Miracle-dz/UniFAR-FTUs huggingface dataset:
Bifidobacterium Is Enriched in Gut Microbiome of Kashmiri Women with Polycystic Ovary Syndrome

Polycystic ovary syndrome (PCOS) is a common endocrine condition in women of reproductive age understudied in non-European populations. In India, PCOS affects the life of up to 19.4 million women of age 14-25 years. Gut microbiome composition might contribute to PCOS susceptibility. We profiled the microbiome in DNA isolated from faecal samples by 16S rRNA sequencing in 19/20 women with/without PCOS from Kashmir, India. We assigned genera to sequenced species with an average 121k reads depth and included bacteria detected in at least 1/3 of the subjects or with average relative abundance ≥0.1%. We compared the relative abundances of 40/58 operational taxonomic units in family/genus level between cases and controls, and in relation to 33 hormonal and metabolic factors, by multivariate analyses adjusted for confounders, and corrected for multiple testing. Seven genera were significantly enriched in PCOS cases: Sarcina, Alkalibacterium and Megasphaera, and previously reported for PCOS Bifidobacterium, Collinsella, Paraprevotella and Lactobacillus. We identified significantly increased relative abundance of Bifidobacteriaceae (median 6.07% vs. 2.77%) and Aerococcaceae (0.03% vs. 0.004%), whereas we detected lower relative abundance Peptococcaceae (0.16% vs. 0.25%) in PCOS cases. For the first time, we identified a significant direct association between butyrate producing Eubacterium and follicle-stimulating hormone levels. We observed increased relative abundance of Collinsella and Paraprevotella with higher fasting blood glucose levels, and Paraprevotella and Alkalibacterium with larger hip and waist circumference, and weight. We show a relationship between gut microbiome composition and PCOS linking it to specific reproductive health metabolic and hormonal predictors in Indian women.
PHYSICOCHEMICAL AND MICROBIOLOGICAL PROPRIETIES OF SOME MEAT PRODUCTS IN SHARKIA GOVERNORATE, EGYPT

Meat and meat products differ in their physical and chemical properties dependingon the characteristic of meat cuts, the additional material and the method of manufacture. The presentinvestigation was planned to evaluate the physical and chemical quality for some types of local meatproducts, such as beef burger and luncheon, collected from local markets in Zagazig city, SharkiaGovernorate, Egypt. Microbiological and physicochemical proprieties of nine meat products (3samples of beef burger of Americana, Halwani and Fragello, 3 samples of beef luncheon ofAmericana, Halwani and Fragello and 3 samples of chicken luncheon of Americana, Halwani andFragello) were carried out. The obtained results declared that samples of beef burger produced byFragello contained the lowest parameter of total protein (14.7%), while samples of beef burgerproduced by Americana showed the highest values (16.90%). Beef and chicken luncheon produced byFragello contained the highest values of total protein (16.0% and 15.05%) respectively. Also, samplesof beef burger and beef, chicken luncheon produced by Fragello contained the highest values of totalfat. Regarding the microbiological evaluation, results showed that the lowest content of total bacteriacount was observed in different meat products such as luncheon Halwani, coliform group andstaphylococci were not detected in all products. Also, beef burger, beef and chicken luncheon samplesof Halawani had high values of yellowness (b), and redness (a). However, the microbiologicalevaluation indicated that Halwani products were the best.
Inhibitory Effect of Certain Chemical Food Preservatives against Cercospora Leaf Spot Disease of Sugar Beet

The antifungal activity of citric acid and its salt (sodium citrate) as chemical food preservatives was evaluated against Cercospora beticola in vitro and in vivo. The inhibitory effect of both compounds was studied against mycelial growth of the pathogen in vitro at concentrations, i.e. 0, 10, 20, 30, 40 and 50 mM. Both of citric acid and sodium citrate were able to inhibit the mycelial growth of the pathogen when they were added to the medium at the tested concentrations. Citric acid at 50 mM had the highest effect on the inhibition growth of the pathogen being 83.70% and also had antifungal activity. The percentage of inhibition growth increased as the tested compounds concentration increased. Data also indicate that microscopic examination of treated plates with citrate shows that this treatment reduced the numbers of C. beticola spores on the medium at all tested concentrations and reached its maximum reducing at concentration 50 mM of citric acid compared to untreated plates. The results revealed that spraying of diseased plants with citric acid and sodium citrate either alone or in combination at concentration 50 mM was effective in decreasing disease severity of Cercospora leaf spot compared to untreated plants. The highest reduction in disease severity was observed in case of citric acid treatment. The results revealed that foliar application of these compounds enhanced significantly root yield and sugar percentage as compared to the control.
NEK7 Regulates NLRP3 Inflammasome Activation and Neuroinflammation Post-traumatic Brain Injury

As one of the most common causes of mortality and disability, traumatic brain injury (TBI) is a huge psychological and economic burden to patients, families, and societies worldwide. Neuroinflammation reduction may be a favorable option to alleviate secondary brain injuries and ameliorate the outcome of TBI. The nucleotide-binding oligomerization domain, leucine-rich repeat and pyrin domain-containing 3 (NLRP3) inflammasome, has been shown to be involved in TBI. NIMA-related kinase 7 (NEK7) has been verified as an essential mediator of NLRP3 inflammasome activation that is recruited upstream of the formation of inflammasomes in response to NLRP3 activators. However, the underlying mechanism by which NEK7 operates post-TBI remains undefined. In this study, we performed both in vivo and in vitro experiments. Using an in vivo mouse TBI model, mice were administered an intracerebroventricular injection of NEK7-shRNA virus. For the in vitro analysis, primary cortical neurons with NEK7-shRNA were stimulated with lipopolysaccharide (LPS)/ATP or potassium (K+). We evaluated the effects of NEK7 knock-down on neurological deficits, NLRP3 inflammasomes, caspase-1 activation, and neuronal injury. During the 0–168 h post-TBI period in vivo, NEK7 and NLRP3 inflammasome activation increased in what appeared to be a time-dependent manner. As well as pyroptosis-related markers, caspase-1 activation (p20) and interleukin-1β (IL-1β) activation (p17) were up-regulated. NEK7 down-regulation attenuated neurological deficits, NLRP3 inflammasomes, caspase-1 activation, and neuronal injury. The same phenomena were observed during the in vitro experiments. Furthermore, NEK7 knock-down suppressed NLRP3 inflammasome activation and pyroptosis, which were triggered by K+ efflux, and the LPS + ATP-triggered NEK7–NLRP3 complex was reversed in primary cortical neurons placed in 50 mM K+ medium. Collectively, the data demonstrated that NEK7, as a modulator, regulates NLRP3 inflammasomes and downstream neuroinflammation in response to K+ efflux, through NEK7–NLRP3 assembly, pro-caspase-1 recruitment, caspase-1 activation, and pyroptosis in nerve injuries, post-TBI. NEK7 may be a potential therapeutic target for attenuating neuroinflammation and nerve injury post-TBI.
Antimicrobial activity and toxicity of Eucalyptus globulus Labill. essential oil against vaginal microorganisms

The antimicrobial potential of commercial essential oil (EO) of Eucalyptus globulus L. was evaluated against six bacterial vaginal isolates (E. coli 1 and E. coli 2, S. aureus 1 and S. aureus 2, P. aeruginosa and P. mirabilis) and two isolates of Candida strains (C. albicans 1 and C. albicans 2). The antimicrobial activity was assessed through double-dilution micro-plate assay to determine the minimum inhibitory (MIC) and minimum bactericidal/fungicidal (МВС/ MFC) concentration. In addition, brine shrimp toxicity assay was performed in order to determine acute toxicity of the examined EO. The isolated strains of pathogens have shown strain specificity to the tested EO. Certain pathogens resistance was noticed toward the tested antibiotic, as well. E. coli isolates showed resistance to the tested antibiotics but did not show resistance against the Eucalyptus EO (E. coli 1 MIC/MBC 12.5/12.5 μL/mL; E. coli 2 MIC/ MBC 25/25 μL/mL). Moreover, the Eucalyptus EO showed effectiveness in application against S. aureus 2 (MIC/MBC 6.25/6.25 μL/mL), and C. albicans 1 strains (MIC/MFC 6.25/6.25 μL/mL). Furthermore, brine shrimp lethality bioassay revealed the Eucalyptus oil toxicity at an LC50 value of 2.66 mg/mL. The chemical composition of the separated essential oil was analyzed by gas chromatography combined with mass spectrometry (GC-MS) showing eucalyptol (59.63%), p-cymene (15.55%) and DL-limonene (14.90%) as dominant constituents. Although a number of toxicology trials are needed, these results provide scientific support to examination of Eucalyptus EO as an antimicrobial agent in alternative treatment of multiresistant human pathogens of vaginal origin.
Efficacy of newer insecticides against Leucinodes orbonalis (Guen.) on brinjal

The present work entitled, “efficacy of newer insecticides against Leucinodes orbonalis (Guen.) on brinjal” were planned to study the efficacy of newer molecules for the management of brinjal shoot and fruit borer on Phule Harit cultivar of brinjal and yield performance by using insecticides. The experiment was conducted in kharif season of 2017-18 on the Insectary field of Department of Entomology, College of agriculture, Nagpur. The experiment was laid out in Randomized Block Design (RBD) with eight treatments including control (water spray) replicated thrice. All the treatments were found significantly superior over (T8) control plot. The treatment (T1) chlorantraniliprole 18.5 SC @ 0.3 ml/lit was found most promising in reducing the BSFB incidence on which recording observations on 3rd, 7th, 10th and 14th DAS to the tune of 8.16, 8.31, 9.27 and 9.83 per cent lowest shoot damage with 71.01, 72.18, 66.16 and 63.01 per cent reduction in infestation over control respectively. The second best treatment was (T3) emamectin benzoate 5 SG @ 0.4 gm/lit which showed effective to curb menace of BSFB and registered shoot infestation on 3rd, 7th 10th and 14 DAS to the tune of 11.27, 12.10, 12.27 and 13.65 per cent with 59.96, 59.50, 55.20 and 48.65 per cent reduction over control.
Effect of Some Antioxidants and Nutrients on Growth of Carnation Plants (Dianthus caryophyllus. L) Cv.''Giant Pink'' under High Temperature Stress

An experiment was conducted to compare the ability of some antioxidants namely salicylic and ascorbic acids at 0.010. 02g/l for each and nutrients namely boric, calcium, magnesium at 0.05-0.10g/l for each and potassium as a foliar spray at 0.71. 4 g/l to decrease high temperature stress and to improve flower productivity of carnation plants. Calcium nitrite at 0.05 g/l was more effective than most of the other treatment for increasing plant height, leaf and flower numbers, fresh and dry weight of plants, pigments content of leaves and chemical composition. Calcium nitrate at 0.05 g/l as three foliar sprays at fifteen days intervals reduced the high temperature stress and improved number and quality of flowers of carnation plants.
Genome-wide development of miRNA-based SSR markers in Cleistogenes songorica with their transferability analysis to gramineae and non- gramineae species

SSR markers are commonly used for many genetic applications, such as map construction, fingerprinting and genetic diversity analysis due to their high reproducibility, levels of polymorphism and abundance. As endogenous, small RNAs, miRNAs have essential roles in plant development and gene expression under diverse stress conditions, including various biotic and abiotic stress conditions. In the present study, we predicted 110 pre-miRNAs sequences from 287 precursor miRNAs and used them as queries for SSR marker development. Among 110 primer pairs, 85 were successfully amplified and examined for transferability to other gramineae and non-gramineae species. The results showed that all 82 primer pairs yielded unambiguous and strong amplification, and across the 23 studied Cleistogenes accessions, a total of 385 alleles were polymorphic. The number of alleles produced per primer varied from 3 to 11, with an average of 4.69 per locus. The expected heterozygosity (He) ranged from 0.44 to 0.88, with an average of 0.74 per locus, and the PIC (Polymorphism Information Content) values ranged from 0.34 to 0.87, with an average of 0.69 per locus. In this study, 1422 miRNA target genes were predicted and analyzed using the GO (Gene Ontology) and KEGG (Kyoto Encyclopedia of Genes and Genomes) databases. The results showed that this miRNA-based microsatellite marker system can be very useful for genetic diversity and marker-assisted breeding studies.
Do parasitoids reduce cereal losses? Estimating the impact of parasitoids on stem borer pest infestation and maize yield

Chilo partellus (spotted stem borer) is an economically important stem borer pest in Eastern Africa causing high yield losses in maize and sorghum. The larval endoparasitoid, Cotesia flavipes (parasitic wasp) was released in Kenya to manage C. partellus and post release studies showed it had established and stem borer parasitism was steadily increasing. Despite the rise in parasitism, doubts on whether parasitoids can effectively reduce stem borer populations have been raised.Objective: This study was carried out to estimate the impact of C. flavipes on stem borer infestation and the resultant effect on maize yield in Kenya. Methodology and results: Using insecticidal check method, selective insecticides were used to exclude stem borer pests and natural enemies in Treatments A and B respectively with controls designated as Treatment C. Results revealed significant differences in stem borer infestation (F2,9=5.835; p<0.05) and parasitism (F2,9 =91.97; p<0.0001) among the three treatments. Significantly higher infestation was recorded in treatment B (2.0±0.2%) compared to A (0.5±0.3%) and C (1.5±0.4%). Parasitism was significantly higher in treatment C (23.5±6.8%) compared to A (0.0±0.0%) and B (0.3±0.1%). However, there was no significant difference in yield among treatments showing that parasitoid action did not translate into changes in yield. Conclusions and application of findings: The parasitoid C. flavipes has made an important contribution towards suppressing stem borer population. This was shown by high infestation recorded in treatment B which was as a result of partial elimination of parasitoids. This deduction was further supported by the results which showed that pest exclusion using chemicals did not have a significant difference from parasitoid action as shown by insignificant difference in infestation between treatment A and C fields. Percentage infestation and parasitism results obtained from this study thus provide quantitative data on the impact of C. flavipes. Release of C. flavipes can therefore be done in other areas both within and beyond the country’s borders where C. partellus is still a problem. However, since reduced infestation and increased parasitism did not translate into yield increase, more suppressive effect may be achieved if the pest’s multiple developmental stages are targeted, most especially before it reaches the destructive larval stage. There is need to carry out further research on C. partellus’ egg parasitoids. Optimum yield may then be realized.Key words: Classical biological control; Chilo partellus ; Cotesia flavipes; parasitism; insecticidal check technique; Kenya
Vps4 triggers sequential subunit exchange in ESCRT-III polymers that drives membrane constriction and fission

ESCRT-III is a ubiquitous complex which catalyzes membrane fission from within membrane necks via an as yet unknown mechanism. Here, we reconstituted in vitro the ESCRT-III complex onto membranes. We show that based on variable affinities between ESCRT-III proteins and the ATPase Vps4, subunits are recruited to the membrane in a Vps4-driven sequence that starts with Snf7 and ends with Did2 and Ist1 which, together, form a fission-active subcomplex. Sequential recruitment of ESCRT-III subunits is coupled to membrane remodeling. Binding of Did2 promoted the formation of membrane protrusions which later constricted and underwent fission mediated by the recruitment of Ist1. Overall, our results provide a mechanism to explain how a sequence of ESCRT-III subunits drives membrane deformation and fission.
Fine‐scale hierarchical genetic structure and kinship analysis of the ascidian Pyura chilensis in the southeastern Pacific

Abstract Studying population structure and genetic diversity at fine spatial scales is key for a better understanding of demographic processes that influence population connectivity. This is particularly important in marine benthic organisms that rely on larval dispersal to maintain connectivity among populations. Here, we report the results of a genetic survey of the ascidian Pyura chilensis from three localities along the southeastern Pacific. This study follows up on a previous report that described a genetic break in this region among localities only 20 km apart. By implementing a hierarchical sampling design at four spatial levels and using ten polymorphic microsatellite markers, we test whether differences in fine‐scale population structure explain the previously reported genetic break. We compared genetic spatial autocorrelations, as well as kinship and relatedness distributions within and among localities adjacent to the genetic break. We found no evidence of significant autocorrelation at the scale up to 50 m despite the low dispersal potential of P. chilensis that has been reported in the literature. We also found that the proportion of related individuals in close proximity (<1 km) was higher than the proportion of related individuals further apart. These results were consistent in the three localities. Our results suggest that the spatial distribution of related individuals can be nonrandom at small spatial scales and suggests that dispersal might be occasionally limited in this species or that larval cohorts can disperse in the plankton as clustered groups. Overall, this study sheds light on new aspects of the life of this ascidian as well as confirms the presence of a genetic break at 39°S latitude. Also, our data indicate there is not enough evidence to confirm that this genetic break can be explained by differences in fine‐scale genetic patterns among localities.
Genome-wide identification, phylogenetic and biochemical analysis of the APYRASE family members, and gene expression analysis in response to the abiotic and biotic stresses in bread wheat (Triticum aestivum)

APYRASEs, which directly regulated the intra- and extra-cellular ATP homeostasis, plays a pivotal role in the regulation of the adaptations to various stresses in mammals, bacteria and plants. In the present study, we identified and characterized the wheat APYRASE family members at the genomic level. The results showed that a total of eight APY homologs with conserved ACR domains were identified. The wheat APYs were further analyzed bioinformatically of their sequence alignment, phylogenetic relations and conserved motifs. Although they share highly conserved secondary structure and tertiary structure, the wheat APYs could be mainly categorized into three groups, according to the phylogenetic and structural analysis. Further, these APYs exhibited similar expression patterns in the root and shoot, among which TaAPY3-1 and TaAPY3-3 had the highest expression level. The time-course expression patterns of the eight APYs in the wheat seedlings in response to the biotic stress and abiotic stress were also investigated. TaAPY3-2, TaAPY3-3, and TaAPY6 exhibited strong sensitivity to all kinds of stresses in the leaves. Some APYs showed specific expression responses, such as TaAPY6 to the heavy metal stress, and TaAPY7 to the heat and salt stress. These results suggested that the stress-inducible APYs could have potential roles in the regulation of the adaptation to the environmental stresses. Moreover, the catalytic activity of TaAPY3-1 was further analyzed in the in vitro system. The results showed that TaAPY3-1 protein exhibited high catalytic activity in degradation of ATP and ADP, but not GTP, CTP and TTP. It also has an extensive range of temperature adaptability, but rather preferred relative acid pH conditions. In this study, the genome-wide identification and characterization of the APYs in wheat could be useful for further genetic modifications to generate high-stress tolerant wheat cultivars.
Indarctos and other Caniformia fossils of G.E. Lewis’ YPM collection from the Siwaliks

ABSTRACT Material of Indarctos and other Caniformia fossils from the Yale Peabody Museum G.E. Lewis Siwalik expedition collections from Pakistan and northern India are described herein. The M2 of a newly described cranium of Indarctos from the Dhok Pathan Zone is extremely similar to the holotype of Indarctos salmontanus, and both materials are similar to European I. atticus, thus both the holotype of I. ‘salmontanus’ and the new material from the Siwaliks can be assigned to I. atticus. ‘Indarctos’ punjabiensis from the Dhok Pathan Zone is markedly different from I. atticus and other known species of Indarctos in having a much shorter M2 talon and probably represents another genus. A hemicyonid from the Chinji Zone is reported in the Siwaliks for the first time. Plesiogulo from the Dhok Pathan Zone is identified as Plesiogulo aff. crassa, differing slightly from Chinese Plesiogulo crassa, P. brachygnathus and all North American species. The earliest member of the small clawed otter lineage, Amblonyx barryi sp. nov., from the Tatrot Zone in the Siwaliks already shows several mandibular and dentition traits characteristic of the genus. An amphicyonid (aff. Magericyon sp.), a gulonine mustelid (aff. Iberictis sp.), and the lutrine mustelid Sivaonyx gandakasensis are also reported.
Major plants foraged by bees for honey production in Ghana: mapping of bee floral sources for the development of the apicultural industry

Abstract Honey is increasingly being used as a food supplement and to treat various diseases and disorders in Ghana. Information on floral nectar preferences of foraging honeybees is, therefore, imperative to increase production to keep pace with demand. However, in Ghana, these floral nectar preferences are yet to be investigated and identified. This study was conducted to determine bee forage sources in the three main agro-ecological honey-producing zones of Ghana. Forty-eight unblended honey samples sourced from beekeepers were analysed. Pollen spectra of the honey samples revealed 27 different pollen types of which eight were identified to family level, while 15 and four were at the level of genus and species, respectively. The results also showed that, in general, 48% of the analysed samples were unifloral honeys with the most important pollen types coming from Sapotaceae/Meliaceae, Anacardiaceae and Burkea africana. Combretaceae, Sapotaceae/Meliaceae and Anacardiaceae, as well as Lannea-type and Burkea africana were found to be the most frequent (with occurrence greater than 50%) sources of nectar utilised by bees to produce honey. The predominant pollen sources of the honeys in the three main apicultural zones of the country were Sapotaceae/Meliaceae and Anacardiaceae (Forest zone), Sapotaceae/Meliaceae and Lannea-type (Savannah–Forest transition zone) and Sapotaceae/Meliaceae, Anacardiaceae and Gynandropsis gynandra (Savannah zones). Identification of the major bee floral sources can be used as a guide by beekeepers in the location of their apiaries as well as reforesting disturbed sites with these plants to act as sources of bee forage.