Miracle-dz/UniFAR-FTUs huggingface dataset:
Variations existing in protein-coding genes of the complete mitochondrial genomes of two highly morphological similarity fish: Periophthalmus magnuspinnatus and P. modestus (Perciformes, Gobiidae)

Abstract Periophthalmus magnuspinnatus is a new record species of Gobiidae in China. It had been misidentified as P. modestus for long time early before 2006. Here, the complete mitochondrial genome (mtDNA) sequences of the two species were first reported and analyzed comparably. The two genomes were both consisted of 13 protein-coding genes, 22 tRNA genes, two rRNA genes and a control region. Except for eight tRNA and ND6 genes, all other mitochondrial genes were encoded on the heavy strand. It was 16,496 bp and 16,803 bp, respectively, and P. modestus had a 238 bp-gap between tRNAleu and ND5. There were high variations (10–19%) in the protein-coding genes. In the initiation condon and stop codons, the two fish also had tiny difference. Phylogenetic analysis showed that P. magnuspinnatus and P. modestus first clustered together and then they constituted Gobiidae clade with other 12 fish. Whereas Odontobutidae and Rhyacichthyidae formed the sister group, then clustered with Eleotridae, and finally joined with Gobiidae, which is consist with previous phenotypic report. The study will contribute to the phylogenetic analysis of the Gobiidae and natural resources conservation of P. magnuspinnatus and P. modestus.
Effect of Organic Manures on Seed Germination and Seedling Growth of Khirni

An experiment was conducted to study the effect of organic manures on germination and growth behaviour of khirni seedlings. The experiment comprised of eight media formulated by mixing soil, sand, FYM, vermicompost, poultry manure, cocopeat and spent mushroom compost in different combinations. The study indicated that seed germination and seedling growth parameters of khirni seeds were greatly influenced by the growing media. The results revealed that the combination of Soil + Sand + FYM proved superior in terms of seed germination, seedling length, number of leaves, root length, root dry weight, seedling dry weight, seedling vigour index-l and II whereas greater shoot length, stem diameter and dry weight of shoots were recorded in the media containing Soil+ Sand+ Vermicompost.
Control of Translation by mRNA Secondary Structure in Escherichia coli: A Quantitative Analysis of Literature Data

Abstract Translational efficiency in Escherichia coli is strongly controlled by the secondary structure of the mRNA in the translational initiation region. We have previously shown that protein production from the coat-protein gene of RNA bacteriophage MS2 is directly related to the fraction of mRNA molecules in which the ribosome binding site is unfolded. This fraction is dictated by the free energy (Δ G f 0 ) of the local secondary structure. We now present a similar analysis of published data on four other ribosome binding sites. The results conform quantitatively to the same relationship as found for the MS2 coat-protein gene. The efficiency of translation is determined by the overall stability of the structure at the ribosome binding site, whether the initiation codon itself is base-paired or not. Structures weaker than -6 kcal/mol usually do not reduce translational efficiency. Below this threshold, all systems show a tenfold decrease in expression for every -1.4 kcal/mol, as predicted from theory.
Enhancement of growth in mangrove plant (Ceriops tagal) by Rhizophagus clarus

ABSTRACT The present study was conducted to investigate the growth response of Ceriops tagal Perr. ) C.B. Robinson a mangrove species belonging to the family Rhizophoraceae. Three dominant native arbuscular mycorrhizal (AM) fungal species viz., Rhizophagus clarus, R. intraradices, and Acaulospora laevis were selected. The results revealed that the Mycorrhizal Plant Responsiveness (MGR) was greater in AM inoculated plants compared to control plants. Among AM fungal treatments, plants inoculated with R. clarus recorded significant increase in growth responses compared to remaining AM treatments. The study suggests that R. clarus was the most efficient AM species exhibiting greater influence on growth and biomass. Differences in growth parameters between AM inoculated treatments and control are reasonably linked to colonization levels. The result of the present study indicates that potential native AM fungal species can be use in mangrove reforestation programs as bio-inoculum.
Cinnamomum iners Leaves as an Alternative Therapy for Diabetes

This study was designed to investigate the antidiabetic property of Cinnamomum iners leaves which were used traditionally to combat diabetes. Firstly, the antidiabetic activity of petroleum ether, chloroform, methanol and water extract of C. iners leaves was evaluated. Next, the potential extract which was the methanol extract was fractionated to obtain ethyl acetate, n-butanol, chloroform and aqueous fraction. The active chloroform fraction was subjected to subfractionation process to obtain subfraction 1 (SF 1) and subfraction 2 (SF 2). Cinnamomum iners leaves active portion (methanol extract, chloroform fraction and subfraction 1) was standardized using cinnamic aldehyde. The antidiabetic activity of standardized C. iners leaves was assessed by using Intra-Peritoneal Glucose Tolerance Test (IPGTT). The antidiabetic mechanism of active portion of C. iners leaves were also determined by measuring glucose absorption from the intestine. This study showed significant glucose tolerance effect of active portion of C. iners leaf after repeated oral administration in STZ-induced diabetic rats. The antidiabetic mechanism of subfraction 1 and chloroform fraction of C. iners leaf is by inhibiting glucose absorption from intestine.
Effect of Selection for Weight of Early Eggs on Egg Production Traits in Japanese Quail

The present study aimed to measure the direct response of selection for high egg weight of the first 10 eggs laid at the beginning of egg production period in Japanese quail through three generations of selection. The egg weight of the first 10 eggs (EW10) as direct response increased in the selected line when compared with control line from 10.43 g in the base generation to 12.52 g in the second generation after selection with rate of 0.69 g per generation. The Age at Sexual Maturity (ASM) trait increased in the selected line from 49.47 days in the base generation to 52.63 days in the second generation after selection for EW10 with rate of 1.05 days per generation. The Body Weight at Sexual Maturity (BWSM) trait increased, after selection in the selected line from 240.09 g in the base generation to 251.45 and 243.67 g in the first and second generation, respectively. Egg number during the first 45 days of production was significantly higher in selected line than the control line throughout the 3 generations of selection. The overall mean of egg weight through the first 45 days of laying period were11.27, 12.01 and 12.29 g for the base, 1st and 2nd generation while it was 11.51 and 12.13 g for control and selected lines, respectively, with a significant difference among generations and between line. Average feed consumption was 31.50 and 29.03 g/female/day for the control and selected line, respectively. The females in selected line had better Feed Conversion Ratio (FCR) than the control females. Selection for EW10 in Japanese quail improved egg number, egg weight and FCR during the first 45 days of laying.
Uncovering the variability, regulatory roles and mutation rates of short tandem repeats

Over the past decade, the advent of next-generation DNA sequencing technologies has ushered in an exciting era of biological research. Through large-scale sequencing projects, scientists have begun to unveil the variability and function of millions of DNA mutations called single nucleotide polymorphisms. Despite this rapid growth in understanding, short tandem repeats (STRs), genomic elements consisting of a repeating pattern of 2-6 bases, have remained poorly understood. Mutating orders of magnitude more rapidly than most of the human genome, STRs have been identified as the causal variants in diseases such as Fragile X syndrome and Huntington’s disease. However, in spite of their potentially profound biological consequences, STRs remain systematically understudied due to difficulties associated with obtaining accurate genotypes. To address this issue, we developed a series of bioinformatics approaches and applied them to populationscale whole-genome sequencing data sets. Using data from the 1000 Genomes Project, we performed the first genome-wide characterization of STR variability by analyzing over 700,000 loci in more than 1000 individuals. Next, we integrated these genotypes with expression data to assess the contribution of STRs to gene expression in humans, uncovering their substantial regulatory role. We then developed a state-of-the-art algorithm to genotype STRs, resulting in vastly improved accuracy and uncovering hundreds of replicable de novo mutations in a deeply sequenced trio. Lastly, we developed a novel approach to estimate mutation rates for STRs on the Y-chromosome (Y-STR), resulting in rates for hundreds of previously uncharacterized markers. Collectively, these analyses highlight the extreme variability of STRs and provide a framework for incorporating them into future studies. Thesis Supervisor: Yaniv Erlich, PhD Title: Assistant Professor of Computer Science, Columbia University Thesis Supervisor: Manolis Kellis, PhD Title: Associate Professor of Computer Science, MIT
Comparing tree‐ring and permanent plot estimates of aboveground net primary production in three eastern U.S. forests

Forests account for a large portion of sequestered carbon, much of which is stored as wood in trees. The rate of carbon accumulation in aboveground plant material, or aboveground net primary productivity (aNPP), quantifies annual to decadal variations in forest carbon sequestration. Permanent plots are often used to estimate aNPP but are usually not annually resolved and take many years to develop a long data set. Tree rings are a unique and infrequently used source for measuring aNPP, and benefit from fine spatial (individual trees) and temporal (annual) resolution. Because of this precision, tree rings are complementary to permanent plots and the suite of tools used to study forest productivity. Here we evaluate whether annual estimates of aNPP developed from tree rings approximate estimates derived from colocated permanent plots. We studied a lowland evergreen (Howland, Maine), mixed deciduous (Harvard Forest, Massachusetts), and mixed mesophytic (Fernow, West Virginia) forest in the eastern United States. Permanent plots at the sites cover an area of 2–3 ha, and we use these areas as benchmarks indicative of the forest stand. We simulate random draws of permanent plot subsets to describe the distribution of aNPP estimates given a sampling area size equivalent to the tree-ring plots. Though mean tree-ring aNPP underestimates permanent plot aNPP slightly at Howland and Fernow and overestimates at Harvard Forest when compared with the entire permanent plot, it is within the 95% confidence interval of the random draws of equal-sized sampling area at all sites. To investigate whether tree-ring aNPP can be upscaled to the stand, we conducted a second random draw of permanent plot subsets simulating a twofold increase in sampling area. aNPP estimates from this distribution were not significantly different from results of the initial sampling area, though variance decreased as sampling area approaches stand area. Despite several concerns to consider when using tree rings to reconstruct aNPP (e.g., upscaling, allometric, and sampling uncertainties), the benefits are apparent, and we call for the continued application of tree rings in carbon cycle studies across a broader range of species diversity, productivity, and disturbance histories to fully develop this potential.
Growth and physiology of peanut ( Arachis hypogaea L . ) irrigated with saline water and biofertilizer application times

The peanut crop has adaptive features to high salinity levels in the soil, due to its morphological and physiological characteristics. The objective of this study was to evaluate the use of biofertilizer in reducing the effects of irrigation water salinity on the vegetative and physiological behavior of the peanut crop, as well as the crop development under saline conditions. The experiment was conducted in a greenhouse, in an experimental design with randomized blocks, adopting a 6 × 3 factorial scheme, concerning the irrigation water salinity (CEa) in six levels (0.5, 1.5, 2.5, 3.5, 4.5 and 5.5 dS m -1 ) and three doses of biofertilizer (applied at 15, 30 and 45 days after germination), with four replications, totaling 72 experimental units. The variables analyzed were: plant height; fresh and dry weight of shoots; stem diameter; length, fresh weight and dry weight of roots; number of branches; leaf area; photosynthetic radiation, chlorophyll a, b, and total chlorophyll. The use of biofertilizer had no influence on reducing the effects of irrigation water salinity in the development of the peanut crop. Salinity negatively affected all physiological and growth variables.
Triazole-induced drought stress amelioration on growth, yield, and pigments composition of Helianthus annuus L. (sunfl ower)

In this investigation, a pot culture experiment was conducted to estimate the ameliorating effect of drought stress and drought with triazole compounds (hexaconazole, propiconazole, and tebuconazole) response on growth analysis, pigment composition, and yield parameters of Helianthus annuus L. (Sunflower). Sunflower is one of the most important oil crops and due to its high content of unsaturated fatty acids and a lack of cholesterol, the oil benefits from a desirable quality. Plant growth and productivity are unfavorably affected by nature’s wrath in the form of various biotic and abiotic stress factors. Water deficit is one of the major abiotic stresses, which adversely affects crop growth and yield. Drought stress during vegetative phase, flowering or seed filling period causes considerable decreases in yield and oil content of sunflower. These changes are mainly related to altered metabolic functions, one of those is either loss of or reduced synthesis of photosynthetic pigments and biochemical modifications. From 30 days after sowing (DAS), the plants were subjected to 4 days interval drought stress and drought with triazole compounds and daily irrigation kept as a control. The plant samples were collected on 40, 50, and 60 DAS. Growth, yield parameters, and pigment variations were analyzed. Drought stress decreased growth, yield, and pigments composition chlorophyll, carotenoid, and anthocyanin when compared to control. The triazole ameliorated drought stress by increasing the growth and biochemical potentials and bring into being the way for overcoming drought stress in H. annuus L. plants.
BIOCHEMICAL EFFECTS OF SUBLETHAL DOSES OF PHOSPHINE ON THE SIXTH- INSTAR LARVAE OF SUSCEPTIBLE AND RESISTANT POPULATIONS OF Trogoderma granarium EVERTS (COLEOPTERA: DERMESTIDAE)

Khapra beetle, Trogoderma granarium Evertsis a serious stored grain pest throughout the world. Misuse of pesticides and fumigants to control this pest is the major cause of resistance development. This study was planned to investigate susceptible and resistant populations of T. granarium by determining the LC 50 doses and biochemical differences in the susceptible and resistant populations. For this purpose, two different populations i.e. Lahore (Lhr) and Khanewal (Khw) collected from various regions of Punjab province of Pakistan. Phosphine was generated in laboratory by FAO method. The LC 50 values of Phosphine were determined against 6 th instar larvae of these two populations of T. granarium in air tight glass desiccators. Following collection, they were transferred to lab and used to develop pure lab culture at 30±1°C and 65±5 R.H. of these populations used in this study. Mortality was calculated and subjected to probit analysis described. The LC 50 of Phosphinefor 6 th instar larvae was 8.4ppm in Lhr population while in Khw LC 50 was 5.6ppm. On the basis of LC 50 results it was concluded that Lhr was the resistant population. Toxicity of three doses (LC 10 , LC 20 , LC 30 ) of Phosphine used by analyzing the activities of the enzymes acid phosphatase (AcP), alkaline phosphatase (AkP), amylase, alanine aminotransferases (ALAT), aspartate aminotransferase (ASAT), lactate dehydrogenases (LDH), Isocitrate dehydrogenases (ICDH), cholinesterase (ChE), protease, aminopeptidase and trehalase. in T. granarium . The ASAT, aminopeptidase, trehalase and protease were increased in resistant population. Enzymes which increase in susceptible population are AcP, AkP, ALAT, LDH and ICDH. This study will help in understanding the biochemical basis of Phosphine resistance in T. granarium andprovide information for improving pests control programs.
Laboratory biology and impact of a stem-boring weevil Apocnemidophorus pipitzi (Coleoptera: Curculionidae) on Schinus terebinthifolia

ABSTRACT Brazilian peppertree, Schinus terebinthifolia Raddi (Anacardiaceae), was introduced into Florida, USA, from South America as an ornamental plant in the late 19th and early 20th centuries. It eventually escaped cultivation and is a serious threat to the state’s biodiversity. In the 1980s, this invasive weed was targeted for classical biocontrol. Surveys for natural enemies of Brazilian peppertree conducted in the native range resulted in the discovery of several candidate biocontrol agents. A stem-boring weevil identified as Apocnemidophorus pipitzi (Faust) was collected in Paraguay and transported under permit to Florida, USA. A laboratory colony of A. pipitzi was established in April 2007 by caging adults on cut branches of Brazilian peppertree supplemented with leaf bouquets. Adults are defoliators that feed mainly on the upper surface of subterminal leaflets. Females deposit eggs singly inside the stems and larvae feed under the bark where they damage the vascular cambium. There are five instars, pupation occurs inside the stem and a new generation is produced in 3–4 months. Growth of potted plants with and without exposure to weevil herbivory was compared over an 11-month period. Feeding damage by adults and larvae significantly increased leaf abscission and reduced leaf and root biomass accumulation.
Rates, application intervals and rotation of four granular pesticides to control nematodes and the corm-weevil (Cosmopolites sordidus Germar) in plantain

The efficacy of the nematicide-insecticides aldicarb, carbofuran, ethoprop and phenamiphos was studied in plantain using recommended and lower label rates, shorter application intervals and rotation. These compounds were effective in reducing Radopholus similis and Pratylenchus coffeae populations when lower than recommended rates were applied at the shortened interval of four months or when the chemicals were rotated. Except for ethoprop, these compounds were also effective in controlling the corm-weevil when applied at below recommended label rates and intervals. However, the insecticide efficacy of phenamiphos and the rotation of aldicarb, phenamiphos and carbofuran was particularly high when applied at planting time and every six months thereafter. Yield components were not significantly affected by the various nematicide-insecticide treatments in the plant crop.
Odds ratio of dystocia in Holstein cows in Iraq

The objective of this research was to determine the effect of some factors on dystocia in Holstein cows. The analysis consist of 19090 records of parturitions belonged to 3181 cows from 1990 to 2004 in the Nasr Dairy Cattle Station in Iraq. A logistic regression model was used to predict dystocia. The model included effects of year of birth, season (winter or other seasons), parity (first or later), birth weight (kg), and sex of calf. Results revealed that odds of dystocia decreased by 5% per year. Calves born in the winter have higher risk of dystocia by 27% than calves born in the other seasons. Male calves associated with dystocia were greater than female calves by 39%. First parity cows had a 2.04 times higher risk of dystocia than cows in later parities. Odds of dystocia increased with increasing birth weight by 16%/kg. It was concluded that dystocia was affected by all the factors under consideration.
Endocannabinoid receptor blockade increases vascular endothelial growth factor and inflammatory markers in obese women with PCOS

Context: Animal studies suggest that cannabinoid receptor-1 (CB-1) blockade reduces inflammation and neovascularization by decreasing vascular endothelial growth factor (VEGF) levels associated with a reduction in inflammatory markers, thereby potentially reducing cardiovascular risk. Objective: To determine the impact of CB1 antagonism by rimonabant on VEGF and inflammatory markers in obese PCOS women. Design: Randomised, open-labelled parallel study. Setting: Endocrinology outpatient clinic in a referral centre. Subjects: Twenty patients with PCOS and biochemical hyperandrogenaemia with a body mass index of ≥ 30kg/m2 were recruited. Patients were randomised to 1.5g daily of metformin or 20mg daily of rimonabant. Main Outcome Measures: Post hoc review to detect VEGF and pro-inflammatory cytokines TNF-α, IL-1β, IL-1ra, IL-2, IL6, IL-8, IL-10 and MCP-1 before and after 12 weeks treatment. Results: After 12 weeks of rimonabant there was a significant increase in VEGF (99.2±17.6 vs 116.2±15.8pg/ml, p<0.01) and IL-8 (7.4±11.0 vs 18.1±13.2pg/ml, p<0.05) but not after metformin (VEGF p=0.7; IL-8 p=0.9). There was no significant difference in the proinflammatory cytokines TNF-α, IL-1β, IL-1ra, IL-2, IL6, IL-8, IL-10 and MCP-1 following
Mitochondrial DNA relationships among North Palaearctic Eptesicus (Vespertilionidae, Chiroptera) and past hybridization between Common Serotine and Northern Bat

Interspecific hybridization was proposed as one of the explanations for the lack of differentiation between mtDNA of the morphologically divergent bats Eptesicus serotinus and E. nilssonii. However, only West European populations of these species were examined so far. The cytochrome b mitochondrial gene sequences of E. serotinus originating from Russia were compared with those of other North Palaearctic Eptesicus. Common serotines from the Caucasus, Central and South Russia constitute a separate monophyletic group, distinct from western E. serotinus populations, E. nilssonii, and also from E. isabellinus. Only a common serotine from Kaliningrad region proved to be a member of the West European clade. According to these results one may suppose that most of Russian population of E. serotinus escaped the hybridization event that led to fixation of alien mitochondrial genome in the West European populations. Given that (i) preliminary nuclear data support the distinction between E. serotinus and E. nilssonii and (ii) E. serotinus appears morphologically homogeneous throughout the European part of its range, we consider that this past mtDNA introgression has no direct taxonomic implications. For the first time included in a molecular phylogenetic analysis, E. gobiensis was shown to be a full species, related to E. nilssonii. From our mtDNA phylogenetic tree, the taxonomic validity of the subgenus Amblyotus appears doubtful.