Miracle-dz/UniFAR-FTUs huggingface dataset:
Developmental epigenetics in humans : can maternal nutritional status mediate DNA methylation in their offspring?

Animal studies show that periconceptional maternal supplementation with nutrients involved in the provision of methyl-groups can alter DNA methylation patterns in the offspring. This thesis examines possible associations between maternal nutrition and offspring DNA methylation patterns in humans in the context of seasonal influences. Two complementary studies were conducted in rural Gambia. The ‘indicator’ group enrolled 30 non-pregnant women and followed them monthly for one year, to measure dietary intakes and blood biomarker levels of choline, betaine, folate, methionine and vitamins B2, B6 and B12, as well as plasma homocysteine, S-adenosyl-methionine (SAM), S-adenosyl-homocysteine (SAH), cysteine and dimethylglycine (DMG). The ‘main’ group enrolled 136 mother-infant pairs, with infants conceived at the peak of the rainy (July to September) or dry (February to April) season. The same panel of blood biomarkers were measured on maternal samples collected early in pregnancy. In the infants, DNA methylation at seven metastable epialleles (MEs) was assessed. Significant seasonal variation was observed within the indicator group for dietary intakes of choline, betaine, folate and B2 and all metabolic biomarkers. A possible change in dependence between the betaine and folate pathways between seasons was identified. Within the main group, a seasonal variation was observed in both maternal biomarker levels and infant DNA methylation. The rainy season was associated with a higher maternal SAM:SAH ratio, higher concentrations of most methyl-donors (folate, betaine and methionine) and cofactors (B2 and B6) and higher infant DNA methylation. DNA methylation at the MEs studied was associated with B2, cysteine and the SAM:SAH and DMG:betaine ratios, but not with the other biomarkers. These data suggest that Gambian seasonality influences maternal methyl-group supply, which may be linked to DNA methylation patterns in offspring. Future work is required to confirm this observation, and understand precise mechanisms, so optimal nutrition at critical phases can be determined.
Controlled-Release Fertilizer on Growth of Melanoxylon brauna Schott Seedlings

Melanoxylon brauna is a tree species native to the Atlantic Forest of high ecological and economic value. The objective of this study was to evaluate the growth and nutritional status of seedlings of two Melanoxylon brauna cultivars grown in substrate with different controlled-release fertilizer doses (CRF). The experiment was arranged in a randomized block 4 × 2 factorial design, with four CRF doses (0, 2, 4, and 8 kg m-3) and two seed origins (Viçosa-MG and Linhares-ES), with four replicates and 126 seedlings per plot. At 60, 90, and 120 days after emergence, seedlings were collected to measure variables related to emergence, growth, and nutrition. The greatest growth and best nutritional status were found for seedlings originated from seeds collected in Linhares at CRF dose of 8 kg m-3. On the other hand, seedlings originated from seeds collected in Viçosa showed low emergence and high plant mortality.
Culture under normoxic conditions and enhanced virulence of phase II Coxiella burnetii transformed with a RSF1010-based shuttle vector

Coxiella burnetii is a Gram-negative, facultative intracellular microorganism that can cause acute or chronic Q fever in human. It was recognized as an obligate intracellular organism until the revolutionary design of an axenic cystine culture medium (ACCM). Present axenic culture of C. burnetii strictly requires a hypoxic condition (<10% oxygen). Here we investigated the normoxic growth of C. burnetii strains in ACCM-2 with or without tryptophan supplementation. Three C. burnetii strains - Henzerling phase I, Nine Mile phase II and a Nine Mile phase II transformant, were included. The transformant contains a pMMGK plasmid that is composed of a RSF1010 ori, a repABC operon, an eGFP gene and a kanamycin resistance cassette. We found that, under normoxia if staring from an appropriate concentration of fresh age inocula, Nine Mile phase II can grow significantly in ACCM-2 with tryptophan, while the transformant can grow robustly in ACCM-2 with or without tryptophan. In contrast, long-term frozen stocks of phase II and its transformant, and Henzerling phase I of different ages had no growth capability under normoxia under any circumstances. Furthermore, frozen stocks of the transformant consistently caused large splenomegaly in SCID mice, while wild type Nine Mile phase II induced a lesser extent of splenomegaly. Taken together, our data show that normoxic cultivation of phase II C. burnetii can be achieved under certain conditions. Our data suggests that tryptophan and an unknown temperature sensitive signal are involved in the expression of genes for normoxic growth regulated by quorum sensing in C. burnetii.
Assessment of School-Based Sexual and Reproductive Health Education in Secondary Schools in Klang Valley, Malaysia

The general purpose of this study was to assess school-based sexual and reproductive health education among female secondary school students.Subsequently the study examined the perspective of Science teachers and their views on school-based sexual and reproductive health education, as well as sex education in the current curriculum. This research had been designed with multiple studies conducted using a mixed methods approach. In phase I of the quantitative study, 520 female students were selected for this cross-sectional study by using a two-stage stratified random sampling. In all, 10 secondary schools were randomly selected as study sites from a total of 276.Subsequently, in phase II; a generic qualitative data gathering was conducted. The participants were science teachers selected by purposeful sampling from selected government secondary schools in phase I. Data were also harvested from semi-structured interviews with science teachers, and a contextual textbook analysis. The findings, in regards to the female student’s knowledge about sexual and reproductive health, revealed that the level of total knowledge was moderate. Additionally, the findings of this study revealed that female students were only moderately aware about issues regarding puberty and condom use. The conclusion drawn from the student participants suggested that a majority of respondents fell into the moderate sexual attitude category which clearly indicates that the surveyed subjects were “uncertain” about their attitudes towards sexual matters. Besides, the findings from this study clearly demonstrated that specially trained teachers are necessary for delivering this course. The results of the current study were in line with literature which found that most of the teachers for this subject did not receive any special training. On the other hand, regarding the constraints of the current school-based sexual and reproductive health education program, the majority of participants named teaching strategy and capacity of teachers, the lack of co-operation from the school and parents, limited resources in teaching and students themselves as some of the challenges. Thus, before a school-based health program can be introduced into the classrooms, the training of specialized teachers becomes a key consideration.
Ant Morphology Mediates Diet Preference in a Neotropical Toad (Rhinella alata)

Despite the widespread occurrence of myrmecophagy in anurans, it is unclear whether ant-specialists feed on ants opportunistically or whether they prefer species with specific morphological, ecological, or nutritional traits. We flushed 105 stomachs of a lowland neotropical toad, Rhinella alata, and identified each consumed ant to species level. We calculated linear selectivity to determine predator preference for ants by comparing the abundances of consumed species to their relative abundances in the leaf litter community on Barro Colorado Island, Panama. We conducted linear regression models to test whether linear selectivity or general predator preference related to seven morphological characteristics and two measurements of nutritional content. Rhinella alata preferentially ate 24 ant species. Other species were either avoided (n = 34) or were eaten opportunistically (n = 26). Preferred ant species were large and textured with hair and/or rugosity. We found that prey preference did not relate to prey nutritional content, that small ants were avoided even if they were superabundant in the environment, and that chemically defended and aggressive ants were preferred if they were large enough. We propose that R. alata prefers large ants because they represent a more efficient prey item in terms of prey handling time and because they are easier to see than are smaller ants. Furthermore, we hypothesize that predation attempts are more successful when prey are textured because microstructures on the tongue and prey surface may increase prey adhesion. The ant specialist R. alata is not specializing on any particular ant species but rather maximizing prey quantity over quality by only eating the largest ants, despite their scarcity in the environment.
Soil respiration dynamics in forage-based and cereal-based cropping systems in central Italy

Studies that have investigated soil carbon dynamics under Mediterranean conditions are scarce and fragmented and contrasting results have often been reported. This study aimed to fill some gaps in our knowledge by: (i) determining annual dynamics of total (RS) and heterotrophic (RH) soil respiration; (ii) estimating annual cumulative RS and RH; and (iii) investigating the relationships between RS and RH and soil temperature and water content. The study was carried out in central Italy, for a plain and a hilly site, with the focus on two main cropping systems: an alfalfa-based forage system and a wheat-based rotation system. RS and RH showed different dynamics, with spatial and temporal variability across these sites. Estimated annual cumulative RS fluxes were 8.97 and 7.43 t C ha –1 yr–1 for the plain and hilly alfalfa-based sites, respectively, and 4.67 and 5.22 t C ha–1 yr–1 for the plain and hilly wheat-based sites, respectively. The RH components of RS were 4.26 and 3.52 t C ha –1 yr–1 for the plain and hilly alfalfa-based sites, respectively, and 3.89 and 2.45 t C ha–1 yr–1 for the plain and hilly wheat-based sites, respectively. A model with a combination of soil temperature and soil water content explained 43 % to 49 % and 33 % to 67 % of the annual variation of RS and RH, respectively. These findings help to extend our knowledge of Mediterranean cropping systems, although further studies are needed to clarify the effects of management practices on the modelling of soil respiration efflux.
Conjugated linoleic acid supplementation for 8 weeks fails to impact body composition , lipid profile , or safety parameters in overweight , hyperlipidemic men

1 The usefulness of conjugated linoleic acid as a nutraceutical remains ambiguous. Our objective 2 was, therefore, to investigate the effect of CLA on body composition, blood lipids and safety 3 parameters in overweight, hyperlipidemic men. A double-blinded, 3-phase crossover trial was 4 conducted in overweight (BMI ≥ 25 kg/m); borderline hypercholesterolemic (LDL-C ≥ 2.5 5 mmol/L) men aged 18-60 y. During three 8-wk phases, each separated by a 4-wk washout period, 6 27 subjects consumed under supervision in random order 3.5 g/d of (i) safflower oil: Control, (ii) 7 50:50 mixture of trans 10, cis 12 (t10, c12) and cis 9, trans 11 (c9, t11) CLA: Clarinol G-80 and 8 (iii) c9, t11 isomer: c9, t11 CLA. At baseline and endpoint of each phase body weight, body fat 9 mass and lean body mass were measured by DXA. Blood lipid profiles and safety biomarkers, 10 including insulin sensitivity, blood concentrations of adiponectin, and inflammatory [hs-C11 reactive protein (CRP), TNF-α, IL-6] and oxidative (oxidized-LDL) molecules were measured. 12 Effect of CLA consumption on fatty acid oxidation was also assessed. Results show that CLA 13 treatments did not affect body weight, body composition or blood lipids compared to control, 14 either at phase end or as change from baseline to endpoint. CLA failed to impact β-oxidation rate 15 of fatty acids. No significant alterations were observed in any of the safety parameters tested. In 16 conclusion, while no detrimental effects were observed with supplementation, these results fail to 17 confirm a role for CLA in either body weight or blood lipid regulation in humans. 18 19 20
Prediction of some peroxidase functions in Arabidopsis thaliana L. by bioinformatic search

Peroxidases of class III are common in various organisms. They are involved in lignin biosynthesis and plant protection against stressors. Peroxidases are presented in many isoforms, whose role is not always clear. The aim of this study is to analyze the amino acid sequences of reference peroxidases with known functions and peroxidases from Arabidopsis thaliana L. whose functions are unknown and to consider their putative roles in lignin biosynthesis. The structural and functional organization of peroxidases was analyzed by bioinformatical methods applied to open Internet sources. Seven reference peroxidases were chosen from four plant species: Zinnia sp. , Armoracia rusticana P.G. Gaertn. , Lycopersicon esculentum L. и Populus alba L. Twenty-four amino acid sequences of homologous peroxidases from A. thaliana were selected for the analyses with the BLAST service. Their molecular weights and isoelectric points were calculated. Multiple alignments of amino acid sequences and phylogenetic analysis were done. Sites of binding to monolignol substrates were identified in seven peroxidases from A. thaliana, and the enzymes were assigned to the groups of Sor G-peroxidases. Amino acid replacements in the primary structures of peroxidases were analyzed. Peroxidases from A. thaliana were clustered with reference peroxidases. They formed six clusters on the phylogenetic tree, three of which contained only A. thaliana peroxidases. Peroxidases within each cluster had similar molecular weights and isoelectric points, common localization of expression, and similar functions. Thus, the use of bioinformatics, databases, and published data bring us to assumptions as to the functions of several A. thaliana class III peroxidases. AtPrx39 peroxidase was shown to be affine to sinapyl alcohol; AtPrx54, to p-coumaryl and coniferyl alcohols. They are likely to participate in lignin biosynthesis.
Regulatory Genes and Enzymatic Complex of Flowering Time in Rice

Flowering time (heading date) of the rice plant is considered an important agronomic trait for environmental adaptation and grain yield. It is controlled by multiple genes and is regulated by different environmental factors, such as day length, temperature, soil moisture, etc. So far, approximately 125 genes regulating flowering process and floral organ identity or development directly or indirectly have been reported in rice. Among these genes, Heading date 3a ( Hd3a ), RICE FLOWERING LOCUS T1 ( RFT1 ), Heading date 5 ( Hd5 ), MORF-RELATED GENE702 ( MRG702 ), Casein kinases, CKI and CK2  , Pseudo-Response Regulator 37 ( PRR37 ), Hd gene family have been reported as the key genes regulating flowering time in rice; however, their functions are mostly inter-related. Hd3a and RFT1 that encode florigens, are known as the floral transition genes in rice. In rice, florigen immediately induces downstream genes in the shoot apical meristem (SAM) to start the transition from vegetative to reproductive phase. RFT1 gene regulates flowering time with pivotal action while Hd3a , regulates under long day conditions. The Hd5 gene regulates flowering time in variation of early heading for adaptation depending on environmental signals. MRG702, a reader protein, promotes flowering. Casein kinases, CKI and CK2  directly influence the function of the early heading regulator PRR37 . Hd16/CKI hinders flowering time in the Ehd1 -concerned pathway through phosphorylation of Ghd7 and PRR37. Natural variants of Hd1 , PRR37 , Ghd7 , DTH8 , Hd6 , and Hd16 were found in the rice varieties that are cultivated presently in Asia and Europe, and their variants play significant roles in the down streaming of Ehd1 expression to delay flowering time in natural long day
Complete mitochondrial genome of the sharp-snouted pitviper Deinagkistrodon acutus (Reptilia, Viperidae)

Abstract The sharp-snouted pitviper, Deinagkistrodon acutus, belongs to the monotypic genus Deinagkistrodon of the family Viperidae. It is one of the important species of snakes for its commercial and medicinal value. Complete mitochondrial genome sequence of the D. acutus was sequenced by next-generation sequencing technology. The total mitochondrial genome is 17,538 bp in length, containing 13 protein-coding genes, 22 tRNA genes, 2 ribosome RNA genes, and 2 control regions. Most of the genes of D. acutus are encoded on the H-strand, except for the ND6 subunit gene and eight tRNA genes which distribute on the L-strand. Phylogenetic reconstruction result indicated that our newly determined mitochondrial genome sequence could meet the demands. The complete mitochondrial genome sequence presented here will be useful to study the evolutionary relationships and genetic diversity of D. acutus.
DISTANCE AND DOSAGE OF ORGANIC FERTILIZER INFLUENCE RESULTS OF EGG CABBAGE PLANT (BRASSICA OLERACEAE VAR. CAPITATA L)

The low yield of cabbage is often associated with the low content of soil organic matter. The inappropriate planting distance also contributes to the low yield of the cabbage plant. The provision of organic fertilizer with the right dosage and setting the right spacing is also expected to increase soil fertility and ultimately increase results of cabbage plants. This research was conducted in the field from April to July 2018 in Subak Gede Bungan Kapal, Tunjuk Village, Tabanan District, Tabanan Regency. Treatment was arranged in a factorial manner in a Randomized Block Design (RBD). Two treatments studied in this study were plant spacing (30 cm x 40 cm; 30 cm x 40 cm; 30 x 50 cm) and organic fertilizer (Petroganic) (0 t ha-1; 1 t ha-1; 2 t ha -1; 3 t ha-1). The treatment was repeated three times. The results showed that the interaction between the treatment of spacing and the use of doses of organic fertilizer had no significant effect on all observed parameters. The treatment of spacing has a significant effect on the diameter of the commercial crop -1, the weight of fresh stover ha-1, and has a very significant effect on the weight of crop ha-1, and the weight of commercial crop ha-1. The highest weight of commercial k-ha ha-1 was obtained at a plant spacing of 30 x 50 cm (J3) of 525.86 kg, significantly increasing by 74.80% compared to a spacing of 30 x 30 cm (J1) which was 299.12 kg. The treatment of organic fertilizer dosage has a very significant effect on the weight of crop ha-1, weight of commercial crop ha-1, commercial crop diameter-1 but has no significant effect on the fresh weight of stover ha-1. The highest weight of commercial ha-1krop obtained at the dose of organic fertilizer 2 t ha-1 of 444.23 kg (P2) increased by 58.30% compared to the dose of 0 t ha-1 (P0) of 280.62 kg
Activity Patterns of Cave-Dwelling Bat Species During Pre-Hibernation Swarming and Post-Hibernation Emergence in the Central Appalachians

In North America, bat research efforts largely have focused on summer maternity colonies and winter hibernacula, leaving the immediate pre- and post-hibernation ecology for many species unstudied. Understanding these patterns and processes is critical for addressing potential additive impacts to White-nose Syndrome (WNS)-affected bats, as autumn is a time of vital weight gain and fat resources are largely depleted in early spring in surviving individuals. Our study sought to examine autumn and spring bat activity patterns in the central Appalachian Mountains around three hibernacula to better understand spatio-temporal patterns during staging for hibernation and post-hibernation migration in the post-WNS environment. From early September through November 2015 and 2016, and from early March through April 2016 and 2017, we assessed the effects of distance to hibernacula and ambient conditions on nightly bat activity for Myotis spp. and big brown bats (Eptesicus fuscus) using zero-crossing frequency division bat detectors near cave entrances and 1 km, 2 km, and 3 km distant from caves. Following identification of echolocation calls, we used generalized linear mixed effects models to examine patterns of activity across the landscape over time and relative to weather. Overall bat activity was low at all sample sites during autumn and spring periods except at sites closest to hibernacula. Best-supported models describing bat activity varied, but date and ambient temperatures generally appeared to be major drivers of activity in both seasons. Total activity for all species had largely ceased by mid-November. Spring bat activity was variable across the sampling season, however, some activity was observed as early as mid-March, almost a month earlier than the historically accepted emergence time regionally. Current timing of restrictions on forest management activities that potentially remove day-roosts near hibernacula when bats are active on the landscape may be mismatched with actual spring post-hibernation emergence. Adjustments to the timing of these restrictions during the spring may help to avoid potentially additive negative impacts on WNS-impacted bat species.
MLSTar: automatic multilocus and core 1 genome sequence typing in R 2

8 Multilocus sequence typing (MLST) is a standard tool in population genetics and bacterial epidemiology that assesses the genetic variation present in a reduced number of housekeeping genes (typically seven) along the genome. This methodology assigns arbitrary integer identiﬁers to genetic variations at these loci allowing to efﬁciently compare bacterial isolates using allele-based methods. Now, the increasing availability of whole-genome sequences for hundreds to thousands of strains from the same bacterial species has motivated to upgrade the resolution of traditional MLST schemes using larger gene sets or even the core genome (cgMLST). The PubMLST database is the most comprehensive resource of described MLST and cgMLST schemes available for a wide variety of species. Here we present MLSTar as the ﬁrst R package that allows to i) connect with the PubMLST database to select a target scheme, ii) screen a desired set of genomes to assign alleles and sequence types and iii) interact with other widely used R packages to analyze and produce graphical representations of the data. We applied MLSTar to analyze a set of 400 Campylobacter coli genomes, showing great accuracy and comparable performance with previously published command-line tools. MLSTar can be freely downloaded from http://github.com/iferres/MLSTar .