A six-amino-acid motif is a major determinant in functional evolution of HOX1 proteins.

Gene duplication and divergence is a major driver in the emergence of evolutionary novelties. How variations in amino acid sequences lead to loss of ancestral activity and functional diversification of proteins is poorly understood. We used cross-species functional analysis of Drosophila Labial and its mouse HOX1 orthologs (HOXA1, HOXB1, and HOXD1) as a paradigm to address this issue. Mouse HOX1 proteins display low (30%) sequence similarity with Drosophila Labial. However, substituting endogenous Labial with the mouse proteins revealed that HOXA1 has retained essential ancestral functions of Labial, while HOXB1 and HOXD1 have diverged. Genome-wide analysis demonstrated similar DNA-binding patterns of HOXA1 and Labial in mouse cells, while HOXB1 binds to distinct targets. Compared with HOXB1, HOXA1 shows an enrichment in co-occupancy with PBX proteins on target sites and exists in the same complex with PBX on chromatin. Functional analysis of HOXA1-HOXB1 chimeric proteins uncovered a novel six-amino-acid C-terminal motif (CTM) flanking the homeodomain that serves as a major determinant of ancestral activity. In vitro DNA-binding experiments and structural prediction show that CTM provides an important domain for interaction of HOXA1 proteins with PBX. Our findings show that small changes outside of highly conserved DNA-binding regions can lead to profound changes in protein function.

A chickpea genetic variation map based on the sequencing of 3,366 genomes.

Zero hunger and good health could be realized by 2030 through effective conservation, characterization and utilization of germplasm resources1. So far, few chickpea (Cicer arietinum) germplasm accessions have been characterized at the genome sequence level2. Here we present a detailed map of variation in 3,171 cultivated and 195 wild accessions to provide publicly available resources for chickpea genomics research and breeding. We constructed a chickpea pan-genome to describe genomic diversity across cultivated chickpea and its wild progenitor accessions. A divergence tree using genes present in around 80% of individuals in one species allowed us to estimate the divergence of Cicer over the last 21 million years. Our analysis found chromosomal segments and genes that show signatures of selection during domestication, migration and improvement. The chromosomal locations of deleterious mutations responsible for limited genetic diversity and decreased fitness were identified in elite germplasm. We identified superior haplotypes for improvement-related traits in landraces that can be introgressed into elite breeding lines through haplotype-based breeding, and found targets for purging deleterious alleles through genomics-assisted breeding and/or gene editing. Finally, we propose three crop breeding strategies based on genomic prediction to enhance crop productivity for 16 traits while avoiding the erosion of genetic diversity through optimal contribution selection (OCS)-based pre-breeding. The predicted performance for 100-seed weight, an important yield-related trait, increased by up to 23% and 12% with OCS- and haplotype-based genomic approaches, respectively.

Characterization of Chemotaxis-Associated Gene Dysregulation in Myeloid Cell Populations in the Lungs during Lipopolysaccharide-Mediated Acute Lung Injury.

During endotoxin-induced acute lung injury (ALI), immune cell recruitment resulting from chemotaxis is mediated by CXC and CC chemokines and their receptors. In this study, we investigated the role of chemokines and their receptors in the regulation of myeloid cell populations in the circulation and the lungs of C57BL/6J mice exhibiting LPS-mediated ALI using single-cell RNA sequencing. During ALI, there was an increase in the myeloid cells, M1 macrophages, monocytes, neutrophils, and other granulocytes, whereas there was a decrease in the residential alveolar macrophages and M2 macrophages. Interestingly, LPS triggered the upregulation of CCL3, CCL4, CXCL2/3, and CXCL10 genes associated with cellular migration of various subsets of macrophages, neutrophils, and granulocytes. Furthermore, there was an increase in the frequency of myeloid cells expressing CCR1, CCR3, CCR5, and CXCR2 receptors during ALI. MicroRNA sequencing studies of vehicle versus LPS groups identified several dysregulated microRNAs targeting the upregulated chemokine genes. This study suggests that chemokine ligand-receptors interactions are responsible for myeloid cell heterogenicity and cellular recruitment to the lungs during ALI. The single-cell transcriptomics allowed for an in-depth assessment and characterization of myeloid cells involved in immune cell trafficking during ALI.

Rationale and design of the NODE-303 study: evaluating the safety of symptom-prompted, self-administered etripamil for paroxysmal supraventricular tachycardia episodes in real-world settings.

BACKGROUND: Paroxysmal supraventricular tachycardia (PSVT) is a common episodic arrhythmia characterized by unpredictable onset and burdensome symptoms including palpitations, dizziness, chest pain, distress, and shortness of breath. Treatment of acute episodes of PSVT in the clinical setting consists of intravenous adenosine, beta-blockers, and calcium channel blockers (CCBs). Etripamil is an intranasally self-administered L-type CCB in development for acute treatment of AV-nodal dependent PSVT in a nonmedical supervised setting. METHODS: This paper summarizes the rationale and study design of NODE-303 that will assess the efficacy and safety of etripamil. In the randomized, double-blinded, placebo-controlled, Phase 3 RAPID trial, etripamil was superior to placebo in the conversion of single PSVT episodes by 30 minutes post initial dose when administered in the nonhealthcare setting; this study required a mandatory and observed test dosing prior to randomization. The primary objective of NODE-303 is to evaluate the safety of symptom-prompted, self-administered etripamil for multiple PSVT episodes in real-world settings, without the need for test dosing prior to first use during PSVT. Secondary endpoints include efficacy and disease burden. Upon perceiving a PSVT episode, the patient applies an electrocardiographic monitor, performs a vagal maneuver, and, if the vagal maneuver is unsuccessful, self-administers etripamil 70 mg, with an optional repeat dose if symptoms do not resolve within 10 minutes after the first dose. A patient may treat up to four PSVT episodes during the study. Adverse events are recorded as treatment-emergent if they occur within 24 hours after the administration of etripamil. RESULTS: Efficacy endpoints include time to conversion to sinus rhythm within 30 and 60 minutes after etripamil administration, and the proportion of patients who convert at 3, 5, 10, 20, 30, and 60 minutes. Patient-reported outcomes are captured by the Brief Illness Perception Questionnaire, the Cardiac Anxiety Questionnaire, the Short Form Health Survey 36, the Treatment Satisfaction Questionnaire for Medication and a PSVT survey. CONCLUSIONS: Overall, these data will support the development of a potentially paradigm-changing long-term management strategy for recurrent PSVT.

Magnetically recoverable Ni-doped iron oxide/graphitic carbon nitride nanocomposites for the improved photocatalytic degradation of ciprofloxacin: Investigation of degradation pathways.

Developing efficient and effective photocatalysts is essential for organic dyes and antibiotic degradation in wastewater. Ni-doped α-Fe2O3/g-C3N4 (NFGCN) photocatalysts were synthesised through a simple co-precipitation technique and used for the ciprofloxacin (CIP) and methylene blue (MB) degradation through photocatalysis. The XRD data indicated the crystallinity of the synthesised iron oxide and its composites with rhombohedral structures with the nature of high purity. The morphology of the NFGCN composite revealed the construction of Ni-doped α-Fe2O3 (NFO) nanoparticles onto the g-C3N4 (GCN) sheet surface along with the close interface that induced a Z-scheme heterojunction. The synthesised photocatalysts showed photocatalytic activity with good degradation efficiency of 82.1 % and 92.0 % for CIP and MB, respectively, within 120 min under solar light exposure. The improved photocatalytic degradation efficiency was attained owing to the synthesised composite's enhanced light absorption in the visible range. The narrow band gap energies and interaction between Ni-doped α-Fe2O3 and g-C3N4 displayed by these materials result in enhanced visible light absorption, effective charge carrier separation and transportation to the pollutants. CIP degradation pathways were investigated utilising the LC-MS analysis. NFGCN composites showed good recyclability (5 cycles), magnetic retrievability, and stability for degrading organic and emerging pollutants from wastewater through photocatalysis.

Efficacy of a Structured Yoga Intervention Integrated with Routine Care versus Exercise on Pulmonary Function and Quality of Life of Asthma Patients: A Randomized Controlled Trial.

Context: Asthma is a chronic disease and its chronicity demands therapy with minimal harm and a good impact on the quality of life of asthmatics. Objective: This study evaluates the efficacy of structured yoga intervention integrated with routine care on asthma patients in improving their pulmonary function and quality of life. Design: The study was a single-blind (outcome assessor) hospital-based randomized controlled trial. Participants: Adults between 18 to 60 years, diagnosed with mild to moderate asthma as per Global Initiative for Asthma guidelines, with no exacerbation in the past month before screening, were included in the study. Intervention: A thirty-minute structured yoga intervention was delivered daily by a qualified yoga instructor through a virtual platform. Outcome measures: Questionnaires were utilized to assess the quality of life, and Breath-o-meter equipment was used to measure peak expiratory flow rate (PEFR). It was tested at baseline and then at 15 days, 45 days, and 90 days, whereas the quality of life was evaluated once a month. Statistical analysis: Intention to treat analysis was performed to compare the mean outcome between the yoga and control groups using an independent sample t test and repeated measures analysis of variance. Results: The yoga group significantly improved their PEFR and asthma-related quality of life scores compared to the control group (P < .001). A significant difference (F = 539.72, degree of freedom = 1.1618; P < .001) was detected between PEFR values at several time intervals (baseline, day 15, day 45, day 90) in the intervention group on repeated measures analysis of variance. The difference in quality-of-life scores between yoga and control was also statistically significant (P < .001), with an improvement in the quality-of-life domain of external stimuli. Conclusion: When combined with normal asthma treatment, the findings of this study show that structured yoga intervention integrated with routine care is more beneficial than traditional breathing exercises in increasing PEFR and quality of life.

Decoding temporal patterns and trends of PM10 pollution over Delhi: a multi-year analysis (2015-2022).

The current study delved into an extensive analysis of multi-year observations on PM10 to have trends at various time scales in Delhi, India. High-resolution ground observations from all 37 monitoring stations from 2015 to 2022 were used. This study used non-parametric generalized additive model (GAM) based smooth-trend and Theil-Sen slope estimator techniques to analyze temporal trends and variations. The long-term PM10 concentration, both in its ambient and de-seasonalized forms, exhibited a statistically significant decreasing trend. An average decrease of - 7.57 [95% confidence interval (CI) - 16.51, 0.18] µg m-3 year-1 for ambient PM10 and - 8.45 [95% CI - 11.96, - 5.58] µg m-3 year-1 for de-seasonalized PM10 mass concentration was observed. Breaking it down into seasons, we observed significant declines in PM10 concentrations during monsoon (- 10.71 µg m-3 year-1, p < 0.1) and post-monsoon (- 7.49 µg m-3 year-1, p < 0.001). On the other hand, summer and winter displayed statistically insignificant declining trends of - 5.32 µg m-3 year-1 and - 6.06 µg m-3 year-1, respectively. Remarkably, all months except March displayed declining PM10 concentrations, suggesting a gradual reduction in particle pollution across the city. Further analysis of PM10 across various wind sectors revealed a consistent decreasing trend in all wind directions. The most substantial decrease was observed from the northwest (- 10.24 µg m-3 year-1), while the minimum reduction occurred from the east (- 5.67 µg m-3 year-1). Throughout the 8-year study period, the daily average PM10 concentration remained at 228 ± 124 µg m-3, ranging from 33 to 819 µg m-3. Seasonal variations were apparent, with concentrations during winter, summer, monsoon, and post-monsoon seasons averaging 279 ± 133, 224 ± 117, 135 ± 95, and 323 ± 142 µg m-3, respectively. November had the highest and August had the lowest concentration. Weekend PM10 concentration is slightly lower than weekdays. These findings emphasize the need for more stringent government action plans.

Lessons Learned in Implementing an Aging Research Training Program for Underrepresented Minority Students.

This brief report provides an overview of lessons learned through evaluation of the first five years of the NIA-funded South Carolina-Advancing Diversity in Aging Research (SC-ADAR) undergraduate program, whose goal is to increase the number of qualified underrepresented minority (URM) students who pursue scientific graduate studies in programs focusing on medicine, science, technology, engineering, and mathematics and aging. Partnering with five Historically Black Colleges and Universities in South Carolina, we implemented a research training approach that included two consecutive summers of research training in a University of South Carolina faculty laboratory, as part of a comprehensive 24-month research education program. In addition to the mentored research experience in a laboratory, students had coursework in the biology of aging and social gerontology, with additional workshops tailored to emergent student needs including basic academic skills development, work-life management skills, reflective social experiences, and enhanced support in the transition from undergraduate to graduate school. We provide an overview of lessons learned throughout the early program period, and a description of the iterative changes we made in the program in response to this learning, all of which have been incorporated into the existing SC-ADAR program.

Low-Dose Methotrexate for the Prevention of Atherosclerotic Events.

BACKGROUND: Inflammation is causally related to atherothrombosis. Treatment with canakinumab, a monoclonal antibody that inhibits inflammation by neutralizing interleukin-1ß, resulted in a lower rate of cardiovascular events than placebo in a previous randomized trial. We sought to determine whether an alternative approach to inflammation inhibition with low-dose methotrexate might provide similar benefit. METHODS: We conducted a randomized, double-blind trial of low-dose methotrexate (at a target dose of 15 to 20 mg weekly) or matching placebo in 4786 patients with previous myocardial infarction or multivessel coronary disease who additionally had either type 2 diabetes or the metabolic syndrome. All participants received 1 mg of folate daily. The primary end point at the onset of the trial was a composite of nonfatal myocardial infarction, nonfatal stroke, or cardiovascular death. Near the conclusion of the trial, but before unblinding, hospitalization for unstable angina that led to urgent revascularization was added to the primary end point. RESULTS: The trial was stopped after a median follow-up of 2.3 years. Methotrexate did not result in lower interleukin-1ß, interleukin-6, or C-reactive protein levels than placebo. The final primary end point occurred in 201 patients in the methotrexate group and in 207 in the placebo group (incidence rate, 4.13 vs. 4.31 per 100 person-years; hazard ratio, 0.96; 95% confidence interval [CI], 0.79 to 1.16). The original primary end point occurred in 170 patients in the methotrexate group and in 167 in the placebo group (incidence rate, 3.46 vs. 3.43 per 100 person-years; hazard ratio, 1.01; 95% CI, 0.82 to 1.25). Methotrexate was associated with elevations in liver-enzyme levels, reductions in leukocyte counts and hematocrit levels, and a higher incidence of non-basal-cell skin cancers than placebo. CONCLUSIONS: Among patients with stable atherosclerosis, low-dose methotrexate did not reduce levels of interleukin-1ß, interleukin-6, or C-reactive protein and did not result in fewer cardiovascular events than placebo. (Funded by the National Heart, Lung, and Blood Institute; CIRT ClinicalTrials.gov number, NCT01594333.).

Occurrence, molecular characterization and antimicrobial-resistance pattern of Staphylococcus species isolates from buck semen.

Staphylococcus aureus is one of the most prevalent pathogens, and a causative agent of a variety of infections in humans and animals. Most studies concentrated on characterization of staphylococcus isolates and its antimicrobial resistance from various illness of veterinary importance, but there is no specific study that is available on isolates from reproductive tract of small ruminants and especially its semen. Hence, in the current study, a total of 48 semen samples were collected from healthy bucks of different breeds to investigate the occurrence of S. aureus. Antimicrobial resistance and virulence of the Staphylococcus isolates were determined to assess the adverse effects of them on buck fertility. The bacterial isolates were tentatively confirmed as Staphylococcus spp. based on the Gram's staining, growth on Mannitol salt agar and catalase test. Overall, 75% (n = 36) of the samples were positive for Staphylococcus spp. from the total 48 buck semen ejaculates from different breeds and among them 23 (63.89%) were coagulase-negative (CoNS) and 13 (36.11%) were coagulase-positive Staphylococcus (CoPS) strains. The species identified by molecular characterization are S. aureus, S. chromogenes, S. haemolyticus, S. sciuri, S. simulans, and S. epidermidis from buck semen. Further, these isolates exhibited varying degrees of multidrug resistance genotypically as well as phenotypically. The presence of antibiotic resistance and virulence genes may pose a potential threat to reproductive health of animals, the animal handlers and livestock keepers, while simultaneously highlighting the need for vigilant monitoring of these isolates at the time of semen cryopreservation.

Machine learning product state distributions from initial reactant states for a reactive atom-diatom collision system.

A machine-learned model for predicting product state distributions from specific initial states (state-to-distribution or STD) for reactive atom-diatom collisions is presented and quantitatively tested for the N(4S) + O2(X3Σg -) → NO(X2Π) + O(3P) reaction. The reference dataset for training the neural network consists of final state distributions determined from quasi-classical trajectory (QCT) simulations for ∼2000 initial conditions. Overall, the prediction accuracy as quantified by the root-mean-squared difference (∼0.003) and the R2 (∼0.99) between the reference QCT and predictions of the STD model is high for the test set, for off-grid state-specific initial conditions, and for initial conditions drawn from reactant state distributions characterized by translational, rotational, and vibrational temperatures. Compared with a more coarse grained distribution-to-distribution (DTD) model evaluated on the same initial state distributions, the STD model shows comparable performance with the additional benefit of the state resolution in the reactant preparation. Starting from specific initial states also leads to a more diverse range of final state distributions, which requires a more expressive neural network compared with DTD. A direct comparison between QCT simulations, the STD model, and the widely used Larsen-Borgnakke (LB) model shows that the STD model is quantitative, whereas the LB model is qualitative at best for rotational distributions P(j') and fails for vibrational distributions P(v'). As such, the STD model can be well-suited for simulating nonequilibrium high-speed flows, e.g., using the direct simulation Monte Carlo method.

Utility of Cerebrospinal Fluid and Serum Procalcitonin for the Diagnosis of Neonatal Meningitis.

OBJECTIVE: Positive CSF culture is the gold standard for the diagnosis of meningitis but it carries poor sensitivity. CSF procalcitonin (PCT) is shown to have some utility for the diagnosis of meningitis though there are limited studies in neonatal age group. We planned this study to compare CSF, serum, and CSF to serum PCT levels in neonates with confirmed, probable, and nonmeningitis groups to determine its optimal cut-off in CSF and serum for diagnosing meningitis. STUDY DESIGN: Sixty-seven neonates who qualified for lumbar puncture were enrolled in the study. Neonates were categorized into confirmed meningitis, i.e., CSF cytochemistry and culture positive (N = 17), probable meningitis, i.e., CSF cytochemistry positive but culture negative (N = 25) and nonmeningitis, i.e., both cytochemistry and culture negative (N = 25). CSF and serum samples were stored at -80°C for PCT assay. RESULTS: Significant difference was seen in mean of CSF PCT in neonates with confirmed (0.31 ng/mL), probable (0.22 ng/mL), and nonmeningitis (0.11 ng/mL) groups. Similarly, significant difference was observed in serum PCT levels also, though the ratio of serum to CSF PCT was comparable. At cut-off of 0.2 ng/mL, CSF PCT had sensitivity of 95.2% and specificity of 96% in the diagnosis of meningitis. CONCLUSION: CSF PCT is more specific marker for the diagnosis of neonatal meningitis as compared with serum PCT and CSF to serum PCT ratio. KEY POINTS: · CSF procalcitonin is a better marker than serum procalcitonin for diagnosing neonatal meningitis.. · It is better than serum procalcitonin and CSF to serum procalcitonin ratio.. · At cut-off of >0.2 ng/mL CSF procalcitonin can diagnose neonatal meningitis with 96% specificity..

Characterizing plant trait(s) for improved heat tolerance in field pea (Pisum sativum L.) under subtropical climate.

Field pea is highly sensitive to climatic vagaries, particularly high-temperature stress. The crop often experiences terminal heat stress in tropical climates indicating the need for the development of heat-tolerant cultivars. Characterization and identification of stress-adaptive plant traits are pre-requisites for breeding stress-tolerant/adaptive cultivar(s). In the study, a panel of 150 diverse field pea genotypes was tested under three different temperature environments (i.e., normal sowing time or non-heat stress environment (NSTE), 15 days after normal sowing time or heat stress environment-I (LSHTE-I), and 30 days after normal sowing time or heat stress environment-II (LSHTE-II)) to verify the effect of high-temperature environment, genotype, and genotype × environment interaction on different plant traits and to elucidate their significance in heat stress adaptation/tolerance. The delayed sowing had exposed field pea crops to high temperatures during flowering stage by + 3.5 °C and + 8.1 °C in the LSHTE-I and LSHTE-II, respectively. Likewise, the maximum ambient temperature during the grain-filling period was + 3.3 °C and + 6.1 °C higher in the LSHTE-I and LSHTE-II over the NSTE. The grain yield loss with heat stress was 25.8 ± 2.2% in LSHTE-I, and 59.3 ± 1.5% in LSHTE-II compared to the NSTE. Exposure of crops to a high-temperature environment during the flowering stage had a higher impact on grain yield than the heat stress at the grain filling period. Results suggested that the reduced sink capacity (pod set (pod plant-1), seed set (seed pod-1)) was the primary cause of yield loss under the heat stress environments, while, under the NSTE, yield potential was mostly attributed to the source capacity (plant biomass). The high-temperature stress resulted in forced maturity as revealed by shrinkage in crop period (5-11%) and reproductive period (15-36%), prominently in long-duration genotypes. The failure of pod set in the upper nodes and higher ovule abortion (7-16%) was noticed under the high-temperature environments, particularly in the LSHTE-II. Multivariate analysis results revealed seed set, pods plant-1, last pod bearing node, and plant biomass as a critical yield determinant under the heat stress. The GGE biplot suggested that the genotypes G-112, G-114, and G-33 had higher potential to sustain yield coupled with higher stability across the environments and, thus, could serve as a source for breeding heat-tolerant high yielding cultivars.

Prediction models for evaluating the impacts of ambient air pollutants on the biochemical response of selected tree species of Haridwar, India.

This study aimed to assess the spatio-temporal impact of selected ambient air pollutants (SO2, NO2, PM10, and PM2.5) on the biochemical response of four tree species including Neem (Azadirachta indica), Mountain cedar (Toona ciliate), Bottlebrush (Callistemon citrinus), and Guava (Psidium guajava) in the province of Haridwar City, Uttarakhand, India. The study was performed in 2020 and 2021 over three selected sites (S1: institutional; S2: industrial; and S3: urban). Purposely, seasonal data of ambient air pollutants and biochemical parameters (ascorbic acid, carotenoid, chlorophyll, pH, relative water content, and dust load) of selected tree species were collected and analyzed using multiple linear regression (MLR) tool to develop prediction models. The results indicated that biochemical parameters of all tree species were negatively impacted by the polluted ambient air quality in the industrial and urban (S2 and S3) sites as compared to the non-polluted institutional (S1) site. The models were characterized by high prediction performance as indicated by the coefficient of determination (R2) values greater than 0.80. Moreover, A. indica was found to be more 'tolerant' based on the air pollution tolerance index (APTI) followed by T. ciliate, P. guajava, and C. citrinus. Similarly, the anticipated performance index (API) was reported higher for A. indica (75 to 81.25%) followed by T. ciliate (68.75 to 75.00%), P. guajava (56.25%), and C. citrinus (37.50%), respectively. This study revealed that the selected tree species are being negatively impacted by the induced pollutant exposure in the urban and industrial region of Haridwar, India which needs sufficient mitigation measures to conserve their diversities.

Genome-wide comparative transcriptome analysis of the A4-CMS line ICPA 2043 and its maintainer ICPB 2043 during the floral bud development of pigeonpea.

Cytoplasmic male sterility (CMS) offers a unique system to understand cytoplasmic nuclear crosstalk, and is also employed for exploitation of hybrid vigor in various crops. Pigeonpea A4-CMS, a predominant source of male sterility, is being used for efficient hybrid seed production. The molecular mechanisms of CMS trait remain poorly studied in pigeonpea. We performed genome-wide transcriptome profiling of A4-CMS line ICPA 2043 and its isogenic maintainer ICPB 2043 at two different stages of floral bud development (stage S1 and stage S2). Consistent with the evidences from some other crops, we also observed significant difference in the expression levels of genes in the later stage, i.e., stage S2. Differential expression was observed for 143 and 55 genes within the two stages of ICPA 2043 and ICPB 2043, respectively. We obtained only 10 differentially expressed genes (DEGs) between the stage S1 of the two genotypes, whereas expression change was significant for 582 genes in the case of stage S2. The qRT-PCR assay of randomly selected six genes supported the differential expression of genes between ICPA 2043 and ICPB 2043. Further, GO and KEGG pathway mapping suggested a possible compromise in key bioprocesses during flower and pollen development. Besides providing novel insights into the functional genomics of CMS trait, our results were in strong agreement with the gene expression atlas of pigeonpea that implicated various candidate genes like sucrose-proton symporter 2 and an uncharacterized protein along with pectate lyase, pectinesterase inhibitors, L-ascorbate oxidase homolog, ATPase, ß-galactosidase, polygalacturonase, and aldose 1-epimerase for pollen development of pigeonpea. The dataset presented here provides a rich genomic resource to improve understanding of CMS trait and its deployment in heterosis breeding in pigeonpea.

Transgenic chickpea (Cicer arietinum L.) harbouring AtDREB1a are physiologically better adapted to water deficit.

BACKGROUND: Chickpea (Cicer arietinum L.) is the second most widely grown pulse and drought (limiting water) is one of the major constraints leading to about 40-50% yield losses annually. Dehydration responsive element binding proteins (DREBs) are important plant transcription factors that regulate the expression of many stress-inducible genes and play a critical role in improving the abiotic stress tolerance. Transgenic chickpea lines harbouring transcription factor, Dehydration Responsive Element-Binding protein 1A from Arabidopsis thaliana (AtDREB1a gene) driven by stress inducible promoter rd29a were developed, with the intent of enhancing drought tolerance in chickpea. Performance of the progenies of one transgenic event and control were assessed based on key physiological traits imparting drought tolerance such as plant water relation characteristics, chlorophyll retention, photosynthesis, membrane stability and water use efficiency under water stressed conditions. RESULTS: Four transgenic chickpea lines harbouring stress inducible AtDREB1a were generated with transformation efficiency of 0.1%. The integration, transmission and regulated expression were confirmed by Polymerase Chain Reaction (PCR), Southern Blot hybridization and Reverse Transcriptase polymerase chain reaction (RT-PCR), respectively. Transgenic chickpea lines exhibited higher relative water content, longer chlorophyll retention capacity and higher osmotic adjustment under severe drought stress (stress level 4), as compared to control. The enhanced drought tolerance in transgenic chickpea lines were also manifested by undeterred photosynthesis involving enhanced quantum yield of PSII, electron transport rate at saturated irradiance levels and maintaining higher relative water content in leaves under relatively severe soil water deficit. Further, lower values of carbon isotope discrimination in some transgenic chickpea lines indicated higher water use efficiency. Transgenic chickpea lines exhibiting better OA resulted in higher seed yield, with progressive increase in water stress, as compared to control. CONCLUSIONS: Based on precise phenotyping, involving non-invasive chlorophyll fluorescence imaging, carbon isotope discrimination, osmotic adjustment, higher chlorophyll retention and membrane stability index, it can be concluded that AtDREB1a transgenic chickpea lines were better adapted to water deficit by modifying important physiological traits. The selected transgenic chickpea event would be a valuable resource that can be used in pre-breeding or directly in varietal development programs for enhanced drought tolerance under parched conditions.

Identification of microRNAs and their gene targets in cytoplasmic male sterile and fertile maintainer lines of pigeonpea.

MAIN CONCLUSION: Comparative analysis of genome-wide miRNAs and their gene targets between cytoplasmic male sterile (CMS) and fertile lines of pigeonpea suggests a possible role of miRNA-regulated pathways in reproductive development. Exploitation of hybrid vigor using CMS technology has delivered nearly 50% yield gain in pigeonpea. Among various sterility-inducing cytoplasms (A1-A9) reported so far in pigeonpea, A2 and A4 are the two major sources that facilitate hybrid seed production. Recent evidence suggests involvement of micro RNA in vast array of biological processes including plant reproductive development. In pigeonpea, information about the miRNAs is insufficient. In view of this, we sequenced six small RNA libraries of CMS line UPAS 120A and isogenic fertile line UPAS 120B using Illumina technology. Results revealed 316 miRNAs including 248 known and 68 novel types. A total of 637 gene targets were predicted for known miRNAs, while 324 genes were associated with novel miRNAs. Degradome analysis revealed 77 gene targets of predicted miRNAs, which included a variety of transcription factors playing key roles in plant reproduction such as F-box family proteins, apetala 2, auxin response factors, ethylene-responsive factors, homeodomain-leucine zipper proteins etc. Differential expression of both known and novel miRNAs implied roles for both conserved as well as species-specific players. We also obtained several miRNA families such as miR156, miR159, miR167 that are known to influence crucial aspects of plant fertility. Gene ontology and pathway level analyses of the target genes showed their possible implications for crucial events during male reproductive development such as tapetal degeneration, pollen wall formation, retrograde signaling etc. To the best of our knowledge, present study is first to combine deep sequencing of small RNA and degradome for elucidating the role of miRNAs in flower and male reproductive development in pigeonpea.

Resveratrol-mediated attenuation of superantigen-driven acute respiratory distress syndrome is mediated by microbiota in the lungs and gut.

Acute Respiratory Distress Syndrome (ARDS) is triggered by a variety of agents, including Staphylococcal Enterotoxin B (SEB). Interestingly, a significant proportion of patients with COVID-19, also develop ARDS. In the absence of effective treatments, ARDS results in almost 40% mortality. Previous studies from our laboratory demonstrated that resveratrol (RES), a stilbenoid, with potent anti-inflammatory properties can attenuate SEB-induced ARDS. In the current study, we investigated the role of RES-induced alterations in the gut and lung microbiota in the regulation of ARDS. Our studies revealed that SEB administration induced inflammatory cytokines, ARDS, and 100% mortality in C3H/HeJ mice. Additionally, SEB caused a significant increase in pathogenic Proteobacteria phylum and Propionibacterium acnes species in the lungs. In contrast, RES treatment attenuated SEB-mediated ARDS and mortality in mice, and significantly increased probiotic Actinobacteria phylum, Tenericutes phylum, and Lactobacillus reuteri species in both the colon and lungs. Colonic Microbiota Transplantation (CMT) from SEB-injected mice that were treated with RES as well as the transfer of L. reuteri into recipient mice inhibited the production of SEB-mediated induction of pro-inflammatory cytokines such as IFN-γ and IL-17 but increased that of anti-inflammatory IL-10. Additionally, such CMT and L. reuteri recipient mice exposed to SEB, showed a decrease in lung-infiltrating mononuclear cells, cytotoxic CD8+ T cells, NKT cells, Th1 cells, and Th17 cells, but an increase in the population of regulatory T cells (Tregs) and Th3 cells, and increase in the survival of mice from SEB-mediated ARDS. Together, the current study demonstrates that ARDS induced by SEB triggers dysbiosis in the lungs and gut and that attenuation of ARDS by RES may be mediated, at least in part, by alterations in microbiota in the lungs and the gut, especially through the induction of beneficial bacteria such as L. reuteri.

Comprehensive RNAseq analysis for identification of genes expressed under heat stress in lentil.

Lentils are highly sensitive to abrupt increases in temperature during the mid to late reproductive stages, leading to severe biomass and seed yield reduction. Therefore, we carried out an RNAseq analysis between IG4258 (heat tolerant) and IG3973 (heat sensitive) lentil genotypes at the reproductive stage under both normal and heat stress conditions in the field. It resulted in 209,549 assembled transcripts and among these 161,809 transcripts had coding regions, of which 94,437 transcripts were annotated. The differential gene expression analysis showed upregulation of 678 transcripts and downregulation of 680 transcripts between the tolerant and sensitive genotypes at the early reproductive stage. While 76 transcripts were upregulated and 47 transcripts were downregulated at the late reproductive stage under heat stress conditions. The validation of 12 up-or downregulated transcripts through RT-PCR corresponded well with the expression analysis data of RNAseq, with a correlation of R2  = 0.89. Among these transcripts, the DN364_c1_g1_i9 and DN2218_c0_g1_i5 transcripts encoded enzymes involved in the tryptophan pathway, indicating that tryptophan biosynthesis plays a role under heat stress in lentil. Moreover, KEGG pathways enrichment analysis identified transcripts associated with genes encoding proteins/regulating factors related to different metabolic pathways including signal transduction, fatty acid biosynthesis, rRNA processing, ribosome biogenesis, gibberellin (GA) biosynthesis, and riboflavin biosynthesis. This analysis also identified 6852 genic-SSRs leading to the development of 4968 SSR primers that are potential genomic resources for molecular mapping of heat-tolerant genes in lentil.