Miracle-dz/UniFAR-FTUs huggingface dataset:
Mutations in rpoB gene and their association with Rifampicin resistance levels in clinical isolates of Mycobacterium tuberculosis

Present study was aimed to identify most frequent mutations in rpoB gene region and to evaluate the association between mutations in rpoB gene and resistance levels to Rifampicin in clinical isolates of Mycobacterium tuberculosis of different geographical regions of India. A total of 100 clinical isolates of Mycobacterium tuberculosis were included in this study. Drug susceptibility testing against first line anti-tuberculosis drugs was performed on LJ medium by conventional minimal inhibitory concentration (MIC) method and the mutation(s) in rpoB gene of M. tuberculosis isolates were analyzed by sequencing method. Of the 100 M. tuberculosis isolates, 31 (31.0%) and 18 (18.0%) were found resistant and susceptible for all four first-line anti-TB drugs. The genetic mutations were observed in 96% (72/75) rifampicin resistant M. tuberculosis isolates, while 4% (3/75) of rifampicin resistant isolates did not have any mutation in rpoB gene. The mutation TCG531TTG (Ser531Leu) was found as most common and frequent mutation in 69.3% (52/75) of rifampicin resistant isolates of M. tuberculosis with MIC level (≥ 512mg/l). The mutation at codon 511 was associated with low degree (128mg/l) of rifampicin resistance, deletions at codons 514-516 or substitution at codon 516 were found to be associated with moderate degree (256mg/l) of rifampicin resistance and mutations at codon 526, 531 were associated with the high degree (512mg/l) of rifampicin resistance in M. tuberculosis isolates of Indian origin. The findings of this study will be useful for the development of raid and more specific indigenous molecular tools for the early diagnosis of MDR-TB in the country.
Rice straw biochar affects water retention and air movement in a sand-textured tropical soil

ABSTRACT Despite the current global attention on biochar (BC) as a soil amendment, knowledge is limited on how BC impacts the physical properties of coarse-textured soils (sand > 95%), particularly in tropical regions. A two-season field-study was conducted to investigate the effect of rice straw BC (3% w/w) on water retention, gas transport and structure of a sand-textured tropical soil. We sampled 3 months and 15 months after BC application and measured wet- and dry-region soil water retention, air permeability and gas diffusivity at selected matric potentials. At all measured potentials and for both sampling times, soil water retention was significantly higher (20–150%) for the BC treatment due to increased fraction of smaller pores (< 30 µm) at the expense of macropores (< 100 µm). Although there was no consistent effect of BC on air-filled porosity, BC significantly reduced air permeability and gas diffusivity (~20%) at −30 kPa matric potential. After 15-months, air permeability decreased by ~15% after BC amendment, but analyses of the pore structure revealed a more tortuous and complex soil structure. Thus, application of rice straw BC to similar coarse-textured soils will improve soil-water relations and over time provide better structure for agricultural purposes.
Status of scientific knowledge, recovery progress, and future research directions for the Gulf Sturgeon, Acipenser oxyrinchus desotoi Vladykov, 1955

Summary The Gulf Sturgeon, Acipenser oxyrinchus desotoi, is an anadromous species of Acipenseridae and native to North America. It currently inhabits and spawns in the upper reaches of seven natal rivers along the northern coast of the Gulf of Mexico from the Suwannee River, Florida, to the Pearl River, Louisiana, during spring to autumn. Next to the Alligator Gar (Atractosteus spatula), the Gulf Sturgeon is currently the largest fish species occurring in U.S. Gulf Coast rivers, attaining a length of 2.35 m and weights exceeding 135 kg, but historically attained a substantially larger size. Historically, the spawning populations existed in additional rivers from which the species has been wholly or nearly extirpated, such as the Mobile and Ochlockonee rivers, and possibly the Rio Grande River. Most Gulf Sturgeon populations were decimated by unrestricted commercial fishing between 1895–1910. Subsequently most populations remained unrecovered or extirpated due to continued harvest until the 1970s–1980s, and the construction of dams blocking access to ancestral upriver spawning grounds. Late 20th Century harvest bans and net bans enacted by the several Gulf Coast states have stabilized several populations and enabled the Suwannee River population to rebound substantially and naturally. Hatchery supplementation has not been necessary in this regard to date. Sturgeon are resilient and adaptable fishes with a geological history of 150 million years. Research undertaken since the 1970s has addressed many aspects of Gulf Sturgeon life history, reproduction, migration, population biology, habitat requirements, and other aspects of species biology. However, many knowledge gaps remain, prominently including the life history of early developmental stages in the first year of life. Natural population recovery is evident for the Suwannee River population, but seems promising as well for at least four other populations. The Pascagoula and Pearl River populations face a challenging future due a combination of natural and anthropogenic factors. These two populations, and perhaps the Escambia River population, are particularly vulnerable to periodic mass mortality due to major stochastic events including hurricanes, flooding, hypoxia, and toxic spills. The present manuscript provides a comprehensive synthesis of knowledge regarding the Gulf Sturgeon at the organismal and population levels, identifying knowledge gaps as priorities for future research. Topics not treated in the present synthesis include morphology, internal biology, physiology, and endocrinology. Topics only briefly treated include parasites and diseases, contaminants, and sturgeon aquaculture.
Role of Fat Soluble Vitamins in the Development of Neural Pathways Regulating Feeding Behaviour in Male Wistar Rat Offspring

High multivitamin (10-fold AIN-93G levels, HV) intake by Wistar rats during pregnancy results in increased male offspring’s body weight and food intake and characteristics of the metabolic syndrome. The hypothesis of this research is that fat soluble vitamins, primarily due to vitamin A, are partially responsible for this effect through modification of development of brain pathways regulating food intake and reward in utero and post-weaning. Three studies were conducted. In study 1, dams were fed AIN-93G diets containing the recommended vitamins (RV) or RV with 10-fold fat soluble vitamins (HFS). In study 2, the dams were fed RV, RV with 10-fold vitamin A (HA) or HV diet with only the recommended vitamin A diets. Male offspring were weaned to a high fat diet for 14 weeks. In study 3, dams were fed the HV diet, while their male offspring were weaned to RV, HV or HA diets for 29 weeks. Study 1 showed that the HFS diet does not reproduce the effects of the HV gestational diet on body weight or food intake of the offspring, but affected development of their higher hedonic regulatory pathways associated with food preference. In study 2, HA intake alone in gestational diets had long-lasting programming effects on the dopaminergic system and decreased sucrose preference but not food intake in the offspring. In study 3, HA in the post-weaning diet reduced the effect of the HV dam’s diet on the offspring and modified gene expression in food intake and reward pathways. In conclusion, fat soluble vitamins, explain little of the effect of the HV diet consumed during gestation on the male offspring phenotype, but primarily, due to vitamin A, are important modulators of brain pathways regulating reward both in utero and post-weaning.
Deceptive ecological status of urban streams and rivers-evidence from diatom indices

Urbanization directly affects the ecological status of streams and rivers: Their beds and drainage basins are often heavily transformed and their habitat conditions disturbed. The aim of the study was to evaluate the extent of human impact in streams in the city of Łodź, Central Poland (~700,000 inhabitants), by pattern recognition analysis of benthic diatom assemblage samples using a Kohonen artificial neural network, principal component analysis, and indicator species analysis. The study also determined the ecological status of the streams using five diatom indices: Multimetric Diatom Index, Specific Pollution Sensitivity Index, Generic Diatom Index, Biological Diatom Index, and Trophic Diatom Index. The samples demonstrated considerable variation in ecological status. Examples of poor and bad ecological status were observed, clearly resulting from strong human pressure; however, good status and moderate status were also recorded, both at natural sites and, unexpectedly, those which were severely transformed, whose beds were covered with concrete and which were located downstream from combined sewer overflows. Such sites demonstrated high water conductivity of up to 1440 μS/cm, but this was accompanied by other more favorable conditions: The water flowed from upstream stretches enclosed in downtown underground canals with a fast current, low water temperature, and high average concentration of dissolved oxygen (approximately 10 mg/dm³). These conditions had a mitigating effect, shaping the diatom assemblages to a specific form with the highest species richness and the highest number of indicator taxa observed in the study. In summary, the hydromorphological transformation of streambeds may result in seemingly good ecological status at heavily degraded sites. Therefore, conclusions based on diatom‐based biomonitoring of urban streams and rivers should be drawn with caution.
Effects of dietary copper nanoparticles and vitamin C supplementations on growth performance, immune response and stress resistance of red sea bream, Pagrus major

A 60-day feeding trial was conducted to determine the effects of copper nanoparticles (Cu-NPs) and vitamin C (VC) on red sea bream. Besides the control diet (D1), six diets were supplemented with Cu-NPs and VC [0/800 (D2), 0/1,000 (D3), 0/1,200 (D4), 2/800 (D5), 2/1,000 (D6) and 2/1,200 (D7) mg Cu-NPs/VC per kg]. Cu-NP was a significant factor on final weight (FBW), weight gain (WG) and specific growth rate (SGR), feed intake (FI), feed (FER) and protein efficiency ratios (PER), protein gain (PG) and protein retention (PR), body protein and lipid contents, protease (PA) and bactericidal activities (BA) and tolerance against stress (LT50%) (p < .05). In addition, BA and LT50% were significantly affected by either Cu-NPs or VC (p < .05). Fish fed Cu-NPs or/and VC-supplemented diets showed higher FBW, WG, SGR, PG, PR, FI, PA, LA and BA values when compared with the control group (p < .05). FER, PER and body lipid content were significantly enhanced in D4, D5, D6 and D7 groups; meanwhile, body protein and LT50% were significantly enhanced in D5, D6 and D7 groups when compared with D1 group (p < .05). In conclusion, dietary Cu-NPs or/and VC improved growth and health of red sea bream.
Phytochemical screening and in vitro antioxidant activities of the ethanolic extract of Hibiscus rosa sinensis L

The study was aimed at evaluating the antioxidant activity of the ethanolic extract of Hibiscus rosa sinensis flowers at varying concentration in vitro. The extract was found to contain large amounts of phenolic compounds and flavonoids. Additionally, the reducing power (capacity to reduce Fe3+ to Fe2+), the capacity to scavenge hydrogen peroxide, superoxide radicals and nitric oxide were evaluated. The extract exhibited a concentration dependent scavenging activity. The GC-MS study carried out showed the presence of phytochemicals like hexadecanoinc acid (RT: 26.02) hexanedioic acid (RT: 33.57) and squalene (RT: 41.55).
Genetic and Morphological Variation in Non-Polyphenic Southern African Populations of the Desert Locust

This study addresses geographic variation of body size and shape and of allele frequencies at 21 microsatellite loci in southern African populations of the desert locust, Schistocerca gregaria. These populations, which belong to the subspecies S. g. flaviventris, lack the capacity to change phase and to swarm relative to the northern populations of the nominate subspecies, S. g. gregaria. We reported overall genetic and morphological similarities among localities that cover most of the subspecies range. Of particular interest, the level of genetic diversity was moderately lower than in the swarming subspecies of the northern range. In addition, S. g. flaviventris populations were genetically homogeneous, such as observed in the northern range of the nominate subspecies. This result can be explained by north—southwest seasonal migration to follow rainfall.
Detection of Genes Encoding of Extended-Spectrum and AmpC β-Lactamases in Klebsiella pneumoniae Isolates from Clinical Specimens

Klebsiella pneumoniae is an important pathogen of nosocomial infections and has rapidly become the most common producing beta lactamases that resistance for many antimicrobial agents. Thus, our study aimed to identify K. pneumoniae isolates harboring SHV, TEM, CTX-M and AmpC β-lactamase genes and the relation between them and with some antimicrobial resistance to avoid treatment failure. Sensitivity disc test and PCR technique were done on 24 clinical isolates of K. pneumoniae. The PCR results showed that blaSHV, blaTEM, blaCTX-M and blaAmpC genes were present in 91.67% of the isolates. Significance appearance of resistance genes was 75% for each blaSHV and blaCTX-M, 62.5% for blaTEM, while blaAmpC in 16.7%. Finding pointed out that blaAmpC gene present with highly significant in bacterial isolates which lacking the blaSHV and blaCTX-M. Moreover, blaSHV and blaTEM occurred on significant correlation with blaCTX-M. Antimicrobial discs (CTX, CDZ, CRO and CL) correlating with resistance genes (blaCTX-M, blaSHV and blaTEM). Remarkably, 41.67% of bacterial isolates have three of cephalosporine β-lactamase genes due to the common used of cephalosporine third generation for treatment.
Contributions of macrophages in lymph nodes and gut mucosa to SIV disease control and progression

The lymph nodes and gastrointestinal tract are principal sites of inflammation and T cell dysfunction in progressive human immunodeficiency virus type 1 (HIV) infection, and a leading hypothesis is that aberrant responses by innate immune cells, such as macrophages, are actively involved in this process. Macrophages promote and resolve tissue inflammation in health and in response to pathogen insult through cytokine release, phagocytosis, and wound repair, but currently their role in HIV/AIDS pathogenesis remains unclear. Using the pathogenic simian immunodeficiency virus (SIV)-rhesus macaque model, I investigated the macrophage response at different stages of SIV infection and AIDS, as well as longitudinally in macaques anticipated to control or progress to disease based on set-point viral load. I hypothesized that macrophages promote a protective response during acute SIV infection that becomes inadequate and/or detrimental to the host in chronic infection and associates with disease progression. I found that macrophage density uniformly increased in lymph nodes and gut mucosa in acute SIV infection and then declined at the onset of chronic infection except for in gut mucosa of SIV progressors, where macrophage numbers remained elevated and were increased above pre-infection in AIDS. Lymph node macrophages were activated, apoptotic, and inflammatory, spontaneously secreting TNF-α, IL-6, and IFN-α in the acute and chronic stages of infection with minor differences between groups. In contrast, macrophages in small intestine were functionally non-inflammatory, except in AIDS, and macrophage phagocytic capacity in SIV progressors was markedly impaired, inversely correlating with gut macrophage abundance, enteropathy, and plasma but not tissue viral burden. Collectively, these data suggest an inflammatory function for macrophages in lymph nodes that participates in SIV-associated inflammation and T cell loss but does not contribute to disease outcome. At the same time, macrophages in gut mucosa appear to resolve rather than promote inflammation through phagocytosis, and their impairment is associated with hallmarks of progressive SIV infection and eventual harmful activity in AIDS. Defining macrophage involvement in HIV/AIDS pathogenesis could elucidate novel pathways for adjunctive therapeutic intervention through direct or indirect augmentation of macrophages and therefore has considerable public health significance.
Blackleg in cattle: current understanding and future research needs

EnglishBlackleg is an endogenous acute infection that principally affects cattle, whose etiologic agent is the anaerobic bacterium Clostridium chauvoei. In recent years, the major virulence factors of C. chauvoei have been discovered and described. However, the pathogenesis of blackleg in cattle, and in particular, the movement of the pathogen from the point of entry to the affected tissues is not yet fully elucidated. Disease control is based on appropriate management and vaccination. This review summarizes the latest research findings that contribute toward the understanding of the disease in cattle, provide a foundation to preventive strategies, and identify future research needs. Key words: Clostridium chauvoei; sudden death; myonecrosis portuguesO carbunculo sintomatico e uma infeccao endogena, aguda, que acomete principalmente bovinos, cujo agente etiologico e a bacteria anaerobica Clostridium chauvoei. Recentemente, os principais fatores de virulencia do C. chauvoei foram descobertos e descritos. Contudo, a patogenese do carbunculo sintomatico em bovinos, especialmente a circulacao do patogeno desde o ponto de entrada ate os tecidos acometidos ainda nao esta completamente elucidada. O controle desta enfermidade e baseado em medidas adequadas de manejo e vacinacao. Esta revisao reune as mais recentes descobertas que contribuiram para o entendimento da doenca em bovinos, fornece embasamento para medidas preventivas e aponta futuras necessidades de pesquisa. Palavras-chave: Clostridium chauvoei; morte subita; mionecrose
Immuogenic Potency of LPS Actinobacillus Actinomycetemcomitans Local Isolate on Iga, Siga, and Igg Titre in Aggressive Periodontitis

The incidence of periodontitis which is varied in different countries around the world shows an increasing tendency in lipopolysaccharide (LPS) of Actinobacillus actinomycetemcomitans which is part of the cell wall of one of the virulence factors. The purpose of this study is to obtain and to characterize LPS of Surabaya isolates A. actinomycetemcomitans as the main cause of aggressive periodontitis and and to analyze the effect of LPS on the induction of IgA and IgG titers in serum and saliva. The method used in this study uses phenol to obtain and to characterize and purification LPS A. actinomycetemcomitans. Furthermore, it conducted in experimental animals (Wistar rats). This is done by calculating the levels of IgA, sIgA, and IgG with ELISA technique. This study results LPS of A. actinomycetemcomitans which is in accordance with LPS of E. coli O127 which is the standard of LPS. In experimental animals, the results show that the level of IgA in serum has increased although there is no significant difference with the control group from the statistical test, whereas the level of IgA in saliva shows significant differences if they are compared from the control group and the treatment group. The level of IgG in the treatment group also seems increasing although the statistical analysis did not show any significant difference from the controlled group. LPS of A. actinomycetemcomitans can increase the antibody of Wistar rats, especially the level of IgA in saliva (sIgA). This suggests that sIgA roles in local immune defense.
Pulmonary Smooth Muscle

Matrix Metalloproteinase-2-Mediated Inhibition of Na -Dependent Ca Uptake by Superoxide Radicals (O2 .7 ) in Microsomes of Pulmonary Smooth Muscle Amritlal Mandal, Tapati Chakraborti, Sudip Das, Biswarup Ghosh, Amarnath Ghosh and Sajal Chakraborti Department of Biochemistry and Biophysics, University of Kalyani, Kalyani 741235, West Bengal, India Division of Electron Microscopy, National Institute of Cholera and Enteric Diseases, P-33, CIT Road, Scheme XM, Kolkata 700010, India
Determination of some parameters of landrace green bean (Phaseolus vulgaris L.) genotypes collected from Western Mediterranean Region of Turkey

Dunyada en fazla yetistirilen ve tuketilen tarimsal urunlerden biri olan fasulye, anavatani olmamasina ragmen Turkiye'de genis bir uretim alani ve cesitlilik sergilemektedir. Turkiye'de fasulye uretimi, bazi bolgelerle sinirli olsa da hem dusuk hem de yuksek rakimli alanlarda genellikle aile tuketimi icin yetistirilmektedir. Bununla birlikte, gunumuzde ticari tohumlara olan talep artmaktadir ve bu durum yerel taze fasulye genotiplerinin varligini tehdit etmektedir. Genetik kaynaklardan bir tanesi olan yerel genotipler, genetik degiskenlik, gida guvenligi ve islah uygulamalari icin oldukca onemlidir. Bu acidan bakildiginda calisma, 2013-2014 yillari arasinda Bati Akdeniz'de yer alan Antalya, Burdur ve Isparta illerinden toplanan yerel taze fasulye ( Phaseolus vulgaris L.) genotiplerinin bazi ozelliklerini belirlemek amaciyla yurutulmustur. Gen havuzu ve islah calismalarina baslangic materyali olusturmak icin hem dusuk hem de yuksek rakimli alanlara adapte olmus 124 tane fasulye genotipi toplanmis ve kayit altina alinmis. Calisma sonucunda en fazla genotip Antalya ilinden toplanmistir. Yuksek rakimli bolgelerde daha fazla yerel fasulye cesidi bulundugu (%56.5) ve tirmanici buyume ozelligine sahip olan cesitlerin(%85.5) bodur buyume ozelliginde ki cesitlerden daha yaygin oldugu belirlenmistir. Ayrica, toplanan genotiplerin %62.9’unun tohumlari tek renklidir ve tohum renginde beyaz rengin baskin oldugu tespit edilmistir.
Genetic Studies of Yield Variation in mid duration irrigated rice

Genetic variability and character association were estimated for ten quantitative characters in 22 mid duration irrigated rice genotypes during kharif 2010.High estimates of heritability coupled with high genetic advance as percent of mean were recorded for most of the characters indicating the presence of additive gene effects in them.The genotypic and phenotypic coefficient of variation were maximum for flag leaf area, grain yield, number of effective tillers per plant , number of fertile grains per panicle,100 seed weight and harvest index indicating selection for such characters would be more reliable.In the present study all the component traits exhibited positive association with grain yields except plant height and panicle length although the level of association varied.Path analysis revealed that number of effective tillers/plant followed by fertile grains/panicle ,100 seed weight and panicle length were the important characters contributing for grain yield.
509-45-1, a Capsicum annuum Pepper Germplasm Containing High Concentrations of Capsinoids

Germplasm release 509-45-1 is a smallfruited Capsicum annuum L. pepper released in 2013 by the Agricultural Research Service (ARS) of the U.S. Department of Agriculture (USDA). Fruit of 509-45-1 contain high concentrations of capsiate [(4-hydroxy-3methoxybenzyl (E)-8-methyl-6-nonenoate/ CAS No. 205687-01-0] and dihydrocapsiate (4hydroxy-3-methoxybenzyl 8-methylnonanoate/ CAS No. 205687-03-2) in both immature and mature fruit. Concentrations of total capsinoids in immature fruit of 509-45-1 exceeded 1000 ug·g fresh weight (FW), in the absence of capsaicinoids, in 2011. The release of 509-45-1 will provide researchers and plant breeders with a new source of capsinoids, thus facilitating the production of and further research on these non-pungent biologically active compounds.