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The California Pipevine, Aristolochia californica Torr., is the only endemic California species within the cosmopolitan birthwort family Aristolochiaceae. It occurs as an understory vine in riparian and chaparral areas and in forest edges and windrows. The geographic range of this plant species almost entirely overlaps with that of its major specialized herbivore, the California Pipevine Swallowtail Butterfly Battus philenor hirsuta. While this species pair is a useful, ecologically well-understood system to study co-evolution, until recently, genomic resources for both have been lacking. Here, we report a new, chromosome-level assembly of A. californica as part of the California Conservation Genomics Project (CCGP). Following the sequencing and assembly strategy of the CCGP, we used Pacific Biosciences HiFi long reads and Hi-C chromatin proximity sequencing technology to produce a de novo assembled genome. Our genome assembly, the first for any species in the genus, contains 531 scaffolds spanning 661 megabase (Mb) pairs, with a contig N50 of 6.53 Mb, a scaffold N50 of 42.2 Mb, and BUSCO complete score of 98%. In combination with the recently published B. philenor hirsuta reference genome assembly, the A. californica reference genome assembly will be a powerful tool for studying co-evolution in a rapidly changing California landscape.

Transposable elements (TE) play critical roles in shaping genome evolution. Highly repetitive TE sequences are also a major source of assembly gaps making it difficult to fully understand the impact of these elements on host genomes. The increased capacity of long-read sequencing technologies to span highly repetitive regions promises to provide new insights into patterns of TE activity across diverse taxa. Here we report the generation of highly contiguous reference genomes using PacBio long-read and Omni-C technologies for three species of Passerellidae sparrow. We compared these assemblies to three chromosome-level sparrow assemblies and nine other sparrow assemblies generated using a variety of short- and long-read technologies. All long-read based assemblies were longer (range: 1.12 to 1.41 Gb) than short-read assemblies (0.91 to 1.08 Gb) and assembly length was strongly correlated with the amount of repeat content. Repeat content for Bell's sparrow (31.2% of genome) was the highest level ever reported within the order Passeriformes, which comprises over half of avian diversity. The highest levels of repeat content (79.2% to 93.7%) were found on the W chromosome relative to other regions of the genome. Finally, we show that proliferation of different TE classes varied even among species with similar levels of repeat content. These patterns support a dynamic model of TE expansion and contraction even in a clade where TEs were once thought to be fairly depauperate and static. Our work highlights how the resolution of difficult-to-assemble regions of the genome with new sequencing technologies promises to transform our understanding of avian genome evolution.

The little pocket mouse, Perognathus longimembris, and its nine congeners are small heteromyid rodents found in arid and seasonally arid regions of Western North America. The genus is characterized by behavioral and physiological adaptations to dry and often harsh environments, including nocturnality, seasonal torpor, food caching, enhanced osmoregulation, and a well-developed sense of hearing. Here we present a genome assembly of Perognathus longimembris longimembris generated from PacBio HiFi long read and Omni-C chromatin-proximity sequencing as part of the California Conservation Genomics Project. The assembly has a length of 2.35 Gb, contig N50 of 11.6 Mb, scaffold N50 of 73.2 Mb, and includes 93.8% of the BUSCO Glires genes. Interspersed repetitive elements constitute 41.2% of the genome. A comparison with the highly endangered Pacific pocket mouse, P. l. pacificus, reveals broad synteny. These new resources will enable studies of local adaptation, genetic diversity, and conservation of threatened taxa.

Abstract An alkaline active L-glutaminase (BALG) producing bacterium was screened and identified from seamount sediment samples of the Arabian Sea. The isolate was confirmed to be Bacillus australimaris NIOT30 based on morphological characteristics and 16 S rRNA gene sequencing. The glutaminase gene, balg was PCR amplified, cloned and expressed in E. coli BL21 (DE3) host. The molecular weight of purified BALG was estimated to be 36 kDa and the enzyme showed a specific activity of 507 ± 27 Umg−1 against L-glutamine under optimal assay conditions of pH 7.0 and temperature at 37 °C for 15 min. The enzyme showed maximum activity at pH 7 and retained 95% activity at pH 10. BALG retained a relative activity of about 82% and 45% at 45 °C and 60 °C respectively. The kinetic parameters of BALG, Km and Kcat/Km were determined to be of 210 ± 11 mM and 4.4 × 102 M s−1 respectively. Homology modeling and substrate ligand interaction studies revealed the stability of the enzyme-substrate complex. The present study highlights the characterization of a highly active L-glutaminase from B. australimaris NIOT30. Further, mutational analyses of ligand binding residues would show insights into the affinity of L-Glutaminase.

Abstract Pulses are essential components of vegetarian diet and play a pivotal role in addressing malnutrition by providing a vital source of dietary protein. However, weed competition remains as a significant obstacle to blackgram (Vigna mungo L) production, resulting in 25 to 35% yield losses. A field experiment was carried out at the National Pulses Research Centre, Tamil Nadu Agricultural University, Vamban, Pudukkottai, India during Kharif seasons of 2020 and 2021, to assess the suitable post-emergence herbicides for appropriate weed control in blackgram grown under irrigated conditions. The experimental field was observed to contain notable grass weed flora, specifically Dactyloctenium aegyptium and Chloris barbata, as well as broadleaved weeds, such as Flaveria australica, Cleome gynandra, Eclipta alba, Convolvulus arvensis, Digera arvensis, Vicia spp., and Celosia argentea. The results demonstrated that among the chemical weed management methods, spraying of Fomesafen @ 220 g + Fluzifop p-butyl @ 220 g ha−1 at 20 days after sowing (DAS) as a post-emergence herbicide treatment exhibited superior weed control efficiency, recording 66.80% and 68.53% at 30 and 45 DAS, respectively and recorded higher seed yield of 1088 kg ha−1. Additionally, this method generated 8.1% higher net income and 12.5% more benefit–cost ratio than hand weeding, making it an economically profitable strategy for maximizing blackgram yield and effective labour management.

Background Childhood is the most essential phase in a person’s life as the foundations laid at this stage decide the future. Children are one of the vulnerable groups during any disaster. It is a stressful event that is not easily understood. It is emotionally confusing and frightening and results in children needing significant instrumental and emotional support from adults. Aim To understand the psychosocial impact of the COVID-19 pandemic on school-going adolescents. Methods This study adopted a cross-sectional research design in which sociodemographic characteristics and the CRIES-13 were administered to all the 312 children studying in 9th and 10th grade from the five selected schools. Statistical Analysis Descriptive statistics such as frequencies, mean, and percentages were employed to analyse participants’ demographic characteristics. Chi-square, independent t-test, and ANOVA were used for comparison of the data. Results The mean age of the respondents was 15 years (SD 0.98). It was found that most of the children (90.4%) had disturbances in their education, with 10th grade children having more disturbance than 9th grade ones (P value < 0.05). Further, intrusion and arousal were found to be significantly higher among male children than female children (P value < 0.05). Also, intrusion and arousal are significantly higher among 9th grade students, whereas avoidance is higher among 10th grade students (P value < 0.05). Conclusion The study identified that COVID-19 has a profound psychosocial impact on school going-adolescents. This finding highlights the importance of understanding the pandemic’s impact on children from a psychosocial perspective and designing appropriate interventions for them.

Abstract Background Social vulnerability is a multidimensional concept based on multivariate factors in domains of physical, social, economic, environmental, etc., and the subsets that constitute it. When addressed effectively, it paves the way for resolving and recorrecting certain facets that play a key role in determining the degree of susceptibility and potentiality of a population to address adverse situations. Aim The current study aims at synthesising research works and providing a comprehensive overview of social vulnerability assessment in the health and disease arena. Subject and methods It incorporates the concept of vulnerability, approaches, indices, indicators, and methodologies regarding social vulnerability in the health and disease arena from selected associated research articles accessed from digital database sources. Results There is an evident trend in associating new tools and techniques with the assessment of social vulnerability, along with conventional methods. Conclusion The results provide a theoretical background for subsequent research and an update on the recent trends in this topic of interest.

Biogenic synthesis of papain-conjugated copper metallic Nanoparticles and their antibacterial and antifungal activities Papain metallic conjugated nanoparticles (Papain-CuNPs) were synthesised using Papain and CuSO4.5H2O. Papain-CuNPs were characterized using UV-visible spectroscopy, FT-IR, HR-TEM, XRD, FE-SEM, zeta potential, and a zeta sizer. The antibacterial activity of papain-CuNPs against human infectious microorganisms (Citrobacter spp, Pseudomonas aeruginosa and Candida albicans) was investigated. The mechanism of action of papain-CuNPs was evaluated using FE-SEM and HRTM. UV spectroscopy confirmed the plasma resonance (SPR) at 679 nm, which indicated the formation of papain-CuNPs. The FT-IR spectrum absorbance peaks at 3927, 3865, 3842, 3363, 2978, and 2900 cm-1 indicate the presence of O-H and N-H of the secondary amine, and peaks at 1643 and 1572 cm-1 represent C=O functional groups in Papain-CuNPs. EDAX analysis confirmed the presence of copper in the papain-CuNPs. The zeta potential (-42.6 mV) and zeta size (99.66 d. nm) confirmed the stability and size of the nanoparticles. XRD confirmed the crystalline nature of the papain-CuNPs. FE-SEM and HRTM showed an oval structure, and the nano particles' 16.71244–34.84793 nm. The synthesized papain-NPs showed significant antibacterial activity against clinical P. aeruginosa (15 mm). MIC 125 µg/ml) showed bactericidal activity against P. aeruginosa and the mechanism of action of Papain-NPs was confirmed using an electron microscope by observing cell damage and cell shrinking. Papain-CuNPs have significant antibacterial activity and are thus used in the treatment of P. aeruginosa infections

Abstract Background PAF1/PD2 deregulation contributes to tumorigenesis, drug resistance, and cancer stem cell maintenance in Pancreatic Cancer (PC). Recent studies demonstrate that metabolic reprogramming plays a role in PC progression, but the mechanism is poorly understood. Here, we focused on examining the role of PAF1/PD2 in the metabolic rewiring of PC. Methods Cell lines were transfected with shRNAs to knockdown PAF1/PD2. Metabolic genes regulated by PAF1/PD2 were identified by qPCR/western blot, and metabolic assays were performed. Immunoprecipitations/ChIP were performed to identify PAF1/PD2 protein partners and confirm PAF1/HIF1α sub-complex binding to LDHA. Results PAF1 and LDHA showed progressively increased expression in human pancreatic tumor sections. Aerobic glycolysis genes were downregulated in PAF1-depleted PC cells. Metabolic assays indicated a decreased lactate production and glucose uptake in knockdown cells. Furthermore, PAF1/PD2 depletion showed a reduced glycolytic rate and increased oxidative phosphorylation by ECAR and OCR analysis. Interestingly, we identified that HIF1α interacts and co-localizes with PAF1, specifically in PC cells. We also observed that the PAF1/PD2-HIF1α complex binds to the LDHA promoter to regulate its expression, reprogramming the metabolism to utilize the aerobic glycolysis pathway preferentially. Conclusion Overall, the results indicate that PAF1/PD2 rewires PC metabolism by interacting with HIF1α to regulate the expression of LDHA.

Small hydro technology is playing a crucial role in advancing sustainable, clean energy policies as part of the global hydro development strategy. Its contribution to social and economic development is becoming more prominent, particularly in ensuring electricity access for rural communities and supporting industrial expansion. The main causes of bulb turbine failures under high operating conditions are frequently attributed to variations in pressure in the draft tubes, which are aggravated when a spinning vortex rope is formed under load operation. Different fluid injection techniques, namely compressed air and water jet injection, address these issues and reduce the negative results of cavitation. The investigation covers the flow visualization on the suction side of a single hydrofoil utilizing a cavitation tunnel and a bulb turbine. This study assesses the effectiveness of compressed air injection in reducing vibration generated by cavitation in bulb turbines. Positive results of the experimental studies suggest a decrease in noise and vibration by air injection that prevents oscillations of the vortex rope. This research also considers how the hydrofoil design of bulb runner blades influences flow characteristics. Hence, it provides knowledge on cavitation structures in diverse cavitation numbers. Different studies that compare the original and modified hydrofoil designs reveal remarkable improvements that may be due to changes in the key parameters of the hydrofoil, such as later cavitation initiation and reduced intensity. To obtain the optimal output of a bulb turbine by considering air injection for vibration reduction and hydrofoil design changes to limit the negative effect of cavitation, the Reynolds number and cavitation number are to be defined. This multidisciplinary approach possesses enormous potential to increase the reliability and efficiency of bulb turbines in challenging operating conditions.

We announce the assembly of the first de novo reference genome for the California Scrub-Jay (Aphelocoma californica). The genus Aphelocoma comprises four currently recognized species including many locally adapted populations across Mesoamerica and North America. Intensive study of Aphelocoma has revealed novel insights into the evolutionary mechanisms driving diversification in natural systems. Additional insights into the evolutionary history of this group will require continued development of high-quality, publicly available genomic resources. We extracted high molecular weight genomic DNA from a female California Scrub-Jay from northern California and generated PacBio HiFi long-read data and Omni-C chromatin conformation capture data. We used these data to generate a de novo partially phased diploid genome assembly, consisting of two pseudo-haplotypes, and scaffolded them using inferred physical proximity information from the Omni-C data. The more complete pseudo-haplotype assembly (arbitrarily designated "Haplotype 1") is 1.35 Gb in total length, highly contiguous (contig N50 = 11.53 Mb), and highly complete (BUSCO completeness score = 97%), with comparable scaffold sizes to chromosome-level avian reference genomes (scaffold N50 = 66.14 Mb). Our California Scrub-Jay assembly is highly syntenic with the New Caledonian Crow reference genome despite ~10 million years of divergence, highlighting the temporal stability of the avian genome. This high-quality reference genome represents a leap forward in publicly available genomic resources for Aphelocoma, and the family Corvidae more broadly. Future work using Aphelocoma as a model for understanding the evolutionary forces generating and maintaining biodiversity across phylogenetic scales can now benefit from a highly contiguous, in-group reference genome.

Rattlesnakes play important roles in their ecosystems by regulating prey populations, are involved in complex coevolutionary dynamics with their prey, and exhibit a variety of unusual adaptations, including maternal care, heat-sensing pit organs, hinged fangs, and medically-significant venoms. The western rattlesnake (Crotalus oreganus) is one of the widest ranging rattlesnake species, with a distribution from British Columbia, where it is listed as threatened, to Baja California and east across the Great Basin to western Wyoming, Colorado and New Mexico. Here, we report a new reference genome assembly for one of six currently recognized subspecies, C. oreganus helleri, as part of the California Conservation Genomics Project (CCGP). Consistent with the reference genomic sequencing strategy of the CCGP, we used Pacific Biosciences HiFi long reads and Hi-C chromatin-proximity sequencing technology to produce a de novo assembled genome. The assembly comprises a total of 698 scaffolds spanning 1,564,812,557 base pairs, has a contig N50 of 64.7 Mb, a scaffold N50 of 110.8 Mb, and BUSCO complete score of 90.5%. This reference genome will be valuable for studies on the genomic basis of venom evolution and variation within Crotalus, in resolving the taxonomy of C. oreganus and its relatives, and for the conservation and management of rattlesnakes in general.

Snakes in the family Colubridae include more than 2,000 currently recognized species, and comprise roughly 75% of the global snake species diversity on Earth. For such a spectacular radiation, colubrid snakes remain poorly understood ecologically and genetically. Two subfamilies, Colubrinae (788 species) and Dipsadinae (833 species), comprise the bulk of colubrid species richness. Dipsadines are a speciose and diverse group of snakes that largely inhabit Central and South America, with a handful of small-body-size genera that have invaded North America. Among them, the ring-necked snake, Diadophis punctatus, has an incredibly broad distribution with 14 subspecies. Given its continental distribution and high degree of variation in coloration, diet, feeding ecology, and behavior, the ring-necked snake is an excellent species for the study of genetic diversity and trait evolution. Within California, six subspecies form a continuously distributed "ring species" around the Central Valley, while a seventh, the regal ring-necked snake, Diadophis punctatus regalis is a disjunct outlier and Species of Special Concern in the state. Here, we report a new reference genome assembly for the San Diego ring-necked snake, D. p. similis, as part of the California Conservation Genomics Project. This assembly comprises a total of 444 scaffolds spanning 1,783 Mb and has a contig N50 of 8.0 Mb, scaffold N50 of 83 Mb, and BUSCO completeness score of 94.5%. This reference genome will be a valuable resource for studies of the taxonomy, conservation, and evolution of the ring-necked snake across its broad, continental distribution.

Acarospora socialis, the bright cobblestone lichen, is commonly found in southwestern North America. This charismatic yellow lichen is a species of key ecological significance as it is often a pioneer species in new environments. Despite their ecological importance virtually no research has been conducted on the genomics of A. socialis. To address this, we used long-read sequencing to generate the first high-quality draft genome of A. socialis. Lichen thallus tissue was collected from Pinkham Canyon in Joshua Tree National Park, California and deposited in the UC Riverside herbarium under accession #295874. The de novo assembly of the mycobiont partner of the lichen was generated from Pacific Biosciences HiFi long reads and Dovetail Omni-C chromatin capture data. After removing algal and bacterial contigs, the fungal genome was approximately 31.2 Mb consisting of 38 scaffolds with contig and scaffold N50 of 2.4 Mb. The BUSCO completeness score of the assembled genome was 97.5% using the Ascomycota gene set. Information on the genome of A. socialis is important for California conservation purposes given that this lichen is threatened in some places locally by wildfires due to climate change. This reference genome will be used for understanding the genetic diversity, population genomics, and comparative genomics of A. socialis species. Genomic resources for this species will support population and landscape genomics investigations, exploring the use of A. socialis as a bioindicator species for climate change, and in studies of adaptation by comparing populations that occur across aridity gradients in California.

The California Pipevine Swallowtail Butterfly, Battus philenor hirsuta, and its host plant, the California Pipevine or Dutchman's Pipe, Aristolochia californica Torr., are an important California endemic species pair. While this species pair is an ideal system to study co-evolution, genomic resources for both are lacking. Here, we report a new, chromosome-level assembly of B. philenor hirsuta as part of the California Conservation Genomics Project (CCGP). Following the sequencing and assembly strategy of the CCGP, we used Pacific Biosciences HiFi long reads and Hi-C chromatin proximity sequencing technology to produce a de novo assembled genome. Our genome assembly, the first for any species in the genus, contains 109 scaffolds spanning 443 mega base (Mb) pairs, with a contig N50 of 14.6 Mb, a scaffold N50 of 15.2 Mb, and BUSCO complete score of 98.9%. In combination with the forthcoming A. californica reference genome, the B. philenor hirsuta genome will be a powerful tool for documenting landscape genomic diversity and plant-insect co-evolution in a rapidly changing California landscape.

Abstract Blackgram, a protein-rich pulse crop (24%), is crucial for combating food insecurity, particularly in malnourished and economically weak countries. Enhancing blackgram production requires improved, input-saving management practices. Given the challenges of climate change and population growth, efficient water management is vital for increasing pulse productivity and water use efficiency with minimal investment. This study aimed to identify cost-effective irrigation methods to optimise blackgram yields. Experiments were conducted at the National Pulses Research Centre in Vamban, Pudukkottai, and the Agricultural College and Research Institute in Kumulur, Tiruchirappalli, during the kharif season of 2021 and 2022. The study compared different treatments of irrigation methods, such as check basin, raised bed, drip, sprinkler and rain hose irrigation. Results showed that the rain hose system maintained the highest soil moisture (23.93% at 10 cm depth and 19.71% at 20 cm depth). Even though drip irrigation resulted in a higher seed yield (1363 kg ha−1), the rain hose system proved to be more cost-effective, saving 27.09% in costs and achieving a 15.23% higher benefit–cost ratio. These findings suggest that the rain hose method, combined with current agronomic practices, is a viable low-cost technique for sustainable blackgram cultivation, optimising water use and maximising profits. This research provides valuable insights into water-saving irrigation methods for pulse crops.

Objectives. Knee injuries are prevalent among professional tennis players and have a significant impact on their athletic performance and longevity. This study aimed to evaluate the dynamic and postural balance differences between injured and healthy professional tennis players, reflecting the broader implications of knee injuries on player stability and performance. Materials and methods. A total of 80 professional tennis players, comprising 40 individuals in the knee injury group (IG) and 40 individuals in the non-injury group (NIG), were selected to participate in this cross-sectional study. Participants’ postural sway was assessed under various conditions, including standing on different surfaces with open and closed eyes using a Wii Balance Board. The Y-Balance Test was performed to evaluate the player’s dynamic balance. An Independent t-test was used to examine the difference in postural sway and dynamic balance between the two groups. Results. The results of this study indicated that players with knee injuries showed significantly worse performance in both dynamic balance (p

Introduction: Coronavirus disease 2019 (COVID-19), caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), presents a broad spectrum of clinical manifestations, from asymptomatic cases to severe pneumonia and acute respiratory distress syndrome (ARDS). Chest computed tomography (CT) has become a critical diagnostic tool, especially in regions with high disease prevalence. This study aims to assess the common CT findings, patterns of lung involvement, and severity of disease in RT-PCR positive COVID-19 patients to better understand and manage this pervasive disease. Materials and Methods: This observational cross-sectional study was conducted at Dr. Kamakshi Memorial Hospital, Chennai, from 2020 to 2021. The study included RT-PCR positive COVID-19 patients aged 18 to 95 years who presented to the fever clinic or COVID casualty and were referred to the radiology department for chest CT evaluation. Exclusion criteria included pregnancy, age under 18 years, and refusal to consent. Non-contrast chest CT scans were performed using a TOSHIBA Aquilion Lightening 16-slice CT machine. Scans were acquired in a single inspiratory breath-hold from the lung apex to the costophrenic angle. CT findings were analyzed and reported by two experienced radiologists, with discrepancies resolved through consensus. Results: Out of 349 patients, 213 (61%) were male and 136 (39%) were female, with a mean age of 47.7 years. The distribution of CT findings showed significant variability among the four groups. Group A had the highest percentage of normal CT scans (22%) and ground-glass opacities (52%). Group B exhibited a reduction in normal CT scans (9%) and an increase in ground-glass opacities (57%). Group C showed further decrease in normal CT scans (10.6%) with increased crazy paving (17.3%) and reticulation (14.6%). Group D had similar normal CT scans (10.8%) but significantly higher incidences of reticulation (24.3%) and ground-glass opacities (64%). Conclusion: This study highlights the critical role of chest CT in monitoring the progression of COVID-19 pneumonia. The findings demonstrate a clear temporal evolution of lung involvement, from ground-glass opacities in the early stages to more complex patterns such as crazy paving and reticulation in later stages.