Miracle-dz/UniFAR-FTUs huggingface dataset:
Isolation and characterization of lactic acid bacteria from Ukrainiantraditional dairy products

The aim of this study was to isolate, identify and analyze the diversity of the predominantlactic acid bacteria (LAB) genera occurring in Ukrainian traditionally prepared dairy products and toassess their potential for industrial application. Fermented milk, soured cream, cottage cheese andbryndza made from raw cow’s, goat’s or sheep’s milk were prepared on traditional way without theaddition of a starter culture. The samples were collected from 9 regions in Ukraine. In total 950strains of LAB strains were isolated and identified using phenotypic and genotypic methods. Among allisolates, Enterococcussp. strains represented 60%,Lactococcussp. —27%,Lactobacillussp. —6%,Leuconostocsp. —3.5% andPediococcussp. —3%. The diversity of the isolated LAB strains wascorrelated with the type of product and the source of milk. The milk clotting activity of isolated LABstrains was preliminary tested to assess their potential for industrial application as starter cultures.Most (54%) of the LAB strains isolated from Ukrainian traditional dairy products showed apotentially good acidifying activity and coagulated milk within 12 h. The milk coagulation rate wasnot strongly dependent on the LAB genus and was strain dependent. The time of milk clotting wascorrelated with product, from which strains were isolated. This is the first systematic study of theLAB diversity in Ukrainian artisanal dairy products, which can be a source of new LAB strains withgood technological and functional properties
Evolutionary Dynamics of 5S rDNA and Recurrent Association of Transposable Elements in Electric Fish of the Family Gymnotidae (Gymnotiformes): The Case of Gymnotus mamiraua

Gymnotidae is a family of electric fish endemic to the Neotropics consisting of 2 genera: Electrophorus and Gymnotus. The genus Gymnotus is widely distributed and is found in all of the major Brazilian river systems. Physical and molecular mapping data for the ribosomal DNA (rDNA) in this genus are still scarce, with its chromosomal location known in only 11 species. As other species of Gymnotus with 2n = 54 chromosomes from the Paraná-Paraguay basin, G. mamiraua was found to have a large number of 5S rDNA sites. Isolation and cloning of the 5S rDNA sequences from G. mamiraua identified a fragment of a transposable element similar to the Tc1/mariner transposon associated with a non-transcribed spacer. Double fluorescence in situ hybridization analysis of this element and the 5S rDNA showed that they were colocalized on several chromosomes, in addition to acting as nonsyntenic markers on others. Our data show the association between these sequences and suggest that the Tc1 retrotransposon may be the agent that drives the spread of these 5S rDNA-like sequences in the G. mamiraua genome.
Trinexapac-ethyl Restricts Shoot Growth and Improves Quality of `Diamond' Zoysiagrass Under Shade

Turfgrass is grown under extremely variable light intensities. This presents difficult management problems, and methods are needed to improve turf performance under variable shade conditions. Two experiments were conducted to determine the influence of trinexapac-ethyl (TE) on turf performance and physiological responses of 'Diamond' zoysiagrass [Zoysia matrella (L.) Merr. ] under several light intensities. In a polyethylene-roofed greenhouse, 'Diamond as sodded in 12 wooden boxes (1.2 x 1.2 x 0.16 m) (Expt. 1) and 18 fiber containers (55 x 38 x 12 cm) (Expt. 2). Treatments applied to boxes or containers included three levels of shade (40%, 75%, and 88%) with and without multiple TE applications at 48 g.ha -1 of active ingredient. Without TE treatment, vertical shoot growth increased linearly with increasing shade levels. Excessive shoot growth under 75% and 88% shade exacerbated energy depletion, as evidenced by the 45% and 67% lower rhizome mass and the 37% and 65% lower total nonstructural carbohydrate content (TNC), respectively, compared with turf under 40% shade. Trinexapac-ethyl reduced excessive vertical shoot growth and increased rhizome mass and TNC. Mean turf quality was increased by 0.7 and 1.4 units for turf receiving multiple TE applications under 75% and 88% shade, respectively. Trinexapac-ethyl did not increase turf quality or TNC under 40% shade. Canopy photosynthetic rate (Pn) was not affected 4 weeks after the initial TE treatment under any shade level. However, 34 weeks after the initial TE treatment a 50% higher Pn was observed for turf treated with TE under 88% shade, possibly because of higher tiller density. Repeated TE application increased turf quality and provided more favorable physiological responses (such as TNC and Pn) under 75% and 88% shade, here conditions favored vertical shoot growth. However, little or no improvement in turf quality as observed under 40% shade, where conditions favored slow vertical shoot growth. Chemical name used: 4-(cyclopropyl-α-hydroxy-methylene)-3,5-dioxo-cyclohexanecarboxyli acid ethyl ester (trinexapac-ethyl).
Assessment of renal functions with different glomerular filtration rate formulas in children with acute exposure of mercury

Abstract Objective: Our aim was to determine whether cystatin C level has a superiority to creatinine to assess kidney functions in rapid decreases of glomerular filtration rate due to acute mercury exposure in children. Eight different glomerular filtration rate calculation formulas which have been used creatinine and/or cystatin C were also compared. Methods: Serum urea, creatinine and cystatin C values of 39 mercury exposed children were measured. Glomerular filtration rates were calculated by eight different formulas. Patient group was divided into three subgroups according to mercury levels. Results: Cystatin C and mercury levels of the patients were found significantly different from control group (p<0.001). There was not a significant difference in creatinine and urea values between two groups (p=0.913, p=0.236). There was not a significant difference between patient and control groups in GFR calculations which have been used serum creatinine and height or which have been used urea additional to them (p=0.069, p=0.559, p=0.424, p=0.945, respectively), but there was a significant difference between patient and control groups in GFR calculations which have been used cystatin C only or creatinine, urea and height in addition to this (p<0.001, p<0.001, p=0.042, p<0.001, respectively). In sugroup analysis, cystatin C results and the results of three GFR calculations of four GFR calculations which were used cystatin C were found different in control group according to subgroups but there was not a difference between subgroups. Conclusion: Cystatin C level is a better indicator than creatinine to assess kidney functions in rapid decreases of glomerular filtration rate due to acute exposure of mercury. Formulas using cystatin C gave better results than formulas using creatinine and height in estimation of glomerular filtration rate.
Dynamics of genetic differentiation in experimental Drosophila metapopulations

As a result of the fragmentation of their habitats, many organisms live in small and relatively isolated populations. In my thesis, I investigate the interplay of migration and local adaptation. Migration promotes genetic exchange among populations, thus contributing to the maintenance of genetic variation. Moreover, migration is a homogenising process that reduces the differences between local populations. Local adaptation (the adaptation of populations to their local circumstances) occurs when the direction of natural selection differs between habitats (diversifying selection). Hence, local adaptation results in the diversification of populations. By means of Drosophila experiments and computer simulations, I surveyed the interrelation between migration and local adaptation. I found that diversifying selection strongly reduces the efficiency of migration. In the presence of local adaptation, migrants are not well-adapted to their new environment and therefore less able to spread their genes to future generations. This applies to all their genes, and not only to the genes involved in local adaptation. Hence, despite considerable migration, local populations become genetically isolated (‘isolation-by-adaptation’). In the presence of regular extinction and recolonisation, migration is more efficient in preventing genetic isolation. However, efficient migration is often associated with the loss of local adaptation and therefore may reduce population viability. Already under the highly standardized conditions of my lab experiments and my simulations the interplay between migration and local adaptation turned out to be very intricate, with many surprising facets. This pleads for caution when making inferences and predictions in natural settings.
Evidence of positive selection in the mitochondrial cytochrome B gene of cetaceans

Mitochondrial genomes (mitogenomes) code for, in part, the enzymes involved in the creation of energy for cellular function. Altering these highly conserved genes even slightly can have a biochemical impact on this pathway. Analyzing the mitogenome for positive selection using models that take biochemically significant changes into account can identify adaptive alterations presumably under selection due to energetic costs that vary across lineages due to physiological divergence, environmental factors, or ecological drivers. This study was conducted on the mitochondrial cytochrome B (CYTB) gene of 45 cetacean species. Using TreeSAAP, I identified evidence of positive selection based on five physicochemical properties acting on several of the transmembrane helical regions of CYTB. In addition to these broad regional findings, 88 codon sites were identified to have undergone radical and significant changes. Further computational analysis will be necessary in order to better resolve which codons are undergoing adaptive changes. This study was not able to conclusively identify any singular metabolic driver for amino acid alterations among lineages
Preparation of Mitochondria from Candida albicans

[Abstract] Based on the methods of (Daum et al., 1982) and (Hewitt et al., 2012), we have established the use of Candida albicans as a new model system to study mitochondrial biogenesis. This dimorphic yeast provides an excellent system to investigate the coordination of mitochondrial biogenesis with other cellular networks including cellular metabolism and the cell cycle. Unlike the model lab yeast Saccharomyces cerevisiae, which has been widely used in the mitochondrial biogenesis field, C. albicans is not subject to the Crabtree effect, hence grows aerobically in glucose when oxygen is present. Therefore the control of mitochondrial biogenesis in C. albicans is more typical of eukaryotic cells. C. albicans has a fully sequenced genome and there are many published tools for genetic manipulation facilitating Systems Biology approaches. The isolation of mitochondria as described in this protocol produces a more simplified system that can be interrogated using the standard tools of molecular biology. In addition the import of radiolabelled proteins as described in the protocol: Candida albicans Mitochondrial Protein Import Assay (Hewitt et al., 2013) is a sensitive technique that can be used to determine details of kinetics and interactions of imported proteins.
Predominance of N-acetyl transferase 2 slow acetylator alleles in children less than ten years experiencing adverse treatment events following artemisinin-based combination therapy in North and South West Regions of Cameroon

The human N -acetyltransferase II (NAT2) gene may vary between individuals resulting in variability in the incidence of adverse drug reactions. We set out in this adhoc analysis to determine the distribution of allele frequencies of NAT2 gene variants among children less than ten years treated with artemisinin-based combinations in Cameroon. Children with uncomplicated malaria were deparasitized with artemisinin based combination therapy (artesunate amodiaquine, dihydroartemisinin-piperaquine and artemether-lumefantrine) and followed up for 42 days and adverse events recorded. Blood was spotted on filter paper prior to drug administration for DNA extraction by chelex method. Standard nested PCR followed by restriction enzyme analysis with KpnI , TaqI , and BamHI for detection of polymorphisms in the NAT2 was performed. Allelic frequencies and acetylator phenotypes were compared between participants with or without adverse drug events. The prevalence of slow, intermediate and fast acetylators was 54, 34 and 12% respectively. Significant clustering of mutant alleles ( NAT2*5 , NAT2*6 and NAT2*7 ) occurred among those who experienced skin rash and tiredness (OR = 5.765, P = 0.046) (OR = 13.280, P = 0.020). No significant difference was observed between fast and slow acetylators with respect to the development of other recorded adverse events. Overall, producers of the slow acetylator alleles were more likely to develop any adverse events (OR = 8.286, P = 0.017) during the study period. Mutant alleles of the wild type NAT2*4 associated with the slow acetylator phenotype were the most predominant NAT2 allelic type and individuals with the phenotype were more likely to develop adverse events to ACTs. Keywords: N -Acetyltransferase 2, Artemisinin based combination therapy, adverse events, slow acetylators, allele
Molecular Detection of Mycobacterium tuberculosis Rifampicin Drug Resistance Using rpoB Gene Sequencing in Zimbabwe

This work carried out collaboration between all authors. Author NC designed the study. Author EM isolated the bacteria and performed DNA extractions. Authors NC and WM performed RpoB gene amplification and the bioinformatics analysis of the results. Author NC wrote the protocol and the first draft of the manuscript. All authors contributed to the writing of the manuscript. All authors read and approved the final manuscript. ABSTRACT Aim: To detect Mtb rifampicin drug resistance mutations in Zimbabwe by rpoB gene sequencing. Study Design: This was a retrospective study. Place of Study: The study was conducted in Zimbabwe in 2015 using archived Mtb isolates previously isolated throughout Zimbabwe during a national TB Survey. Methodology: Archived Mtb isolates at the National Microbiology Reference Laboratory were retrieved. Genomic DNA from the isolates was extracted by the boiling method. The 81 bp region of rpoB gene that contains rifampicin drug resistance mutations was amplified by polymerase chain reaction (PCR). The PCR products were sequenced and sequences analyzed to determine mutations in the rpoB protein. Results: RpoB mutations in 30 Mtb isolates were analyzed. Out of the 30 Mtb isolates, 19 (63.3%) had at least one codon mutation in the rpoB gene that resulted in a change of amino acid. The commonest mutation was on codons 531 (S>L), with a prevalence of 20%. Other mutations were detected at codons 511 (L>P) (3.3%), 516 (D>Y) (10.0%), 516 (D>V) (3.3%), 518 (N>H) (3.3%), 526 (H>D) (10.0%), 526 (H>L) (3.3%), 526 (H>C) (3.3%), 526 (H>Y) (3.3%) and 533 (L>P) (6.6%). The other 11 Mtb isolates (36.7%) did not have any mutations in the gene coding for drug resistance. Conclusion: Genetic mutations that code for rifampicin drug resistance are prevalent in Mtb isolates from Zimbabwe. Further studies need to be instituted to ascertain the scope and threat of the Mtb drug resistance.
Evaluation of canola meal derived from Brassica juncea and Brassica napus on rumen fermentation and nutrient digestibility by feedlot heifers fed finishing diets

Abstract: Five yearling heifers (387 ± 6.5 kg) were utilized in a 5 × 5 Latin square to evaluate the substitution of canola meal (CM) derived from Brassica (B.) napus and B. juncea seed for barley grain on feed intake and nutrient utilization. The control diet (CONTROL) consisted of 88.3% barley grain, 4.4% barley silage, and 7.3% supplement [dry matter (DM) basis]. The four CM treatments included 10% and 20% B. napus or B. juncea meal, with CM replacing barley grain. Dry matter intake was not affected (P > 0.05) by treatment. Total duration and area under rumen pH 5.8, 5.5, and 5.2 increased (P < 0.05) with greater inclusion of CM, regardless of type. Cattle fed 20% CM had elevated rumen ammonia-N concentration and urinary N excretion. Cattle fed B. juncea meal exhibited greater (P < 0.05) apparent nutrient digestibility compared with those fed B. napus meal. In conclusion, meal derived from B. napus or B. juncea can be used to replace barley grain at levels up to 20% (DM) in finishing diets without compromising rumen fermentation or total tract nutrient digestibility. However, animal performance and possible economic benefits need to be balanced against the increasing N excretion resulting from over-feeding protein to cattle.
Ski-piste revegetation promotes partial bird community recovery in the European Alps

ABSTRACT Capsule: Restoration of grasslands on ski-pistes caused a recovery in the bird community, but not to the extent that it was equivalent to a natural Alpine grassland community. Aim: To test whether revegetation of ski-pistes in open habitat areas results in bird community recovery. Methods: The bird communities in two ski resorts in the Italian Maritime Alps were surveyed using a standardized area count method in three different plot types: non-restored ski-pistes (newly constructed), restored ski-pistes and control plots in grassland far from ski-pistes. Results: In 49 independent plots, 32 species were recorded. Species richness and abundance of birds were significantly higher on restored than on non-restored ski-pistes, independently of the species group considered and the analyses carried out. Bird community parameters of restored ski-pistes were still lower than those of natural grassland, as shown by results of typical grassland species. Conclusion: Our results suggest that an apparently successful restoration of ski-pistes may be not enough to promote a complete recovery of bird communities. The complete recovery of local bird communities may be promoted only if an integral recovery of the original vegetal communities is achieved. We suggest the best conservation option is to adopt techniques to maintain as far as possible original grassland if construction of new ski-pistes is unavoidable.
Inability of Pediococcus pentosaceus to Inhibit Clostridium botulinum in sous vide Beef With Gravy at 4 and 10°C.

The ability of Pediococcus pentosaceus to inhibit Clostridium botulinum toxigenesis in minimally heat-treated, vacuum-packaged sous vide-type beef with gravy was investigated. The bacteriocinogenic strain P. pentosaceus ATCC 43200 and the nonbacteriocinogenic strain P. pentosaceus 43NP1 were coinoculated with proteolytic and nonproteolytic C. botulinum types A and B spores into minimally processed meat with gravy. Toxin was present in samples inoculated with C. botulinum alone by day 31 at 4°C and by day 6 at 10°C. When coinoculated with C. botulinum , neither strain of Pediococcus was capable of significantly delaying the appearance of toxin. Although an enzyme-linked immunosorbent assay method for botulinal toxin was useful for screening toxin-positive samples, a high proportion of false negatives was revealed by confirmatory mouse bioassays. This research confirms that, if botulinal spores are present, sous vide beef does present a botulinal hazard, even when kept under adequate refrigeration.
Decoding the cellular zipcode : Functional analysis of transit peptide motifs and mechanistic implications in plastid targeting and import

5 Over 95% of plastid proteins are nuclear-encoded as precursors containing an N-terminal 6 extension known as the transit peptide (TP). Although highly variable, TPs direct the 7 precursors through a conserved, posttranslational mechanism involving translocons in 8 the outer (Toc) and inner envelope (Tic). The organelle import specificity is mediated by 9 one or more components of the Toc complex. However, the high TP diversity creates a 10 paradox on how the sequences can be specifically recognized. An emerging model of TP 11 design is that they contain multiple loosely conserved motifs that are recognized at 12 different steps in the targeting and transport process. Bioinformatics has established that 13 many TPs contain semi-conserved physicochemical motifs, termed FGLK. In order to 14 characterize FGLK motifs in TP recognition and import, we have analyzed two well15 studied TPs from the precursor of RuBisCO small subunit (SStp) and ferredoxin (Fdtp). 16 Both SStp and Fdtp contain two FGLK motifs. Analysis of large set mutations (~85) in 17 these two motifs using in vitro, in organello, and in vivo approaches support a model in 18 which the FGLK domains mediate interaction with Toc34 and possibly other TOC 19 components. In vivo import analysis suggests that multiple FGLK motifs are functionally 20 redundant. Furthermore, we discuss how FGLK motifs are required for efficient precursor 21 protein import and how these elements may permit a convergent function of this highly 22 variable class of targeting sequences. 23
Genetic similarities among certain freshwater mussel populations of the Lampsilis genus in North Carolina

The objective of this research was to explore ecological and genetic similarities among several southeastern freshwater mussel populations, focusing especially on two rare and potentially endangered «subspecies» of lampsilis radiata residing in river systems in the Piedmont and coastal plain of North Carolina. Conchological analyses and the examination of genetic identity patterns derived from 11 electrophoretic loci in six different populations or species formed the basis of our interpretations. Two currently recognized subspecies of lampsilis radiata (radiata and conspicua) are now quite rare in North Carolina waters, and one, L. r. conspicua, may be endemic to the state
CULTURING AND SPAWNING STRATEGIES FOR CULTIVATION OF GANODERMA LUCIDUM Short Communication

Results: Malt Agar Extract medium and Glucose Asparagine Solution supported the best mycelial growth among the solid and liquid media screened for the purpose. Barley grains were the best for the spawn development. Maximum yield was observed on the Oak sawdust and the wheat bran (4:1 w/w) mixture used as a substrate. Conclusion: The study revealed that this pharmacologically important mushroom can be grown under lab conditions, and more yield of the mushroom can be obtained using barley based spawn.