Miracle-dz/UniFAR-FTUs huggingface dataset:
Mating, epigenetics, and evolution: Genomic dissection of three transcriptional circuits in fungi

Author(s): Galgoczy, David J | Advisor(s): Johnson, Alexander D | Abstract: The coordination of cellular processes is largely controlled at the level of transcriptional regulation. Previous work, dating back over forty years, has focused on a few details of transcriptional regulation, providing a window through which to view the basic workings of transcriptional regulation. Recent developments have allowed broader analyses, providing new views into how whole transcriptional programs mold cellular processes.To provide the first complete example of a transcriptional circuit, we completely dissected the transcriptional regulation that underlies the specification of the three cell types in Saccharomyces cerevisiae. In addition to providing an example of a completely mapped circuit, this analysis uncovered genes not expected to be associated with specific cell types. We have extended this approach to a second fungal species, uncovering processes of molecular evolution on a whole circuit level.We adopted a similar approach to describe the transcriptional regulatory mechanism that governs the switch between the white and opaque states in Candida albicans, the primary fungal pathogen in humans. This process modulates the virulence properties and mating competence of this species, and involves the regulation of hundreds of genes. We showed that one transcriptional regulator, Wor1 governs the mechanism underlying the switch. Our analysis revealed that Wor1 directs an extensive and complex transcriptional program to set up the opaque state.Finally, to understand how changes in transcriptional regulation shape evolution of organisms, we explored the evolution of a large transcriptional circuit in fungi. This is an important endeavor, since phenotypic differences between evolutionarily divergent species are thought to be largely due to differences in gene expression. While several anecdotal examples of molecular evolution events exist, a broad analysis would yield insights into what types of changes figure importantly in shaping evolution on a systems level. To this end, we mapped the large combinatorial circuit controlled by Mcm1 in three fungal species; this provided an unprecedented view into the evolution of a large transcriptional circuit, and offered two examples where circuitry had been dramatically restructured. Ongoing informatics analysis is refining this view, allowing us to distill out the molecular processes that are important in the evolution of circuits.
Les trichothécènes : nature des toxines, présence dans les aliments et moyens de lutte

Ce travail est consacre a l'etude de la nature et des proprietes des trichothecenes des groupes A et B. Ces composes contaminent les cereales du monde entier. Si des concentrations importantes de toxines peuvent etre ponctuellement rencontrees, la quasi-totalite des denrees se revelent contaminees par de faibles concentrations. Le tri selectif des grains contamines et sains est une des rares methodes applicable a l'industrie. Les methodes chimiques et biologiques de decontamination sont insuffisamment evaluees pour avoir de reelles applications. Les principaux moyens de lutte visent donc a prevenir la contamination fongique des matieres premieres.
Spatial variations in responses of vegetation autumn phenology to climate change on the Tibetan Plateau

Aims Information about changes in the start and end of the vegetation growing season (SOS and EOS) is crucial for assessing ecosystem responses to climate change because of the high sensitivity of both to climate and their extensive influence on ecological processes in temperate and cold regions. climatic warming substantially advanced SOS on the tibetan Plateau from 1982 to 2011. However, it is unclear why EOS showed little delay despite increasing temperature over this period. Methods We used multiple methods to determine EOS from the satelliteobserved normalized-difference vegetation index and investigated the relationships between EOS and its potential drivers on the tibetan Plateau over 1982–2011. Important findings We found a slight but non-significant delay in regionally averaged EOS of 0.7 day decade−1 (P = 0.18) and a widespread but weak delaying trend across the Plateau over this period. the inter-annual variations in regionally averaged EOS were driven mainly by preseason temperature (partial R = 0.62, P < 0.01), and precipitation and insolation showed weak impact on EOS (P > 0.10). Pre-season warming delayed EOS mainly in the eastern half and north-western area of the plateau. In the south-west, EOS was significantly and positively related to SOS, suggesting potentially indirect effects of winter weather conditions on the following autumn’s phenology through regulation of spring phenology. EOS was more strongly related with pre-season temperature in colder and wetter areas, reflecting vegetation adaptation to local climate. Interestingly, preseason temperature had weaker delaying effects on EOS for vegetation with a shorter growing season, for which SOS had a stronger control on inter-annual variations in EOS than for vegetation with a longer growing season. this indicates that shorter-season tibetan Plateau vegetation may have lower plasticity in adjusting the length of its growing season, whenever it begins, and that climate change is more likely to shift the growing season than extend it for that vegetation.
Regressão linear múltipla e modelo Random Forest para estimar a densidade do solo em áreas montanhosas

The objective of this work was the development of models with different sets of data for estimating soil bulk density in tropical mountainous regions, from soil attributes commonly found in the analyses of soil profiles described in regional surveys. The complete dataset is composed of 163 samples and it was divided into six groups, of which three groups have 73 samples and the maximum of 32 covariables, and three have 163 samples and the maximum of 18 covariables. The linear regression (RLM) and randomForest (RF) models were tested. The lowest uncertainty between the models was achieved by RLM2, with R2 of 0.56, 13 covariables, and 73 samples. Considering the groups with 163 samples, the best models were the RFs with mean R2 of 0.48. The root mean squared error ranged between 0.09 and 0.14. The most important covariables in the RF model were: organic carbon, hydrogen, fine and coarse sand, base saturation, and cation exchange capacity. By the stepwise backward regression, the main covariables were: silt and clay relation; fine and coarse sand; organic carbon; base saturation; and potassium.
Self-generated microbial population or cultured microflora – an important criterion toward development of an effective and economically viable road map for organic soil management

ABSTRACT Huge depletion of soil microflora under conventional farming practice has become the primary contributory factor toward the present depletion of soil and crop productivity. Reconstitution of soil microbial dynamics has been identified as the only way out, but there has been a debate regarding the most effective pathway for soil rejuvenation i.e. whether to create the environment for natural proliferation or opt for inoculation of laboratory generated microbes. In this respect, a study was undertaken at Maud T.E. (Assam) under FAO-CFC-TBI Project, where bio-fertilizer (microbial inoculant, MI), vermicompost (organic food source, OF), vermicompost + bio-fertilizer (OF+MI), and Novcom compost (representing self-generated native microflora in the order of 1016c.f.u. along with organic food source, SNM); were taken as treatments for a yield target of 1500 kg made tea/ha. The highest crop yield (1500 kg ha−1) along with high and consistent soil quality development was noted under SNM treatment; while MI influenced lowest yield (1268 kg ha−1) and minimal soil response. Addition of the organic food source with cultured microbes (MI+OF) was found to improve crop performance (1427 kg ha−1), but with 7.60 times higher cost (Rs. 39.97 kg−1 made tea). Economic viability study indicated that except SNM, all other treatments were vulnerable toward crop loss or market downfall.
AUTOIMMUNE MECHANISMS IN THE PATHOGENESIS OF THE PRIMARY OPEN ANGLE GLAUCOMA (The literature review)

Numerous researches testify to presence of autoimmune aggression in pathogenesis POAG. Antibodies to various fabric components of an eyeball, both in forward, and in a back piece of an eye are found out. There are qualitative changes in collagenic structure of a sclera. There are products of pathological synthesis of the collagenic fibers having diagnostic, toxic, prognostic value. Change of a spectrum of immunoglobulins, cellular structure of immunocompetent cells testify that are involved in pathogenesis POAG not only autoimmune mechanisms of an autoaggression, but also change of natural immunity, and weakening of regulating functions.
Screening of Entomopathogenic Fungi Against Citrus Mealybug, Plannococcus citri (Hemiptera: Pseudococcidae)

Planococcus citri (citrus mealybug) is a common and damaging citrus crop pest which has proven difficult to control using conventional methods, such as chemical pesticides and insect growth regulators, particularly late in the citrus growing season. The virulence of two entomopathogenic fungal species was studied in laboratory bioassays against the crawlers and adults of P. citri. Isolates of Metarhizium anisopliae and Beauveria bassiana, collected from citrus orchards in the Eastern Cape Province in SouthAfrica, were verified using and molecular techniques. Mealybug bioassays were performed in 24-well plates. Beauveria bassiana (GAR 17 B3) and M. anisopliae (FCM AR 23 B3) isolates both resulted in 67.5 % mortality of mealybug crawlers and B. bassiana (GB AR 23 13 3) resulted in 64 % crawler mortality with concentrations of 1 × 107 conidia/ml. These three isolates were further tested in multipledose bioassays to determine the median lethal concentration (LC50), which were 5.29 × 105 conidia/ml for the M. anisopliae isolate (FCM AR 23 B3), 4.25 × 106 conidia/ml for B. bassiana (GAR 17 B3), and 6.65 × 107 conidia/ml B. bassiana (GB AR 23 13 3) for crawlers, respectively. The results of this study suggested that two isolates (M. anisopliae FCM AR 23 B3 and B. bassianaGAR 17 B3) showed potential for further development as biological control agents against citrus mealybug. Further research would be required to determine their ability to perform under field conditions.
Improved peptide generation from milk fermented by heat‐shocked Lactobacillus helveticus

Summary High macromolecular protein content in bovine milk produces a firm and dense coagulum in the stomach. To increase the number of easily digested peptides, we were the first to introduce heat-shocked Lactobacillus helveticus to fermented milk. The results showed that acid production was inhibited significantly (P < 0.01) over 14 h of fermentation; the content of small peptides and nonapeptide increased 28.03% and 27.78%, respectively, including three specific and fifteen common bioactivity peptides. The identified type of peptides from α-casein, β-casein and κ-casein increased by 12.05%, 30.73% and 19.30%, respectively, and the distribution of peptides was similar to intestinal digestion. Therefore, this attenuated strain could improve the generation of small molecular peptides and bioactive peptides to promote the degradation of proteins and accelerate milk protein digestion and absorption. This approach might be used to develop functional dairy products.
Analysis of apple (Malus domestica Borkh.) wax by means of chromatographic techniques and confocal microscopy

The wax of three economically important Belgian apple cultivars, 'Jonagold', 'Jonagored' and 'Elstar', was analysed chemically and structurally before and after 4 and 8 months of optimal ultra low oxygen (ULO) storage and during shelf life. Macroscopically and microscopically the surface properties of 'Elstar' were clearly different from the two other cultivars. These properties changed similarly for all cultivars during storage and shelf life. Chromatographic patterns of the three cultivars were dominated by the carbohydrate fraction with nonacosane (C29) as the major component. Again 'Elstar' differed in composition compared to 'Jonagold' and 'Jonagored'. For the non-destructive structural analysis confocal microscopy was used, and this led to the development of a new technique for the determination of the wax layer thickness. This technique was compared with the chemical technique known for determination of wax layer thickness. With the confocal technique 'Elstar', 'Jonagold' and 'Jonagored' could be significantly (p=0.05) discriminated based on wax-layer thickness, showing values of 4.14 mum, 2.58 mum and 3.41 mum, respectively.
Hydrolyzation of Edible Starches: Their Preparations and Properties

Starch is the most important polysaccharide and has become the major component of many food industries as well as textile, paper, cosmetic and certain industries that engage in adhesive, thickening, stiffening and gelling agents. However, native starch has limited function and therefore is recommended to modify its physical and chemical properties to meet the consumers’ needs. In this study, the native starch was chemically modified to determine its behavior and characteristics after using hydrolysis process of acid hydrolysis method. There were three types of starch that has been studied - potato, cassava and corn. These starches undergone hydrolysis process using hydrochloric acid and their characteristics were determinedthrough moisture absorption test and Fourier Transform Infrared Spectroscopy (FT-IR) analysis. For moisture absorption test, hydrolyzed starch tends to absorb more surrounding moisture than native starch. This behavior resulted from the increase of hydrophilic character of starch after being modified. The FT-IR analysis shows that hydrolyzed starch content got more hydroxyl group than the native starch due to the breakdown of hydrogen bond between the starch molecules after the acid hydrochloric treatment.
The lesser prairie chicken (Tympanuchus pallidicinctus) in southeastern New Mexico: A population survey

To provide an assessment of the current status of populations of the lesser prairie chicken (Tympanuchus pallidicinctus) in southeastern New Mexico, this study monitored 4,368 sites along 3,428 km of transects, which surveyed a total of 548,608 hectares, in search of active leks during April 2000 and 2001. Of 249 monitoring sites along 195 km of transects north of US380, vocalizations originating at active leks were heard at 46 sites on 31,232 hectares surveyed. Of 4,119 monitoring sites along 3,233 km of transects south of US380, one prairie chicken was observed at one site and vocalizations from one active lek were heard at two sites on 517,376 hectares surveyed. As has been documented in other parts of its range, the lesser prairie chicken in extreme southeastern New Mexico (area south of US380) appears to have experienced a significant decline in size of population.
Anti‐epiphyte defences in the red seaweed Gracilaria vermiculophylla: non‐native algae are better defended than their native conspecifics

Epibiosis in the marine environment is a stressor that may determine invasion success in introduced species. Previous comparisons showed resistance to epibionts can be higher in non‐native than in resident seaweed species, but we do not know whether it is an intrinsic trait of the non‐natives or it has been acquired during the invasion process. To elucidate this question, a comparison between native and non‐native populations of the same species is needed. Resistance against two groups of epiphytes was assessed in living thalli and in artificial substrata coated with surface extracts, both gained from four Asian (native) and four European (non‐native) populations of the red alga Gracilaria vermiculophylla. Two diatom species and two filamentous macroalgae were used as micro‐ and macro‐epiphytes, and one of each type was collected in Asia, while the other came from Europe. Laboratory assays were done in both distributional ranges of G. vermiculophylla and in different seasons. We used G. vermiculophylla from four populations in each range and used a fully crossed design with the factors (i) ‘Origin of Gracilaria’, (ii) ‘Origin of epiphytes’, (iii) ‘Season’ and (iv) ‘Solvent used for extraction’. Both groups of epiphytes, regardless of their origin, attached less to living thalli and to surface extracts from non‐native G. vermiculophylla. Fewer diatoms attached to hexane‐based extracts, while fewer Ceramium filaments settled on extracts gained with dichloromethane. Synthesis. Our results show for the first time that non‐native individuals of a marine organism are better defended against epiphytes than native conspecifics. Furthermore, we found evidence that at least a part of the defence is based on extractable secondary metabolites. We discuss several mechanisms that could explain the increased resistance to epiphytes in non‐native individuals, including the release from enemies in the non‐native range, which could lead to an increase in algal performance during the invasion process. We suggest that an enhanced defence against epiphytes after introduction is one reason for G. vermiculophylla's invasion success. Our observation may also apply to other basibiont–epibiont and host–enemy systems, including plant–plant, plant–animal and animal–animal interactions, in aquatic environments and could be a key feature of bioinvasions.
Structural and functional characterisation of dioxolane A3, a new eicosanoid generated by cycooxygenase-1 in platelets

Platelet-derived eicosanoids play important signalling roles in haemostasis and innate immunity and have major medical implications in cardiovascular disease, inflammation and cancer. Therefore, identification and characterisation of novel platelet lipids is an important goal. Prior to my PhD, our group identified a novel cyclooxygenase-1 (COX-1) product generated by platelets upon agonist activation in an aspirin–sensitive manner. Preliminary structural data suggested this lipid to be 8-hydroxy-9,11-dioxolane eicosatrienoic acid (DXA3) (Aldrovandi, unpublished). However, this required further investigation and its biology was unknown. In this study, I undertook a detailed structural characterisation of DXA3. Using GC/MS, high resolution LC/MSn and UV enabled structural characterisation of the lipid. Through pharmacological studies on isolated platelets and using mutant COX-2 enzymes, I revealed a distinct enzymatic mechanism of COX where the dioxolane forms within the COX catalytic site, then a radical escapes from the enzyme to form DXA3 possibly via a peroxidase. I developed a quantitative assay and showed that DXA3 is generated in ng amounts by thrombin-activated platelets (human and murine) with 77% of DXA3 esterified to phosphatidylethanolamine (PE). In addition to platelets, I detected the lipid in human serum derived from whole blood following clot formation in vitro and the macrophage cell line RAW246.7 in response to calcium ionophore A23187 stimulation. Last, DXA3 stimulated expression of the integrin Mac-1 on human neutrophils. In conclusion, DXA3 represents a novel eicosanoid, generated by activated platelets that activates neutrophils and may play a role in early immune responses.
Domestic violence: a hidden problem

Domestic violence has presently drawn maximum attention in our country where male dominated society is predominant. However women undergo as much agony in the dominantly matrilineal tribal societies in Meghalaya, as their counterpart in the rest of the country. Majority of the victims were in the age group of 20 to 30 years. Tribals constitute 69.23% of the cases; more in rural areas. The perpetrators were mostly the husbands. 61.54% of the perpetrators were alcoholics. The commonest assault was physical abuse. Socio-cultural factors associated with such violence need to be addressed to prevent such crimes.
Demonstration of receptor sites with electron microscope autoradiography —distribution of receptors for estradiol and its ligands in the mouse and rat uteri—

A large number of developed silver grains accumulated on the nuclei and some were scattered in the cell organelles of mouse endometrial, interstitial, and myometrial cells, 30min after 3H-17-β-6, 7-estradiol administration. 2hr later, they showed distinct active reactions in their cytoplasmic fine structures, although developed silver grains were still located in their nuclei. A single fixation method with 2 to 4/osmium tetroxide seemed very effective to preserve the carrier bound estradiol.Female rats were perfused with PLP (periodate-lysine-paraformaldehyde) or PG (paraformaldehyde and glutaraldehyde) before incubation in radioactive estradiol or its ligands. The perfused uteri were cut in small pieces and incubated in 3H-estradiol or 3H-moxestrol with a 10μCi/ml in phosphate buffer for 2hr at 37°C. They were post-fixed with a mixture of glutaraldehyde and osmium tetroxide for 2hr, then embedded in Epon after dehydration. In both cases, the developed silver grains were homogenously on the cell surfaces, in the cytoplasm, and on the nuclear membranes of endometrial, interstitial, and myometrial cells.No nuclear accumulation was observed in those experiments. However, a very strong accumulation of labeled compounds was observed in the granules of eosinophilic leucocytes and in the lysosomal granules of tissue macrophages.These data suggest that the receptors for the estradiol or ligands in the endometrial cells, especially in the nuclei, cannot accept directly without carrier proteins, except in the eosinophilic leucocyte or macrophages. The results may support facts obtained by many biochemical studies. Furthermore, it is possible that the primary receptors for estradiol or its ligands are distributed in the cytoplasm and on the membrane surface of cells, with only a small number in the nuclei. In this case, secondary receptors should exist in the nuclei, which only accept the carrier-bound estradiol or its ligands.