Miracle-dz/UniFAR-FTUs huggingface dataset:
Fusarium graminearum‐induced shoot elongation and root reduction in maize seedlings correlate with later seedling blight severity

Fusarium graminearum seedling blight is a common disease of maize (Zea mays). Development of genetic resistance to seedling blight in maize germplasm requires efficient and accurate quantitative assessment of disease severity. Through artificial inoculation experiments under controlled growth conditions, we determined that host genotype, pathogen genotype, and infection dose influence the extent to which F. graminearum induces shoot elongation and inhibits root growth in maize seedlings. A comparison of fifteen maize inbred lines showed independent variation of these two fungus-induced effects on seedling growth. In a broader survey with nine commercial maize hybrids and three field-collected fungal isolates, there was significant correlation between these seedling growth responses, as well as with later seedling blight severity. Analysis of variance suggested that this variation and the observed correlative relationships were primarily driven by differing pathogenicity of the three fungal isolates. Together, our results indicate that F. graminearum-induced shoot elongation and root reduction in maize seedlings have distinct underlying physiological mechanisms, and that early observations of seedling growth responses can serve as a proxy for investigating natural variation in host resistance and pathogen aggressiveness at later growth stages.
Prevalence of antibodies against leptospires in the wild boar (Sus scrofa L., 1758)

A total of 307 blood sera of the wild boar from different localities of the Břeclav district (Czech Republic) were examined in 1999 to 2002. Antibodies against leptospires were found in 16.9% of blood sera examined. The incidence of antibodies in the wild boar varied both in individual years (26.1, 5.3, 25.0 and 12.0%, respectively) and age categories (7.8, 17.3 and 35.7%, respectively) with older individuals being more o�en positive. There were found no differences in relation to sex (18.2 and 15.0% of positives in males and females, respectively). Positive reactions at low titres (i.e., 100 and 200) predominated in 71.3%. Higher titres (3 200) were only exceptionally found in older individuals (3.8%). All positive reactions concerned only the L. grippotyphosa serotype (100%). The other 11 serotypes tested were negative. On the basis of the results it can be stated that the wild boar is susceptible to infection by leptospires and the occurrence of specific antibodies correlates to a large extent with the presence of leptospires in the environment. In our opinion, the wild boar could be used for purposes of monitoring natural foci of leptospirosis.
Characterization and categorization of Indian mustard genotypes for agro-morphological traits

A total of sixty genotypes and germplasm lines were evaluated and characterized for 14 quantitative and 8 qualitative traits in Brassica juncea. Observations were recorded on the basis of scores given in the DUS descriptor. Majority of accessions were very late in maturity and medium in flowering. No variability was observed for leaf length and leaf width. On the basis of branches, most of the genotypes were classified under intermediate category. Long main shoot length (31), medium number of siliquae on main shoot (46), medium density on main shoot (52), short siliqua length (51), very tall plant height (38), few numbers of seeds per siliqua (33), medium 1000-seed weight (38), medium seed yield per plant (32) and low oil content (40) were observed in most of the genotypes. For qualitative traits, most of the genotype showed dark green leaf color, sparse hairs, dentation of leaf margin lyrate type, open leaf growth habit, yellow petal color, semi-appressedsiliqua angle with main shoot and intermediate siliqua surface texture. Wide (Yellow, Dull grey, Reddish brown, Brown and Black) diversity has been observed for seed color.
Pseudomonas aeruginosa Can Inhibit Growth of Streptococcal Species via Iron Sequestration

Cystic Fibrosis (CF) is a genetic disease that causes patients to accumulate thick, dehydrated mucus in the lung and develop chronic, polymicrobial infections due to reduced mucociliary clearance. These chronic polymicrobial infections and subsequent decline in lung function are significant factors in the morbidity and mortality of CF. Pseudomonas aeruginosa and Streptococcus spp. are among the most prevalent pathogens in the CF lung; the presence of P. aeruginosa correlates with lung function decline and the Streptococcus milleri group (SMG) is associated with exacerbations in CF patients. Here we characterize the interspecies interactions that occur between these two genera. We demonstrated that multiple P. aeruginosa laboratory strains and clinical CF isolates promote the growth of multiple SMG strains and oral Streptococci in an in vitro coculture system. We investigated the mechanism by which P. aeruginosa enhances growth of streptococci by screening for mutants of P. aeruginosa PA14 unable to enhance Streptococcus growth, and we identified the P. aeruginosa pqsL::TnM mutant, which failed to promote growth of S. constellatus and S. sanguinis. Characterization of the P. aeruginosa ΔpqsL mutant revealed that this strain cannot promote Streptococcus growth. Our genetic data and growth studies support a model whereby the P. aeruginosa ΔpqsL mutant outcompetes Streptococcus sanguinis for limited iron. We propose a model whereby competition for iron represents one important means of interaction between P. aeruginosa and Streptococcus spp.
Spatial distribution and seasonal variation in fluoride enrichment in groundwater and its associated human health risk assessment in Telangana State, South India

ABSTRACT Groundwater is a vital source of drinking water in Siddipet rural and urban regions of Central Telangana, South India and it is a major cause of fluoride toxicity in humans. The intake of elevated fluoride has a significant impact on human health, especially immediate problems that are seen in children's teeth. The primary aim of the study was to identify the seasonal variation in fluoride concentration and associated health risks in the residents of the study region. To assess the fluoride contamination in groundwater, a total of 158 samples were analyzed in two seasons. The mean concentrations of fluoride 1.26 mg/L and 2.21 mg/L were 1.46 and 2.8 times higher than the acceptable limit of 1.5 mg/L, before and after monsoon respectively. To estimate the human health risks due to the ingestion of elevated fluoride through drinking water, hazard quotient fluoride (HQFluoride) was calculated using the United States Environmental Protection Agency method. HQFluoride values were 0.44–2.44 and 0.89–4.67 for children, 0.36–2.00 and 0.73–3.82 for females, and 0.41–2.26 and 0.82–4.31 for males in pre- and post-monsoon seasons respectively, suggesting emphatically greater risk than the acceptable limits (HQFluoride > 1), which generates health risks.
Pathological Alterations in Hepatocytes of Dairy Cows With a Tendency to Emaciation and Fattening

Abstract The aim of this study was to demonstrate the histochemical and histopathological alterations in the livers of cows with a tendency to become emaciated (body condition score - BCS1 and 2) and a tendency to become fattened (BCS4 and 5) in comparison to the cows of average body condition (BCS3) presented as a control. The histochemical analysis (PAS reaction) showed that the influence of emaciation and fattening in our study was manifested by a decreased occurrence of glycogen and a decreased level of the PAS-positive matter in the hepatocytes of dairy cows with BCS1, 2, 4 and 5. An abundant accumulation of lipids in the form of large lipid droplets, liposomes and lipoproteins observed in the hepatocytes of emaciated and fattened (BCS1 and 5) cows may be related to moderate-severe steatosis. These observations suggest a relationship between liver steatosis and the occurrence of lipoproteins in cows with a tendency toward emaciation and fattening.
Pan-cancer analysis of RNA binding proteins (RBPs) reveals the involvement of the core pre-mRNA splicing and translation machinery in tumorigenesis

RNA binding proteins (RBPs) are key regulators of posttranscriptional processes such as RNA maturation, transport, localization, turnover and translation. Despite their dysregulation in various diseases including cancer, the landscape of RBP expression and regulatory mechanisms in human cancer has not been well characterized. Here, we analyzed mRNA expression of 1487 RBPs in ~6700 clinical samples across 16 human cancer types and found that there were significantly more upregulated RBPs than downregulated ones in tumors when compared to their adjacent normal tissues. Across almost all of the 16 cancer types, 109 RBPs were consistently upregulated (cuRBPs) while only 41 RBPs were consistently downregulated (cdRBPs). Integrating expression with the copy number and DNA methylation data, we found that the overexpression of cuRBPs is largely associated with the amplification of copy number, whereas the downregulation of cdRBPs may be a result of epigenetic silencing mediated by DNA methylation. Furthermore, our results indicated that cuRBPs could work together to promote cancer progression potentially through the involvement of splicing and translation machinery, while cdRBPs might function independently to suppress tumorigenesis. Additionally, we focused on colon cancer and identified several novel potential oncogenic RBPs, such as PABPC1L which might promote cancer development via regulating the core splicing machinery. In summary, we showed distinct expression landscapes, regulatory mechanisms and characteristics of cuRBPs and cdRBPs and implicated several novel RBPs in cancer pathogenesis. Moreover, our results suggest that the involvement of the core pre-mRNA splicing and translation machinery could be critical in tumorigenesis.
Dissolved black carbon in aquatic ecosystems

The incomplete combustion of organic molecules produces a chemically diverse suite of pyrogenic residues termed black carbon (BC). The significance of BC cycling on land has long been recognized, and the recognition of dissolved BC (DBC) as a major component of the aquatic carbon cycle is developing rapidly. As we seek a greater understanding of DBC cycling, our interpretation of environmental DBC concentrations and molecular composition should take into account both the formation conditions of charred residues, and the physico‐chemical transformation of DBC that occurs during transit within aquatic systems. We present the current state of knowledge concerning sources, processing, and sinks of DBC in inland, coastal/estuarine, and ocean waters. We feature studies and new methodologies which focus specifically on the aquatic cycling of DBC, explore the relationship between particulate and dissolved BC, and highlight research gaps which should be targeted to advance our current knowledge of DBC biogeochemistry.
Spearfishing modulates flight initiation distance of fishes: the effects of protection, individual size, and bearing a speargun

In a landscape of fear, humans are altering key behaviours of wild-living animals, including those related to foraging, reproduction, and survival. When exposed to potentially lethal human actions, such as hunting or fishing, fish, and wildlife are expected to behaviourally respond by becoming shyer and learning when to be cautious. Using a rich dataset collected in temperate rocky reefs, we provide evidence of spearfishing-induced behavioural changes in five coastal fish taxa, exposed to different levels of spearfishing exploitation, by using flight initiation distance (FID) as a proxy of predator avoidance. We detected a significant increase of mean and size effects of FID when the observer was equipped with a speargun. Such effects were more evident outside marine protected areas where spearfishing was allowed and was commensurate to the historically spearfishing pressure of each investigated taxon. Our results demonstrate the ability of fish to develop fine-tuned antipredator responses and to recognize the risks posed by spearfishers as human predators. This capacity is likely acquired by learning, but harvest-induced truncation of the behavioural diversity and fisheries-induced evolution may also play a role and help to explain the increased timidity shown by the exploited fishes in our study.
Expression of ovine ubiquitin C-terminal hydroxylase 1, pH and colour of variety meats from head-stunned Dohne Merino sheep

Ubiquitin C-terminal hydroxylase (UCH-L1) has been identified in few transcriptome studies as a biomarker coding for trauma and perception of pain in non-meat species. For the first time, real-time polymerase chain reaction (qPCR) assay was used to quantitate the expression of ovine ubiquitin C-terminal hydroxylase 1 (ovUCH-L1 mRNA) from head-stunned Dohne Merino ewes and lambs presented for slaughter at a high-throughput abattoir. The correlation between ambient environment and quality of variety meats from those ovine species was also determined. The level of ovUCH-L1 mRNA expression found in lambs was high, based on the outcome of qPCR quantification. The effect of head stunning shows that ewes exhibited higher capacity to impede electric insults than lambs. Except for the trachea and heart, ambient conditions had a negative correlation with pH of most variety meats. Similarly, a negative correlation was observed between total colour difference (ΔE*) for fillet and dew point. Saturation index of a few variety meats showed a moderate relationship with ambient temperature. Industrially, the results on ambient conditions are important for post-mortem control of pH, colour, and preservation of other physiochemical properties of variety meats. Findings from qPCR quantification indicated that ovUCH-L1 is a novel candidate marker for pain detection in head-stunned ovine species. Keywords: Biomarker, edible offal, halal slaughter, ovine species, stunning
Application of Arbuscular Mycorrhizae Glomus iranicum var. tenuihypharum var. nova in Intensive Agriculture: A Study Case

Intensive agriculture contributes to a decrease in microbial biomass and crop yields, while accelerating soil degradation. Arbuscular mycorrhizae associations have direct benefits for plant nutrition, and may be considered a useful tool in modern agriculture. Notwithstanding the widespread knowledge of these benefits, their use in intensive farming systems has until now been ineffectual, because most mycorrhizal species have low tolerance toward high concentrations of nutrients and are poorly adapted to the soil and/or mycorrhizal functioning. The aim of this work was to test the efficacy of an arbuscular mycorrhizal (AM) fungus, Glomus iranicum var. tenuihypharum on lettuce and table grape crops in different intensive farming systems. The variables studied were root colonization percentage, external mycelium concentration, gas exchange, photosynthetic activity, root starch concentration and plant nutrition. The main finding was that the fungus is tolerant of a wide range of soil pH values, high salinity levels and abundant external mycelium. In lettuce, it produced significant increases in plant physiological activity and productivity (10%-15%); and in table grapes, increases of 12%-45% in yield were achieved for more than three years in Crimson variety, and significant increases in fruit cluster weight, color uniformity and Brix (°Bx). The AM species is protected by two patents and is a component of MycoUp, MycoUp Activ, Resid HC and Resid MG, whose commercial application has spread to more than 30 countries, with increments in crop yields of 8%-45% in lines as varied as leaf vegetables, berries, fruit, olives, grapes, greenhouse crops and cereals.
A novel histone H4 variant regulates rDNA transcription in breast cancer

Histone variants, present in various cell types and tissues, are known to exhibit different functions. For example, histone H3.3 and H2A.Z are both involved in gene expression regulation, whereas H2A.X is a specific variant that responds to DNA double-strand breaks. In this study, we characterized H4G, a novel hominidae-specific histone H4 variant. H4G expression was found in a variety of cell lines and was particularly overexpressed in the tissues of breast cancer patients. H4G was found to localize primarily to the nucleoli of the cell nucleus. This localization was controlled by the interaction of the alpha helix 3 of the histone fold motif with the histone chaperone, nucleophosphomin 1. In addition, we found that H4G nucleolar localization increased rRNA levels, protein synthesis rates, and cell cycle progression. Furthermore, micrococcal nuclease digestion of H4G-containing nucleosomes reconstituted in vitro indicated that H4G destabilizes the nucleosome, which may serve to alter nucleolar chromatin in a way that enhances rDNA transcription in breast cancer tissues.
Betaines and N-Methylprolines from Venezuelan Plants

A collection of tropical Angiosperms, mainly collected in Amazonas and Apure States in Venezuela, has been examined for the presence of betaines and N-methylprolines, which were found in 58 out of the 65 species investigated. Betaine yields were generally low, but in the species that contained N-methylprolines, the yields of these compounds were generally in excess of 0.5% of the plant dry weight. N-methylprolines were isolated from four species of Loranthaceae, all four examined species of Miconia (Melastomataceae), Pleonotema variabilis (Bignoniaceae), Gustavia augusta and Lecythis corrugata (Lecythidaceae), and Machaerium humboldtianum (Fabaceae). Trans-4-hydroxyprolinebetaine was isolated in high yields from Amphilophium paniculatum, Arrabidaea candidans and Clytostoma binatum (Bignoniaceae), Combretum laxum (Combretaceae) and Gustavia augusta (Lecythidaceae).
Origins and early evolution of photosynthetic eukaryotes

Primary plastids derive from a cyanobacterium that entered into an endosymbioticrelationship with a eukaryotic host. This event gave rise to the supergroup Archaeplastida whichcomprises Viridiplantae (green algae and land plants), Rhodophyta (red algae) and Glaucophyta. Afterprimary endosymbiosis, red and green algae spread the ability to photosynthesize to other eukaryoticlineages via secondary endosymbioses. Although considerable progress has been made in theunderstanding of the evolution of photosynthetic eukaryotes, important questions remained debatedsuch as the present-day closest cyanobacterial lineage to primary plastids as well as the number andidentity of partners in secondary endosymbioses.The main objectives of my PhD were to study the origin and evolution of plastid-bearing eukaryotesusing phylogenetic and phylogenomic approaches to shed some light on how primary and secondaryendosymbioses occurred. In this work, I show that primary plastids evolved from a close relative ofGloeomargarita lithophora, a recently sequenced early-branching cyanobacterium that has been onlydetected in terrestrial environments. This result provide interesting hints on the ecological setting whereprimary endosymbiosis likely took place. Regarding the evolution of eukaryotic lineages with secondaryplastids, I show that the nuclear genomes of chlorarachniophytes and euglenids, two photosyntheticlineages with green alga-derived plastids, encode for a large number of genes acquired by transfersfrom red algae. Finally, I highlight that SELMA, the translocation machinery putatively used to importproteins across the second outermost membrane of secondary red plastids with four membranes, has asurprisingly complex history with strong evolutionary implications: cryptophytes have recruited a set ofSELMA components different from those present in haptophytes, stramenopiles and alveolates.In conclusion, during my PhD I identified for the first time the closest living cyanobacterium to primaryplastids and provided new insights on the complex evolution that have undergone secondary plastid-bearing eukaryotes
Estimation of type i collagen structure dissolved in inorganical acids from circular dichroism spectra

Usually, weak inorganic acids have been used to disperse collagen as green solvents for fabricating kinds of biomaterials all the time. However, it is an open question how much the dissolving process preserves or alters the native structure of collagen till now. Herein, we have examined the effect of three different solvents (HAc, HCl, H3PO4) on the secondary structures of collagen, based on circular dichroism (CD) spectra of collagen from 185 to 260 nm together with CDNN programs. We have found that collagen almost completely preserved its triple helical structure in the three inorganic acids at pH=3.0 or so, which demonstrated that it was the concentration of free H in the above three solutions whose pH was fixed at 3.0 that can maintain an proper amount of surface charge on the collagen colloidal particles and appropriately loose the three-helix structure, which can not only lead to a better dispersion behavior, but also maximize the preservation of the integrity of the collagen structure. Although the fractions of kinds of secondary structures in collagen were different from all the three solvents based on CDNN data, which gave very similar results for each other. These results was tested for the first time in this work to estimate the secondary structures for collagen in the different common inorganic acids, which provides a new avenue for green collagen solvents to prepare collagen-based composite with well triple-helical structure for tissue engineering.
Detecting Protein Variants within Mass Spectrometry Datasets

An important aim of cancer proteomics is to understand how the cancer proteome, with all its variation in both protein sequence and protein abundance, emerges from aberrations characterized within cancer genomic and transcriptomic datasets. A challenge in reaching this goal is that standard mass-spectrometry-based onco-proteomic strategies typically ignore variations in protein sequences, instead characterizing cancer proteomes in terms of changing abundances of standard reference proteins. In this thesis, I assess strategies for incorporating information about protein sequence variation within standard proteomics analysis strategies. I develop a pipeline for the characterization of variations within protein sequences and assess the best methodology to do so.
Gamma rays induced chromosomal aberrations in tomato ( Solanum lycopersicum L.)

Gamma irradiation is one of the physical mutagens that are widely used for induced mutations, food sterilization and medicinal healing. In the present study, irradiation techniques were applied to investigate the effect of gamma irradiation on seed germination, meiotic behavior and pollen fertility of tomato (Solanum lycopersicum L.). The seeds of Solanum lycopersicum (var. Bharat ratan -221) were irradiated with different doses of gamma rays (10, 15, 20, 25, 30, 35 and 40 kR). Results showed that seed germination and pollen fertility in M1 generation reduced steadily with the increasing doses of gamma rays. During the study, increases in meiotic abnormalities with increasing doses were noticed in mutagenic population of gamma rays in M1 generation. The most common chromosome abnormalities observed include univalents, multivalents, bridges, laggards, fragments, micronuclei and disturbed polarity, etc.