Miracle-dz/UniFAR-FTUs huggingface dataset:
Development and use of genomics mining and visualization tools for prokaryotes

Mining bacterial genomes for bacteriocins is a challenging task due to the substantial structure and sequence diversity, and generally small sizes, of these antimicrobial peptides. Major progress in the research of antimicrobial peptides and the ever-increasing quantities of genomic data, varying from (un)finished genomes to metagenomic data, led us to develop the significantly improved genome mining software BAGEL2, as a follow-up of our previous BAGEL software. BAGEL2 identifies putative bacteriocins on the basis of conserved domains, physical properties and the presence of biosynthesis, transport and immunity genes in their genomic context. The software supports parameter-free, class-specific mining and has high-throughput capabilities. Besides building an expert validated bacteriocin database, we describe the development of novel Hidden Markov Models (HMMs) and the interpretation of combinations of HMMs via simple decision rules for prediction of bacteriocin (sub-)classes. Furthermore, the genetic context is automatically annotated based on (combinations of) PFAM domains and databases of known context genes. The scoring system was fine-tuned using expert knowledge on data derived from screening all bacterial genomes currently available at the NCBI. BAGEL2 is freely accessible at http://bagel2.molgenrug. nl.
The complete mitochondrial genome of the yellow-spotted triggerfish (Pseudobalistes fuscus)

Abstract The yellow-spotted triggerfish (Pseudobalistes fuscus), a member of the genus Pseudobalistes, belongs to the family Balistidae. Here, we describe the complete mitochondrial genome sequence of P. fuscus. The genome, 16,480 bp in length, is comprised of 13 protein-coding genes, 22 tRNAs, 2 rRNAs and a major non-coding region. The gene content and order are in accord with the common vertebrate form. A phylogenic tree was constructed based on the complete mitogenomes of P. fuscus and six closely related species to estimate their phylogenic relationship. Our data present an important genetic resource for the biological studies of the family Balistidae.
In vitro antimicrobial activity of three medicinal plants of Ethiopia against some selected bacterial isolates

Medicinal plants constitute natural source of antimicrobial drugs that will provide essential compounds to fight against disease. In this study, the antibacterial activity of ethanol extracts of Moringa stenopetala, Thymus serrulatus, and Terminalia brownii were investigated against selected pathogenic Gram positive and Gram negative bacteria. In vitro antibacterial activities of the ethanol extracts were tested at a concentration of 50, 25, and 12.5 mg/ml by using agar disc diffusion method and zone of inhibitions were determined. Furthermore, minimum inhibitory concentrations were determined for plants that showed antibacterial activity (>15 mm zone of inhibition). The results indicated that only T. serrulatus and T. brownii exhibited antimicrobial activity against one or more test pathogens. Both extracts of these plants showed strong and dose dependent activity when compared with M. stenopetala which demonstrated no activity. Interestingly, T. serrulatus showed broad spectrum activity against the tested bacteria. Therefore, ethanol extracts of T. serrulatus and T. brownii showed promising antimicrobial activity justifying their usage in traditional medicine. Key words: Antibacterial, Ethiopia, Moringa stenopetala, Terminalia brownii, Thymus serrulatus.
Production and Use Sorghum: A Literature Review

Sorghum bicolor (L). Moench is the crop for grain for human and animal consumption. The aim of this study is to document the production and use Sorghum in Senegal through a literature review. Medline database and scholar Google were used. To be selected, the manuscripts were to address the use and production of sorghum and their health implications. World sorghum production is about 60 million tons per year; the main producing countries are the USA, Nigeria, and India. In Senegal there is on the one hand of traditional sorghum varieties and on the other, those improved by the Senegalese Institute of Agricultural Research (ISRA) that are adapted to our soil and productive. Sorghum grains are used by people in semi-arid countries in Africa and Asia, for consumption as pasta, boiled and traditional drinks. Studies have shown the virtues of this cereal on the health of men, hence the need for further studies to be eligible for any of the therapeutic potential of the latter.
Development of a diagnostic molecular marker for Philonema spp. (Nematoda; Dracunculoidea) infecting salmonids in British Columbia

We developed a species specific DNA probe based on differential PCR amplification that distinguishes two congeneric nematode parasites of salmonids in British Columbia: Philonema agubernaculum Simon and Simon, 1936, usually parasitic in lake resident rainbow trout, Oncorhynchus mykiss; and P. oncorhynchi Kuitunen-Ekbaum, 1933, parasitic in anadromous sockeye salmon, O. nerka. The region differentially amplified was the D3 expansion domain of the 28S rDNA. Sequences of the two species differ in two parts of the domain, one a single base substitution and the other a three base duplication in P. oncorhynchi. A primer specific to P. oncorhynchi (amplifying P. oncorhynchi, not P. agubernaculum) was defined in the duplication region. Using differential amplification, we showed that sockeye smolts are infected with P. agubernaculum, although returning adults harbour only P. oncorhynchi. This technique could conceivably be used to quantify the frequency of heterologous infections in the wild, before infecting wor.
VEGF induces signalling and angiogenesis by directing VEGFR2 internalisation through macropinocytosis

Endocytosis plays critical role in receptor signalling. VEGFR2 and its ligand VEGFA are fundamental in neovascularization. Yet, our understanding of the role of endocytosis in VEGFR2 signalling remains limited. Despite the existence of diverse internalisation routes, the only known endocytic pathway of VEGFR2 is the clathrin-mediated. Here, we show that this pathway is the predominant internalisation route of VEGFR2 only in the absence of ligand. Intriguingly, VEGF introduces a novel internalisation itinerary for VEGFR2, the pathway of macropinocytosis, which becomes the prevalent endocytic route of the receptor in the presence of ligand, while the route of clathrin becomes minor. Macropinocytic internalisation of VEGFR2, which mechanistically is mediated via the small GTPase CDC42, takes place via macropinosomes generated at ruffling areas of the membrane. Interestingly, macropinocytosis plays critical role in VEGF-induced signalling, endothelial cell functions in vitro and angiogenesis in vivo, while clathrin-mediated endocytosis is not essential for VEGF signalling. These findings expand our knowledge on the endocytic pathways of VEGFR2 and suggest that VEGF-driven internalisation of VEGFR2 via macropinocytosis is essential for endothelial cell signalling and angiogenesis. INTRODUCTION It has been originally thought that the plasma membrane is the exclusive place from where the ligand/receptor complexes activate downstream signalling cascades. In this view, endocytosis was considered to cause termination of signalling via directing the receptors to lysosomes for degradation. However, it is now evident that a number of receptors explore the endocytic routes in order to tune the duration, amplitude and specificity of the signalling process (McMahon and Boucrot, 2011; Miaczynska et al., 2004; Sorkin and von Zastrow, 2009). VEGFR2 is a major angiogenic receptor that plays crucial role in blood vessel homeostasis and vascular diseases (Herbert and Stainier, 2011; Olsson et al., 2006). Additionally, VEGFR2-triggered angiogenesis is a hallmark of cancer progression and metastasis (Herbert and Stainier, 2011; Olsson et al., 2006). Numerous previous studies
‘Toothbrush’ plant bugs and allies: Protemiris gen. nov., a new genus and five new species of Proteaceae‐associated Australian Phylinae (Hemiptera : Miridae)

Due to substantial recent field and taxonomic research, the true biodiversity of plant bugs in the subfamily Phylinae in Australia is only beginning to emerge. This study is a contribution to advancing our understanding of the diversity of plant bugs in Australia. A new genus and five new species of Australian Phylinae are here described, where all species are associated with host plants in the Proteaceae, a family of plants with few well‐documented plant bug associates. The new genus Protemiris gen. nov. and the new species P. adenanthi sp. nov., P. conospermi sp. nov., P. distichi sp. nov., P. grevillae sp. nov. and P. isopogoni sp. nov. are mostly restricted to Western Australia, with one species also occurring in the Northern Territory. A morphology‐based cladistic analysis confirms the monophyly of this new genus and places it in the recently described subtribe Exocarpocorina of the tribe Semiini, among other Australian phylines with similarly elaborate male and female genitalia. Habitus and scanning electron images, genitalic illustrations, host associations and distribution maps for the new plant bug species are provided.
Microbial community composition in deep marine subsurface sediments of ODP Leg 201: Sequencing surveys and cultivations

Recent molecular analyses of Leg 201 subsurface sediments show that microbial communities of deep marine sediments harbor members of distinct, uncultured bacterial and archaeal lineages, in addition to Gram-positive bacteria (Firmicutes and Actinobacteria), members of the Cytophaga-Flavobacterium-Bacteroides phylum, and Proteobacteria that are detected by cultivation surveys. Several of these subsurface lineages show cosmopolitan occurrence patterns; they can be found in cold marine sediments and in hydrothermal habitats, suggesting a continuous deep subsurface and hydrothermal biosphere. Some archaeal and bacterial lineages appear to be well-diversified generalists that occur in subsurface sediments as well as in a wide range of terrestrial and aquatic habitats.
Nutrient dilution and removal bioassays to estimate phytoplankton response to nutrient control

Nutrient addition and dilution bioassays were performed in a large eutrophic reservoir. Experiments were conducted in situ in 10 L carboys and 1256 L mesocosms. By day 4 in carboy experiments, addition of N alone stimulated chlorophyll-a by 403 %, simultaneous N and P addition by 929 %, and secondary sewage effluent addition by 188 %. P added alone had little stimulatory effect. Dilution of 15 % per day with 1 μm filtered lake water or reverse osmosis water had an insignificant effect on productivity, algal biovolume, and chlorophyll-a concentrations compared to controls. The results from the mesocosms were consistent with the carboy experiments; addition of N and N + P stimulated chlorophyll-a, and 12 % dilution per day with filtered lake water or reverse osmosis water had little effect. Increasing or decreasing zooplankton numbers had only small effects on productivity and chlorophyll-a. Nutrient addition and dilution bioassays may provide valuable information when evaluating measures to reduce eutrophication in lakes.
Different cells make different proteins: a laboratory exercise illustrating tissue-specific protein expression in animals

Abstract All the cells of higher organisms have the same DNA but not the same proteins. Each type of specialised cell that forms a tissue has its own pattern of gene expression and, consequently, it contains a particular set of proteins that determine its function. Here, we describe a laboratory exercise addressed to undergraduate students that aims to reinforce the following concept: what makes cells different is they make different proteins. The students performed a denaturing polyacrylamide gel electrophoresis (SDS–PAGE) to separate the proteins extracted from different animal tissues, and then obtained and compared the corresponding protein profiles. In addition, the students performed a Western blot analysis to detect the presence or absence of a tissue-specific protein in the different tissue extracts. This laboratory exercise allowed students to understand the basis of the cell differentiation better and also provided them the opportunity to learn a variety of analytical laboratory techniques.
Detection of local DNA copy number changes in lung cancer population analyses using a multi-scale approach

ABSTRACT Emerging advances in genomic sequencing have prompted the development of new computational methods for studying the genomic sources of human diseases. This article presents a recent statistical approach for detection of local regions with significant copy number alterations (CNAs) in a population of lung cancer patients. Mapping such regions is of interest as they are potentially associated with lung cancer. Conventional application of multiple testing methods corresponds to testing for CNAs at each probe separately and thresholding the t-statistics as test statistics. Due to the large number of probes, this approach often fails to detect CNA regions. In contrast, the proposed method uses the heights of located peaks and improves the detection power. This is achieved by taking advantage of the spatial structure in the data as well as reducing the number of tests in the multiple comparisons problem. In copy number analysis, it is common to apply segmentation or change detection tools to each individual genomic sample. However, since segmentation results vary among subjects, it becomes difficult to find the common genomic regions in population analyses. Our approach solves this problem by performing the analysis using summary statistics to study at the population level directly. Hence, the region detection is performed on the summary t-statistic map. The proposed method is applied to lung cancer data and shows promise for detection of local regions with significant CNAs.
Some Rapid Methods for Oral Treponema Detection

The present study investigates the presence of four oral Treponemal species using rapid molecular methods. Subgingival fluid samples were obtained before and after one week of scaling and the nucleic acid was liberated from the bacterial cells to be used as a template for PCR. Specific primers for each Treponemal species targeted to16SrDNA sequence was depended.89% of samples were positive for Treponema sp. , 88% of them were positive to the presence of more than one type. T. amylovorum, T. medium, T.socranskii, and T. vincentii were detected in 72%, 87%, 76 % , and 28% respectively with higher percentage at pocket depths >5 mm. Molecular method was able to detect Treponemal species even after scaling, however, in lower percentage than before it.
The Positioning and Function of Bazooka Polarity Landmarks

Epithelial sheets line the surfaces of the body and our organs, acting as semi-permeable barriers between the internal and external environment. Epithelial polarity is critical for epithelial function. In Drosophila, epithelial polarity is established at the onset of embryogenesis by a network of polarity, cytoskeletal, and junctional complexes. The scaffold protein Bazooka (Baz; mammalian partitioning-defective (PAR)-3), localizes to the site of adherens junction (AJ) assembly, where it acts as an early polarity landmark to position downstream AJ components. My work addressed how Baz positions AJ components, and how Baz is localized and positioned within the apicolateral region. The focus of my first study was to understand how Baz affects AJ assembly and what precursors were involved. The quantification of Baz and AJ components in combination with a photobleaching analysis suggested that early AJs are subdivided into Baz clusters and cadherin/catenin clusters with independent protein numbers and dynamics. Consistent with
Cell‐penetrating peptide–labelled smart polymers for enhanced gene delivery

Highly efficient gene delivery vehicles are pursued to progress gene therapy. In this study, we developed the cell‐penetrating peptide‐labelled and degradable gene carriers for efficient external gene transfection. The cationic carriers were prepared by coupling low‐molecular‐weight polyethylenimine (PEI800) with 4ʹ4‐dithiodibutyric acid (DA), and HIV‐1 Trans‐Activator of Transcription (TAT) was conjugated to the carriers as a penetrating peptide. The resulted PEI‐DA‐TAT was able to condense plasmid DNA (pDNA) into a complex with a hydrodynamic size of around 150 nm under a neutral condition. PEI‐DA‐TAT showed negligible cytotoxicity to both Hela and HEK 293 cells with the cell viability of more than 80% beyond the carrier concentration of 50 μg/mL. This new carrier displayed better performance in regard to DNA transfection efficiency in comparison with the carriers of non‐TAT labelled PEI‐DA, commercial PEI25K and low‐molecular‐weight PEI (PEI800). The transfection efficiency of PEI‐DA‐TAT was increased by 8% compared with PEI‐DA and PEI25K. The experimental findings suggested that the developed PEI‐DA‐TAT is a promising carrier for efficient DNA delivery with low cytotoxicity for gene therapy.
How the AFF1/4 scaffold recruits the elongation factor ELL2 to promote HIV-1 proviral transcription

The intrinsically disordered scaffold proteins AFF1/4 and the transcription elongation factors ELL1/2 are core components of the superelongation complex required for HIV-1 proviral transcription. We determined the 2.0-Å resolution crystal structure of the human ELL2 C-terminal domain bound to its 50-residue binding site on AFF4, the ELLBow. The ELL2 domain has the same arch-shaped fold as the tight junction protein occludin. The ELLBow consists of an N-terminal helix followed by an extended hairpin that we refer to as the elbow joint, and occupies most of the concave surface of ELL2. This surface is important for the ability of ELL2 to promote HIV-1 Tat-mediated proviral transcription. The AFF4-ELL2 interface is imperfectly packed, leaving a cavity suggestive of a potential binding site for transcription-promoting small molecules.
Cloning and characterization of xerC gene of Streptococcus suis

XerC and XerD are members of the tyrosine recombinase farnily and mediate site specific recombination which contributes to the stability of circular chromosomes in bacteria by resolving plasmid multimers and chromosome dimers to monomers prior to ceil division. Homologues of xerC/xerD genes have been found in many bacteria. In this paper, an open reading frame in Streptococcus suis with a strong homology to xer genes found in streptococcal bacteria was discovered. The gene, designated xerC, was cloned, overexpressed and purified as a maltose binding protein fusion. The purified XerC-MBP fusion showed specific DNA binding activity to the df site of Bacillus subtilis, as well as df site of S. suis. xerC mutants of S. suis showed significant growth and morphological changes.
Molecular mechanism on two fluoroquinolones inducing oxidative stress: evidence from copper/zinc superoxide dismutase

Fluoroquinolones (FQs) are very important agents in human health as antibiotics. Regardless of their potential side effects, displayed by all medicines, their value to promote human health cannot be denied. In this paper, we determined the oxidative stress-induced effects of two FQs, ciprofloxacin (CPFX) and enrofloxacin (ENFX), via the essential antioxidant enzyme copper/zinc superoxide dismutase (Cu/Zn-SOD) at its macromolecular and functional level. Cellular study indicated that both FQs elevated vulnerability towards oxidative stress, and CPFX exhibited more of an oxidative threat than ENFX. The analysis using the spectroscopic and computational methods confirmed that both FQs could bind into the interface of two subdomains and alter the microenvironmental and structure of the enzyme. Furthermore, the inhibition of Cu/Zn-SOD activity from the molecular tests was consistent with that in the cellular study. This work provides direct evidence that the increased risk of cellular oxidative stress by two FQs was closely related to the conformational and functional changes of the Cu/Zn-SOD molecule.
First Report of Pleoanamorphy in Gyrothrix verticiclada with an Idriella-Like Synanamorph

Abstract Pleoanamorphy with two types of conidia is reported for the first time in Gyrothrix verticiclada. The first conidial type has the normal morphology already known for G. verticiclada, but the second conidial type is identified here as an Idriella-like synanamorph. Both conidial types were isolated, then cultivated separately, photographed, and deposited in the Mycothèque de l'Université Catholique de Louvain (BCCM™/MUCL). The morphological similarities of both types of conidia were examined in comparison with conidia in other species of Idriella and Gyrothrix guided by a phylogenetic analysis of DNA sequences from three gene regions and morphological data. Phylogenetic analyses were performed with maximum parsimony as the optimality criterion using the program TNT. Results indicated that one individual of Gyrothrix verticiclada is associated with Idriella cubensis and seven with species of both genera. Both types of conidia, Gyrothrix verticiclada (MUCL54065) and the Idriella-like synanamorph (MUCL54064) were recovered as homologous. In addition to knowledge about pleomorphism of G. verticiclada, a BLAST search was made using ITS and LSU sequences in order to find the teleomorphic relationship of G. verticiclada. The teleomorphic connection suggests a correspondence with named genera belonging to the order Xylariales.
Myosin II Isoforms in Breast Cancer: Role of Contractility in Matrix Organization, Cell Migration, and Endothelial Barrier Function

Myosin II Isoforms in Breast Cancer: Role of Contractility in Matrix Organization, Cell Migration, and Endothelial Barrier Function Bridget R. Hindman Breast cancer is a devastating and complicated disease. A large proportion of breast cancer related deaths are due to metastasis. Metastasis is when cancer cells leave the primary tumor, travel through the bloodstream, and proliferate in distant sites. Cell contractility is involved in a number of cellular processes associated with metastasis including matrix organization, tumor cell migration, and endothelial cell barrier function. The main regulator of contractility in nonmuscle cells is nonmuscle myosin II. There are three isoforms of this protein: myosin IIA, IIB, and IIC. The specific roles of the individual isoforms in cancer progression and metastasis have yet to elucidated. This works aims to determine if myosin II isoforms play separate roles in three functions associated with cancer progression: tumor cell organization of a collagen matrix, tumor cell migration, and endothelial cell barrier function. In Study 1, the ability of breast cancer cells lacking myosin II isoforms to organize a collagen matrix was assessed. In addition, the migration potential of these cells in 3D matrices was measured. Myosin II isoforms were found to play distinct roles in cancer cell matrix organization and cell migration. In Study 2, the barrier function of endothelial cells lacking myosin II isoforms was tested. This cell function is involved in metastasis when cancer cells cross the blood vessel wall to enter and exit the bloodstream. Both myosin II isoforms were found to be involved in endothelial cell contractility, and the IIA isoform was found to be necessary for barrier function. Collectively, these studies indicate that myosin II isoforms play distinct and non-redundant roles in cell processes associated with cancer metastasis.