Miracle-dz/UniFAR-FTUs huggingface dataset:
DNA Barcoding on Cardinalfishes (Apogonidae) of Thoothukudi Coast

India is one of the largest heritage resources for marine fishery resources. In India, there are nearly 1570 species of known marine fishes with the exploited area of 2.02 million sq.km of the Exclusive Economic Zone (EEZ). Also, Indian seas have many unexploited habitats like mesopelagic zone and deep waters that may harbor many species of fishes which is yet to be documented. Most of the species were not correctly identified from the Indian waters as taxonomic ambiguity exists in several groups of Indian finfishes. In India, marine ornamental fishes are distributed in the Gulf of Mannar/Palk Bay, Gulf of Kutch along the mainland coast and in reefs around Andaman & Nicobar and Lakshadweep International Journal of Current Microbiology and Applied Sciences ISSN: 2319-7706 Volume 8 Number 08 (2019) Journal homepage: http://www.ijcmas. com
Direct Metatranscriptome RNA-seq and Multiplex RT-PCR Amplicon Sequencing on Nanopore MinION – Promising Strategies for Multiplex Identification of Viable Pathogens in Food

Viable pathogenic bacteria are major biohazards that pose a significant threat to food safety. Despite the recent developments in detection platforms, multiplex identification of viable pathogens in food remains a major challenge. A novel strategy is developed through direct metatranscriptome RNA-seq and multiplex RT-PCR amplicon sequencing on Nanopore MinION to achieve real-time multiplex identification of viable pathogen in food. Specifically, this study reports an optimized universal Nanopore sample extraction and library preparation protocol applicable to both Gram-positive and Gram-negative pathogenic bacteria, demonstrated using a cocktail culture of E. coli O157:H7, Salmonella enteritidis, and Listeria monocytogenes, which were selected based on their impact on economic loss or prevalence in recent outbreaks. Further evaluation and validation confirmed the accuracy of direct metatranscriptome RNA-seq and multiplex RT-PCR amplicon sequencing using Sanger sequencing and selective media. The study also included a comparison of different bioinformatic pipelines for metatranscriptomic and amplicon genomic analysis. MEGAN without rRNA mapping showed the highest accuracy of multiplex identification using the metatranscriptomic data. EPI2ME also demonstrated high accuracy using multiplex RT-PCR amplicon sequencing. In addition, a systemic comparison was drawn between Nanopore sequencing of the direct metatranscriptome RNA-seq and RT-PCR amplicons. Both methods are comparable in accuracy and time. Nanopore sequencing of RT-PCR amplicon has higher sensitivity, but Nanopore metatranscriptome sequencing excels in read length and dealing with complex microbiome and non-bacterial transcriptome backgrounds. To the best of our knowledge, this is the first report of metatranscriptome sequencing of cocktail microbial RNAs on the emerging Nanopore platform. Direct RNA-seq and RT-PCR amplicons sequencing of metatranscriptome enable the direct identification of nucleotide analogs in RNAs, which is highly informative for determining microbial identities while detecting ecologically relevant processes. The information pertained in this study could be important for future revelatory research, including predicting antibiotic resistance, elucidating host-pathogen interaction, prognosing disease progression, and investigating microbial ecology, etc.
Har-P, a short P-element variant, weaponizes P-transposase to severely impair Drosophila development

Without transposon-silencing Piwi-interacting RNAs (piRNAs), transposition causes an ovarian atrophy syndrome in Drosophila called gonadal dysgenesis (GD). Harwich (Har) strains with P-elements cause severe GD in F1 daughters when Har fathers mate with mothers lacking P-element-piRNAs (i.e. ISO1 strain). To address the mystery of why Har induces severe GD, we bred hybrid Drosophila with Har genomic fragments into the ISO1 background to create HISR-D or HISR-N lines that still cause Dysgenesis or are Non-dysgenic, respectively. In these lines, we discovered a highly truncated P-element variant we named “Har-P” as the most frequent de novo insertion. Although HISR-D lines still contain full-length P-elements, HISR-N lines lost functional P-transposase but retained Har-P’s that when crossed back to P-transposase restores GD induction. Finally, we uncovered P-element-piRNA-directed repression on Har-P’s transmitted paternally to suppress somatic transposition. The Drosophila short Har-P’s and full-length P-elements relationship parallels the MITEs/DNA-transposase in plants and SINEs/LINEs in mammals.
Characterization of the complete mitochondrial genome of Eysarcoris aeneus (Heteroptera: Pentatomidae), with its phylogenetic analysis

Abstract In this study, the complete 16,065 bp mitochondrial genome of Eysarcoris aeneus was determined from China using next-generation sequencing technology. It consists of 13 protein-coding genes, 22 tRNAs, 2 ribosomal RNAs, and a control region. Among them, 23 genes were located on J-strand, and the other genes (nad5, nad4, nad4L, nad1, trnQ, trnC, trnY, trnF, trnH, trnP, trnL1, trnV, 12S rRNA, and 16S rRNA) were located on the N-strand. The phylogenetic tree was constructed using MrBayes method based on the 13 protein-coding genes (PCGs) showed the present species clustered within the Pentatomidae. The complete mitogenome data would be useful for further study of Pentatomoidea and Pentatomomorpha.
Modeling cell-specific dynamics and regulation of the common gamma chain cytokines

Many receptor families exhibit both pleiotropy and redundancy in their regulation, with multiple ligands, receptors, and responding cell populations. Any intervention, therefore, has multiple effects and is context specific, confounding intuition about how to carry out precise therapeutic manipulation. The common γ-chain cytokine receptor dimerizes with complexes of the cytokines interleukin (IL)-2, IL-4, IL-7, IL-9, IL-15, and IL-21 and their corresponding “private” receptors. These cytokines have existing uses and future potential as immune therapies due to their ability to regulate the abundance and function of specific immune cell populations. Here, we build a binding-reaction model for the ligand-receptor interactions of common γ-chain cytokines enabling quantitative predictions of response. We show that accounting for receptor-ligand trafficking is essential to accurately model cell response. Using this model, we visualize regulation across the family and immune cell types by tensor factorization. This model accurately predicts ligand response across a wide panel of cell types under diverse experimental designs. Further, we can predict the effect of ligands across cell types. In total, these results present a more accurate model of ligand response validated across a panel of immune cell types, and demonstrate an approach for generating interpretable guidelines to manipulate the cell type-specific targeting of engineered ligands. Summary points A dynamical model of the γ-chain cytokines accurately models responses to IL-2, IL-15, IL-4, and IL-7. Receptor trafficking is necessary for capturing ligand response. Tensor factorization maps responses across cell populations, receptors, cytokines, and dynamics. An activation model coupled with tensor factorization creates design specifications for engineering cell-specific responses.
Inhibition of the mitochondrial permeability transition exerts sex-specific stimulatory effect on fracture repair

Bone fracture is accompanied by mechanical stresses and inflammation – conditions that impair mitochondria via the phenomenon of permeability transition. This phenomenon occurs due to opening of the mitochondrial permeability transition pore (MPTP) promoted by cyclophilin D (CypD). MPTP opening exacerbates inflammation and cell death and, thus can disrupt fracture repair. Here we tested a hypothesis that protecting mitochondria from MPTP opening via inhibition of CypD improves fracture repair. Our data indicate that osteoblast activity, bone formation, and biomechanical properties of repaired bones were significantly increased in CypD knock-out mice when compared to controls during fracture repair. These effects were observed in male but not female mice, thus showing sexual dimorphism. Pharmacological inhibition of CypD with NIM811 in male mice also stimulated fracture repair. In addition, CypD knock-out or pharmacological inhibition produced pro-osteogenic effect in isolated bone marrow osteoprogenitors. This in vitro effect was associated with higher mitochondrial respiration and increased β-catenin activity regulated by mitochondria-dependent acetylation. Our findings implicate a sex-specific role of MPTP in bone fracture and suggest CypD inhibition as a modality to promote fracture repair.
Mechanism of immune escape from CD8+ T cell response in hepatitis delta virus infection

Hepatitis D virus (HDV) infection affects 20 million humans worldwide. A failure of T cell responses is associated with chronicity, but little is known about this. We found that HLA-B alleles exert stronger selection pressure on HDV than HLA-A alleles and identified two new HLA-B*27-restricted HDV epitopes. Patients with resolved infection showed T cell responses against these epitopes, and viral escape mutations resulted in viral evasion proving their immunodominance.
Improvement of the specific detection of Xanthomonas phaseoli pv. manihotis based on the pthB gene

Modifications were made in the PCR conditions aiming to overcome the problem of non-amplification of the Xanthomonas phaseoli pv. manihotis (Xpm) fragment, using the primer pair XV / XK described in the literature. The objective of this study was to propose changes in the primers already described (XV / XK_MOD) and validate the use of these new primers in identifying Xpm. The validation procedure was carried out with the primer pair XV and XK_MOD, using different strains of Xpm, other plant pathogenic and endophytic bacteria genera and one isolate of X. phaseoli pv. passiflorae. As a control, additional reactions were conducted in multiplex with the universal primers for the 16S rRNA gene of the bacteria together with XV / XK and XV / XK_MOD. Using the forward primer (XV) described in the literature together with the modified reverse primer (XK_MOD), it was possible to achieve amplification from DNA extracted from in vitro cultures and from infected tissue, but no amplification was noticed for the primer pair described in the literature, confirming the effectiveness of the proposed modification.
In vivo and in vitro antidiabetic and antioxidant activity of spirulina

Objective: This study aims to evaluate the effect of spirulina, a biomass produced by cyanobacteria, on the level of plasma glucose, oxidative stress, and other biochemical parameters in diabetes in streptozocin (STZ) 50 mg/kg-induced diabetic-induced rat model. Materials and Methods: The in vitro antioxidant property of spirulina was assessed by measuring its ability to scavenge free radicals and reactive oxygen species (ROS) such as superoxide anion, nitric oxide, and hydroxyl and lipid peroxyl radicals. The inhibition of diabetic link enzymes alpha-glucosidase, alpha-amylase, and dipeptidyl peptidase-4 inhibitor (DPP-IV) were tested in vitro. Thirty female Sprague-Dawley rats weighing 150–250 g were divided into five groups: normal, diabetes (negative control), metformin in single dose of 300 mg/kg, spirulina in a single dose of 300 mg/kg and spirulina combined with metformin at dose of 150 mg/kg, and spirulina at dose of 150 mg/kg (spirulina + metformin 300 mg/kg) (n = 6). After an acclimation period of 2 weeks, diabetes was induced in the rats through STZ intraperitoneal injection. Spirulina (300 mg/kg) was dissolved in water and was administered orally for 12 weeks, and the rats' that plasma glucose level reached ≥11 mmol/L after 12 weeks treatment was selected for the study. After the treatment, the blood and liver were used for the evaluation of antioxidant enzyme activities, lipid, liver, kidney, and hematology profile. Results: Spirulina was able to reduce hyperglycemia-induced oxidative stress by reducing plasma glucose levels and scavenging or reducing the production of ROS and free radicals. It was also able to inhibit the activities of the alpha-glucosidase, alpha-amylase, and DPP-IV. With this, it significantly reduced the effect of STZ on the liver and kidney at the organ level and on antioxidant enzymes at the cellular level. Conclusion: Spirulina is able to reduce the lipid, liver, and kidney disease markers in STZ-induced rats and therefore is a potential supplement for diabetic patients. The antidiabetic effect of spirulina may be based on the antioxidant effect of the biomass as a whole, or it is based on specific bioactive components present in spirulina.
Zymobacter palmae Pyruvate Decarboxylase is Less Effective Than That of Zymomonas mobilis for Ethanol Production in Metabolically Engineered Synechocystis sp. PCC6803

To produce bioethanol from model cyanobacteria such as Synechocystis, a two gene cassette consisting of genes encoding pyruvate decarboxylase (PDC) and alcohol dehydrogenase (ADH) are required to transform pyruvate first to acetaldehyde and then to ethanol. However the partition of pyruvate to ethanol comes at a cost, a reduction in biomass and pyruvate availability for other metabolic processes. Hence strategies to divert flux to ethanol as a biofuel in Synechocystis are of interest. PDC from Zymobacter palmae (ZpPDC) has been reported to have a lower Km then the Zymomonas mobilis PDC (ZmPDC), which has traditionally been used in metabolic engineering constructs. The Zppdc gene was combined with the native slr1192 alcohol dehydrogenase gene (adhA) in an attempt to increase ethanol production in the photoautotrophic cyanobacterium Synechocystis sp. PCC 6803 over constructs created with the traditional Zmpdc. Native (Zppdc) and codon optimized (ZpOpdc) versions of the ZpPDC were cloned into a construct where pdc expression was controlled via the psbA2 light inducible promoter from Synechocystis sp. PCC 6803. These constructs were transformed into wildtype Synechocystis sp. PCC 6803 for expression and ethanol production. Ethanol levels were then compared with identical constructs containing the Zmpdc. While strains with the Zppdc (UL071) and ZpOpdc (UL072) constructs did produce ethanol, levels were lower compared to a control strain (UL070) expressing the pdc from Zymomonas mobilis. All constructs demonstrated lower biomass productivity illustrating that the flux from pyruvate to ethanol has a major effect on biomass and ultimately overall biofuel productivity. Thus the utilization of a PDC with a lower Km from Zymobacter palmae unusually did not result in enhanced ethanol production in Synechocystis sp. PCC 6803.
Trends in extreme rainfall events in Sri Lanka, 1961 - 2010

Many parts of Sri Lanka are vulnerable to extreme rainfall events leading to floods and droughts. This study was focused on a trend analysis of climate extremes derived from daily rainfall records. The daily rainfall data from 13 meteorological stations representing different geographical regions in Sri Lanka for the period 1961–2010 were chosen. The analysis was carried out separately for summer half year (March-August) and winter half year (September-February) to capture the possible changes in two growing seasons, Yala and Maha. Magnitudes of trends were derived using linear regression analysis while the statistical significance was determined using the Mann-Kendall test. Spatial maps were used to study the regional differences in climate extremes. Extreme rainfall events were found to be isolated events without coherent increasing or decreasing trends. However, statistically significant increasing (decreasing) trends were observed for number of dry days (wet days) ranging from 1.1 to 3.1 days/decade in most parts of the island during the summer half year, except for the coastal areas of the dry zone. No increasing or decreasing trends in extremes were observed for the winter half year. Based on the analysis, it was concluded that there is widespread climate change leading to increasing (decreasing) dry days (wet days) during the summer half year receiving rainfall predominantly from the South-West monsoon. However, mixed results were obtained for the winter half year.
Genetic divergence in basil cultivars and hybrids

ABSTRACT Basil is an aromatic herb that stands out for its economic importance. It is consumed in natura and used to obtain essential oil. The cultivation of this species in several regions of the world has allowed variations by natural crosses and euploidy, leading to the wide genetic variability found nowadays. Considering the importance of this species, we aimed to analyze the genetic diversity of 27 basil genotypes using ISSR molecular markers. Fourteen primers were employed for DNA amplification, resulting in 86% polymorphism. Based on the Jaccard’s dissimilarity index, the highest index (0.80) was observed between the individuals BAS001 and BAS012, while the lowest index (0.18) was detected between the genotypes BAS014 and BAS015. The genetic similarity among individuals was calculated, forming four distinct clusters. Most individuals (40.7%) were allocated in cluster I. The polymorphic information content (PIC) (0.89) indicated considerable levels of genetic diversity among genotypes. In this sense, the ISSR markers were efficient in the detection of polymorphisms between the accessions, suggesting the genetic variability of the collection. This result demonstrates the importance of the use of molecular markers and the advantages that this information provides to the breeding of the species.
Muntjac chromosome evolution and architecture

Despite their recent divergence, muntjac deer show striking karyotype differences. Here we describe new chromosome-scale genome assemblies for the Chinese and Indian muntjacs, Muntiacus reevesi (2n=46) and Muntiacus muntjak (2n=6/7), and analyze their evolution and architecture. We identified six fusion events shared by both species relative to the cervid ancestor and therefore present in the muntjac common ancestor, six fusion events unique to the M. reevesi lineage, and twenty-six fusion events unique to the M. muntjak lineage. One of these M. muntjak fusions reverses an earlier fission in the cervid lineage. Although comparative Hi-C analysis revealed differences in long-range genome contacts and A/B compartment structures, we discovered widespread conservation of local chromatin contacts between the muntjacs, even near the fusion sites. A small number of genes involved in chromosome maintenance show evidence for rapid evolution, possibly associated with the dramatic changes in karyotype. Analysis of muntjac genomes reveals new insights into this unique case of rapid karyotype evolution and the resulting biological variation.
The complete mitochondrial genome of Thalassoma lunare (Labriformes, Labridae)

Abstract Thalassoma lunare is one of most important genera of Labridae. However, the systemically classification and taxonomic studies have so far been limited. In this study, we report the complete mitochondrial genome sequence of T. lunare. The mitogenome has 17,073 base pairs (57.7% A + T content) and made up of total of 37 genes (13 protein-coding, 22 transfer RNAs and 2 ribosomal RNAs), and a putative control region. This study will provide useful genetic information for future phylogenetic and taxonomic classification of Labridae.
Vegetation recovery on neighboring tidal flats forms an Achilles' heel of saltmarsh resilience to sea level rise

Coastal wetlands such as saltmarshes are valued as prominent buffering ecosystems to global climate change and sea level rise (SLR), yet their long‐term persistence may also be threatened by these global change stressors. While saltmarshes are increasingly thought to be resilient to SLR owing to high vertical marsh adaptability, their long‐term stability remains uncertain due to our poor understanding of marsh resilience at the marsh‐tidal flat interface, where wave disturbance can progressively shift vegetated marsh toward a bare tidal flat state. Here, we explore how SLR affects vegetation recoverability on tidal flats using cordgrass, a globally common saltmarsh foundation species, as a model plant. Combined field and model results demonstrate that small increases in wave forcing due to raised water depth over tidal flats can dramatically weaken or even block vegetation recovery from eroding marsh edges, through hampering seed persistence. Vegetation recovery on tidal flats next to the marsh edge thus represents an unrecognized Achilles' heel of marsh resilience to SLR, which if ignored may cause underestimation of marsh vulnerability. These findings are highly relevant for a more comprehensive assessment of marsh susceptibility to SLR in systems where seeds play an essential role in revegetation of tidal flats, and highlight the importance of maintaining either a wave‐protected or well‐elevated tidal flat near the marsh edge that allows for quick vegetation recovery for supporting resilient marshes.
Synergic action of Vitamin D3 and 17β-estradiol on behavioral impairments induced by unpredictable mild stress in the adult ovariectomized female rats

The aim of the present study was study changes in antidepressant-like responses to Vitamin D3 (VD3) supplementation in three different doses (1.0, 2.5, and 5.0 mg/kg, s.c.) in long-term ovariectomized (OVX) rats treated with low dose of 17β-E2 (0.5 μg/rat, s.c.) during chronic unpredictable mild stress (CUMS). Sucrose preference (SPT), forced swimming (FST), and open-field (OFT) tests were administered to measure depression-like behavior. Brain-derived neurotrophic factor (BDNF), and serotonine (5-HT) and 5-hydroxyindoleacetic acid (5-HIAA) levels in the hippocampus were measured by ELISA, western blotting analysis, and by using high performance liquid chromatography (HPLC), respectively. The findings demonstrated that VD3 (5.0 mg/kg, s.c.) in a combination with low dose of 17β-E2 increased sucrose consumption in the SPT and decreased depression-like in the FST of the long-term OVX rats exposed to CUMS. VD3 (5.0 mg/kg) resulted in significant elevated levels of hippocampal BDNF protein expression, as well as to the normalization of 5-HT and 5-HIAA levels in long-term OVX rats plus 17β-E2 compared to the OVX rats plus solvent or 17β-E2 submitted to CUMS. There were no significant effects of VD3 (1.0 and 2.5 mg/kg) treatment on both BDNF protein levels and 5-HT turnover in the hippocampus of the long-term OVX rats treated with 17β-E2 exposed to CUMS compared to the long-term OVX with CUMS rats plus solvent. In conclusion, VD3 (5.0 mg/kg, s.c.) in a combination with low dose of 17β-E2 had a synergic antianhedonic- and antidepressant-like effects in the adult female rats following long-term ovariectomy submitted to CUMS. This is the first study in long-term OVX female rats showing beneficial effects of VD3 on depression-like behavior that are depended on the presence/absence of stressful factors.