Role of Urinary Biomarkers (Transforming Growth Factor ß1, Neutrophil Gelatinase-Associated Lipocalin, and Cystatin C) as a Prognostic Factor of Renal Outcome in the Posterior Urethral Valve.

Background: The urinary biomarker response precedes the appearance of any renal structural or functional derangement. Transforming growth factor-ß1 (TGF-ß1), neutrophil gelatinase associated lipocalin (NGAL), and Cystatin C (CysC) can act as the early prognostic markers in posterior urethral valve (PUV) patients. Aim: To compare the urinary levels of TGF-ß1, NGAL, and CysC between PUV cases and age matched controls and to correlate these with renal structural and functional parameters. Materials and Methods: This prospective study included children with PUV diagnosed using the standard investigations and an equal number of age-matched controls with nonurological problems. For the study subjects, the urinary samples were collected at three different time points (pre- and postoperatively at 3 and 6 months), whereas for controls, only single-voided samples were studied. The urinary levels of TGF-ß1, NGAL, and CysC were estimated by the standardized techniques using the ELISA kits. Statistical methods were used to drive the comparisons between cases and controls. Results: Fifteen children with a median age of 10 (5-48) months were enrolled in each of the two groups. The mean uTGF-ß1 in the case group was significantly higher at all three time points (43.20 ± 6.13 pg/ml, 43.33 ± 11.89 pg/ml and 40.71 ± 9.01 pg/ml) as compared to the control group (29.12 ± 8.31 pg/ml) (P ≤ 0.001). The median uNGAL in the case group was also higher (17.78 ng/ml, 2.35 ng/ml and 2.536 ng/ml) as compared to the control group (1.31 ng/ml). However, the difference was significant only preoperatively (P = 0.02). The median uCysC in case group was similarly higher (0.347 µg/ml, 0.439 µg/ml, and 0.382 µg/ml) than the control group (0.243 µg/ml) (P > 0.05). Serum creatinine in the case group (0.49 mg/dl) showed no significant rise above that of control (0.24 mg/dl). A cutoff value of uTGF-ß1 = 36.55 pg/ml (P < 0.001), uNGAL = 0.879 ng/ml (P = 0.02), and uCysC = 0.25 µg/ml (P = 0.22) was found to be associated with renal damage in PUV. A significant correlation was found between uNGAL and S. creatinine at 3 months (r = 0.43, P = 0.017) and 6 months (r = 0.47, P = 0.08). Conclusion: The elevated uTGF-ß1, a decline in uNGAL and an increase in uCysC suggests ongoing inflammation, improvement in hydronephrosis and a prolonged proximal tubular dysfunction in PUV patients, respectively.

DeepPlnc: Bi-modal deep learning for highly accurate plant lncRNA discovery.

We present here a bi-modal CNN based deep-learning system, DeepPlnc, to identify plant lncRNAs with high accuracy while using sequence and structural properties. Unlike most of the existing software, it works accurately even in conditions with ambiguity of boundaries and incomplete sequences. It scored consistently high for performance metrics while breaching accuracy of >98% when tested across a large number of validated instances. During multiple benchmarkings DeepPlnc consistently outperformed all the compared tools and maintained a highly significant lead in the range of 2.5%- 4.6% from the second best performing tool (p-value << 0.01). DeepPlnc was used to annotate a de novo assembled transcriptome of a himalayan species where again it suggested its much better suitability for genome and transcriptome annotation purposes than the existing tools. DeepPlnc has been made freely available as a web-server and stand-alone program at https://scbb.ihbt.res.in/DeepPlnc/.

Epigenetic silencing of SOCS5 potentiates JAK-STAT signaling and progression of T-cell acute lymphoblastic leukemia.

Activating mutations in cytokine receptors and transcriptional regulators govern aberrant signal transduction in T-cell lineage acute lymphoblastic leukemia (T-ALL). However, the roles played by suppressors of cytokine signaling remain incompletely understood. We examined the regulatory roles of suppressor of cytokine signaling 5 (SOCS5) in T-ALL cellular signaling networks and leukemia progression. We found that SOCS5 was differentially expressed in primary T-ALL and its expression levels were lowered in HOXA-deregulated leukemia harboring KMT2A gene rearrangements. Here, we report that SOCS5 expression is epigenetically regulated by DNA methyltransferase-3A-mediated DNA methylation and methyl CpG binding protein-2-mediated histone deacetylation. We show that SOCS5 negatively regulates T-ALL cell growth and cell cycle progression but has no effect on apoptotic cell death. Mechanistically, SOCS5 silencing induces activation of JAK-STAT signaling, and negatively regulates interleukin-7 and interleukin-4 receptors. Using a human T-ALL murine xenograft model, we show that genetic inactivation of SOCS5 accelerates leukemia engraftment and progression, and leukemia burden. We postulate that SOCS5 is epigenetically deregulated in T-ALL and serves as an important regulator of T-ALL cell proliferation and leukemic progression. Our results link aberrant downregulation of SOCS5 expression to the enhanced activation of the JAK-STAT and cytokine receptor-signaling cascade in T-ALL.

De novo UBE2A mutations are recurrently acquired during chronic myeloid leukemia progression and interfere with myeloid differentiation pathways.

Despite the advent of tyrosine kinase inhibitors, a proportion of chronic myeloid leukemia patients in chronic phase fail to respond to imatinib or to second-generation inhibitors and progress to blast crisis. Until now, improvements in the understanding of the molecular mechanisms responsible for chronic myeloid leukemia transformation from chronic phase to the aggressive blast crisis remain limited. Here we present a large parallel sequencing analysis of 10 blast crisis samples and of the corresponding autologous chronic phase controls that reveals, for the first time, recurrent mutations affecting the ubiquitin-conjugating enzyme E2A gene (UBE2A, formerly RAD6A). Additional analyses on a cohort of 24 blast crisis, 41 chronic phase as well as 40 acute myeloid leukemia and 38 atypical chronic myeloid leukemia patients at onset confirmed that UBE2A mutations are specifically acquired during chronic myeloid leukemia progression, with a frequency of 16.7% in advanced phases. In vitro studies show that the mutations here described cause a decrease in UBE2A activity, leading to an impairment of myeloid differentiation in chronic myeloid leukemia cells.

BCR/ABL1 and BCR are under the transcriptional control of the MYC oncogene.

BACKGROUND: Chronic Myeloid Leukaemia (CML) is caused by the BCR/ABL1 fusion gene. Both the presence and the levels of BCR/ABL1 expression seem to be critical for CML progression from chronic phase (CP) to blast crisis (BC). After the oncogenic translocation, the BCR/ABL1 gene is under the transcriptional control of BCR promoter but the molecular mechanisms involved in the regulation of oncogene expression are mostly unknown. METHODS: A region of 1443bp of the functional BCR promoter was studied for transcription factor binding sites through in-silico analysis and Chromatin Immunoprecipitation experiments. BCR and BCR/ABL1 expression levels were analysed in CML cell lines after over-expression or silencing of MYC transcription factor. A luciferase reporter assay was used to confirm its activity on BCR promoter. RESULTS: In the present study we demonstrate that MYC and its partner MAX bind to the BCR promoter, leading to up-regulation of BCR and BCR/ABL1 at both transcriptional and protein levels. Accordingly, silencing of MYC expression in various BCR/ABL1 positive cell lines causes significant downregulation of BCR and BCR/ABL1, which consequently leads to decreased proliferation and induction of cell death. CONCLUSIONS: Here we describe a regulatory pathway modulating BCR and BCR/ABL1 expression, showing that the BCR promoter is under the transcriptional control of the MYC/MAX heterodimer. Since MYC is frequently over-expressed in BC, this phenomenon could play a critical role in BCR/ABL1 up-regulation and blast aggressiveness acquired during CML evolution.

Analytical code sharing practices in biomedical research.

Data-driven computational analysis is becoming increasingly important in biomedical research, as the amount of data being generated continues to grow. However, the lack of practices of sharing research outputs, such as data, source code and methods, affects transparency and reproducibility of studies, which are critical to the advancement of science. Many published studies are not reproducible due to insufficient documentation, code, and data being shared. We conducted a comprehensive analysis of 453 manuscripts published between 2016-2021 and found that 50.1% of them fail to share the analytical code. Even among those that did disclose their code, a vast majority failed to offer additional research outputs, such as data. Furthermore, only one in ten articles organized their code in a structured and reproducible manner. We discovered a significant association between the presence of code availability statements and increased code availability. Additionally, a greater proportion of studies conducting secondary analyses were inclined to share their code compared to those conducting primary analyses. In light of our findings, we propose raising awareness of code sharing practices and taking immediate steps to enhance code availability to improve reproducibility in biomedical research. By increasing transparency and reproducibility, we can promote scientific rigor, encourage collaboration, and accelerate scientific discoveries. We must prioritize open science practices, including sharing code, data, and other research products, to ensure that biomedical research can be replicated and built upon by others in the scientific community.

Comparative evaluation of periodontal health status of pre and postmenopausal females.

BACKGROUND: Menopause in females is a corporeal stage that gives rise to a number of adaptive changes both at systemic and oral levels, prototypically occurring in the late fourth or fifth decade of life. Though physiological aging affects the oral tissue, the hormonal changes due to menopause also act as a major contributing factor in deteriorating the health of oral tissues. Thus, the main aim of our study was to compare the overall periodontal status and alkaline phosphatase levels in the saliva of females in their pre and postmenopausal ages. MATERIAL AND METHODS: This study was conducted on 200 female subjects coming to the Department of Periodontology at Rajendra Institute of Medical Science for oral prophylaxis. The subjects were arbitrarily selected in the age group ranging from 15 to 70 years and were further divided based on the inclusion criteria. Group A included 100 subjects with age ranging from 15 to 45 years, and group B, 100 subjects with age 54 to 70 years. Signs of periodontitis including clinical attachment loss, furcation involvement, and probing depth and salivary alkaline levels were obtained, evaluated, compared, and analyzed. RESULTS: In group A 65% of patients had grade 0 and 28% had grade 1 of clinical attachment level. Similarly in group B, 44% of the total had grade 0 of clinical attachment loss, 38% had grade 1, and 18% were of grade 2. On evaluating grades of furcation involvement, around 45% of the total patients in group A were grade 1 (incipient, pocket formation), while in group B, 51% of the total patients were grade 1. At least 46% in group A and only 20% in group B had no signs of furcation involvement. Salivary alkaline phosphatase levels in pre and postmenopausal patients showed a significant difference between the two groups was obtained. CONCLUSION: The study concluded a major difference in the periodontal health of pre and postmenopausal women with many influencing factors apart from menopause itself.

Knowledge, Attitude and Practice towards COVID-19 Pandemic among Patients Attending Dental Outpatient Department of M.G.M. Medical College and Hospital, Jamshedpur, Jharkhand, India.

Background: The 2019 coronavirus disease (COVID-19) is an extremely contagious illness that spreads mostly via the dentistry practice. Patients in need of dental care are at a higher risk of becoming infected with and becoming carriers of the illness. Aim: To assess the COVID-19-related knowledge, attitude, and practice (KAP) of patients visiting dental outpatient department of M.G.M. Medical College and Hospital, Jamshedpur, Jharkhand, India. Materials and Methods: In this cross-sectional study, patients visiting dental outpatient department of M.G.M. Medical College and Hospital, Jamshedpur, Jharkhand, India were included. The questionnaire had four sections including demographic information, knowledge, attitudes, and practice in relation to COVID-19. Along with computation of descriptive statistics, data analysis was performed using unpaired t-test. Results: A total of 332 people took part in the research. The female respondents were higher in number (53.01%) and the highest percentage of the respondents belongs to the age group 18-40 years (55.72%). Nearly, 98% of respondents were vaccinated. The highest percentage of KAP level was recorded for knowledge (74.95%) followed by that of attitude (50.84%) and practices (37.05%). Conclusion: While respondents' overall knowledge was high but their enthusiasm for taking preventative measures was low, and their efforts to stem the pandemic were lagging at best. Future campaigns should focus more on reaching out to marginalized populations, such as those with less education or higher poverty rates.

DBPMod: a supervised learning model for computational recognition of DNA-binding proteins in model organisms.

DNA-binding proteins (DBPs) play critical roles in many biological processes, including gene expression, DNA replication, recombination and repair. Understanding the molecular mechanisms underlying these processes depends on the precise identification of DBPs. In recent times, several computational methods have been developed to identify DBPs. However, because of the generic nature of the models, these models are unable to identify species-specific DBPs with higher accuracy. Therefore, a species-specific computational model is needed to predict species-specific DBPs. In this paper, we introduce the computational DBPMod method, which makes use of a machine learning approach to identify species-specific DBPs. For prediction, both shallow learning algorithms and deep learning models were used, with shallow learning models achieving higher accuracy. Additionally, the evolutionary features outperformed sequence-derived features in terms of accuracy. Five model organisms, including Caenorhabditis elegans, Drosophila melanogaster, Escherichia coli, Homo sapiens and Mus musculus, were used to assess the performance of DBPMod. Five-fold cross-validation and independent test set analyses were used to evaluate the prediction accuracy in terms of area under receiver operating characteristic curve (auROC) and area under precision-recall curve (auPRC), which was found to be ~89-92% and ~89-95%, respectively. The comparative results demonstrate that the DBPMod outperforms 12 current state-of-the-art computational approaches in identifying the DBPs for all five model organisms. We further developed the web server of DBPMod to make it easier for researchers to detect DBPs and is publicly available at https://iasri-sg.icar.gov.in/dbpmod/. DBPMod is expected to be an invaluable tool for discovering DBPs, supplementing the current experimental and computational methods.

The Genomic Landscape of Colorectal Cancer in the Saudi Arabian Population Using a Comprehensive Genomic Panel.

PURPOSE: Next-generation sequencing (NGS) technology detects specific mutations that can provide treatment opportunities for colorectal cancer (CRC) patients. PATIENTS AND METHODS: We analyzed the mutation frequencies of common actionable genes and their association with clinicopathological characteristics and oncologic outcomes using targeted NGS in 107 Saudi Arabian patients without a family history of CRC. RESULTS: Approximately 98% of patients had genetic alterations. Frequent mutations were observed in BRCA2 (79%), CHEK1 (78%), ATM (76%), PMS2 (76%), ATR (74%), and MYCL (73%). The APC gene was not included in the panel. Statistical analysis using the Cox proportional hazards model revealed an unusual positive association between poorly differentiated tumors and survival rates (p = 0.025). Although no significant univariate associations between specific mutations or overall mutation rate and overall survival were found, our preliminary analysis of the molecular markers for CRC in a predominantly Arab population can provide insights into the molecular pathways that play a significant role in the underlying disease progression. CONCLUSIONS: These results may help optimize personalized therapy when drugs specific to a patient's mutation profile have already been developed.

Genome-Wide Single-Nucleotide Polymorphism-Based Genomic Diversity and Runs of Homozygosity for Selection Signatures in Equine Breeds.

The horse, one of the most domesticated animals, has been used for several purposes, like transportation, hunting, in sport, or for agriculture-related works. Kathiawari, Marwari, Manipuri, Zanskari, Bhutia, Spiti, and Thoroughbred are the main breeds of horses, particularly due to their agroclimatic adaptation and role in any kind of strong physical activity, and these characteristics are majorly governed by genetic factors. The genetic diversity and phylogenetic relationship of these Indian equine breeds using microsatellite markers have been reported, but further studies exploring the SNP diversity and runs of homozygosity revealing the selection signature of breeds are still warranted. In our study, the identification of genes that play a vital role in muscle development is performed through SNP detection via the whole-genome sequencing approach. A total of 96 samples, categorized under seven breeds, and 620,721 SNPs were considered to ascertain the ROH patterns amongst all the seven breeds. Over 5444 ROH islands were mined, and the maximum number of ROHs was found to be present in Zanskari, while Thoroughbred was confined to the lowest number of ROHs. Gene enrichment of these ROH islands produced 6757 functional genes, with AGPAT1, CLEC4, and CFAP20 as important gene families. However, QTL annotation revealed that the maximum QTLs were associated with Wither's height trait ontology that falls under the growth trait in all seven breeds. An Equine SNP marker database (EqSNPDb) was developed to catalogue ROHs for all these equine breeds for the flexible and easy chromosome-wise retrieval of ROH along with the genotype details of all the SNPs. Such a study can reveal breed divergence in different climatic and ecological conditions.

Analytical code sharing practices in biomedical research.

Data-driven computational analysis is becoming increasingly important in biomedical research, as the amount of data being generated continues to grow. However, the lack of practices of sharing research outputs, such as data, source code and methods, affects transparency and reproducibility of studies, which are critical to the advancement of science. Many published studies are not reproducible due to insufficient documentation, code, and data being shared. We conducted a comprehensive analysis of 453 manuscripts published between 2016-2021 and found that 50.1% of them fail to share the analytical code. Even among those that did disclose their code, a vast majority failed to offer additional research outputs, such as data. Furthermore, only one in ten papers organized their code in a structured and reproducible manner. We discovered a significant association between the presence of code availability statements and increased code availability (p=2.71×10-9). Additionally, a greater proportion of studies conducting secondary analyses were inclined to share their code compared to those conducting primary analyses (p=1.15*10-07). In light of our findings, we propose raising awareness of code sharing practices and taking immediate steps to enhance code availability to improve reproducibility in biomedical research. By increasing transparency and reproducibility, we can promote scientific rigor, encourage collaboration, and accelerate scientific discoveries. We must prioritize open science practices, including sharing code, data, and other research products, to ensure that biomedical research can be replicated and built upon by others in the scientific community.

Effect of Yoga on the Stress, Anxiety, and Depression of COVID-19-Positive Patients: A Quasi-Randomized Controlled Study.

The spread of COVID-19 has resulted in reports of increase in stress, anxiety, and depression across society, especially in people who have tested positive for COVID-19, which affects their mental health and well-being. This article reports a quasi-randomized controlled study conducted in the COVID wards of a hospital to examine the efficacy of add-on yoga intervention in reducing stress, anxiety, and depression in COVID-affected patients under quarantine. The peripheral capillary oxygen saturation level and heart rate of the COVID-19-affected patients were also measured. A total of 62 COVID-19-positive patients participated in the study. The participants were randomized into a control group (n = 31), which received conventional medical treatment alone, and a yoga intervention group (n = 31), which received 50 minutes of yoga intervention along with the conventional medical treatment. Standardized Hospital Anxiety and Depression Scale, Generalized Anxiety Disorder-7 Item, Patient Health Questionnaire-9, and Perceived Stress Scale were administered at the beginning and end of the quarantine period. A significant decrease in stress, anxiety, and depression was observed in the patients who undertook the add-on yoga intervention. There was also a significant decrease in anxiety in the control group, but the intervention group had a larger decrease compared to the control group. Further significant improvements in oxygen saturation and heart rate levels were observed in the group of patients who were practicing yoga, but no significant improvement was observed in the control group. Findings of this study suggest that yoga intervention can be an effective add-on practice in reducing stress, anxiety, and depression levels of COVID-19 patients.

Metabolic Reprogramming and Cell Adhesion in Acute Leukemia Adaptation to the CNS Niche.

Involvement of the Central Nervous System (CNS) in acute leukemia confers poor prognosis and lower overall survival. Existing CNS-directed therapies are associated with a significant risk of short- or long-term toxicities. Leukemic cells can metabolically adapt and survive in the microenvironment of the CNS. The supporting role of the CNS microenvironment in leukemia progression and dissemination has not received sufficient attention. Understanding the mechanism by which leukemic cells survive in the nutrient-poor and oxygen-deprived CNS microenvironment will lead to the development of more specific and less toxic therapies. Here, we review the current literature regarding the roles of metabolic reprogramming in leukemic cell adhesion and survival in the CNS.

Yoga an effective strategy for self-management of stress-related problems and wellbeing during COVID19 lockdown: A cross-sectional study.

This cross-sectional research aims to study the effect of yoga practice on the illness perception, and wellbeing of healthy adults during 4-10 weeks of lockdown due to COVID19 outbreak. A total of 668 adults (64.7% males, M = 28.12 years, SD = 9.09 years) participated in the online survey. The participants were grouped as; yoga practitioners, other spiritual practitioners, and non-practitioners based on their responses to daily practices that they follow. Yoga practitioners were further examined based on the duration of practice as; long-term, mid-term and beginners. Multivariate analysis indicates that yoga practitioners had significantly lower depression, anxiety, & stress (DASS), and higher general wellbeing (SWGB) as well as higher peace of mind (POMS) than the other two groups. The results further revealed that the yoga practitioners significantly differed in the perception of personal control, illness concern and emotional impact of COVID19. However, there was no significant difference found for the measure of resilience (BRS) in this study. Yoga practitioners also significantly differed in the cognitive reappraisal strategy for regulating their emotions than the other two groups. Interestingly, it was found that beginners -those who had started practicing yoga only during the lockdown period reported no significant difference for general wellbeing and peace of mind when compared to the mid- term practitioner. Evidence supports that yoga was found as an effective self- management strategy to cope with stress, anxiety and depression, and maintain wellbeing during COVID19 lockdown.

miRbiom: Machine-learning on Bayesian causal nets of RBP-miRNA interactions successfully predicts miRNA profiles.

Formation of mature miRNAs and their expression is a highly controlled process. It is very much dependent upon the post-transcriptional regulatory events. Recent findings suggest that several RNA binding proteins beyond Drosha/Dicer are involved in the processing of miRNAs. Deciphering of conditional networks for these RBP-miRNA interactions may help to reason the spatio-temporal nature of miRNAs which can also be used to predict miRNA profiles. In this direction, >25TB of data from different platforms were studied (CLIP-seq/RNA-seq/miRNA-seq) to develop Bayesian causal networks capable of reasoning miRNA biogenesis. The networks ably explained the miRNA formation when tested across a large number of conditions and experimentally validated data. The networks were modeled into an XGBoost machine learning system where expression information of the network components was found capable to quantitatively explain the miRNAs formation levels and their profiles. The models were developed for 1,204 human miRNAs whose accurate expression level could be detected directly from the RNA-seq data alone without any need of doing separate miRNA profiling experiments like miRNA-seq or arrays. A first of its kind, miRbiom performed consistently well with high average accuracy (91%) when tested across a large number of experimentally established data from several conditions. It has been implemented as an interactive open access web-server where besides finding the profiles of miRNAs, their downstream functional analysis can also be done. miRbiom will help to get an accurate prediction of human miRNAs profiles in the absence of profiling experiments and will be an asset for regulatory research areas. The study also shows the importance of having RBP interaction information in better understanding the miRNAs and their functional projectiles where it also lays the foundation of such studies and software in future.

First wave of covid-19 in India using IoT for identification of virus.

Internet of Things (IoT) are evolving rapidly and making it possible for many uses, such as manufacturing, military, education and health, to link different intelligent objects. Coronavirus has recently spread widely around the globe and no effective therapies are currently available. It is also very necessary to avoid infection and to control the symptoms, such as fever and shortness of breath. As Coronavirus is a disease that is circulating very rapidly and the social distancing to deter an outbreak is very significant, it is essential to provide a system that is intelligent enough to monitor the effects of individuals with little direct contact. This document contains an IoT-based and wireless sensor network architecture and simulation of the COVID-19 Monitoring Mechanism (CSMM) for the monitoring of people in their quarantine, particularly the elderly who are living under chronic diseases and immune failure, and are therefore more likely to contract severe diseases. The mechanism relies on patient health data remotely. A doctor or care practitioner may carry out the monitoring process. For starters, where there is high fire or trouble breathing, this can conveniently be used for a detected urgent or irregular situation. The process will then give a warning to the health care provider or practitioner, sending urgent SMS with time and condition to act without any delays to save the patient's life.

RBPSpot: Learning on appropriate contextual information for RBP binding sites discovery.

Identifying the factors determining the RBP-RNA interactions remains a big challenge. It involves sparse binding motifs and a suitable sequence context for binding. The present work describes an approach to detect RBP binding sites in RNAs using an ultra-fast inexact k-mers search for statistically significant seeds. The seeds work as an anchor to evaluate the context and binding potential using flanking region information while leveraging from Deep Feed-forward Neural Network. The developed models also received support from MD-simulation studies. The implemented software, RBPSpot, scored consistently high for all the performance metrics including average accuracy of ∼90% across a large number of validated datasets. It outperformed the compared tools, including some with much complex deep-learning models, during a comprehensive benchmarking process. RBPSpot can identify RBP binding sites in the human system and can also be used to develop new models, making it a valuable resource in the area of regulatory system studies.

Comparative transcriptome analysis of Rheum australe, an endangered medicinal herb, growing in its natural habitat and those grown in controlled growth chambers.

Rheum australe is an endangered medicinal herb of high altitude alpine region of Himalayas and is known to possess anti-cancerous properties. Unlike many herbs of the region, R. australe has broad leaves. The species thrives well under the environmental extremes in its niche habitat, therefore an understanding of transcriptome of R. australe to environmental cues was of significance. Since, temperature is one of the major environmental variables in the niche of R. australe, transcriptome was studied in the species growing in natural habitat and those grown in growth chambers maintained at 4 °C and 25 °C to understand genes associated with different temperatures. A total of 39,136 primarily assembled transcripts were obtained from 10,17,74,336 clean read, and 21,303 unigenes could match to public databases. An analysis of transcriptome by fragments per kilobase of transcript per million, followed by validation through qRT-PCR showed 22.4% up- and 22.5% down-regulated common differentially expressed genes in the species growing under natural habitat and at 4 °C as compared to those at 25 °C. These genes largely belonged to signaling pathway, transporters, secondary metabolites, phytohormones, and those associated with cellular protection, suggesting their importance in imparting adaptive advantage to R. australe in its niche.

The first draft genome of Picrorhiza kurrooa, an endangered medicinal herb from Himalayas.

Picrorhiza kurrooa is an endangered medicinal herb which is distributed across the Himalayan region at an altitude between 3000-5000 m above mean sea level. The medicinal properties of P. kurrooa are attributed to monoterpenoid picrosides present in leaf, rhizome and root of the plant. However, no genomic information is currently available for P. kurrooa, which limits our understanding about its molecular systems and associated responses. The present study brings the first assembled draft genome of P. kurrooa by using 227 Gb of raw data generated by Illumina and PacBio RS II sequencing platforms. The assembled genome has a size of n = ~ 1.7 Gb with 12,924 scaffolds. Four pronged assembly quality validations studies, including experimentally reported ESTs mapping and directed sequencing of the assembled contigs, confirmed high reliability of the assembly. About 76% of the genome is covered by complex repeats alone. Annotation revealed 24,798 protein coding and 9789 non-coding genes. Using the assembled genome, a total of 710 miRNAs were discovered, many of which were found responsible for molecular response against temperature changes. The miRNAs and targets were validated experimentally. The availability of draft genome sequence will aid in genetic improvement and conservation of P. kurrooa. Also, this study provided an efficient approach for assembling complex genomes while dealing with repeats when regular assemblers failed to progress due to repeats.