic occurrence resulted in identification of resistant plant Chit 3-13.The plants with higher reflectance also displayed improved disease resistance, implying their early classification into resistant/susceptible. The losses in sucrose content were minimized (up to 4-fold) in inoculated resistant plant Chit 3–13 as compared to susceptible non-transgenic plant, and a fewer pathogen hyphae were detected in vascular cells of the former through optical microscopy. The electron micrographs confirmed sucrose-filled stalk parenchyma cells in Chit 3–13; in contrast, cells of non-transgenic inoculated plant were depleted of sucrose. The active sites involved in cleaving 1–4 β-glycoside bonds of N-acetyl-d-glucosaminein the pathogen hyphal walls were detected through endochitinase protein structural modelling. The transgenic sugarcane is an important source for in trogressingred rot resistance in plant breeding programs.

Yellow mosaic disease (YMD) in bitter gourd ( Momordica charantia ) is a devastating disease that seriously affects its yield. Although there is currently no effective method to control the disease, breeding of resistant varieties is the most effective and economic option. Moreover, quantitative trait locus (QTL) associated with resistance to YMD has not yet been reported. With the objective of mapping YMD resistance in bitter gourd, the susceptible parent “Punjab-14” and the resistant parent “PAUBG-6” were crossed to obtain F 4 mapping population comprising 101 individuals. In the present study, the genotyping by sequencing (GBS) approach was used to develop the genetic linkage map. The map contained 3,144 single nucleotide polymorphism (SNP) markers, consisted of 15 linkage groups, and it spanned 2415.2 cM with an average marker distance of 0.7 cM. By adopting the artificial and field inoculation techniques, F 4:5 individuals were phenotyped for disease resistance in Nethouse (2019), Rainy (2019), and Spring season (2020). The QTL analysis using the genetic map and phenotyping data identified three QTLs qYMD.pau_3.1 , qYMD.pau_4.1 , and qYMD.pau_5.1 on chromosome 3, 4, and 5 respectively. Among these, qYMD.pau_3.1 , qYMD.pau_4.1 QTLs were identified during the rainy season, explaining the 13.5 and 21.6% phenotypic variance respectively, whereas, during the spring season, qYMD.pau_4.1 and qYMD.pau_5.1 QTLs were observed with 17.5 and 22.1% phenotypic variance respectively. Only one QTL qYMD.pau_5.1 was identified for disease resistance under nethouse conditions with 15.6% phenotypic variance. To our knowledge, this is the first report on the identification of QTLs associated with YMD resistance in bitter gourd using SNP markers. The information generated in this study is very useful in the future for fine-mapping and marker-assisted selection for disease resistance.

Leguminous plants are the rich source of dietary proteins that account for 27% of the world primary crop production. Their high vulnerability to the pathogens resulted in the annual loss of ~2.0 - 2.1 million tonnes of crops. Among the various pests, pea aphids represent the highly specialized and most devastating pathogens of the leguminous plants. During the evolution, they evolved themselves in such a manner that showed reduced performance when grown in the alternative host plant. In order to understand their host preference, genome level scan is required. Therefore, in this study, we used the genome-wide SNP scan of five pea aphid biotypes of >70 GB raw sequencing reads. We used the pea aphid genome as a reference having size of ~450 MB. Using quality filtering, BWA alignment, and GATK tool, we identified more than 1.5 million bi-allelic and around 1500 multi-allelic nuclear SNPs with a Ts/Tv ratio of 1.42. A high rate of mutation was observed in T. pratense biotype as compared to the M. Sativa. Their functional classification revealed approximately 26K - 30K missense and ~400 nonsense variation in their nuclear genome. Furthermore, the genome-wide scan revealed that an average of 5.42% of the identified SNPs located in the exon regions while a major portion ~80% were present in the intron region of the genome. This is the first report of genome-wide SNPs analysis on different pea aphid biotypes which in future could be used for host-pathogen interaction, and diversity analysis. Our future goal is the analysis of more biotypes and development of a unique resource of SNP’s present biologically important class of genes playing role in immunity, olfactory response, etc.

Stripe rust disease of wheat, caused by Puccinia striiformis f. sp. tritici , ( Pst ) is one of the most serious diseases of wheat worldwide. In India, virulent stripe rust races have been constantly evolving in the North-Western Plains Zone leading to the failure of some of the most widely grown resistant varieties in the region. With the goal of studying the recent evolution of virulent races in this region, we conducted whole-genome re-sequencing of three prevalent Indian Pst pathotypes Pst46S119, Pst78S84 and Pst110S119. We assembled 58.62, 58.33 and 55.78 Mb of Pst110S119, Pst46S119 and Pst78S84 genome, respectively and found that pathotypes were highly heterozygous. Comparative phylogenetic analysis indicated the recent evolution of pathotypes Pst110S119 and Pst78S84 from Pst46S119. Pathogenicity-related genes classes (CAZyme, proteases, effectors, and secretome proteins) were identified and found to be under positive selection. Higher rate of gene families expansion were also observed in the three pathotypes. A strong association between the effector genes and transposable elements may be the source of the rapid evolution of these strains. Phylogenetic analysis differentiated the Indian races in this study from other known United States, European, African, and Asian races. Diagnostic markers developed for the identification of three Pst pathotypes will help tracking of yellow rust at farmers field and strategizing resistance gene deployment.

We planned this study to compare three approaches to arterial cannulation, i.e., catheter over the needle, catheter over the guidewire, and ultrasound-guided cannulation, in terms of overall success rate, first pass success rate, time for cannulation and incidence of complications. After obtaining informed written consent from the patient, they were randomized into three groups, based on chits in the box technique, to undergo radial artery cannulation as follows: group N (using catheter over needle technique), group W (using catheter over guidewire technique), group U (radial artery cannulations under ultrasound guidance). We calculated a sample size of 50 patients in each group based on the primary endpoint of the overall success rate. The data was analyzed using one-way ANOVA and post hoc Tukey's test. There was a non-statistically significant trend towards a higher overall success rate in groups W and U compared to group N (47 and 46, respectively, compared to 43, p-value 0.35). Similarly, no significant differences were observed concerning any of the characteristics of radial artery cannulation, except the first pass success rate, where the success rate was highest in group W (33, 70.21%), followed by group U (34, 68%) with a p-value of 0.04. Though catheter over guidewire and ultrasound-based techniques offer advantages in terms of higher first-pass success rate, they do not significantly increase the overall success rate or reduce the total incidence of complications.

Bitter gourd ( Momordica charantia L.) is an important vegetable crop having numerous medicinal properties. Earliness and yield related traits are main aims of bitter gourd breeding program. High resolution quantitative trait loci (QTLs) mapping can help in understanding the molecular basis of phenotypic variation of these traits and thus facilitate marker-assisted breeding. The aim of present study was to identify genetic loci controlling earliness, fruit, and seed related traits. To achieve this, genotyping-by-sequencing (GBS) approach was used to genotype 101 individuals of F 4 population derived from a cross between an elite cultivar Punjab-14 and PAUBG-6. This population was phenotyped under net-house conditions for three years 2018, 2019, and 2021. The linkage map consisting of 15 linkage groups comprising 3,144 single nucleotide polymorphism (SNP) markers was used to detect the QTLs for nine traits. A total of 50 QTLs for these traits were detected which were distributed on 11 chromosomes. The QTLs explained 5.09–29.82% of the phenotypic variance. The highest logarithm of the odds (LOD) score for a single QTL was 8.68 and the lowest was 2.50. For the earliness related traits, a total of 22 QTLs were detected. For the fruit related traits, a total of 16 QTLs and for seed related traits, a total of 12 QTLs were detected. Out of 50 QTLs, 20 QTLs were considered as frequent QTLs (FQ-QTLs). The information generated in this study is very useful in the future for fine-mapping and marker-assisted selection for these traits in bitter gourd improvement program.