Miracle-dz/UniFAR-FTUs huggingface dataset:
Bacterial wilt resistance in tomato cultivars in Roraima, Brazil

ABSTRACT Bacterial wilt resistance in tomato cultivars in Roraima, Brazil The bacterial wilt caused by Ralstonia solanacearum is the most important bacterial disease of tomato in the Brazilian North Region. The objectives of this study were to evaluate (1) the resistance level of ten tomato cultivars; (2) the progress of bacterial wilt in these genotypes in order to know the disease behavior in different stages of development of the crop, and (3) determine the critical time to disease development in these cultivars, in Roraima. The experiment was carried out in a field naturally infested with biovar 1 of R. solanacearum , during two years. The area was infested by cultivating susceptible tomato plants to bacterial wilt. The cvs. Majestade, Nemonetta, Carmen, Liliane, Santa Clara, Sensacao, San Vito, Gaucho Melhorado, Hector and Laura were cultivated in the infested field. Six disease incidence evaluations were done in seven plants with irreversible wilt and/or death during the crop cycle. The following variables were determined: area under the disease progress curve (AUPDC) and the progress rate (r), mean incidence (Y50), maximum incidence (Ymax) and the final incidence of the disease. The values of AUDPC and the variable r to ‘Majestade’ were the lowest, although the level of resistance shown by this cultivar was not very high. Therefore, ‘Majestade’ is recommended for planting in the State of Roraima, especially considering the high prices of tomatoes, which are purchased from other regions in the country. However, only the level of resistance of ‘Majestade’ is not sufficient for disease control, being necessary other control measures.
Molecular variation in Drepanocladus aduncus s.l. does not support recognition of more than one species in Europe

Abstract The taxonomically problematic Drepanocladus aduncus (Hedw.) Warnst. s.l. has either been treated as a single phenotypically variable species or as including a variable number of taxa at different levels. In this investigation, the molecular variation within the D. aduncus complex is studied based on the internal transcribed spacer (ITS), the trnL (UAA) 5' exon–trnF (GAA) region, and tRNA-Gly. Relationships among more than 100 specimens are studied by means of neighbor joining (ITS; while potential hybridization was revealed), maximum parsimony (chloroplast markers), and haplotype network reconstruction (all markers). The complex exhibits considerable haplotype variation, but the variation is uncorrelated with recognized taxa. On the other hand, the studied material suggests that a geographic component is present in the variation, especially in Europe. The geographical distributions of some haplotypes suggest a possible relationship with the glacial history of Europe, although this needs to be further investigated based on a larger sample before any firm conclusions can be drawn. Two molecularly strongly deviating plants were revealed; these were collected in salt water streams at high elevations in South America.
The complete mitochondrial genome of the Dongan black chicken and its phylogenetic analyses

Abstract Dongan black chicken (Gallus gallus domesticus, DBC) is one of the famous native breed of Hunan province in China. The complete mitochondrial genome sequence plays an important role in the accurate determination of phylogenetic relationships among metazoans. It is the first time that the complete mitochondrial genome sequence of the DBC was reported. The total length of the mtDNA is 16,785 bp, It contains the typical structure, including 22 transfer RNA genes, 2 ribosomal RNA genes, 13 protein-coding genes and 1 non-coding control region (D-loop region). The overall composition of the mtDNA was estimated to be 30.27% for A, 23.78% for T, 32.46% for C, and 13.49% for G. Phylogenetic analyses using N-J computational algorithms showed that the analyzed 21 Galliformes species are divided into four major clades: Phasianidae, Numidiidae, Odontophoridae, and Megapodiidae. In addition, our work confirmed that DBC and Taoyuan chicken (TYC) have a close genetic relationship with fellow tribal members Xuefeng black-boned chicken (XBC) and Huang Lang chicken (HLC). Meanwhile, we also found that DBC and TYC have highly similar genetic relationship. This work will provide an important data set for the study of genetic mechanism of chicken in Hunan province.
Growth of Crustacean Meiofauna in a Forested Floodplain Swamp: Implications for Biomass Turnover

Microcrustaceans are common in the meiobenthos of many freshwater habitats including wetlands. Quantification of their functional roles, including determination of secondary production, has lagged behind our understanding of macrobenthos because microcrustaceans are small animals with nearly continuous reproduction and often short generation times. Such noncohort populations necessitate independent estimates of growth to quantify secondary production. Growth rates of 3 benthic microcrustaceans from a forested floodplain swamp in Alabama were measured on a diet of natural food at temperatures of 10, 15, 20, and 25°C, which span much of the annual range. For Chydorus brevilabris (Cladocera:Chydoridae), somatic growth rates were as high as 20%/d at all temperatures, and total growth rate (including egg production) was roughly twice the somatic growth rate in the larger size classes. For reproductive-sized individuals, eggs represented >60% of the growth within an instar and >60% of an individual's lifetime production. Multiple regression using individual size and temperature as independent variables explained 76% of the variation in somatic growth rates and 49% of the variation in total growth rates. Somatic growth rates were also measured for Physocypria pustulosa (Ostracoda:Cyprididae) and Cypridopsis vidua (Ostracoda:Cypridopsidae). The ostracod species had lower somatic growth rates than the chydorid, but growth rates of all 3 taxa increased with temperature and decreased with increasing size. Somatic growth rates for ostracods were <20%/d in most size classes, and multiple regressions, using individual mass and temperature as independent variables, explained 50% of the variation in somatic growth for Cypridopsis vidua and 33% for Physocypria pustulosa. Growth rates measured in this study under natural conditions suggest that freshwater meiofauna can have higher annual turnover rates (i.e., >15) than is generally assumed.
Site-specific labeling of DNA sequences containing phosphorothioate diesters

A phosphorothioate diester can be incorporated site-specifically into DNA sequences to provide a nucleophilic site that is amenable to alkylation by labels containing haloacetamide, aziridine sulfonamide, or γ-bromo-α,β-unsaturated carbonyl functionalities. Labeling reactions proceed most efficiently at 50 o C in the pH range 5.0-8.0 and require a number of hours for completion. HPLC techniques employing reversed-phase columns can be used to rapidly purify the labeled materials, and a variety of examples are shown including the purification of a site-specifically labeled 30-mer
Identification of Differentially Expressed Gene Transcripts in Porcine Endometrium during Early Stages of Pregnancy

During the early stages of pregnancy, the uterine endometrium undergoes dramatic morphologic and functional changes accompanied with dynamic variation in gene expression. Pregnancy-stage specific differentially expressed gene (DEG)-transcript-probes were investigated and identified by comparing endometrium transcriptome at 9th day (9D), 12th day (12D) and 16th day (16D) of early pregnancy in Polish large-white (PLW) gilts. Endometrium comparisons between 9D-vs-12D, 9D-vs-16D and 12D-vs-16D of early pregnancy identified 6049, 374 and 6034 highly significant DEG-transcript-probes (p < 0.001; >2 FC). GO term enrichment analysis identified commonly shared upregulated endometrial DEG-transcript-probes (p < 0.001; >2 FC), that were regulating the gene functions of anatomic structure development and transport (TG), DNA-binding and methyltransferase activity (ZBTB2), ion-binding and kinase activity (CKM), cell proliferation and apoptosis activity (IL1B). Downregulated DEG-transcript-probes (p < 0.001; >2 FC) were involved in regulating the gene functions of phosphatase activity (PTPN11), TC616413 gene-transcript and Sus-scrofa LOC100525539. Moreover, blastn comparison of microarray-probes sequences against sus-scrofa11 assembly identified commonly shared upregulated endometrial DEG-transcript-probes (E < 0.06; >2 FC), that were regulating the gene functions of reproduction and growth (SELENOP), cytoskeleton organization and kinase activity (CDC42BPA), phosphatase activity (MINPP1), enzyme-binding and cell-population proliferation (VAV3), cancer-susceptibility candidate gene (CASC4), cytoskeletal protein-binding (COBLL1), ion-binding, enzyme regulator activity (ACAP2) Downregulated endometrial DEG-transcript-probes (E < 0.06; >2FC) were involved in regulating the gene functions of signal-transduction (TMEM33), catabolic and metabolic processes (KLHL15). Microarray validation experiment on selected candidate genes showed complementarity to significant endometrial DEG-transcript-probes responsible for the regulation of immune response (IL1B, S100A11), lipid metabolism (FABP3, PPARG), cell-adhesion (ITGAV), angiogenesis (IL1B), intercellular transmission (NMB), cell-adhesion (OPN) and response to stimuli (RBP4) was confirmed by RT-PCR. This study provides a clue that identified pregnancy-stage specific microarray transcript probes could be considered as candidate genes for recognition and establishment of early pregnancy in the pig.
Differential regulation of actin stress fiber assembly and proplatelet formation by α2β1 integrin and GPVI in human megakaryocytes

The actin cytoskeleton plays a major role in platelet function. In contrast, its precise role in the function of megakaryocytes (MKs) is less understood but may be important for a chemoattractive response and an efficient proplatelet formation. In the marrow microenvironment, mature MKs are in contact with the extracellular matrix, including fibrillar collagen type I. MKs express α2β1 integrin and the immunoglobulin superfamily member glycoprotein VI (GPVI), the main receptors for collagen. Using function-blocking antibodies or specific ligands, we investigated in primary human MKs how α2β1 integrin and GPVI regulate stress fiber formation, the primary actin structures needed for cell contraction. Stress fiber assembly requires synergistic activation of the MAPK/Erk1/2 pathway and the small guanosine triphosphatase Rho via its effector, Rho-associated coiled-coil kinase (ROCK). α2β1 integrin is crucial for stress fiber formation, whereas GPVI triggers rapid and sustained activation of the Erk1/2 pathway. Strikingly, after a longer adhesion time, proplatelet formation was significantly inhibited by the engagement of α2β1 integrin, not by GPVI, likely through the Rho/ROCK pathway. Thus, proplatelet formation in human MKs could be tightly regulated by differential interactions with their collagen receptors. We propose that this interaction with collagen prevents proplatelet formation within the marrow.
Human α2‐globin nonsense‐mediated mRNA decay induced by a novel α‐thalassaemia frameshift mutation at codon 22

We describe a novel α‐thalassaemia determinant in a 3‐year‐old girl presenting a mild microcytic and hypochromic anaemia, and normal haemoglobin A2 level. Molecular studies revealed heterozygosity for a novel microdeletion (−C) at codon 22 of the α2‐globin gene. As the frameshift mutation generates a premature translation termination codon at position 48/49, we investigated the effect of the nonsense codon on the α2‐globin gene expression. Although it does not affect RNA splicing, the premature nonsense codon induces accelerated mRNA degradation. To our knowledge, this is the first time the nonsense‐mediated mRNA decay has been reported to occur in human α‐globin mRNA.
Sclerotherapy in pyogenic granuloma and mucocele

Aim and Objective: To evaluate the effect of intralesional injection of polidocanol for treating pyogenic granuloma and mucocele that commonly in the oral cavity. This study also aimed to analyze the effect of polidocanol in both lesions of various sizes. Materials and Methods: Fifteen clinically diagnosed cases of oral pyogenic granuloma (8 cases) and mucocele (7 Cases) were included in the study. After topical anesthesia application, 0.5–1 ml of polidocanol was injected using an insulin syringe into the lesion till the solution leaked out. Each patient was recalled after 1 week and evaluated; if the lesion did not resolve, second and third injections were given consecutively. Results: All 15 patients showed complete regression of the lesion after 1–3 consecutive injections in a weekly interval. Recurrence of one case of mucocele occurred. Conclusion: Sclerotherapy is simple, minimally invasive, economical, and of minimal discomfort to the patient; there is negligible blood loss, and less surgical expertise is required. Size of the lesion determines the number of weekly injections of sclerotherapy required for complete resolution of the lesion; however, numbers of injections do not depend on age, sex, and site of the lesion.
The complete chloroplast genome sequence of Horsfieldia kingii (Myristicaceae)

Abstract Horsfieldia kingii is a member of Myristicaceae. The H. kingii chloroplast genome is found to be 155,655 bp in length and has a base composition of A (30.03%), G (19.52%), C (19.72%), and T (30.73%). The genome contained two short inverted repeat (IRa and IRb) regions (48,052 bp) which were separated by a large single copy (LSC) region (86,912 bp) and a small single copy (SSC) region (20,691 bp). The genome encodes 123 unique genes, including 85 protein-coding genes, 27 transfer RNA (tRNA) genes, and 8 ribosomal RNA (rRNA) genes. Further, complete chloroplast sequence of H. kingii was aligned together with other 2 species of Myristicaceae and other 5 basal angiosperms species which have reported the complete chloroplast sequence. This complete chloroplast genome will provide valuable information for the development of DNA markers for future species resource development and phylogenetic analysis of H. kingii.
Comparison of two DNA Extraction Protocols Representing Bacterial Community from Bulk Soil by PCR-DGGE

Aims: The objective of this work was to investigate the efficiency of DNA extraction from bulk soil using the Britânia® mini mixer combined with phenol extraction to study bacterial communities, from three sampling sites localized in Sao Goncalo-RJ, Brazil, comparing it to a commercial kit by the PCR-DGGE technique. Study Design: Molecular fingerprints of bacterial communities in bulk soil from three sampling sites were generated by DGGE after 16S rDNA gene amplification. Place and Duration of Study: Faculdade de Formacao de Professores-UERJ and Embrapa Agrobiologia between April 2010 and April 2013. Methodology: Samples of DNA, in triplicate, extracted from bulk soil at three sampling sites localized in Sao Goncalo-RJ, Brazil, were obtained by two protocols of DNA extraction. The DNA
Mammalian Nudix proteins cleave nucleotide metabolite caps on RNAs

Abstract We recently reported the presence of nicotinamide adenine dinucleotide (NAD)-capped RNAs in mammalian cells and a role for DXO and the Nudix hydrolase Nudt12 in decapping NAD-capped RNAs (deNADding) in cells. Analysis of 5′caps has revealed that in addition to NAD, mammalian RNAs also contain other metabolite caps including flavin adenine dinucleotide (FAD) and dephosphoCoA (dpCoA). In the present study we systematically screened all mammalian Nudix proteins for their potential deNADing, FAD cap decapping (deFADding) and dpCoA cap decapping (deCoAping) activity. We demonstrate that Nudt16 is a novel deNADding enzyme in mammalian cells. Additionally, we identified seven Nudix proteins—Nudt2, Nudt7, Nudt8, Nudt12, Nudt15, Nudt16 and Nudt19, to possess deCoAping activity in vitro. Moreover, our screening revealed that both mammalian Nudt2 and Nudt16 hydrolyze FAD-capped RNAs in vitro with Nudt16 regulating levels of FAD-capped RNAs in cells. All decapping activities identified hydrolyze the metabolite cap substrate within the diphosphate linkage. Crystal structure of human Nudt16 in complex with FAD at 2.7 Å resolution provide molecular insights into the binding and metal-coordinated hydrolysis of FAD by Nudt16. In summary, our study identifies novel cellular deNADding and deFADding enzymes and establishes a foundation for the selective functionality of the Nudix decapping enzymes on non-canonical metabolite caps.
Comparing outcomes and costs among warfarin-sensitive patients versus warfarin-insensitive patients using The Right Drug, Right Dose, Right Time: Using genomic data to individualize treatment (RIGHT) 10K warfarin cohort

Oral anticoagulant (OAC) therapy has been the main treatment approach for stroke prevention for decades. Warfarin is the most widely prescribed OAC in the United States, but is difficult to manage due to variability in dose requirements across individuals. Pharmacogenomics may mitigate risk concerns related to warfarin use by fostering the opportunity to facilitate individualized medicine approaches to warfarin treatment (e.g., genome-guided dosing). While various economic evaluations exist examining the cost-effectiveness of pharmacogenomics testing for warfarin, few observational studies exist to support these studies, with even fewer using genotype as the main exposure of interest. We examined a cohort of individuals initiating warfarin therapy between 2004 and 2017 and examined bleeding and cost outcomes for the year following initiation using Mayo Clinic’s billing and administrative data, as well the Mayo Clinic Rochester Cost Data Warehouse. Analyses included descriptive summaries, comparison of characteristics across exposure groups, reporting of crude outcomes, and multivariate analyses. We included N = 1,143 patients for analyses. Just over a third of our study population (34.9%) carried a warfarin-sensitive phenotype. Sensitive individuals differed in their baseline characteristics by being of older age and having a higher number of comorbid conditions; myocardial infarction, diabetes, and cancer in particular. The occurrence of bleeding events was not significantly different across exposure groups. No significant differences across exposure groups existed in either the likelihood of incurring all-cause healthcare costs or in the magnitude of those costs. Warfarin-sensitive individuals were no more likely to utilize cardiovascular-related healthcare services; however, they had lower total and inpatient cardiovascular-related costs compared to warfarin-insensitive patients. No significant differences existed in any other categories of costs. We found limited evidence that warfarin-sensitive individuals have different healthcare spending than warfarin-insensitive individuals. Additional real-world studies are needed to support the traditional economic evaluations currently existing in the literature.
Prenatal anxiety, breastfeeding and child growth and puberty: linking evolutionary models with human cohort studies

Abstract Background: Stress experienced by mothers during pregnancy can have both immediate and long-term effects on child development, potentially mediated by breastfeeding. Aim: Using a UK birth cohort study, we asked how maternal stress relates to breastfeeding and consequences for growth and puberty onset. Subjects and methods: We analysed data from the Avon Longitudinal Study of Parents and Children, collected via questionnaires and clinic visits (N: 698–8,506). We used reports of prenatal anxiety, breastfeeding, early growth and age at menarche or first voice change. Confounding by maternal age, parity, smoking, education and body mass index (BMI) was considered. Results: Mothers with higher levels of reported anxiety were less likely to breastfeed (Odds ratio (OR): 0.83, 95% confidence interval (CI): 0.71, 0.97). Breastfed infants had slower growth before weaning, although growth differences were unclear thereafter. Being breastfed for more than six months was associated with later puberty onset in females (2.76 months later than non-breastfed; CI: 0.9, 4.63), although the association was attenuated by confounders and BMI (1.51 months, CI: −0.38, 3.40). No association between breastfeeding and puberty onset in males was found. Conclusion: Our studies fit results shown previously, and we consider these in light of evolutionary life history theory while discussing key challenges in such an approach.
Growth rate of duckweeds (Lemnaceae) in relation to the internal and ambient nutrient concentrations - testing the Droop and Monod models

The Monod model describes the relationship between growth rate and ambient nutrient concentration, the Droop model focuses on internal nutrient resources as the driving factor. Both were applied mainly to explain phytoplankton dynamics in lakes or in experimental cultures. Our test plants were two species of duckweeds – Lemna minor L. and Spirodela polyrhiza (L.) Schleiden sampled from 18 natural stands situated in 6 different water bodies. Plants were grown outdoor in original lake water or in mineral media of varying N and P concentrations (0–21 mg N-NO3 L-1 and 0–1853 μg P-PO4 L-1 for L.minor and 0–4.2 mg N-NO3 L-1 and 0–371 μg P-PO4 L-1 for S. polyrhiza). Moreover, we analysed concentrations of mineral forms of N and P in lake water and tissue nutrient concentrations in plants. Tissue N of both plants was significantly correlated with ambient inorganic nitrogen sources, no such relationship was observed for tissue P. The growth rate of both plants measured under experimental outdoor conditions was better explained by tissue N and P variability (the Droop model) than by the external nutrient availability (the Monod model). The latter also failed to fit the growth rate of both plants in artificial mineral media with a decreasing gradient of N and P concentrations. The plants grew at the expense of internal N and P resources which remarkably declined during 9-day long experiments. Calculated minimum tissue contents (11.19  1.11 mg N g-1 and 0.97  0.07 mg P g-1 in L. minor and 6.10  1.85 mg N and 1.25  0.37 mg P g-1 in S. polyrhiza) show that the latter species would be a superior competitor under N limiting conditions and the former – under P limitation. We confront obtained results with literature data on N uptake kinetics and postulate that the luxury consumption of nutrients and plant growth dependent mainly on internal N and P resources might be an adaptation of duckweeds to varying habitat conditions typical of astatic water bodies.