Miracle-dz/UniFAR-FTUs huggingface dataset:
Molecular Dynamics and Docking of Biphenyl: A Potential Attachment Inhibitor for HIV-1 gp120 Glycoprotein

Purpose: To develop a new drug that inhibits viral attachment and entry for the treatment of HIV/AIDS patients. Methods: Two Protein Databank (PDB) crystal structures of HIV-1 gp120-CD4 complexes, namely, 1RZK and 1G9N, were mutated at amino acid position 43 to a biphenylalanine (biPhe-43) residue. FireDock web server was used for the docking experiments and 5ns molecular dynamics (MD) using Gromacs 4.0 was performed on the protein complexes to verify the docking results based on the Gibbs free binding energies. Results: Molecular docking by FireDock web server showed that biPhe-43 and Trp-43-mutated CD4 inhibited the binding of gp120 more efficiently, -113.8 and -101.7 kJ/mol (SD = 0, n = 3), respectively, than the alternate aromatic wild type amino acid Phe-43 and the mutant His-43 and Tyr-43. FireDock revealed that electrostatic and Van der Waals interactions were mainly involved in the CD4-gp120 binding and helped to stabilize the protein interactions. In a 5ns MD simulation, biPhe-43 and Trp-43 mutated CD4 demonstrated best Gibbs free binding energies (-16271  29 and -16266 ± 18 kJ/mol, respectively) to gp120 in the identification and confirmation of biPhe-43 and Trp-43 mutated CD4 as excellent inhibitors to gp120. Conclusion: The docked energies and probability outcomes by FireDock anticipated that a ligand for an efficient inhibition of HIV gp120 should involve an extended but conformational flexible aromatic group, i.e. a biphenyl.
Variability in exchange of CO2 across 12 northern peatland and tundra sites

Many wetland ecosystems such as peatlands and wet tundra hold large amounts of organic carbon (C) in their soils, and are thus important in the terrestrial C cycle. We have synthesized data on the carbon dioxide (CO2) exchange obtained from eddy covariance measurements from 12 wetland sites, covering 1–7 years at each site, across Europe and North America, ranging from ombrotrophic and minerotrophic peatlands to wet tundra ecosystems, spanning temperate to arctic climate zones. The average summertime net ecosystem exchange of CO2 (NEE) was highly variable between sites. However, all sites with complete annual datasets, seven in total, acted as annual net sinks for atmospheric CO2. To evaluate the influence of gross primary production (GPP) and ecosystem respiration (Reco) on NEE, we first removed the artificial correlation emanating from the method of partitioning NEE into GPP and Reco. After this correction neither Reco (P= 0.162) nor GPP (P= 0.110) correlated significantly with NEE on an annual basis. Spatial variation in annual and summertime Reco was associated with growing season period, air temperature, growing degree days, normalized difference vegetation index and vapour pressure deficit. GPP showed weaker correlations with environmental variables as compared with Reco, the exception being leaf area index (LAI), which correlated with both GPP and NEE, but not with Reco. Length of growing season period was found to be the most important variable describing the spatial variation in summertime GPP and Reco; global warming will thus cause these components to increase. Annual GPP and NEE correlated significantly with LAI and pH, thus, in order to predict wetland C exchange, differences in ecosystem structure such as leaf area and biomass as well as nutritional status must be taken into account.
In vitro microbial growth and rumen fermentation of different substrates as affected by the addition of disodium malate

The effects of two concentrations of disodium malate on the in vitro fermentation of three substrates differing in their forage: concentrate ratio (0·8: 0·2, 0·5: 0·5 and 0·2: 0·8; g/g dry matter; low-, medium- and high-concentrate substrates, respectively) by rumen micro-organisms were studied using batch cultures. Rumen contents were collected from four Merino sheep offered lucerne hay ad libitum and supplemented daily with 400 g concentrate. Disodium malate was added to the incubation bottles to achieve final concentrations of 0, 4 and 8 mmol/l malate and 15 N was used as a microbial marker. Gas production was measured at regular intervals from 0 to 120 h of incubation to study fermentation kinetics. When gas production values were corrected for gas released from added malate, no effects ( P > 0·05) of malate were detected for any of the estimated gas production parameters. In 17-h incubations, the final pH and total volatile fatty acid (VFA) production were increased ( P P > 0·05) were detected in the final amounts of ammonia-N and lactate. When net VFA productions were corrected for the amount of VFA produced from malate fermentation itself, adding malate did not affect ( P > 0·05) the production of acetate, propionate and total VFA. Malate reduced methane (CH 4 ) production by proportionately 0·058, 0·013 and 0·054 for the low-, medium- and high-concentrate substrates, respectively. Adding malate to batch cultures increased ( P P > 0·05) its efficiency of growth (55·5, 56·7 and 54·3 mg of microbial N per g of organic matter apparently fermented for malate at 0, 4 and 8 mmol/l, respectively). There were no interactions ( P > 0·05) malate × substrate for any of the measured variables, and no differences ( P > 0·05) in pH, CH 4 production and microbial growth were found between malate at 4 and 8 mmol/l. The results indicate that malate had a beneficial effect on in vitro rumen fermentation of substrates by increasing VFA production and microbial growth, and that only subtle differences in the effects of malate were observed between substrates. Most of the observed effects, however, seem to be due to fermentation of malate itself.
Foraging of Buthus occitanus (Scorpiones: Buthidae) on shrub branches in an arid area of southeastern Spain

Abstract Little is known about the climbing habits of scorpions on plants, despite the interest in this behavior for understanding the connection between above- and below-ground food webs in deserts and to uncover the importance of prey availability and predator avoidance on foraging and habitat selection. Here we report on the foraging of Buthus cf. occitanus (Amoreux 1789) on shrub branches in an arid area in southeastern Spain. Black-light censuses were carried out within six 50 m × 4 m areas in one full and two new moon nights during September and October 2011. Shrub availability was estimated by counting shrubs in 50 m × 1 m areas within each census area. Results showed that nearly 40% of the scorpions, mostly small, 10–20-mm-long individuals, were found foraging on both inner and outer shrub branches up to 80 cm in height. The probability of finding a scorpion on a shrub was inversely related to scorpion size. Selectivity analysis showed that scorpions selected four shrub species, a result that may be related to prey size and availability. Foraging of B. occitanus on shrubs may be favored if this behavior not only allows access to shrub-inhabiting prey, but also reduces predation risk.
IDENTIFICATION OF SCLEROTIUM DELPHINII CAUSING SEEDLING ROT IN COTTON

Sclerotium delphinii (syn. Sclerotium rolfsii var. delphinii) is a serious pathogen infecting plants in the genus Ajuga, Arachis, Hosta, Iris, Malus and many additional herbaceous ornamental species but there has been no report of this pathogen infecting cotton. Plants infected with S. delphinii were first noticed in the fields of Wardha, India, during 2011- 2012. The causal agent was isolated in PDA medium and identified by sequencing the ITS region and its pathogenicity was determined by fulfilling Koch’s postulates
LOWER DOSES OF VANADATE IN COMBINATION WITH AZADIRACHTA INDICA LEAF EXTRACT RESTORE ALTERED ANTIOXIDANT STATUS IN THE BRAIN OF STREPTOZOTOCIN INDUCED DIABETIC RATS

Azadirachta indica leaf extract has been reported to have hypoglycemic effects. Sodium orthovanadate also exerts antidiabetic effects but at relatively high doses with several toxic effects. So, in the present study we investigate the effects of oral administration of Azadirachta indica leaf extract and vanadate, separately and in combination, on the activities of antioxidant enzymes in streptozotocin induced diabetic rats. Diabetes was induced by a single intraperitoneal injection of streptozotocin (55mg/kg body wt). Animals were divided into six groups namely non diabetic control, diabetic control, diabetic treated with insulin (2U), diabetic treated with leaf extract (500mg/kg body weight),diabetic treated with vanadate (0.6mg/ml) and diabetic treated with both vanadate (0.2mg/ml) and Azadirachta indica leaf extract (500mg/kg body weight). After treatment, the activities of superoxide dismutase (SOD), catalase (CAT), glutathione peroxidase (GPx) and glutathione reductase (GR) were determine in cytosolic fraction of brain tissue. Treatment with different antidiabetic compounds restored the above enzymes activity to normal. Combined dose of Azadirachta indica and vanadate was found to be the most effective in normalizing these Enzyme activities.
Nutrient Changes During the Fermentation of African Oil Bean (Pentaclethra macrophylla Benth) Seeds

The prepared seedslices of African oil bean (Pentaclethra macrophylla Benth) were subjected to a 72-hour traditional fermentation to produce 'ugba' a popular food condiment consumed in the rain forest areas of West tropical Africa. The fermentation brought about slight increases in crude protein and ash contents, and a slight decrease in the oil content of the seeds. Amino nitrogen increased steadily from 1.23 mgNg DM prior to fermentation to 13.68 mg Ng DM after 72-hours, showing a strong indication of -1 -1 appreciable protein hydrolysis. Gas chromatographic analysis of the seed oil showed the principal fatty acid, linoleic acid, increasing from 60.68 to 67.57% of total fatty acids while oleic acid decreased from 26.95 to 22.59%. Palmitic acid and other saturated fatty acids in the seed oil were also slightly affected by th e fermentation; while palmitic increased steadily, others decreased markedly. Total titratable acidity increased gradually as fermentation progressed. A further analysis using thin-layer chromatography revealed the accumulation of formic, acetic, lactic and butyric acids in the fermenting seedslices. At the end of 72 hours, 'ugba' contained 0.41 mgg butyric acid, 0.35mgg lactic acid, 0.18 mgg acetic acid and 0.20 mgg formic -1 -1 -1 -1
A PRIMITIVE ACTINOPTERYGIAN NEUROCRANIUM FROM THE EARLY DEVONIAN OF SOUTHEASTERN AUSTRALIA

Abstract A well-preserved neurocranium with attached partial skull roof is described from the Early Devonian Taemas Formation at Wee Jasper, southern New South Wales, Australia. The dermal ornament, skull roof pattern, and general proportion and structure of the endocranium are typically actinopterygian and the specimen is tentatively assigned to the actinopterygian genus Ligulalepsis. Other features more closely resemble some other groups, such as sarcopterygians (widely-spaced orbital walls, and short, broad telencephalon cavity), acanthodians (position of hyomandibular facet), and placoderms (many similarities including position of foramina for oculomotor, profundus, and trigeminal nerves, pituitary vein, and ophthalmic and orbital arteries in and around the orbit). This specimen is the first early osteichthyan to demonstrate the presence of an eyestalk, previously known only in placoderms and chondrichthyans. The unusual mix of characters and presence of an eyestalk provide new insights into primitive osteichthyan anatomy.
Molecular evolution of phosphoeno/pyruvate carboxylase

Phosphoenolpyruvate carboxylase is an enzyme involved in a wide variety of important metabolic pathways of plants such as anaplerotic reactions and C4 and CAM photosynthetic pathways. The accumulation of molecular sequence data of phosphoenolpyruvate carboxylases has enabled us to investigate the function and molecular evolution of the enzymes by computer-assisted sequence comparison. Here we report the results of sequence comparison of phosphoenolpyruvate carboxylases: (1) Phosphoenofpyruvate carboxylases were classified into four groups; a subgroup of bacterial enzymes and three subgroups of plants enzymes. (2) The divergence time of the monocot enzymes involved in the C4 pathways was roughly estimated to be 150—300 million years. On the other hand, the phylogenetic tree of the enzymes suggested that those for the dicot enzymes involved in the C4 and CAM pathways might be close to the divergence time between the monocots and the dicots. (3) The evolutionary positions of the enzymes prevalent in roots or root nodules were identified. (4) Although sorghum and maize contained at least three genes for the enzymes in their genomes, the rates of amino acid substitution of the enzymes were different from gene to gene. The difference could not be explained by either lineage effects nor bias in base contents.
Performance studies of free-living tomato (Lycopersicon exculentum L.) rhizospheric Bacillus for their multiple plant growth promoting activity

The present investigation is based on the study of the diversity of Bacillus spp. isolated from tomato rhizosphere and their evaluation as plant growth promoter. A total of twenty eight rhizospheric gram positive rod-shaped bacteria (DPNSB-1 to DPNSB-28) were isolated on nutrient agar and confirmed as Bacillus spp. on the basis of phenotypic characterization. Carbon source utilization pattern based on BIOLOG and 16S rDNA-RFLP analysis of these isolates using three tetra cutter restriction enzymes (AluI, HaeIII and MspI) was employed for diversity studies. All the 28 strains deliberated with multiple plant growth promotion (PGP) attributes such as production of Indole acetic acid (IAA), siderophore, ammonia, HCN and phosphate solubilization. The diversity pattern followed amongst isolates was based on carbon utilization profiling, which revealed 9 distinct clusters ranging from 10 to 50%, whereas RFLP based resulted into pattern 5 determined distinct clusters with a range of 10 to 70%. However, all the isolates were endowed with variable range of PGP activities. Among them, DPNSB-2, DPNSB-11 and DPNSB-28 produced significant levels of IAA production 503.65, 687.94 and 845.28 µg mg -1 respectively. While 19 (67%) isolates were capable of solubilizing phosphate, 13 (46%) isolates produced siderophore, 21 (75%) isolates produced Ammonia and 20 (71%) were produced HCN. The positive isolates appeared attractive for exploring their plant growth- promoting activity and may be useful for control of Fusarium wilt in tomato field.
Importance of Microhabitats for Preservation of Species Diversity, on the Basis of Mesostigmatid Mites (Mesostigmata, Arachnida, Acari)

Mesostigmatid mites were studied in 50 microhabitats in a moderately humid pine-oak forest, markedly transformed by human activity, in the Rybnik Forest District (southern Poland). This study was aimed to show differences in species composition and abundance of mite communities in the studied microhabitats. In total, 1,936 mesostigmatid mites were collected of 65 species and 15 families. The most abundant and frequent species were Paragamasus vagabundus and Gamasellodes bicolor. The largest number of species (16-18) and the highest abundance of the mites (750-1,270 individuals/m 2 ) were found in dead wood (M15), leaf litter (M34), bark (M40), and an anthill (M62). In 30 microhabitats, only exclusive species were found, which significantly increased the mite species diversity in the forest floor.
Engineering a responsive, heterologous mevalonate pathway in Escherichia coli using microarrays

Isoprenoids are a highly diverse class of natural compounds that have received wide spread commercial use as flavors, fragrances, and pharmaceuticals. However, their supply is often limited due to their low abundance in their natural sources and difficult routes of chemical synthesis. To alleviate this limitation, the Keasling Lab has engineered Escherichia coli to produce large quantities of the ultimate precursors, the isoprenyl diphosphates, by introducing the mevalonate pathway from Saccharomyces cerevisiae . Coupled with engineered terpene synthases and tailoring enzymes from their native sources, we now have the ability to make these molecules from simple sugars in a controlled environment. The engineered heterologous pathway however bypassed the native regulation of E. coli 's isoprenoid pathway and the unregulated expression of the pathway resulted in growth inhibition due to the accumulation of the isoprenyl diphosphates. Microarray analysis of the inhibited cells identified the PhoPQ regulon as a concerted response to the toxicity. The PhoPQ regulon is E. coli 's regulatory two component system to respond to magnesium concentrations in the environment. Further analysis of the growth conditions revealed that the toxicity occurred when the magnesium and glucose concentrations in the media were low, validating the microarray results and leading to the hypothesis that the accumulation of the negatively charged diphosphate molecules disrupted the divalent cation's normal role in the cell. Enzyme assays with luciferase, which uses ATP and magnesium as cofactors, confirmed that farnesyl diphosphate was inhibitory at an enzyme level. Fluorescent sensors were designed using promoters of these genes upregulated and downregulated in response to farnesyl diphosphate accumulation. The sensors were tested for their dose dependent response to farnesyl diphoshpate accumulation and these promoters were then used to regulate the heterologous pathway. In the absence of other methods to regulate the pathway in response to the intermediates' accumulation, we have used standard inducible promoters that give a static output in response to an exogenous inducer and have no connection to the flux through the pathway. However, at industrial scale production the use of these exogenous inducers is not feasible. Using the responsive promoters return dynamic regulation to the pathway and obviates the need for an exogenous inducer. When the responsive promoters were cloned 5r of the isoprenyl diphsophates' downstream enzyme and the pathway was still regulated by the inducible promoters, production was less than the inducible promoter regulating the downstream enzyme. However, when the entire pathway was regulated by the responsive promoters, production doubled relative to the inducible pathway. In addition, the responsive pathway reduced acetate accumulation, allowed faster glucose consumption, and increased cell growth.
Canopy-microclimate effects on the antagonism between Trichoderma stromaticum and Moniliophthora perniciosa in shaded cacao

The collective impact of several environmental factors on the biocontrol activity of Trichoderma stromaticum (Ts )a gainst Moniliophthora perniciosa (Mp), the cause of cacao witches’ broom disease, was assessed under field conditions of shaded cacao (Theobroma cacao) in south-eastern Bahia, Brazil. Biocontrol experiments were performed adjacent to an automated weather station, with sensors and Ts-treated brooms placed at different canopy heights. Sporulation occurred at the same dates for all Ts isolates, but in different quantities. Broom moisture >30%, air temperature of approximately 23 ± 3� C, relative humidity >90%, solar radiation intensities <0AE12 KW m )2 and wind speed near zero were the key environmental parameters that preceded Ts sporulation events. A multiple logistic regression indicated that these weather variables combined were capable of distinguishing sporulation from non-sporulation events, with a significant effect of wind speed. Analyses of environmental factors at ground level indicated similar pre-sporulation conditions, with a soil moisture content above a threshold of 0AE34 m 3 m )3 preceding all sporulation events. The sporulation of five selected Ts isolates was compared at four different canopy heights. Isolates responded differently to weather variation in terms of sporulation and antagonism to Mp at different canopy levels, indicating that different microclimates are established along the vertical profile of a shaded cacao plantation. The potential of these findings for development of predictive mathematical models and disease-management approaches is discussed.
PARAMETRIZING SIMPLE MODEL BETWEEN YIELD AND EVAPOTRANSPIRATION FOR AMARANTHUS CRUENTUS UNDER DRIP AND SPRINKLER IRRIGATIONS

Amaranthus cruentus, an annual vegetable crop, is known to be highly productive under rain-fed conditions and during the dry season when supplied with water. However, for good water management, there is need to accurately quantify the water consumed by the crop. This paper investigates the water use and biomass yield of differentially irrigated Amaranthus cruentus at different developmental stages: emergence/vegetative, fruiting and maturity. Field experiments were conducted between January and March of 2005 and 2006. The experiment was a 2×3×3 combination of two irrigation methods (drip and sprinkler systems) three crop phenological stages (Emergence/vegetative, fruiting and maturity), and three water stress levels. A randomized complete block design (RCBD) was adopted. Soil moisture storages within the root zone depth (10-30 cm) of Amaranthus were highest (13.86 and 13.23 cm) on drip plots at the 71 day of year (DOY) during the 2005 and 2006 experiment respectively. This has direct influence on the evapotranspiration of the crop. The highest evapotranspiration were 12.87 and 9.96 mm day -1 during 2005 and 2006 respectively on plots irrigated under drip system. The highest and the lowest crop yield were 13.94 and 4.2 tonha -1 , respectively in plots irrigated under drip irrigation system, and 11.16 and 3.39 tonha 1 , respectively in plots irrigated under sprinkler system. The non-linear model used for yield prediction showed good agreement with the field data with r 2 = 0.94 and 0.74 for A. cruentus grown under drip and sprinkler irrigation systems, respectively. The correlation coefficient (r) between relative yield and relative evapotranspiration were 0.78 and 0.74 for crop under drip and sprinkler irrigation systems, respectively.
Genomic organization of microdissected Y-chromosomal lampbrush loop DNA sequences of Drosophila hydei

We mlcrodlssected а У chromosomal lampbrush loop pair from primary spermatocyte nuclei of Drosophila hydei and cloned the DNA di­ rectly at the microscale. Four of the 12 recombinant DNA clones recovered display In situ hybridization to mitotic metaphase У chromosomes, prefe­ rentially in the chromosomal region identified as the origin of the lampbrush loop pair. All clones, however, also hybridize to autosomal and X chromosomal loci In polytene chromosomes. У chromosomal DNA sequen­ ces of D. hydei again prove to be members of different families of repeated sequences distributed throughout the genome. These microcloning experi­ ments, which were carried out under very unfavourable experimental condi­ tions (low DNA content of the lampbrush loops in the presence of large amounts of RNA) prove that almost any chromosomal structure detected by light microscopy is directly accessible to molecular cloning experiments by micromethods.