Miracle-dz/UniFAR-FTUs huggingface dataset:
Evaluation of Kalmegh (Andrographis Paniculata) Germplasm for Higher Biochemical Constituents Production Under Agro-Climatic Conditions of Jharkhand

Keeping in view the importance of variability in biochemical constituents of Kalmegh germplasm, a systematic research trial was undertaken to assess its biochemical contents thus to screen out its most promising cultivar suited for the climatic and edaphic conditions of Jharkhand. 25 Kalmegh germplasm was collected across its natural growing zone and evaluated under uniform edapho-climatic conditions of Jharkhand. Plants of Kalmegh of all germplasm were harvested before flowering stage to evaluate its different biochemical constituents. At before flowering stage, germplasm like JHAP1 (2.39%), JHAP3 (2.21%), OAP1 (2.00%), CHAP1 (2.36%) and CHAP2 (2.03%) gave maximum andrographolide %. Maximum andrographolide yield was recorded for JHAP3 (35.33 kg/ha) followed by OAP1, OAP5, CHAP1 and MPAP4. Maximum neo-andrographolide % was recorded for JHAP3, (2.93%) followed by JHAP4, OAP1 and OAP2; however maximum neo-andrographolide yield was recorded for JHAP3 (46.78 kg/ha) followed by JHAP4, OAP1 and MPAP4. Maximum diterpenoid yield in Kalmegh plants was recorded for JHAP3 (82.11 kg/ha) and OAP1. So for maximum production of andrographolide, neo-andrographolide and diterpenoid yield from the plants of Kalmegh germplasm harvested before flowering stage; JHAP1, JHAP3, MPAP1, OAP1 and CHAP1 may be screened out as best germplasm under the climatic and edaphic conditions of Jharkhand.
Isolation and purification of wheat germ agglutinin and analysis of its properties

In this paper, the wheat germ agglutinin was isolated and purified by affinity chromatography of chicken ovomucoid as ligand. The physicochemical properties were analyzed. The chicken ovomucoid was isolated from egg white and conjugated to affinity chromatography column agarose gel to prepare affinity adsorbent. The crude extract of wheat germ was freezedried by affinity chromatography. The physicochemical properties were analyzed by SDSpolyacrylamide gel electrophoresis and isoelectric focusing electrophoresis. And the relative molecular mass and isoelectric point of wheat germ agglutinin were obtained, and the high efficiency of purification of wheat germ agglutinin was proved by affinity chromatography.
Changes in expression of neurotrophins and neurotrophic factors in the model of eosinophilic inflammation of the esophageal mucosa

Abstract Esophageal sensory and motor nerves contribute to the symptoms of eosinophilic esophagitis, however, the mechanisms of this neural dysfunction are essentially unknown. We addressed the hypothesis that eosinophilic inflammation in the esophagus alters production of the key regulators of neural function neurotrophins and neurotrophic factors. We developed and optimized the model of allergic eosinophilic inflammation of esophageal mucosa induced by localized administration of allergen ovalbumin into the esophagus in ovalbumin-sensitized guinea pigs. We evaluated changes in expression of nerve growth factor (NGF), brain-derived neurotrophic factor (BDNF), glial cell-derived neurotrophic factor (GDNF) and artemin in esophageal mucosa by quantitative RT-PCR. We found that the administration of ovalbumin into the esophageal wall of sensitized animals induced a massive eosinophilic infiltration restricted to esophageal mucosa (3 ± 1 vs. 97 ± 23 eosinophils per high power filed). This inflammatory response altered the expression profile of selected neurotrophic factors. The BDNF mRNA was increased (to 200%), artemin mRNA was decreased (to 50%) while NGF and GDNF was not changed. We conclude that a strong eosinophilic inflammation can be induced in guinea pigs and alters the expression of neurotrophins and neurotrophic factors. Our findings will aid mechanistic studies of neural dysfunction in eosinophilic esophagitis.
Pervasive chromatin remodeling at X-inactivation escape genes in schizophrenic males

Reanalyzing a large methylome dataset of 225 schizophrenic and 450 control samples derived from the prefrontal cortex revealed that 6 male patients have predominantly hypomethylated probes mostly on chromosome X, affecting the same genes in all six. Network analysis of the differentially methylated genes revealed a dense network of transcription factors, histone and chromatin remodeling proteins, with 15 of the X-located genes expressed at the synapse, including NLGN4X, SYN1 and MECP2. Mapping a recent experimental dataset of G-quadruplexes (G4s) onto the differentially methylated probes revealed that the probes in the group of six overlapping with G4s on chromosome X are significantly more hypomethylated than non-overlapping and non-X probes whereas in the rest of the patients G4-overlapping probes are more methylated than non-overlapping ones, revealing a distinct pathology, involving chromatin remodeling for the six patients. Unexpectedly, the hypomethylated genes in them significantly overlapped with gene locations where X-inactivation escapism was observed in women.
Studies on the mechanism of general anesthesia

Significance Anesthetics are used every day in thousands of hospitals to induce loss of consciousness, yet scientists and the doctors who administer these compounds lack a molecular understanding for their action. The chemical properties of anesthetics suggest that they could target the plasma membrane. Here the authors show anesthetics directly target a subset of plasma membrane lipids to activate an ion channel in a two-step mechanism. Applying the mechanism, the authors mutate a fruit fly to be less sensitive to anesthetics and convert a nonanesthetic-sensitive channel into a sensitive one. These findings suggest a membrane-mediated mechanism will be an important consideration for other proteins of which direct binding of anesthetic has yet to explain conserved sensitivity to chemically diverse anesthetics. Inhaled anesthetics are a chemically diverse collection of hydrophobic molecules that robustly activate TWIK-related K+ channels (TREK-1) and reversibly induce loss of consciousness. For 100 y, anesthetics were speculated to target cellular membranes, yet no plausible mechanism emerged to explain a membrane effect on ion channels. Here we show that inhaled anesthetics (chloroform and isoflurane) activate TREK-1 through disruption of phospholipase D2 (PLD2) localization to lipid rafts and subsequent production of signaling lipid phosphatidic acid (PA). Catalytically dead PLD2 robustly blocks anesthetic TREK-1 currents in whole-cell patch-clamp recordings. Localization of PLD2 renders the TRAAK channel sensitive, a channel that is otherwise anesthetic insensitive. General anesthetics, such as chloroform, isoflurane, diethyl ether, xenon, and propofol, disrupt lipid rafts and activate PLD2. In the whole brain of flies, anesthesia disrupts rafts and PLDnull flies resist anesthesia. Our results establish a membrane-mediated target of inhaled anesthesia and suggest PA helps set thresholds of anesthetic sensitivity in vivo.
Antioxidant Properties of Some Herbal Teas (Green tea, Senna, Corn Silk, Rosemary) Brewed at Different Temperatures

Some non-wood forest products are brewed and consumed as tea. Among the reasons for the consumption of herbal tea, digestive problems are located in the first row. Antioxidants help to human body for arranging digestive and immune system. Herbal tea is brewed in various ways such as boiling at different durations or waiting in hot water at different temperatures etc. Type of brewing can affect to bioactive properties of herbal tea. In this study, it was investigated the bioactive properties (total phenolic content, total flavonoid content, condensed tannin content and antioxidant properties) of some herbals brewed ( Green tea / Camellia sinensis. , senna / Cassia sp., corn silk / Zea mays , rosemary / Rosmarinus officinalis ) at different temperature. These herbs were brewed for 10 minutes at 60 o C, 80 o C and 100 o C temperatures. After cooling, total phenolic, flavonoid content, total condensed tannin content and antioxidant properties of these herbs were determined. Consistently, the highest results were found in the tea brewed at 100 o C. The highest total flavonoid (0.305 ± 0.005 mg QE/g) and ferric reducing ability (670.150 ± 2.121 µmol FeSO 4 7H 2 O/g ) was in Rosmarinus officinalis. The highest condensed tannin (9.443 ± 0.524 mg CE/g) and the highest total phenolic content (4.872 ± 0.005 mg GAE/g) was in Camellia sinensis and Cassia sp. , respectively.
Worrisome isolation: noninvasive genetic analyses shed light on the critical status of a remnant jaguar population

Many carnivore species, particularly felids, are sensitive to land use changes and may disappear from landscapes with reduced natural habitat and increased fragmentation. The jaguar (Panthera onca) is highly affected by these factors and is particularly endangered in the Atlantic Forest (AF) of South America, one of the most threatened biomes in the world. We used noninvasive fecal sampling and microsatellite markers to investigate the genetic diversity of jaguars in one of the last remnant populations of this species in the entire coastal AF. This section of the biome is highly fragmented. We observed low levels of genetic diversity (HO = 0.621, HE = 0.532, AR = 3.195), and estimated a small effective size for the population (Ne = 7.9 individuals). We performed comparative analyses incorporating data from previously surveyed populations located farther inland (interior AF), revealing that the coastal population studied shows significant genetic differentiation. Our results support a scenario of anthropogenic, drift-induced differentiation among jaguar populations in small AF fragments, affecting both the interior and coastal components of this biome. Despite its low diversity, we detected putatively unique alleles present in the coastal population, supporting its importance in the context of maintaining the remaining genetic variability of jaguars in the AF. Our results highlight the urgent need to implement coordinated conservation actions for jaguars in this highly impacted biome, including management interventions that foster the restoration of genetic connectivity among isolated remnant populations.
Plants with purple abaxial leaves: A repository of metrics from stomata distribution

Plants with purple abaxial leaf surfaces are very common in nature but the ecophysiological aspects of this phenotype are not well known. We have shown that the purple color of the abaxial surfaces generates an interesting contrast between the color of the stomata arranged on the epidermis, generally green, and the purple color of the pavement. This contrast makes the stomata completely visible to optic microscopy of the extant plants. This phenomenon made possible the proposition of a strategy to measure the distance between the stomata of the layer. The measurement of the distance between stomata generates accurate information of the distribution of stomata on the epidermis of living purple plants. In future ecophysiological inferences will be established from the information brought about by the measurements of the distance between stomata in purple plants.
Could Wading in Shallow Water Account for the Unique Shape of the Australopithecus afarensis Pelvis

A 3D Geometric Morphometric (GM) analysis of the shape of the pelvis and femur of various extinct hominids and extant humans and apes is described. Observed differences in shape are then discussed in the context of the wading hypothesis, a model of the evolution of hominin bipedalism that has rarely been seriously considered despite some compelling arguments in its favour. The general shape of the pelvis of Australopithecus afarensis is confirmed to be fundamentally different from both Homo and extant great apes, and not intermediate between them. Although it includes some human-like traits indicating a strong propensity to bipedalism, there are also sufficient differences to indicate that australopithecines probably exhibited a different type of bipedality to the relatively efficient striding gait associated with modern humans. An analysis of putative muscle lever arm ratios is described, which generated over 135,000 ratios in all. This data was then explored using the Pivot Table feature of Microsoft Excel. Succinct species summaries of broad lever arm groups, such as those pertaining to abduction compared to those pertaining to extension were generated. The results indicate that the australopithecine hip was more adapted, than modern humans or extant great apes, to adduction, abduction and rotation of the thigh during locomotion. It is argued that this apparent lateral biomechanical advantage complements the broad platypelloid shape as a putative adaptation to side-to-side wading. This adds further evidential weight to the wading hypothesis of bipedal origins in addition to the already compelling arguments from extant ape behaviour in shallow water and the favourable evidence of the paleohabitats of the earliest bipeds.
Seagrass Posidonia oceanica (L.) Delile as a marine biomarker: a metabolomic and toxicological analysis

A human-made environmental disaster due to the shipwrecked of Costa Concordia cruise vessel on the Tuscan Island of Giglio (Italy) coast and the possible pollutants release has been feared, so requiring the activation of removal operations and the monitoring of the marine environment. In the present study, the seagrass Posidonia oceanica (L.) Delile was used as a bioindicator for the impact of the Costa Concordia accident on the marine and coastal habitat. Different P. oceanica samples were collected in the shipwrecked site under different light conditions. Using high-performance thin-layer chromatography, metabolic analysis of the samples was carried out in order to highlight possible changes in the secondary metabolism due to the permanent shading and the presence of pollutant traces. Moreover, sample mutagenicity, as a consequence of the possible absorption of environmental toxicants leaked by the wreck, was assessed by the Ames test. The results highlighted the permanence of the Concordia-induced alter-ation in the plant secondary metabolites. However, absorption of chemical pollutants and carcinogens was not reported; this point was con ﬁ rmed by the lack of mutagenic effects found for the samples tested. Our results clearly evidence that the environmental impact of Costa Concordia wreck and removal operations on P. oceanica was mainly due to the lack of light in the marine habitat. Present methodological approach, which combines metabolomic and genetic ecotoxicological analysis, could represent a suitable strategy to evaluate the impact of human disasters on the ecosystem and to monitor the environmental changes.
Disturbance macroecology: integrating disturbance ecology and macroecology with different-age post-fire stands of a closed-cone pine forest

Macroecological studies have generally restricted their scope to relatively steady-state systems, and as a result, how biodiversity and abundance metrics are expected to scale in disturbance-dependent ecosystems is unknown. We examine macroecological patterns in a fire-dependent forest of Bishop pine (Pinus muricata). We target two different-aged stands in a stand-replacing fire regime, one a characteristically mature stand with a diverse understory, and one more recently disturbed by a stand-replacing fire (17 years prior to measurement). We compare the stands using macroecological metrics of species richness, abundance and spatial distributions that are predicted by the Maximum Entropy Theory of Ecology (METE), an information-entropy based theory that has proven highly successful in predicting macroecological metrics across a wide variety of systems and taxa. Ecological patterns in the mature stand more closely match METE predictions than do data from the recently disturbed stand. This suggests METE’s predictions are more robust in late-successional, slowly changing, or steady-state systems than those in rapid flux with respect to species composition, abundances, and organisms’ sizes. Our findings highlight the need for a macroecological theory that incorporates natural disturbance and other ecological perturbations into its predictive capabilities, because most natural systems are not in a steady state.
CIMMYT's Seeds of Discovery Initiative: Harnessing Biodiversity for Food Security and Sustainable Development

A visionary investment by Mexico's Secretariat of Agriculture, Livestock, Rural Development, Fisheries and Food (SAGARPA) has enabled the Seeds of Discovery (SeeD) initiative to assemble a platform of technologies to facilitate the effective use of genetic resources in breeding to address challenges of climate change and evolving consumer demands to ensuring universal food security. The platform consists of 1) high-density genotypic data and extensive phenotypic data characterizing maize and wheat germplasm bank accessions, 2) software tools to enable bioinformatics analyses of these and relevant germplasm bank data, and 3) maize and wheat lines incorporating novel diversity for priority traits from exotic germplasm into breeder-preferred, elite genetic backgrounds. Each of these platform components was co-developed with partners bringing unique expertise and resources to the project. Sustained impact, and equitable access to the platform and the maize and wheat genetic resources it describes, are pursued via multi-pronged capacity development and proactive intellectual property strategies described herein. After describing the SeeD initiative and some of its products, we conclude by sharing comments and insights from eminent scientists and partners who attended a special session on ‘Harnessing Biodiversity for Food Security and Sustainable Development’ during the 1st International Agrobiodiversity Congress (IAC), in New Delhi, November 2016.
Evolutionary genetics of CYP2J19 in red carotenoid pigmentation

The gene CYP2J19 has been described to be associated with ketocarotenoid pigmentation in two lineages of passerine birds. However, the extent to which CYP2J19 functions in carotenoid ketolation across the entire avian clade is unknown. From 70 avian genomes, I retrieved full length CYP2J19 of 43 species, representing all major avian clades, which is consistent with a conserved function of CYP2J19 in colour vision, and its co-option for red coloration. In addition, I analysed CYP2J19 sequences obtained from 13 species of weaverbirds (Ploceidae), which have variable red C4-ketocarotenoid coloration. I find that the locus has been positively selected throughout the radiation of the birds despite the conserved retinal function and pleiotropy via co-option for red coloration. Analysis on a further eight CYP loci across 25 matched species show that positive selection is common within members of this gene family. In addition, I did not detect a change in selection pressure on CYP2J19 following co-option for red coloration in the weaverbirds. The cause of positive selection on CYP2J19 is unclear, but it may be partly related to selection at the adjacent locus CYP2J40. Chapter 5 CYP2J19: Positive selection in the face of conservation and pleiotropy
Evaluation of Efficacy of Neem Oil, Castor Oil, Carbendazim, Trichoderma harzianum, Trichoderma viride and Pseudomonas fluorescens against Alternaria carthami

The efficacy of two botanicals viz . , Neem oil and castor oil, one fungicide i.e . , carbendazim and three bioagents viz . , Trichoderma harzianum, Trichoderma viride, Pseudomonas fluorescens were tested in vitro and in vivo against Alternaria carthami inciting leaf spot safflower leaf spot/blight. In vitro efficacy of botanicals and fungicide was evaluated by poison food technique against Alternaria carthami. In vitro efficacy of bioagents was evaluated by dual culture technique against Alternaria carthami. In in vitro evaluation of fungicide and botanicals carbendazim found to be most effective and showed maximum inhibition of mycelial growth (43.33%) followed by Neem oil (30.53%). Among the bioagents maximum inhibition of radial growth of the test pathogen was noticed in P. fluorescens (87.36%) which was found on par with T. virde (86.22%). Mycelial growth of test pathogen was inhibited to an extent of 81.08 per cent T. harzianum . In in-vivo evaluation, combined seed treatment with of P. fluorescens (10 g kg-1 seed) + carbendazim (2 g kg -1 seed)+ Neem oil (10 ml kg -1 seed) was effective in controlling Alternaria leaf spot/blight.
Antiviral Activity of Dicrocephala Integrifolia (Kuntze) Against Herpes Simplex Type-1 Virus: An in vitro Study

Introduction: At present, acyclovir is commercially available as the drug of choice for managing herpes simplex type I (HSV-1) viral infection. However, the high prevalence of the infection coupled with the emergence of resistant viral strains has limited its effectiveness. Thus, the development of novel antiviral agents is crucial. Practitioners of herbal medicine in Kenya make use of Dicrocephala integrifolia (DI) for the management of several diseases including viral infections. However, information on the efficacy of this plant against HSV-1 viral infection is not available. The aim of the present study was to determine the in vitro antiviral activity of crude extracts of DI against HSV-1. Methods: Leaves, roots, flowers and stems of DI were extracted using water (W) and methanol (ME) and qualitatively screened to identify the phytoconstituents present. Furthermore, the anti HSV-1 activity of the obtained extracts was evaluated on Vero cell lines using the 3-[4, 5 dimethylthiazol-2-yl]-2, 5-diphenyltetrazolium bromide] assay. The 50% cytotoxic concentration (CC50) and 50% effective concentration (EC50) of each extract was determined using regression analysis. The effects of crude DI extracts on adsorption and post-adsorption stages of the HSV-1 replication cycle was evaluated against acyclovir using a cytopathogenic inhibition assay. Results: Alkaloids, glycosides, flavonoids, phenols, saponins, tannins and terpenoids were found to be present in the extracts. The CC50 values of the aqueous DI extracts was in the range 71.31 ± 2.65 to >100 μg/ml compared to >100 μg/ml of acyclovir. The EC50 values of crude extracts of DI on the pre-adsorptive phase of HSV-1 activity was in the range 54.45±3.45 to >100μg/ml compared to 4.772±7. 81μg/ml of acyclovir whilst the EC50 value of the crude extracts of DI on the post-adsorptive phase of HSV-1 activity was in the range 45.270±4.31 to >100μg/ml compared to >100μg/ml of acyclovir. Conclusion: The results suggest that crude extracts of DI may be a reservoir of phytochemicals with potentially good efficacy against HSV-1.
Étude de la réparation par excision de nucléotides dans le locus des ADN ribosomaux chez la levure Saccharomyces cerevisiae

A strategy amenable to the genome-wide study of DNA damage and repair kinetics is described. The ultraviolet damage endonuclease (UVDE) generates 3’-OH ends at the two major UV induced DNA lesions, cyclobutane pyrimidine dimers (CPDs) and 6,4 pyrimidinepyrimidone dimers (6,4 PPs), allowing for their capture after biotin end-labeling. qPCR amplification of biotinylated DNA enables parallel measuring of DNA damage in a several loci, which can then be combined with high-throughput screening of cell survival to test genotoxic reagents. Alternatively, a library of captured sequences could be generated for a genome wide study of damage sites and large-scale assessment of repair kinetics in different regions of the genome, using next-generation sequencing. The assay is suitable to study any DNA lesion that can be converted into 3’-OH by UVDE, or other enzymes. Toward these goals, we compared UVDE with the classical T4 endonuclease V (T4V) assay. We showed that there is a linear correlation between UV dose, 3’-OH formation and capture by immunoprecipitation, together with its potential application for in vivo studies.