Miracle-dz/UniFAR-FTUs huggingface dataset:
Predicting Evolutionary Transitions in Tooth Complexity With a Morphogenetic Model

The extent to which evolutionary transitions are shaped by developmental bias remains poorly understood. Classically, morphological variation is assumed to be abundant and continuous, but if morphogenesis biases how traits vary than evolutionary transitions might follow somewhat predictable steps. Compared to other anatomical structures, teeth have an exceptional fossil record which documents striking evolutionary trajectories toward complexity. Using computer simulations of tooth morphogenesis, we examined how varying developmental parameters influenced transitions from morphologically simple to complex teeth. We find that as tooth complexity increases, development tends to generate progressively more discontinuous variation which could make the fine-tuning of dietary adaptation difficult. Transitions from simple to complex teeth required an early shift from mesiodistal to lateral cusp patterning which is congruent with patterns of dental complexification in early mammals. We infer that the contributions of primary enamel knot cells to secondary enamel knots which are responsible for patterning lateral cusps may have been an important developmental innovation in tribosphenic mammals. Our results provide evidence that development can bias evolutionary transitions and highlights how morphogenetic modelling can play an important role in building more realistic models of morphological character evolution.
Two common disease-associated TYK2 variants impact exon splicing and TYK2 dosage

TYK2 belongs to the JAK protein tyrosine kinase family and mediates signaling of numerous antiviral and immunoregulatory cytokines (type I and type III IFNs, IL-10, IL-12, IL-22, IL-23) in immune and non-immune cells. After many years of genetic association studies, TYK2 is recognized as a susceptibility gene for some inflammatory and autoimmune diseases (AID). Seven TYK2 variants have been associated with AIDs in Europeans, and establishing their causality remains challenging. Previous work showed that a protective variant (P1104A) is hypomorphic and also a risk allele for mycobacterial infection. Here, we have studied two AID-associated common TYK2 variants: rs12720270 located in intron 7 and rs2304256, a non-synonymous variant in exon 8 that causes a valine to phenylalanine substitution (c.1084 G > T, Val362Phe). We found that this amino acid substitution does not alter TYK2 expression, catalytic activity or ability to relay signaling in EBV-B cell lines or in reconstituted TYK2-null cells. Based on in silico predictions that these variants may impact splicing of exon 8, we: i) analyzed TYK2 transcripts in genotyped EBV-B cells and in CRISPR/Cas9-edited cells, ii) measured splicing using minigene assays, and iii) performed eQTL (expression quantitative trait locus) analysis of TYK2 transcripts in primary monocytes and whole blood cells. Our results reveal that the two variants promote the inclusion of exon 8, which, we demonstrate, is essential for TYK2 binding to cognate receptors. In addition and in line with GTEx (Genetic Tissue Expression) data, our eQTL results show that rs2304256 mildly enhances TYK2 expression in whole blood. In all, these findings suggest that these TYK2 variants are not neutral but instead have a potential impact in AID.
A unique conformational escape reaction of HIV-1 against an allosteric integrase inhibitor

HIV-1 integrase (IN) contributes to HIV-1 RNA binding, which is required for viral maturation. Non-catalytic site integrase inhibitors (NCINIs) have been developed as allosteric IN inhibitors, which perform anti-HIV-1 activity by disrupting IN multimerization. Here, we show that IN undergoes a novel conformational alteration to escape from NCINIs. We observed that NCINI-resistant HIV-1 variants have accumulated amino acid (AA) mutations in the IN-encoding region. We employed HPLC and thermal stability assays to show that the AA mutations affect the folding and dimerization interface of the IN catalytic core domains, resulting in severely decreased multimerization of full-length IN proteins (IN under-multimerization). The under-multimerization of IN was finally restored by HIV-1 RNA in the viral particles. Our study demonstrates that HIV-1 countervails NCINIs by IN under-multimerization as a novel escape mechanism. Our findings provide information on the understanding of IN multimerization and influence the development of unique anti-HIV-1 strategies.
Comparison on the effect of three different methods on preventing PICC ectopic in jugular veins

Objective To compare the effect of three different methods on preventing PICC ectopic in jugular veins.Methods Totally 480 patients with PICC were randomly divided into three groups,160 in each group.The entrance of jugular veins was blocked during PICC placement by using the traditional method,finger-pressure,and pressure device in group A,B and C,respectively.The catheter ectopic rate was compared among the three groups.Result The catheter ectopic rate of PICC was lowest in group C(P0.05). Conclusion Using pressure device to block the entrance of jugular veins is more effective to prevent catheter ectopic of PICC.It is worth to be promoted and used.
Monitoring strawberry production to get grip on strawberry quality : GreenCHAINge Fruit & Vegetables WP3

nature to improve the quality of life” . U nder the banner Wageningen U niversity & Research, Wageningen U niversity and the specialised research institutes of the a enin en e ea o ndation a e oined o e in ont i tin to findin solutions to important questions in the domain of healthy food and living environment. With its roughly 30 branches, 5 ,000 employees and 10,000 students, Wageningen U niversity & Research is one of the leading organisations in its domain. The unique Wageningen approach lies in its integrated approach to issues and the olla o ation et een di e ent di i line Wageningen Food & Biobased Research Bornse Weilanden 9 6708 WG Wageningen The Netherlands www.wur. eu/wfbr E info.wfbr@wur.nl
Effect of Dietary Supplementation of Chicory Root Powder and Avian Specific Lactobacillus spp on the Hematology, Blood Biochemical, Lipid, Enzyme and Antioxidant Profile of Broiler Birds

Poultry production has undergone an enormous expansion during the past decades throughout the world (Praveen et al., 2017). India's poultry industry has shown to grow at a steady rate of around 7-8% per year (Soundararajan, 2017). The poultry industry International Journal of Current Microbiology and Applied Sciences ISSN: 2319-7706 Volume 8 Number 10 (2019) Journal homepage: http://www.ijcmas. com
Sporolithon amadoi sp. nov. (Sporolithales, Rhodophyta), a new rhodolith-forming non-geniculate coralline alga from offshore the northwestern Gulf of Mexico and Brazil

DNA sequence analysis of plastid-encoded psbA and rbcL loci, and nuclear-encoded LSU rDNA of rhodolith-forming specimens of Sporolithales from Brazil and the northwestern Gulf of Mexico reveal that they belong to an unnamed species of Sporolithon (Sporolithaceae). Sporolithon amadoi sp. nov. is morpho-anatomically characterized by a vegetative thallus reaching more than 20 cell layers, a tetrasporophyte with tetrasporangial sori slightly raised above the thallus surface that become overgrown and buried after spore release, and by cruciately divided tetrasporangia with pores surrounded by 9–13 rosette cells. Since these morpho-anatomical features are shared with some other Sporolithon species, identification of this species can only be confirmed by DNA sequences.
5’ splice site GC>GT variants differ from GT>GC variants in terms of their functionality and pathogenicity

In the human genome, most 5’ splice sites (~99%) employ the canonical GT dinucleotide whereas a small minority (~1%) use the non-canonical GC dinucleotide. The functionality and pathogenicity of 5’ splice site GT>GC (i.e., +2T>C) variants have been extensively studied but we still know very little about 5’ splice site GC>GT (+2C>T) variants. Herein, we sought to address this deficiency by performing a meta-analysis of identified +2C>T pathogenic variants together with a functional analysis of +2C>T substitutions using a cell culture-based full-length gene splicing assay. Our results establish a proof of concept that +2C>T variants are qualitatively different from +2T>C variants in terms of their functionality and pathogenicity and suggest that, in sharp contrast with +2T>C variants, most if not all +2C>T variants have no pathological relevance. Our findings have important implications for interpreting the clinical relevance of +2C>T variants but might also improve our understanding of the evolutionary basis of switching between GT and GC 5’ splice sites in mammalian genomes.
Characterization of the complete chloroplast genome of Paederia scandens (Rubiaceae): a Chinese folk medicinal plant

Abstract Paederia scandens has been used as a traditional medicine in Asian countries to treat jaundice, dysentery, and the pain of rheumatism. The complete chloroplast (cp) genome sequence of P. scandens was reported and characterized in this study. The cp genome is 153,626 bp in length, composed of a pair of 26,513 bp inverted repeat (IR) regions separated by a large single-copy (LSC) region of 83,712 bp and a small single-copy (SSC) region of 16,888 bp. There were 131 predicted genes (86 protein-coding genes, 37 tRNA genes, and 8 rRNA genes) in the genome, and the overall GC content of the genome is 37.7%. Phylogenetic analysis based on the cp genome data showed that P. scandens was sister to the clade formed by Galium mollugo and G. aparine.
CELLULAR BIOLOGICAL AND EUMELANIN-RELATED GENE EXPRESSIONAL BASES OF PIGMENT DEVIATION OF LEPTOBOTIA TAENIOPS

Pigmentation is closely associated with various behaviors, and it is also an important feature that influences the popularity and price of ornamental fish. However, the molecular mechanism that regulates the pigmentation of fish is barely understood. There are two clearly different pigmentation phenotypes, i.e. light and dark phenotypes, in the same natural population of Leptobotia taeniops . Type and distribution of chromatophores is the cellular basis of the pigmentation. To analyze the composition of chromatophores in the light and dark phenotypes of L. taeniops and the correlation of the pigmentation to the expressions of pigment synthesis genes, we studied the pigment cell types and distribution in the skin of L. taeniops by microscope, and analyzed the expressions of genes that regulate melanin production using real-time qRT-PCR. Our results showed that the amount of melanophores in the skin was the major factor that caused the pigment deviation of L. taeniops living in the same habitat. The expressions of TYR , Tyrp1 , and Dct genes were significantly higher in the skin of the dark phenotype than those in the light phenotype. This result implied that the amount of melanophores was influenced by the expression of these genes in the skin of L. taeniops .
Complete chloroplast genome sequence of Bougainvillea Spectabilis (Nyctaginaceae)

Abstract Bougainvillea spectabilis is an important ornamental plant in tropical and subtropical regions, whose complex and diverse germplasm has brought great difficulties to variety selection and identification. Here, to provide data support for the identification of the relationship between cultivars of B. spectabilis, we sequenced the chloroplast genome of B. spectabilis. The chloroplast genome is 154,520 bp in length, including a large single-copy (LSC) region of 88,101 bp and small single-copy (SSC) region of 17,729 bp, and a pair of invert repeats (IR) regions of 24,171 bp. The chloroplast genome contains 129 genes, including 83 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. The phylogenetic analysis based on 14 chloroplast genome demonstrated a close relationship between B. spectabilis and other plant species in Caryophyllales. The chloroplast genome will help for further of taxonomy research and provide data support for the identification of genetic relationship among different cultivars of B. spectabilis.
Aislamiento, caracterización y actividad de cepas de Azospirillum brasilense asociadas a la caña de azúcar

Sugarcane is one of the most relevant bioenergy crops in Argentina. Due to its high capacity for biomass production, the crop has a high nitrogen requirement that can be supplied using chemical fertilizers. To ensure the sustainability of bioenergy programs and reduce the environmental issues caused by synthetic fertilizers, it is necessary to replace them in a short term. In this sense, Azospirillum inoculation constitutes the most used alternatives in our region to increase sugarcane plantations yields. The objective of this work was to isolate and characterize Azospirillum bacteria from sugarcane, analyze some of their PGPB characteristics and evaluate the effect of bioproducts formulated with the obtained isolates on crop sprouting. Three endophytic isolates (Ls1, Ls2 and Ls3) and two from the rhizosphere (Tv1 and Tv2) were obtained, with potential ability to fix atmospheric nitrogen and produce total indoles. Using 16S gene restriction and sequencing, the isolates were identified as A. brasilense . Genotyping by BOX-PCR, confirmed that Ls1, Ls2 and Ls3 were different from each other and from Az39 strain, unlike observations for Tv1 and Tv2. On greenhouse bioassays, it was observed that the inoculation with Ls1 biopreparation significantly increased sugarcane germination rate, so it could be used as a biofertilizer in this crop.
Transposable elements contribute to the genomic response to insecticides in Drosophila melanogaster

Most of the genotype–phenotype analyses to date have largely centred attention on single nucleotide polymorphisms. However, transposable element (TE) insertions have arisen as a plausible addition to the study of the genotypic–phenotypic link because of to their role in genome function and evolution. In this work, we investigate the contribution of TE insertions to the regulation of gene expression in response to insecticides. We exposed four Drosophila melanogaster strains to malathion, a commonly used organophosphate insecticide. By combining information from different approaches, including RNA-seq and ATAC-seq, we found that TEs can contribute to the regulation of gene expression under insecticide exposure by rewiring cis-regulatory networks. This article is part of a discussion meeting issue ‘Crossroads between transposons and gene regulation’.
Development and validation of a deep learning framework for Alzheimer’s disease classification

Alzheimer’s disease (AD) is the primary cause of dementia worldwide (1), with an increasing morbidity burden that may outstrip diagnosis and management capacity as the population ages. Current methods integrate patient history, neuropsychological testing and magnetic resonance imaging (MRI) to identify likely cases, yet effective practices remain variably-applied and lacking in sensitivity and specificity (2). Here we report an explainable deep learning strategy that delineates unique AD signatures from multimodal inputs of MRI, age, gender, and mini-mental state examination (MMSE) score. Our framework linked a fully convolutional network (FCN) to a multilayer perceptron (MLP) to construct high resolution maps of disease probability from local brain structure. This enabled precise, intuitive visualization of individual AD risk en route to accurate diagnosis. The model was trained using clinically-diagnosed AD and cognitively normal (NC) subjects from the Alzheimer’s Disease Neuroimaging Initiative (ADNI) dataset (n=417) (3), and validated on three independent cohorts: the Australian Imaging, Biomarker & Lifestyle Flagship Study of Ageing (AIBL, n=382) (4), the Framingham Heart Study (FHS, n=102) (5), and the National Alzheimer’s Coordinating Center (NACC, n=582) (6). Model performance was consistent across datasets, with mean accuracy values of 0.966, 0.948, 0.815, and 0.916 for ADNI, AIBL, FHS and NACC, respectively. Moreover, our approach exceeded the diagnostic performance of a multi-institutional team of practicing neurologists (n=11), and high-risk cerebral regions predicted by the model closely tracked postmortem histopathological findings. This framework provides a clinically-adaptable strategy for using routinely available imaging techniques such as MRI to generate nuanced neuroimaging signatures for AD diagnosis, as well as a generalizable approach for linking deep learning to pathophysiological processes in human disease.
Field observations of the dinoflagellate genus Azadinium and azaspiracid toxins in the south-west Atlantic Ocean

Some dinoflagellate species of the genera Azadinium and Amphidoma (Amphidomataceae) produce azaspiracids (AZA), a group of toxins responsible for gastrointestinal disorders in humans following the consumption of contaminated shellfish. In this study, we investigated the diversity, distribution and abundance of Azadinium and AZA from field plankton samples collected during four oceanographic expeditions that covered an extended area of the Argentine Sea during different seasons. Scanning electron microscopy analyses indicated the presence of five Azadinium species: Az. dexteroporum, Az. luciferelloides, Az. obesum, Az. asperum and Az. cf. poporum. Azadinium-like cells were frequently found and were even an abundant component of plankton assemblages, showing a wide latitudinal distribution, from ~38 to ~55.5°S, and occurring in a wide temperature and salinity range. High cell densities (up to 154000cellsL–1) occurred in northern slope and external shelf waters during spring. AZA-2 was detected in net samples from the 20- to 200-µm fractions by tandem mass spectrometry–liquid chromatography analysis, suggesting a transfer of AZA through the food web. Our results contribute to the knowledge of the worldwide occurrence of Azadinium species and AZA, and highlight the importance of amphidomatacean species as a potential source of AZA shellfish poisoning in the south-west Atlantic Ocean.
Effect of yeast-based selenium on blood progesterone, metabolites and milk yield in Achai dairy cows

Abstract The aim of present study was to find the influence of organic selenium (Se) on blood progesterone, metabolites and milk production in Achai dairy cows. A total of 45 cows were divided into three groups. One of these was control group. The 2nd and 3rd group were supplemented with yeast based Se at the rate of 0.3 and 0.4 mg/kg dry matter intake (DMI) respectively from the start of eighth month of pregnancy until parturition. Animals supplemented with organic Se at the rate of 0.3 and 0.4 mg/kg had significantly (p < .05) higher serum progesterone (P4) concentration (2.98 ng/mL) and milk production (3.94 L/day) respectively, exhibiting 24.8% higher milk production than the control group. Serum cortisol level was significantly lower (0.42 ug/dL) in animals supplemented with yeast based Se at the rate of 0.4 mg/kg DMI. Concentration of serum glucose, triglycerides and cholesterol did not differ among the groups. In conclusion, supplementation of yeast based Se improved the progesterone concentration, milk yield and reduced the stress in Achai dairy cattle. Highlights Organic selenium (Se) improved milk yield in Achai cows Organic Se reduced stress in Achai cows Organic Se had no effect on blood metabolites
Biomolecular AFM viewer

We developed a stand-alone software which allows to transform biomolecular structures and movies of their conformational dynamics into a representation which corresponds to the outcome of biomolecular atomic force microscopy (AFM) experiments, such as high-speed AFM. The software implements a high degree of usability. An integrated highly versatile molecular viewer allows the visualization of structures and their corresponding simulated AFM representations in arbitrary orientations. The obtained results can be conveniently exported as still images and movies. We provide a demonstration of our biomolecular AFM viewer by applying it to several proteins from the Protein Data Bank, and to a molecular movie of conformational transitions between two protein structures obtained from a modelling server.
Seed plant families with diverse mycorrhizal states have higher diversification rates

Most of plant species have mycorrhizas, which can be classified in four types: Arbuscular (AM), Ecto (EM), Orchid (OM) and Ericoid Mycorrhiza (ER). Since the AM ancestral state, some plant lineages have switched partner (EM, OM and ER) or lost the association (NM). Evolutionary transitions to a novel mycorrhizal state (MS) might allow plant lineages to access new resources, enhancing diversification rates. However, some clades are not restricted to one MS, and this variability might promote diversification. Here, we address the relationship between MS diversity and seed plant diversification. Using the Fungal-root database, which compiles plant species and their MS, we assigned a single MS to each plant family, calculated the MS heterogeneity and estimated their diversification rates using the method-of-moments. Our results showed higher diversification rates in families with mixed MS, and a positive relationship between MS heterogeneity and diversification rates, which suggests that MS lability promotes plant diversification.
Bioassay-guided Fractionation of Carica papaya Seed Extracts against Potassium Bromate-induced Nephrotoxicity Detected Fatty Acid-rich Compounds and Prevents Oxidative Stress in Rat’s Kidney

Aim: To evaluate the effect and identify the bioactive constituents of Carica papaya seed with potency against potassium bromate –induced nephrotoxicity and oxidative stress in renal tissue of rat. Study Design: For each state of polarity, twenty male Wistar rats were divided into four groups, five rats per group; normal control, KBrO3 control, papaya fraction control and KBrO3 group administered with required concentration of extract of C. papaya seed for 48 hours. Place and Duration of Study: Department of Biochemistry Laboratory, Faculty of Basic Medical Sciences, Bayero University Kano, Nigeria. Original Research Article Kanadi et al.; IJANR, 2(1): 1-12, 2019; Article no.IJANR. 50202 2 Methodology: A bioassay-guided screening of powdered C. papaya seed and its fractions was carried out against KBrO3 –induced nephrotoxicity and oxidative stress. The tests carried out include serum urea, creatinine, uric acid and electrolytes. Also the following markers of oxidative stress were assayed in renal homogenates; superoxide dismutase (SOD), catalase (CAT), glutathione peroxidase (GPx), reduced glutathione (GSH) and malondialdehyde (MDA). Spectroscopic analysis of the most active fraction was also carried out. Results: Fractionation of C. papaya seed yielded fractions and sub-fractions that prevent KBrO3 – induced increases in serum urea, creatinine, uric acid and electrolytes as well as the level of MDA. Furthermore there were increases in activities of SOD, CAT, GPx and level of GSH. F1 was the most active fraction. Spectroscopic analysis of F1 identified six functional groups and ten compounds. Seven of the compounds have been previously reported to possess antioxidant activities: 9-octadecenoic acid (z)2hydroxyl-1(hydroxymethyl) ethyl ester, 17-octadecynoic acid, Hexadecanoic acid methyl ester, 1,2-benzenedicarboxylic acid butyl 2-ethylhexyl ester, 9,12octadecadienoic acid (z,z) methyl ester, 10-octadecenoic acid methyl ester and 9,17octadecadienal (z). Conclusion: Fractions of C. papaya seed contain bioactive compounds that could prevent KBrO3 – induced nephrotoxicity and oxidative stress in rats however isolation and administration of each compound was recommended for a more convincing result.