Miracle-dz/UniFAR-FTUs huggingface dataset:
Volatile organic compounds produced by Lysinibacillus sp. FJAT-4748 possess antifungal activity against Colletotrichum acutatum

ABSTRACT FJAT-4748 is a bacterial strain isolated from forest soil samples taken from Dongba Valley, Lijiang, Kunming, Yunnan Province, PR China. This strain was identified as Lysinibacillus sp. based on a 16S rRNA gene sequence analysis. FJAT-4748 has been shown to possess antifungal activity against different fungi, including Colletotrichum acutatum, Aspergillus niger, Fusarium solani, Fusarium moniliforme and Fusarium oxysporum. The results of the present study indicate that this antifungal activity results from volatile organic compounds (VOCs) produced by this strain. The observed inhibition rates of VOCs from FJAT-4748 against these fungi were 100%, 100%, 37.20%, 18.94% and 7.64%, respectively. GC-MS analysis identified 24 VOCs from FJAT-4748, which included different categories of compounds, such as aldehydes, ketones, alcohols, aromatic hydrocarbons and alkanes. Of these 24 VOCs, the most abundant compound was 2-ethyl-1-hexanol, which constituted 36.24% of the total VOCs based on the relative peak area. In the in vitro C. acutatum mycelial growth assay, 2-ethyl-1-hexanol exhibited the strongest activity, with an inhibitory rate of 100% using 10 µL/plate of this VOC. The activity of benzaldehyde was lower. 2-decanone showed the weakest activity among the compounds tested. The inhibitory activity of an artificial mixture of three VOCs against the C. acutatum increased with the amount of artificial mixture used. The inhibition rate reached 100% using 30 µL/plate of this artificial mixture in the plate test. Taken together, these results show that the antifungal VOCs produced by Lysinibacillus sp. FJAT-4748 are potentially useful as agents for controlling anthracnose caused by Colletotrichum acutatum.
The identification and characterisation of novel antimicrobial resistance genes from human and animal metagenomes

Antimicrobial resistance genes are harboured by bacteria in the human oral cavity and ruminant faeces and they are shed in particularly high abundances in calf faeces. Furthermore, bacteriocin (antimicrobial peptide) producing bacteria have been isolated from these environments. In recent times bacteriocins have received much attention as potential alternatives to antibiotics. Human saliva and calf faeces harbour ‘yet-to-be cultured bacteria’ that can only be studied by analysing their DNA. To this end, two metagenomic libraries were created from human saliva and calf faeces metagenomic DNA with the aim of identifying novel antimicrobial resistance and bacteriocin genes. Screening these libraries for tetracycline resistance identified two tetracycline resistant clones. Clone PS9 was also tigecycline resistant and contained a 7,765 bp insert that encoded two half-ABC transporter genes; subcloning of these genes showed that they were responsible for the observed resistance phenotype. As the ABC transporter conferred resistance only to tetracyclines and its putative amino acid sequence showed <80 % identity to known tetracycline resistance proteins, it was named TetAB(60). Clone TT31 contained a 14,226 bp insert. 7, 216 bp of the insert had 97 % nucleotide identity to Tn916 and contained part of tet(M) and a full length tet(L) gene. This gene organisation has not been described in Tn916-like elements and it may represent a novel Tn916-like element. The human saliva library was also screened for antiseptic resistance revealing a CTAB resistant clone. Random transposon mutagenesis of the 19.1 Kb insert and subcloning of a UDP-glucose 4-epimerase revealed it to be solely required for the observed resistance. This study identified novel tetracycline, tigecycline and CTAB resistance genes from the human saliva metagenome, demonstrating the importance of this environment as a source of resistance genes that may compromise the effectiveness of these antibiotics and antimicrobials. Additionally, this work highlights the relevance of house-keeping genes to the development of antimicrobial resistance.
Amphipod assemblage found on sublittoral hydroids in the White Sea with the special remarks to symbiotic association of stenothoid Metopa alderi with hydroid Tubularia larynx

Data on amphipod assemblage associated with sublittoral hydroids collected in the Kandalaksha Bay in the White Sea are presented in the paper. Eleven species of amphipods were found, among them only M. alderi (Stenothoidae) could be considered as specific symbionts for 3 species of sublittoral hydroid, namely H. falcate, S. mirabilis and T. larynx. Aquarium and in situ observation showed that adult females of M. alderi occupy hydrants and protect from other invading females, while males are moving between hydrants showing the absence of any strict territoriality. Probably, the species specifically associated with the habitat on the hydroids polyps allowing feed both on tissues of polyp/hydrant and catching floating particles. Females show no negative reaction to juveniles or males presenting on the same hydrants, and normally co-existed during all time of observations. The males during usually actively move inside the colony of hydroids T. larynx between hydrants and migrating to neighboring colonies showing no negative reaction to females or juvenile; they were numerously catch in plankton in September.
Computational analyses of regulatory elements during embryonic development

All animals begin their life from a single initial cell. A cascade of cellular transitions and proliferation events during embryonic development eventually gives rise to tissues and organs. Their functionality is highly dependent on the composition of cellular machines - proteins. Since majority of cells contain same genetic material, the regulation of how this material is used, in other words how genes are expressed, results in a specific protein composition in cells that is critical for their individual function and thereby the proper development of metazoan organisms. During my doctoral studies, I have focused my research efforts on understanding how gene expression is regulated by enhancers, non-coding elements that regulate spatiotemporal gene expression, thus acting as the decisive ‘controllers’ in the establishment of cellular identity during development. My interests revolve around two key topics in enhancer biology: How do specific transcription factors modulate enhancer activity, and what is their role in the formation of tissues such as mesoderm? What is the topological organization of enhancer-to-promoter interactions during development, and how do they relate to other regulatory features, such as the chromatin state? address these questions, I collaborated with experimentalists within the Furlong lab on three projects, each using embryonic development in Drosophila melanogaster as a model system: 1. Characterization of the recruitment of the repressive Polycomb complex (PhoRC) in a specific cell type during development; 2. Dissecting properties of enhancer to promoter interactions in two spatial (whole- embryo and mesoderm), and temporal (3-4h and 6-8h of development) contexts in the largest 4C-seq study up to date; 3. A description of more global chromatin topology, using high-resolution Hi-C data. Using extensive statistical analyses, I found that a significant portion of PhoRC binding sites overlap with mesodermal developmental enhancers, have strong association with other Polycomb proteins, and cause repression of both enhancer and gene activity. The topological studies revealed that these enhancers tend to form a vast amount of long-range interactions, even within the compact Drosophila genome. These interactions remain largely unchanged, even though the embryo undergoes severe morphological transitions from multipotency to cellular specification during these stages, and correlate with the occupancy of paused RNA Polymerase II. Taken together, these results have provided important new insights into how enhancer function, from the recruitment of transcription factors and their role in embryonic development, to the deciphering of the topological organization of chromatin in three-dimensional nuclear space.
Agrobacterium-Mediated Plant Transformation: Biology and Applications

Plant genetic transformation heavily relies on the bacterial pathogen Agrobacterium tumefaciens as a powerful tool to deliver genes of interest into a host plant. Inside the plant nucleus, the transferred DNA is capable of integrating into the plant genome for inheritance to the next generation (i.e. stable transformation). Alternatively, the foreign DNA can transiently remain in the nucleus without integrating into the genome but still be transcribed to produce desirable gene products (i.e. transient transformation). From the discovery of A. tumefaciens to its wide application in plant biotechnology, numerous aspects of the interaction between A. tumefaciens and plants have been elucidated. This article aims to provide a comprehensive review of the biology and the applications of Agrobacterium-mediated plant transformation, which may be useful for both microbiologists and plant biologists who desire a better understanding of plant transformation, protein expression in plants, and plant-microbe interaction.
Is gardening corals of opportunity the appropriate response to reverse Philippine reef decline?

Hard coral cover (HCC) in the Philippines has been declining over the past decades. Restoration practices that utilize “gardening” corals of opportunity (COPs) are actively being adopted throughout the country. However, the use of COPs in coral gardening has not yet been examined in terms of its effectiveness in addressing nationwide‐scale reef decline. The feasibility of using COPs for coral gardening was determined through a spreadsheet model that derives COP numbers needed to increase HCC in a reef. The model showed that 280,112 COPs of 5‐cm radius need to be transplanted to increase HCC in a hectare of reef from 0% to 22%, the current national average. Annual COP mortality must be less than 31.5% to achieve an increase in HCC above 22% over a span of 10 years following a gardening effort. Actual counts and generic composition of available COPs were recorded from transects in 20 reef stations across three locations in the Philippines (Lian, Luzon; Lubang Island; and Balabac, Palawan). Natural COP densities suggest that large areas of healthy reefs must be searched to obtain enough COPs for an effective gardening effort. Furthermore, the COPs measured in Lian were below the recommended fragment size for transplantation, thus needing nursery rearing to attain the 5‐cm radius prescribed for increased probability of transplant survivorship. These findings indicate that applying coral gardening at a nationwide scale is not likely to be feasible, effective, or sustainable.
A Novel Thermotolerant β‐glucosidase from Aspergillus nidulans Has Activity Across a Broad pH Profile and a Likely Bacterial Origin

This study aims at cloning, expression and biochemical characterization of recombinant β‐glucosidases from Aspergillus nidulans AN1804 gene for biofuel production. Purification was conducted using ammonium sulphate precipitation and anion exchange chromatography on a DEAE‐Sephadex A‐50 column. The enzyme was purified 2.25 fold from the crude extract with a 33.33% recovery yield. The protein migrated homogeneously as a single band on SDS‐PAGE stained with Sterling rapid silver stain and the molecular weight was determined to be approximately 100 kDa. It was optimally active at 50 °C and pH 5.5, though it had a broad pH range of pH 3.0 – 10.0. The presence of CoCl2, CaCl2, FeCl3, FeCl2 and ZnCl2 slightly enhanced the activity of β‐glucosidase but was slightly decreased in the presence of HgCl2. β‐glucosidase showed very high affinity to para‐Nitrophenyl β‐D‐glucopyranoside (pNPG). Km and Vmax for the hydrolysis of pNPG by β‐glucosidase was calculated as 0.59 mM and 2.04 μmole/ml/min respectively. An initial bioinformatics studies shows a rare occurrence of introns in AN1804, providing additional support to the argument of horizontal transfer from a bacterial source. The spectacular thermo‐tolerance and very broad pH profile of AN1804 β‐glucosidase could be the reason why the fungus has kept the bacterial gene.
THE ROLE OF SKELETAL MUSCLE MYOSTATIN IN SARCOPENIA IN OLDER ADULTS

Myostatin is a key negative regulator of muscle mass in humans and animals, having direct and indirect influences on molecular regulators of atrophy and hypertrophy, thus may impact fitness and physical function. We have shown that myostatin is elevated in conditions of chronic disability (e.g. paretic limb of stroke). Our hypothesis is that myostatin would be elevated in older adults with sarcopenia The purpose of this study was to examine the role of skeletal muscle myostatin in sarcopenia. Thirty-eight normal-weight to obese (BMI: 33 ± 5 kg/m2, X±SEM, range 21–45 kg/m2) men (n=21) and women (n=17) aged 45–81 years underwent a VO2max test, DXA scan to determine appendicular lean tissue (ALM), and vastus lateralis muscle biopsy. Quantitative real time PCR (Q-RT-PCR) was performed using Taqman probes with 36B4 as a reference to determine myostatin mRNA expression. Rates of sarcopenia were determined using (ALM/BMI) and sarcopenia was defined as < 0.789 in men and < 0.512 in women. Subjects had low fitness (VO2max: 24 ± 1 ml/kg/min) and on average 41 ± 1% body fat. The prevalence of sarcopenia in this cohort was 16%. Myostatin mRNA expression tended to be lower (29%) in those without sarcopenia than those with sarcopenia (68 ± 6 vs. 96 ± 18 AU, P=0.09). Myostatin expression was not related to age or VO2max. While myostatin may be important in muscle atrophy and sarcopenia, further work could address it’s implication in other aging cohorts of disability and chronic disease.
Identification and Prioritisation of Variants in the Short Open-Reading Frame Regions of the Human Genome

As whole-genome sequencing technologies improve and accurate maps of the entire genome are assembled, short open-reading frames (sORFs) are garnering interest as functionally important regions that were previously overlooked. However, there is a paucity of tools available to investigate variants in sORF regions of the genome. Here we investigate the performance of commonly used tools for variant calling and variant prioritisation in these regions, and present a framework for optimising these processes. First, the performance of four widely used germline variant calling algorithms is systematically compared. Haplotype Caller is found to perform best across the whole genome, but FreeBayes is shown to produce the most accurate variant set in sORF regions. An accurate set of variants is found by taking the intersection of called variants. The potential deleteriousness of each variant is then predicted using a pathogenicity scoring algorithm developed here, called sORF-c. This algorithm uses supervised machine-learning to predict the pathogenicity of each variant, based on a holistic range of functional, conservation-based and region-based scores defined for each variant. By training on a dataset of over 130,000 variants, sORF-c outperforms other comparable pathogenicity scoring algorithms on a test set of variants in sORF regions of the human genome. List of Abbreviations AUPRC Area under the precision-recall curve BED Browser Extensible Data CADD Combined annotation-dependent depletion DANN Deleterious annotation of genetic variants using neural networks EPO Enredo, Pecan, Ortheus pipeline GATK Genome analysis toolkit GIAB Genome in a bottle HGMD Human gene mutation database Indels Insertions and deletions MS Mass spectrometry ORF Open reading frame RF Random Forests ROC Receiver Operating Characteristics SEP sORF encoded peptide sklearn Scikit-learn package SNVs Single nucleotide variants sORF Short open-reading frame TF Transcription factor TSS Transcription start site VCF Variant Call Format file
Bone morphology is regulated modularly by global and regional genetic programs

ABSTRACT Bone protrusions provide stable anchoring sites for ligaments and tendons and define the unique morphology of each long bone. Despite their importance, the mechanism by which superstructures are patterned is unknown. Here, we identify components of the genetic program that control the patterning of Sox9+/Scx+ superstructure progenitors in mouse and show that this program includes both global and regional regulatory modules. Using light-sheet fluorescence microscopy combined with genetic lineage labeling, we mapped the broad contribution of the Sox9+/Scx+ progenitors to the formation of bone superstructures. Then, by combining literature-based evidence, comparative transcriptomic analysis and genetic mouse models, we identified Gli3 as a global regulator of superstructure patterning, whereas Pbx1, Pbx2, Hoxa11 and Hoxd11 act as proximal and distal regulators, respectively. Moreover, by demonstrating a dose-dependent pattern regulation in Gli3 and Pbx1 compound mutations, we show that the global and regional regulatory modules work in a coordinated manner. Collectively, our results provide strong evidence for genetic regulation of superstructure patterning, which further supports the notion that long bone development is a modular process. This article has an associated ‘The people behind the papers’ interview. Highlighted Article: The development of protrusions, such as eminences and condyles, along long bones in mice is coordinated by a patterning mechanism involving global and regional genetic regulation.
Protein-protein Interactions of Bacterial Topoisomerase I

Escherichia coli topoisomerase I (EcTopoI), a type IA DNA topoisomerase, physically and functionally interacts with RNA polymerase (RNAP) during the transcription process. EcTopoI, an enzyme responsible for relieving the negative supercoiling, is recruited by RNAP beta’ subunit for resolving the transcription associated hyper-negative supercoiling. Structural information of the RNAP-EcTopoI complex is required for understanding the basis of protein-protein interaction. The potential structure of the complex was predicted by molecular docking, and molecular dynamic simulations. Surface plasmon resonance (SPR) provided a quantitative measure of the interaction (KD=~93 nM). The docking studies predicted salt bridging and hydrogen bonding as the driving force for interaction of the RNA Polymerase beta’ subunit with the C-terminal domain of topoisomerase I in E. coli. Residues 609 (Arginine), 627 (Lysine), and 664 (Lysine) of EcTopoI were predicted, by docking, to be involved in the salt bridge and hydrogen bond formation with RNAP beta’ subunit. Supporting the docking prediction, pull-down assays with a double mutant EcTopoI (K627,664A) created in this study via site-directed mutagenesis confirmed a significant reduction in the interaction with RNA
A Review of the Neotenic Genus Atelius Waterhouse, 1878 from China (Coleoptera: Lycidae)

Abstract. The neotenic genus Atelius Waterhouse, 1878 from China is reviewed and two new species are described: A. brevicornis sp. nov. and A. kadoorieorum sp. nov., both from the tropical rainforests of Yunnan. The general appearance of all Chinese species and the morphology of male genitalia are illustrated and a key to all Atelius species is provided. The distribution of Atelius and other widespread neotenic net-winged beetles in the northern part of the Oriental region indicates their survival in disjunctive regions, which were not affected by aridization and cooling of the climate. The current distribution is hypothesized as a relict of the earlier continuous range of neotenic beetles in the Oriental region.
Deep thinking: a systematic review of mesophotic coral ecosystems

Deep thinking: a systematic review of mesophotic coral ecosystems. Science, 74: 2309–2320. Mesophotic coral ecosystems (MCEs) occur at depths beyond those typically associated with coral reefs. Signiﬁcant logistical challenges associated with data collection in deep water have resulted in a limited understanding of the ecological relevance of these deeper coral ecosystems. We review the trends in this research, covering the geographic spread of MCE research, the focus of these studies, the methods used, how MCEs differ in terms of species diversity and begin to assess connectivity of coral populations. Clear locational biases were observed, with studies concentrated in a few discrete areas mainly around the Atlantic region. The focus of MCE studies has diversiﬁed in recent years and more detailed aspects of MCE ecology are now being investigated in particular areas of research. Advances in technology are also reﬂected in the current range of research, with a wider variety of methods now employed. However, large information gaps are present in entire regions and particularly in relation to the threats, impacts and subsequent management of MCEs. Analysis of species diversity shows that initial deﬁnitions based on depth alone may not be appropriate globally, while further taxonomic resolution may also be required to deduce the full biodiversity of major groups in certain regions. Genetic studies to date show species-speciﬁc results, although distinct deeper populations do appear to exist, which raises questions regarding the potential of MCEs to act as refugia.
Secular changes in sexual and natural selection against deleterious genetic mutations in humans

All genetic variation once arose by mutation. Genetic variation is the substance on which natural selection can act, but mutations are random. Therefore, new variations usually have negative or no effects on an organism’s evolutionary fitness. This dissertation is not about the exciting exceptions to this rule, which drive evolutionary adaptation, but about harmful mutations. We know that the average human child is born with 70-100 genetic variants that its parents did not carry, around 2.2 of which are estimated to be harmful. Why don't these harmful mutations build up irreversibly? Natural and sexual selection may have continuously worked against harmful mutations building up, but do they still? Geneticists commonly worry that human civilisation has sheltered us from the purifying selection against mutations by reducing infant mortality, introducing modern medicine, social transfers, and the like. In this work, I studied whether we can find evidence of changes in purifying selection by examining the relationship between paternal age, an index of de novo mutations, and evolutionary fitness in four large cohorts from before and after the industrial revolution and more than 1.4 million people. We find no evidence for such changes, in so far as paternal age effects are a useful index, nor do we find that contemporary fathers are unprecedentedly old and hence a bigger source of mutations. In a second study, we tested whether the hormonal contraceptive pill interferes with evolutionarily adapted shifts in mate preferences across the menstrual cycle. Although we find changes in sexual desire and behaviour across the menstrual cycle in women who do not use the pill, we find no evidence of changed mate preferences. Our research cannot allay worries about relaxed selection, delayed reproduction, and altered mate choices, but we report evidence that, given proper context and empirical comparisons, these changes do not seem drastic. The balance between mutation and selection may not be as fragile as some have predicted, but it is clearly a topic worth examining. We call for further careful and empirical examination of this topic and the many other factors that may affect strength and efficacy of selection.