Miracle-dz/UniFAR-FTUs huggingface dataset:
Original Article - Molecular characterisation of Cryptosporidium : Anemerging parasite

Purpose: The aim of the present study was to determine the prevalence of Crytposporidium in local population and to understand its epidemiology by molecular methods. Methods: Faecal samples from 681 children and 804 adults, admitted to tertiary care hospitals in twin cities of Hyderabad and Secunderabad with complaints of diarrhoea; and six calves with diarrhoea, were screened for Cryptosporidium oocysts by microscopy and enzyme linked immunosorbent assay (ELISA). Polymerase chain reaction restriction fragment length polymorphism (PCR RFLP) based identification of Cryptosporidium species in positive specimens was done to elucidate epidemiology of Cryptosporidium. Results: Cryptosporidium was found in 52 (7.6%) children and 7(0.9%) adults and 1(16.6%) calf with diarrhoea. The prevalence of Cryptosporidium in children below five years of age was 8.2% and 14.3% in children in the age group of six months to one year. Of the 42 samples genotyped 29 (69%) were C. hominis and 8 (19%) were C. parvum and 5 (11.9%) were mixed infection with the two species. Conclusions : Children in the age group of six months to one year were found to be the most vulnerable. The occurrence of C. parvum, in nearly one third of cases in the present series indicates that the zoonotic transmission is of considerable significance in the epidemiology of Cryptosporidiosis in the study area.
Effect of Body Condition Score during Transition Period on Early Lactation, Postpartum Interval to Estrus and Calf Birth Weight in Sahiwal Cows

A total of 26 purebred Sahiwal cows, 13 cows each from two farms i.e. the BMEF and CBF, Anjora, Durg, Chhattisgarh were studied during extended transition period (56 days prepartum to 84 days postpartum) to investigate variation in body condition score along with birth weight of calf, early lactational yield, postpartum interval to estrus (PPIE) and their interrelationships. In BMEF herd concentrate was not fed to the animals during prepartum stage. In BMEF, the mean BCS at periodical intervals was significantly less than that of CBF herd throughout the transition period. The postpartum mean unit loss in BCS of the cows of BMEF herd (0.54±0.09) was significantly higher than that of CBF cows (0.52±0.09). Significant differences were observed between overall pre-and post-partum means of BCS of each farm. Significantly higher early lactation yield was observed in the Sahiwal cows of CBF (667.23±37.13 kg) than the cows of BMEF herd (476.92±51.59 kg). The average PPIE was non-significantly shorter in CBF cows (228.69±37.36 days) than those of the cows of BMEF herd (241.69±43.51 days). The average birth weight of calf of CBF herd (22.38±0.75 kg) was significantly higher than that of BMEF cows (19.58±0.52 kg). Highly significant (P<0.01) positive correlations were observed between the mean pre-and post-partum BCS with all periodical BCS at different intervals including mean pre-and post-partum BCS in both farms. Early lactation yield has shown negative and non significant correlation with 84 days postpartum BCS in both farms. PPIE was negatively correlated with BCS at 56 and 84 days postpartum in both the farms. PPIE had shown positive correlation with early lactation yield in BMEF (r=0.377) and negative correlation in CBF herd (r=-0.182). It can be concluded that the energy status can be assessed by scoring of body condition periodically in transition Sahiwal cows which were indicative of their early lactation yield, interval to first detected heat and birth weight of calf.
Seasonal changes in diet and lipid content of northern sand lance Ammodytes dubius on Fyllas Bank, West Greenland

: Sandeel ( Ammodytes spp.) are forage fishes and form a crucial link in the flow of energy from phytoplankton to marine top predators in the North Atlantic. The nutritional value of the sandeel is linked to the presence of lipid-rich zooplankton species, which makes their trophic role vulnerable to climate-induced changes in the zooplankton community. We provide the first description of diet and lipid accumulation of the northern sand lance Ammodytes dubius Rein-hardt, 1837 in southwest Greenland (64° N) during a growing season. Sampling occurred in May, August and September 2013, and differences in diet and lipid content were found in relation to season, gender and ontogeny. In terms of numbers and biomass, nauplii constituted the vast majority of prey in May, whereas copepods (primarily large Calanus spp.) dominated in August and September. Groups of larger prey (euphausiids and amphipods) were only found late in the season and primarily in sandeel larger than 16 cm. Mean lipid content (% DW) was at a minimum in May for both mature (males: 5.6%, females: 6.4%) and immature sandeel (3.9%), and peaked in August for mature individuals (males: 21.7%, females: 24.2%) and in September for juveniles (19.8%). Sandeel condition responds quickly to changes in prey availability and can be used as an indicator sensitive to of productivity and environmental change on the banks in West Greenland. In the light of rapid climate changes in Arctic marine ecosystems, the present findings may serve as a baseline for future monitoring of the productivity of pelagic ecosystems in West Greenland.
PURIFICATION OF CATALASE ENZYME FROM PLEUROTUS OSTREATUS

The oyster mushroom Pleurotus ostreatus is the most commonly cultivated mushroom, and are effective for antitumor, antibacterial, anti viral and hematological agents and in immune modulating treatments. Several compounds from oyster mushrooms, potentially beneficial for human health have been isolated and studied. The aim of this research is to purify an enzyme catalase from Pleurotus ostreatus through Sephadox G-75 column, its molecular weight was determined by polyacrylamide gel electrophoresis and the catalase enzyme stability were observed at various temperature and different pH condition. Under denaturing conditions, polyacrylamide gel electrophoresis revealed dissociation of a major component of molecular weight 62,000 kDa, which constituted 90% of the total protein of the stained gel, suggesting that the native enzyme is tetrameric. The optimum temperature and pH for the purified enzyme catalase from Pleurotus ostreatus enzymatic reaction were 30°C and pH 7.5.
Abundance of Baird’s sparrows, Ammodramus bairdii, in native prairie and introduced vegetation

Abstract:Endemic grassland songbirds, including the Baird’s sparrow (Ammodramus bairdii), are adapted to breed in North American native prairie, an extremely rare habitat that is often grazed by cattle and continues to be threatened by cultivation. We determined the degree to which Baird’s sparrow numbers in mixed-grass prairie are associated with plant species composition and grazing pressure. Bird numbers in grazed native prairie correlated positively with grass/sedge cover and negatively with bare ground cover. Mean numbers of singing males were generally highest on ungrazed native prairie and similar in grazed introduced and grazed native vegetation, suggesting that birds are more affected by grazing pressure than by plant species composition. What attracts this species to introduced vegetation remains unclear.
Phycobilisomes and complementary chromatic adaptation in cyanobacteria

Proprietes des phycobilisomes cyanobacterions. Rapport avec l'adaptation chromatique complementaire. Etudes de genetique moleculaire. Autres effets de l'illumination chromatique. Modele hypothetique d'adaptation chromatique complementaire. Remarques en guise de conclusion
Race profiling, genetic diversity, diagnostics and management of Fusarium oxysporum f. sp. ciceris causing wilt in chickpea

Fusarium oxysporum f. sp. ciceris (Foc) is a soil and seed- borne fungal pathogen causing chickpea wilt worldwide and produces typical vascular wilt symptoms in India. The populations were highly variable in their growth pattern and rate, size of macroconida and pigmentation in culture. The studies clearly indicate the need to revise the International differential cultivars standardized in 1982 for characterization of the Indian populations of Foc into races. A set of new differential cultivars namely, C104, JG74, CPS1, BG212, WR315, KWR108, GPF2, DCP92-3, Chaffa and JG62 was identified and based on differential reactions; the Indian populations of Foc were characterized into eight races. Genetic diversity analysis using various molecular markers such as RAPD, URP, ISSR and SSR indicated the existence of variability among the populations predominated by a single race of the pathogen in an area. The groups partially corresponded to the states of origin/chickpea-growing region of the isolates as well as races of the pathogen. Gene specific markers such as TEF-1a, b-tubulin, and ITS were also used to determine the genetic diversity and about 90% populations showed more or less similar grouping pattern with these markers. The groups did not correspond to the state of origin and races of the pathogen. High level of similarity among the populations in respect of these gene sequences was observed. Highly sensitive and specific molecular markers from various genomic regions as well as SCAR markers were developed for detection of the pathogen using both conventional and real-time PCR. For management of the disease, efficacy of various bio-agents was evaluated and Trichoderma harzianum and T. viride were found effective. Novel seed dressing and soil application formulations were developed from these bio-agents. A combination of PBP 4G (T. viride) for soil application and Pusa 5SD (T. harzianum) for seed treatment together with a fungicide, carboxin provided the highest seed germination, shoot and root lengths and grain yield with the lowest incidence of wilt in chickpea under field conditions. The efficacy of seed treatment with Pusa 5SD has been validated at different locations in India. Further, a combination of seeds treated with Pusa 5SD developed from T. harzianum + Pseudomonas fluorescens 80 + Mesorhizobium ciceri + Vitavax power also provided the highest germination, grain yield and the lowest wilt incidence.
Expression profiles of two thaumatin‐like protein (TmTLP) genes in responses to various micro‐organisms from Tenebrio molitor

It is well known that anti‐fungal thaumatin‐like proteins (TLPs) play important roles in plants. Here, we investigated the expression analysis of thaumatin‐like protein genes TmTLPs in response to various pathogens in Tenebrio molitor. Developmental expression patterns of TmTLPs show that TmTLPs are highly expressed in the early pupal and adult stages. Furthermore, tissue‐specific expression patterns of TmTLPs indicate that TmTLP1 is highly expressed in the integument and gut of last instar larvae and the integument and Malpighian tubules of 5‐day old adults. In contrast, TmTLP2 is highly expressed in the gut of both last instar larvae and 5‐day old adults. We hypothesize that the expression of TmTLP genes in developmental stages may be related to molting and body remodeling stresses. In addition, the induction patterns of TmTLP genes indicate that TmTLPs were slightly induced by Escherichia coli, Staphylococcus aureus, Candida albicans and Listeria monocytogenes. Furthermore, TmTLP1 and TmTLP2 were strongly induced in response to E. coli at 9 h post‐injection and L. monocytogenes at 3 h post‐injection. Our results suggest that TmTLPs may possess antimicrobial functions in T. molitor.
Epigenetic Regulation of the Dlk1-Meg3 Imprinted Locus in Human Islets

Type 2 diabetes mellitus (T2DM) is a complex metabolic disease characterized by inadequate insulin secretion by the pancreatic β-cell in response to increased blood glucose levels. Despite compelling evidence that T2DM has a high rate of familial aggregation, known genetic risk variants account for less than 10% of the observed heritability. Consequently, post-transcriptional regulators of gene expression, including microRNAs and other noncoding RNAs, have been implicated in the etiology of T2DM, in part due to their ability to simultaneously regulate the expression of hundreds of targets. To determine if microRNAs are involved in the pathogenesis of human T2DM, I sequenced the small RNAs of human islets from diabetic and non-diabetic organ donors. From this screen, I identified the maternallyexpressed genes in the imprinted DLK1-MEG3 locus as highlyand specifically-expressed in human β-cells, but repressed in T2DM islets. Repression of this noncoding transcript was strongly correlated with hypermethylation of the promoter that drives transcription of all the maternal noncoding RNAs including the long noncoding RNA MEG3, several microRNAs and snoRNAs. Additionally, I identified disease-relevant targets of DLK1-MEG3 microRNAs in vivo using HITS-CLIP, a technique to detect targets of RNA binding proteins. My results provide strong evidence for a role of microRNAs and epigenetic modifications, such as DNA methylation, in the pathogenesis of T2DM. In addition, my data set catalogs human islet microRNAs relevant to human T2DM pathogenesis and characterizes their target transcriptomes. Despite being associated with T2DM and several other diseases, very little is known about the regulation of imprinting of the MEG3-DLK1 locus. Hence, I interrogated a newly described enhancer in this locus, as enhancers are known mediators of mono-allelic expression at other imprinted loci. I discovered allele-specific binding of this enhancer by critical islet transcription factors, including FOXA2 in human islets. In addition, I mapped long-range interactions of this enhancer in human islets using 4C-Seq. Overall, my findings provide novel insights into the regulation of an imprinted locus critical to β-cell health and function. Degree Type Dissertation Degree Name Doctor of Philosophy (PhD) Graduate Group Cell & Molecular Biology First Advisor Klaus H. Kaestner
Auxin cell biology in plant pattern formation

Auxin has been implicated in a vast array of plant processes, and concomitant with a more detailed understanding of the cellular mechanisms underlying its biosynthesis, transport, and perception, it has become increasingly clear that auxin also has instructive roles in plant pattern formation. Moreover, it turns out that in a multitude of instances, from the early establishment of body axes to organogenesis in shoot and root, plant tissue patterns owe their robust flexibility in part to feedback interactions involving auxin. Higher resolution cell biology, molecular genetics, and genomics, as well as live imaging are now used together to define the parameters needed to generate more detailed and precise mathematical models of plant development.
Biogeography of a plant invasion: drivers of latitudinal variation in enemy release

Aim The relationship between herbivory and latitude may differ between native and invasive plant taxa, which can generate biogeographical heterogeneity in the strength of enemy release. Our aim was to compare latitudinal gradients in herbivory between native and invasive plants and investigate whether gradients are driven by local adaptation or phenotypic plasticity. Location North America. Methods Using sympatric native and invasive lineages of the wetland grass Phragmites australis and the specialist gall-fly Lipara rufitarsis, we conducted a field survey to examine whether the relationship between herbivory (the proportion of stems galled) and latitude was parallel between lineages. In a subsequent common garden experiment, we assessed whether latitudinal gradients in herbivory were genetically based or driven by phenotypic plasticity. Results In the field, L. rufitarsis herbivory on the native P. australis lineage increased from 27% of stems galled in southern populations (36.5°) to 37% in northern populations (43.6°), whereas there was no relationship for the invasive lineage. Similar relationships were evident in the common garden experiment, indicating a genetic basis to latitudinal variation in herbivory. Moreover, the invasive lineage suffered five times less herbivory than the native lineage on average, supporting the enemy release hypothesis. However, a genetic basis to this pattern was absent in the common garden experiment, suggesting that local environmental conditions were responsible for the enemy release observed in nature. Specifically, stem height, diameter and density during the L. rufitarsis oviposition period appeared to be important drivers of herbivory. Main conclusions Non-parallel gradients in herbivory may help explain the equivocal results of other studies that examine enemy release and biotic resistance at local scales, and can be an important mechanism promoting biogeographical variation in invasion success. We suggest that these latitudinal patterns in herbivory and other species interactions are likely to be a common phenomenon across a range of invaded systems.
Identification of groundnut genotypes and wild species resistant to stem rot using an efficient field screening technique

Stem rot of groundnut caused by S. rolfsii Sacc. is one of the major constraint to groundnut production in many countries. The fungus is ubiquitous, soil in habitant and non-target. Screening of groundnut genotypes for resistance to stem rot under field conditions is complicated by the non-uniform spatial distribution of the pathogen. While development and maintenance of artificial sick plot with optimum inoculums load under field conditions are also difficult because of sensitivity of the pathogen to temperature, humidity, soil type, cropping system and host preference. In the present study a simple screening technique under field conditions with high disease pressure and greater repeatability has been reported. Twenty-five wild Arachis accessions and 178F3progenies were screened under pot and field conditions, respectively for resistance to stem rot. Two wild Arachis accessions and threeF3 lines were found resistant to stem rot with disease scoring less than 20% and 10%, respectively.
Methods and models for identifying thresholds of habitat loss

&NA; There is mounting evidence that many taxa respond in non‐linear ways to perturbation (i.e. deviations from a natural trajectory brought on by an external agent), and many statistical, physical and ecological methods have been developed to detect the critical points or thresholds of perturbation. The majority of these methods define thresholds as the perturbation points causing abrupt ecological response, but in reality most species or ecosystems do not show a break point response but more gradual transitional change to perturbation. We develop a new method which delineates thresholds as a region in which the slope of the relationship between ecological response (y) and perturbation (x; e.g. habitat loss) is larger than 1: |dy/dx|≥ 1, where both x‐ and y‐axes are scaled to (0, 1) range. The lower end of threshold zones so defined is of particular ecological interest because it is the smallest x that may trigger impending catastrophic response to a small change in x. We derived two landscape models (edge length and the number of patches of species distribution) and two biodiversity models (endemics–area relationship and half‐population curve) to test this method. We applied our zonal thresholding method to these four models fit to empirical data of two forest plots to detect thresholds of species distribution to habitat loss. The two landscape metric models predict that no species could tolerate more than 40% of habitat loss and these thresholds can be much lower for relatively rare species with occupancy < 0.4 and for aggregated habitat loss compared to random habitat loss. The half‐population model leads to a similar threshold level of 40% habitat loss. Overall, we suggest the maximum permissible habitat loss threshold to be between 0–40%, depending on the pre‐disturbed occupancy (or abundance) of a species. This habitat loss threshold falls within the otherwise wide range of thresholds calculated from conventional methods. Our study contributes novel methods and models to quantify the effect of habitat loss on species distribution and diversity in landscapes with potential for conservation applications.
The Phylogenetic Origins and Evolutionary History of Holocentric Chromosomes

Abstract In eukaryotes, we can recognize two kinds of chromosomes, based on the location of the kinetochores. The majority of eukaryotes have monocentric chromosomes, in which kinetochoric activity is concentrated in a single locus. In several unrelated eukaryotic lineages, chromosomes are holocentric, having diffuse centromeric / kinetochoric activity along the length of the chromosome. Whether holocentric chromosomes are derived or ancestral is still under debate. This study uses the phylogenetic tree from Time Tree of Life project, comprising more than 50,000 sampled species, to reconstruct the evolution of holocentry. Asymmetrical two-state Markov (Mk2) models were compared with BiSSE models to assess sensitivity of our conclusions to possible effects of holocentry on lineage diversification rates. Our analyses based on Mk2 and BiSSE models inferred that the rate of transition from holocentric to monocentric chromosomes is two orders of magnitude higher than the reverse direction. The ancestral state of all eukaryotes is ambiguous depending on the model, inferred to be either monocentric (Mk2) or holocentric (BiSSE). Whatever the direction, the multiple transitions and high diversity of centromere organization across the tree of life are what we would expect if there are selective advantages to both chromosome types. Understanding those selective advantages is key to understanding how genetic information is organized and transmitted from one generation to the next, and why these major evolutionary transitions in centromere organization have occurred in the first place.