Miracle-dz/UniFAR-FTUs huggingface dataset:
Assessing eukaryotic biodiversity in the Florida Keys National Marine Sanctuary through environmental DNA metabarcoding

Abstract Environmental DNA (eDNA) is the DNA suspended in the environment (e.g., water column), which includes cells, gametes, and other material derived from but not limited to shedding of tissue, scales, mucus, and fecal matter. Amplifying and sequencing marker genes (i.e., metabarcoding) from eDNA can reveal the wide range of taxa present in an ecosystem through analysis of a single water sample. Metabarcoding of eDNA provides higher resolution data than visual surveys, aiding in assessments of ecosystem health. This study conducted eDNA metabarcoding of two molecular markers (cytochrome c oxidase I (COI) and 18S ribosomal RNA (rRNA) genes) to survey eukaryotic diversity across multiple trophic levels in surface water samples collected at three sites along the coral reef tract within the Florida Keys National Marine Sanctuary (FKNMS) during four research cruises in 2015. The 18S rRNA gene sequences recovered 785 genera while the COI gene sequences recovered 115 genera, with only 33 genera shared between the two datasets, emphasizing the complementarity of these marker genes. Community composition for both genetic markers clustered by month of sample collection, suggesting that temporal variation has a larger effect on biodiversity than spatial variability in the FKNMS surface waters. Sequences from both marker genes were dominated by copepods, but each marker recovered distinct phytoplankton groups, with 18S rRNA gene sequences dominated by dinoflagellates and COI sequences dominated by coccolithophores. Although eDNA samples were collected from surface waters, many benthic species such as sponges, crustaceans, and corals were identified. These results show the utility of eDNA metabarcoding for cataloging biodiversity to establish an ecosystem baseline against which future samples can be compared in order to monitor community changes.
Chronic versus New-Onset Hyponatremia in Geriatric Patients Undergoing Orthopedic Surgery

Background: Hyponatremia is a common electrolyte disorder encountered in geriatric population undergoing an orthopedic surgery and is associated with adverse clinical outcomes. There is a paucity in literature comparing the effects of chronic- and new-onset hyponatremia on patient outcomes. Materials and Methods: A prospective study on 220 patients of age ≥60 years with an orthopedic injury was carried out over 1 year. The aim of this study was to determine the prevalence of chronic hyponatremia during hospitalization and the incidence of new-onset hyponatremia developing perioperatively and compare between the two groups with regard to the severity of hyponatremia, perioperative morbidities, serum sodium level trend in the early postoperative period, and mortality. Results: The prevalence of chronic hyponatremia was 14.1%, with an incidence of new-onset hyponatremia of 22.7%. Patients who developed new-onset hyponatremia were mostly of mild grade (130–134 mmol/L) and were significantly different from those with chronic hyponatremia who were more likely to be of profound grade (<125 mmol/L). When aggressively managed with adequate sodium corrections and strict monitoring, new-onset hyponatremia corrected within 48 h, whereas chronic hyponatremia had a gradual rise in serum sodium levels and did not achieve full correction within 48 h (P < 0.05). Those with chronic hyponatremia had a longer duration of hospital stay (P < 0.0001). No significant differences were obtained in mortality between the two groups. Conclusions: Patients developing new-onset hyponatremia are of milder grade and recover faster. Patients with chronic hyponatremia require a more cautious approach as they are more likely to be of profound grade and take longer time to correct.
Synthesis of MWCNTs using waste toner powder as carbon source by chemical vapor deposition method

Abstract The present work deals with the synthesis of carbon nanotubes (CNTs) from waste toner powder. XRD pattern of waste toner showed peaks related to magnetite and proximate analysis showed higher percentage of volatile matter (56.7%) which confirmed the possibility of using waste toner as a good source of carbon for the synthesis of CNTs. The process involved thermal breakdown of waste toner into hydrocarbons and used as a precursor to synthesize multi-walled carbon-nanotubes (MWCNTs) by chemical vapor deposition (CVD) method. The catalyst containing Ni4Mo0.2MgO1 was used for synthesis of CNTs. The process parameters were optimized using response surface methodology (RSM) and prepared CNTs were studied by using XRD, Raman spectroscopy, FESEM and HRTEM. The results shown the formation of multi walled carbon nanotubes with 40–50 nm from waste toner.
Control of entropy in neural models of environmental state

Humans and animals construct internal models of their environment in order to select appropriate courses of action. The representation of uncertainty about the current state of the environment is a key feature of these models that controls the rate of learning as well as directly affecting choice behaviour. To maintain flexibility, given that uncertainty naturally decreases over time, most theoretical inference models include a dedicated mechanism to drive up model uncertainty. Here we probe the long-standing hypothesis that noradrenaline is involved in determining the uncertainty, or entropy, and thus flexibility, of neural models. Pupil diameter, which indexes neuromodulatory state including noradrenaline release, predicted increases (but not decreases) in entropy in a neural state model encoded in human medial orbitofrontal cortex, as measured using multivariate functional MRI. Activity in anterior cingulate cortex predicted pupil diameter. These results provide evidence for top-down, neuromodulatory control of entropy in neural state models.
Anti-Inflammatory Effects of Aurantiochytrium limacinum 4W-1b Ethanol Extract on Murine Macrophage RAW264 Cells

Aurantiochytrium limacinum 4W-1b (AL4W-1b) is a newly discovered microalgal strain with unique features. In the present study, we investigated the effects of ethanol extracts of AL4W-1b on lipopolysaccharide- (LPS-) induced inflammatory responses in RAW264 murine macrophage cells. Pretreatment of RAW264 cells with the AL4W-1b extract significantly reduced the production of LPS-induced nitric oxide (NO) and the expression of proinflammatory cytokine genes, including tumor necrosis factor α, interleukin- (IL-) 1β, and IL-6. Treatment with the AL4W-1b extract also decreased the production of IL-1β and IL-6. These results suggest that AL4W-1b might have anti-inflammatory effects in RAW264 cells. The NF-κB inhibitor, BAY 11-7082, synergistically prevented LPS-induced NO production after pretreatment with the AL4W-1b extract. Thus, the AL4W-1b extract may affect not only the NF-κB pathway but also other inflammatory pathways. To the best of our knowledge, this is the first study to report the anti-inflammatory effects of AL4W-1b extract and its mechanism of action in LPS-stimulated murine macrophage cells.
Can larvae of a marine fish adapt to ocean acidification? Evaluating the evolutionary potential of California Grunion (Leuresthes tenuis)

Ocean acidification can reduce the growth and survival of marine species during their larval stages. However, if populations have the genetic capacity to adapt and increase their tolerance of low pH and high pCO2 levels, this may offset the harmful effects of ocean acidification. By combining controlled breeding experiments with laboratory manipulations of seawater chemistry, we evaluated genetic variation in tolerance of ocean acidification conditions for a nearshore marine fish, the California Grunion (Leuresthes tenuis). Our results indicated that acidification conditions increased overall mortality rates of grunion larvae, but did not have a significant effect on growth. Groups of larvae varied widely with respect to mortality and growth rates in both ambient and acidified conditions. We demonstrate that the potential to evolve in response to ocean acidification is best described by considering additive genetic variation in fitness‐related traits under both ambient and acidified conditions and by evaluating the genetic correlation between traits expressed in these environments. We used a multivariate animal model to estimate additive genetic (co)variance in larval growth and mortality rates under both ambient and acidified conditions (low pH/high pCO2). Our results suggest appreciable genetic variation in larval mortality rates (h2Ambient = 0.120; h2Acidified = 0.183; rG = 0.460), but less genetic variation in growth (h2Ambient = 0.092; h2Acidified = 0.101; rG = 0.135). Maternal effects on larval mortality rates accounted for 26%–36% of the variation in phenotypes, but maternal effects accounted for only 8% of the variation in growth. Collectively, our estimates of genetic variation and covariation suggest that populations of California Grunion have the capacity to adapt relatively quickly to long‐term changes in ocean chemistry.
Recent progress on the interaction between insects and Bacillus thuringiensis crops

Extensive use of chemical pesticides poses a great threat to the environment and food safety. The discovery of Bacillus thuringiensis (Bt) toxins with effective insecticidal activity against pests and the development of transgenic technology of plants opened a new era of pest control. Transgenic Bt crops, including maize, cotton and soya bean, have now been produced and commercialized to protect against about 30 major coleopteran and lepidopteran pests, greatly benefiting the environment and the economy. However, with the long-term cultivation of Bt crops, some target pests have gradually developed resistance. Numerous studies have indicated that mutations in genes for toxins activation, toxin-binding and insect immunization are important sources in Bt resistance. An in-depth exploration of the corresponding Bt-resistance mechanisms will aid in the design of new strategies to prevent and control pests. Future research will focus on Bt crops expressing new genes and multiple genes to control a broader range of pests as part of an integrated pest management programme. This article is part of the theme issue ‘Biotic signalling sheds light on smart pest management’.
Heat stress compromises epithelial integrity in the coral, Acropora hyacinthus

It is well understood that heat stress causes bleaching in corals. Much work has focused on the way heat stress disrupts corals’ symbiotic relationship with endosymbiotic algal dinoflagellate, Symbiodiniaceae, a process called bleaching. However, the damage to the coral tissue that occurs during the bleaching process and, importantly, the factors that contribute to subsequent recovery, are not well understood. I hypothesize that the host tissue damage created by heat stress initiates cascades of wound healing factors that maintain epithelial integrity. These factors may be found to contribute to the coral’s potential capacity to recover. In this study, I present evidence that heat stress causes damage to the coral host tissue and that collagen is present in the gastrodermis of heat-stressed corals. I found that, during the early stages of bleaching, an important transcription factor for wound healing, Grainyhead, is expressed throughout the gastrodermis, where the cellular and tissue rearrangements occur. Lastly, using phylogenetics, I found that cnidarian Grainyhead proteins evolved three distinct groups and that evolution of this protein family likely happened within each taxonomic group. These findings have important implications for our study of coral resiliency in the face of climate change.
Tetrahymena Comparative Genomics Database (TCGD): a community resource for Tetrahymena

Abstract Ciliates are a large and diverse group of unicellular organisms characterized by having the following two distinct type of nuclei within a single cell: micronucleus (MIC) and macronucleus (MAC). Although the genomes of several ciliates in different groups have been sequenced, comparative genomics data for multiple species within a ciliate genus are not yet available. Here we collected the genome information and comparative genomics analysis results for 10 species in the Tetrahymena genus, including the previously sequenced model organism Tetrahymena thermophila and 9 newly sequenced species, and constructed a genus-level comparative analysis platform, the Tetrahymena Comparative Genomics Database (TCGD). Genome sequences, transcriptomic data, gene models, functional annotation, ortholog groups and synteny maps were built into this database and a user-friendly interface was developed for searching, visualizing and analyzing these data. In summary, the TCGD (http://ciliate.ihb.ac.cn) will be an important and useful resource for the ciliate research community.
The preparation of carbon nanofillers and their role on the performance of variable polymer nanocomposites

ABSTRACT New synergic behavior is always inspiring scientists toward the formation of nanocomposites aiming at getting advanced materials with superior performance and/or novel properties. Carbon nanotubes (CNT), graphene, fullerene, and graphite as carbon-based are great fillers for polymeric materials. The presence of these materials in the polymeric matrix would render it several characteristics, such as electrical and thermal conductivity, magnetic, mechanical, and as sensor materials for pressure and other environmental changes. This review presents the most recent works in the use of CNT, graphene, fullerene, and graphite as filler in different polymeric matrixes. The primary emphasis of this review is on CNT preparation and its composites formation, while others carbon-based nano-fillers are also introduced. The methods of making polymer nanocomposites using these fillers and their impact on the properties obtained are also presented and discussed.
Characterization of the complete chloroplast genomes of five Populus species from the western Sichuan plateau, southwest China: comparative and phylogenetic analyses

Species of the genus Populus, which is widely distributed in the northern hemisphere from subtropical to boreal forests, are among the most commercially exploited groups of forest trees. In this study, the complete chloroplast genomes of five Populus species (Populus cathayana, P. kangdingensis, P. pseudoglauca, P. schneideri, and P. xiangchengensis) were compared. The chloroplast genomes of the five Populus species are very similar. The total chloroplast genome sequence lengths for the five plastomes were 156,789, 156,523, 156,512, 156,513, and 156,465 bp, respectively. A total of 130 genes were identified in each genome, including 85 protein-coding genes, 37 tRNA genes and eight rRNA genes. Seven genes were duplicated in the protein-coding genes, whereas 11 genes were duplicated in the RNA genes. The GC content was 36.7% for all plastomes. We analyzed nucleotide substitutions, small inversions, simple sequence repeats and long repeats in the chloroplast genomes and found nine divergence hotspots (ccsA+ccsA-ndhD, ndhC-trnV, psbZ-trnfM, trnG-atpA, trnL-ndhJ, trnR-trnN, ycf4-cemA, ycf1, and trnR-trnN), which could be useful molecular genetic markers for future population genetic and phylogenetic studies. We also observed that two genes (rpoC2 and rbcL) were subject to positive selection. Phylogenetic analysis based on whole cp genomes showed that P. schneideri had a close relationship with P. kangdingensis and P. pseudoglauca, while P. xiangchengensis was a sister to P. cathayana.
Child Marriage Laws around the World: Minimum Marriage Age, Legal Exceptions, and Gender Disparities

ABSTRACT The marriage of children below 18 is widely recognized in international human rights agreements as a discriminatory global practice that hinders the development and well-being of hundreds of millions of girls. Using a new global policy database, we analyze national legislation regarding minimum marriage age, exceptions permitting marriage at earlier ages, and gender disparities in laws. While our longitudinal data indicate improvements in frequencies of countries with legal provisions that prohibit marriage below the age of 18, important gaps remain in eliminating legal exceptions and gender discrimination.
Investigating novel regulators of mTORC1 activation in human skeletal muscle

The mechanistic target of rapamycin (mTOR), specifically mTOR complex 1 (mTORC1) is believed to be a central regulator of muscle size, however, the upstream mechanisms which activate this kinase in response to anabolic stimuli remain to be fully elucidated. This thesis therefore aimed to investigate the role of several novel regulators of mTORC1 activity in human skeletal muscle. Chapter 3 displays that mTOR translocation to the cell periphery is mTORC1-specific and is greater following resistance exercise (RE) and protein-carbohydrate (PRO-CHO) feeding compared to feeding alone. In chapter 4 we validate and optimise a immunofluorescent staining protocol to visualise L-Type amino acid transporter 1 (LAT1) in human skeletal muscle, where it was more greatly expressed in fast twitch fibres and localised close to sarcolemma and microvasculature. Chapter 5 investigated the role of vacuolar protein sorting 34 (Vps34), a potential nutrient ‘sensor’, in mTORC1 activation in skeletal muscle. Here, both in vitro and in vivo experimental designs were utilised to display that changes in Vps34 cellular location, rather than kinase activity, may be important for nutrient sensing in skeletal muscle. Finally, chapter 6 reports how mTORC1 activation can occur without alterations in Vps34 protein content, kinase activity or LAT1 fibre type distribution in response to RE and/or PRO-CHO feeding. Overall, this thesis enhanced our understanding of the intricate regulation of mTORC1 activity in human skeletal muscle, identifying new potential mechanisms by which anabolic stimuli may regulate this kinase.
Strategies of Phytophthora infestans adaptation to local UV radiation conditions

Expected global changes in environmental conditions underline the need for a better understanding of genetic variation in ecological traits and their strategies of adaptation to the stresses. In this study, evolutionary mechanisms and processes of UV adaptation in plant pathogens were investigated by combining statistical genetics, physiological assays, and common garden experiment approaches in an assessment of the potato late blight pathogen, Phytophthora infestans, sampled from various geographic locations in China. We found spatial divergence caused by diversifying selection in UV tolerance among P. infestans populations. Local UV radiation was the driving force of selection as indicated by a positive correlation between UV tolerance in P. infestans populations and the altitude of collection sites. Plasticity accounted for 68% of population variation while heritability was negligible, suggesting temporary changes in gene expression and/or enzymatic activity play a more important role than permanent modification of gene structure in the evolution of UV adaptation. This adaptation strategy may explain the lack of fitness penalty observed in genotypes with higher UV tolerance.
Rapid evolution and conserved function of the piRNA pathway

Transposons are major genome constituents that can mobilize and trigger mutations, DNA breaks and chromosome rearrangements. Transposon silencing is particularly important in the germline, which is dedicated to transmission of the inherited genome. Piwi-interacting RNAs (piRNAs) guide a host defence system that transcriptionally and post-transcriptionally silences transposons during germline development. While germline control of transposons by the piRNA pathway is conserved, many piRNA pathway genes are evolving rapidly under positive selection, and the piRNA biogenesis machinery shows remarkable phylogenetic diversity. Conservation of core function combined with rapid gene evolution is characteristic of a host–pathogen arms race, suggesting that transposons and the piRNA pathway are engaged in an evolutionary tug of war that is driving divergence of the biogenesis machinery. Recent studies suggest that this process may produce biochemical incompatibilities that contribute to reproductive isolation and species divergence.
Diversity and functional analysis of salivary microflora of Indian Antarctic expeditionaries

ABSTRACT Introduction: The human oral microbiota continues to change phenotype by many factors (environment, diet, genetics, stress, etc.), throughout life with a major impact on human physiology, psychology, metabolism and immune system. Amongst one such factor with unique and extreme environmental conditions is Antarctica. The sea voyage to Antarctica has many risks than at station for expedition members. In this study, we investigated the influence of Antarctic sea voyage and stay at the Indian Antarctic station Maitri, on the health of Indian expedition members by using a metagenomic approach to explore oral biodiversity. Methods: Saliva samples were collected from 12 expedition members, at 3 different time points viz. before the start of the ship voyage, after the completion of the voyage and at the end of the stay at Antarctica. Samples were analyzed for whole genome and 16S rRNA sequencing. Result: The oral microbial diversity of the expedition members was significantly changed, during the days of sailing and after the stay at Antarctica. The oral microbiota comprised mainly of the phyla Firmicutes (46%, 29% & 36%); Proteobacteria (40%, 48%, & 44%), Bacteroidetes (10%, 22%, &14%), Fusobacterium and Actinobacteria (5%-1%) and Unclassified (17%, 25% & 23%), at three time points, respectively. Further, the differential analysis of microbes across all the phyla revealed 89, 157 and 157 OTUs genera. The altered microbiota indicated changes in amino acid, lipid and carbohydrate metabolism. Conclusion: Study suggests that understanding the compositional and functional differences in the oral microbiota of Antarctic expedition members, can lay the foundation to relate these differences to their health status. It will further demonstrate the need for providing improved management during ship voyage and stay in Antarctica.
Complete Genome Sequence of Caldicellulosiruptor changbaiensis CBS-Z, an Extremely Thermophilic, Cellulolytic Bacterium Isolated from a Hot Spring in China

Here, we describe the complete genome sequence of Caldicellulosiruptor changbaiensis, isolated from a hot spring in the Changbai Mountain Range of China. Currently, only one other genome sequence representing a Caldicellulosiruptor species from China is available. ABSTRACT Here, we describe the complete genome sequence of Caldicellulosiruptor changbaiensis, isolated from a hot spring in the Changbai Mountain Range of China. Currently, only one other genome sequence representing a Caldicellulosiruptor species from China is available. Assembly of a continuous single contig used both Oxford Nanopore and Illumina sequencing data.
Nonspecific effects of oral vaccination with live-attenuated Salmonella Typhi strain Ty21a

Vaccination with weakened strains of Salmonella may protect against other infections. Epidemiological and immunological evidence suggests that some vaccines can reduce all-cause mortality through nonspecific changes made to innate immune cells. Here, we present the first data to describe the nonspecific immunological impact of oral vaccination with live-attenuated Salmonella Typhi strain Ty21a. We vaccinated healthy adults with Ty21a and assessed aspects of innate and adaptive immunity over the course of 6 months. Changes to monocyte phenotype/function were observed for at least 3 months. Changes to innate and adaptive immune cell cytokine production in response to stimulation with vaccine and unrelated nonvaccine antigens were observed over the 6-month study period. The changes that we have observed could influence susceptibility to infection through altered immune responses mounted to subsequently encountered pathogens. These changes could influence all-cause mortality.