Miracle-dz/UniFAR-FTUs huggingface dataset:
Studies on Genetic and Non-Genetic Factors Affecting Performance Traits of Frieswal Cows.

A total of 601 lactation records of 205 Frieswal cows (Holstein Friesian and Sahiwal crossbred) from 1st to 4th parity over a period of 9 years from 1998 to 2006 maintained at Military farm, Jammu Cantonment (J&K, India) were used to estimate performance of reproduction and production traits and to study the effect of genetic and non genetic factors on performance traits. The overall averages for age at first service (AFS), age at first calving (AFC), gestation length (GL), dry period (DP), calving interval (CI), lactation length (LL), total lactation milk yield (TLMY) and milk yield per day of lactation length (MYDL) were estimated as 20.53 ± 0.44 months, 29.72 ± 0.45 months, 278.43 ± 1.54 days, 116.85 ± 4.40 days, 423.46 ± 6.15 days, 305.05 ± 4.51 days, 3087.00 ± 62.60 kg and 10.10 ± 0.16 kg, respectively. The effect of genetic group of sire was significant on age at first service, age at first calving, calving interval, lactation length, total lactation milk yield and milk yield per day of lactation length whereas effect of period was significant on all reproduction and production traits except for gestation length and lactation length. The effect of parity was significant only on dry period and milk yield per day of lactation length whereas effect of season was non-significant on all reproduction and production traits except for calving interval where it had significant effect.
Skull variation in Dinaric–Balkan and Carpathian gray wolf populations revealed by geometric morphometric approaches

Abstract Dinaric–Balkan and Carpathian gray wolf (Canis lupus L., 1758) populations, although geographically separated, occupy closely situated areas in the territory of Serbia. We studied morphological variation in the skull to investigate whether the two populations are distinguishable despite the animals being very large and highly mobile and seeming to form one continuous population. The size and shape of the mandible and cranium in the lateral view were compared between sexes and populations using landmark-based geometric morphometrics. Significant differences between sexes and populations were found for size and shape of both structures. Males were larger than females in both populations, and Carpathian were larger than Dinaric–Balkan wolves. Principal component analysis revealed the cranium to be a highly discriminative skull structure. Zygomatic arches were located anteriorly in males and posteriorly in females. Dinaric–Balkan wolves had a more elevated snout and sagittal crest than Carpathian wolves. Difference between Dinaric–Balkan and Carpathian wolves in the cranial flexion was observed for the first time in a comparative study of wolf populations. Present-day separation of Dinaric–Balkan and Carpathian wolf populations could have originated from 2 different glacial refuges. We presume that the observed morphometric divergence between the populations is not only a relic of the last glacial maximum but was further strengthened and shaped by synergistic effects of environmental factors and social behavior (territoriality and a dispersal mechanism influenced by the natal habitat).
Protein phosphorylation in mammalian sperm during capacitation

Subcellular fractionation revealed that pp97, pp96 and pp64 are head protein whereas pp90 and pp55 are tail proteins. Advanced proteomic analysis (GeLC-MS) identified 37 proteins, including AKAP4, AKAP3, CALI, HSPAlL and HSP70 as candidates for the dephosphorylated proteins. AKAP4 was excluded because it was localised to the tail. Two AKAP3 antibodies showed non-specific binding and a better quality antibody will be needed for further investigations. CALI was excluded because it was localised to the tail fraction. HSP70/72 and HSPA1L were strong candidates for pp64. However, immunoprecipitation of dephosphorylated proteins using phospho (S/T) PKA substrate Ab and HSPA1L Ab was unsuccessful and further work is now required to address this.
Diversity studies in the interaction between the anthracnose fungus Colletotrichum gloeosporioides and its host plant Stylosanthes spp. in Mexico

Pests and diseases are important constraints to production in both traditional and modern agricultural systems. It is widely accepted that crop diversity, mainly through use of resistance and tolerance genes, is an important asset in reducing the risk of crop losses related to pests and diseases. However, little is known about the effect of the natural pathogen diversity on the occurrence and severity of phytopathological infestations. This publication summarizes the results of the multidisciplinary project ‘Genetic diversity studies in the interaction between the anthracnose fungus Colletotrichum gloeosporioides and its host plant Stylosanthes spp. ’ The legume Stylosanthes is an important forage crop worldwide and Colletotrichum gloeosporioides is its most important pathogen. This project was a multidisciplinary bi-national effort centred in Mexico, a centre of origin of the host plant, which focused on characterizing both the host plant and the pathogen using different characterization techniques, from macro-morphological through molecular. As anthracnosis is reducing Stylosanthes yields from Africa to Australia, an increased knowledge and understanding of the co-existence of crop and pathogen diversity will benefit stakeholders outside the study area as well. A team of international researchers undertook a coordinated effort to increase the inclusion of information on host and pathogen diversity in areas where the crop and its pathogen are native. The Unite de Phytopathologie de l’Universite catholique de Louvain, Louvain-la-Neuve, Belgium (UCL) focused on the characterization of C. gloeosporioides and other Colletotrichum species associated with wild Stylosanthes species in Mexico, while Stylosanthes diversity and taxonomy were studied by the Laboratorio de Recursos Naturales, Unidad de Biologia, Tecnologia y Prototipos, Facultad de Estudios Superiores Iztacala de la Universidad Nacional Autonoma de Mexico (UNAM) at the morphological level and by the Laboratory of Gene Technology, Katholieke Universiteit Leuven, Belgium (KUL) that studied the material at the molecular level. The Mexican partner, UNAM, was responsible for the collection of materials, both host plant and pathogen, while the Belgian partners, UCL and KUL, carried out the molecular analysis. This study is a clear example of how a collaborative, multidisciplinary effort, including the exchange of plant material, allows for the optimal use of existing synergies between different research centres, leading to a better understanding of a complex theme such as host-pathogen diversity. This will permit a better use of the crop’s genetic diversity, and the corresponding resistance genes available, as well as the application of better screening methods for pest or disease resistance, based on a more extensive pathogen diversity.
Movement ecology of five Afrotropical waterfowl species from Malawi, Mali and Nigeria

Habitat availability for Afrotropical waterbirds is highly dynamic with unpredictable rainfall patterns and ephemeral wetlands resulting in diverse movement strategies among different species. Movement strategies among waterfowl encompass resident, regional and intercontinental migrants, but little quantitative information exists on their specific movement patterns. We studied the movement ecology of five Afrotropical waterfowl species marked with satellite transmitters in Malawi, Mali and Nigeria. Resident species, including White-faced Whistling Ducks Dendrocygna viduata, Fulvous Whistling Ducks Dendrocygna bicolor and Spur-winged Geese Plectropterus gambensis, remained sedentary during the rainy season and only flew limited distances during other months. In contrast, Knob-billed Ducks Sarkidiornis melanotos made short regional movements >50 km in all months and showed little site fidelity to previously used habitats in subsequent years. Garganey Anas quequedula followed an intercontinental strategy and made long-distance jumps across the Sahara and Mediterranean to their Eurasian breeding grounds. Most species flew farthest during the dry season, as mean daily movements varied from 1.5 to 14.2 km and was greatest in the winter months (January–March). Total distance moved varied from 9.5 km for White-faced Whistling Ducks (October–December) to 45.6 km for Knob-billed Ducks (April–June). Nomadic behaviour by Knob-billed Ducks was evidenced by long exploratory flights, but small mean daily movements suggested that they were relying on previous experience. Improving our understanding of these movement strategies increases our ability to assess connectivity of wetland resources that support waterfowl throughout their annual cycle and focuses conservation efforts on their most important habitats.
Response of Rainfed Sunflower (Helianthus annuus L.) to Nitrogen Rates and Plant Population in the Semi-arid Savanna Region of Nigeria

Field experiments were conducted during the wet seasons of 1991, 1992 and 1993 at the Abubakar Tafawa Balewa University Farm, Bauchi (10° 22'N, 09° 47'E) to study the response of sunflower (Helianthus annuus L.) to N rates and plant population under rainfed conditions. Four N rates (0, 50, 100 and 150 kg N ha -1 ) and four plant populations (40 0000, 80 000, 120 000 and 160 000 plants ha -1 ) were factorially combined in a randomized complete block design with three replications. Leaf area index, shoot dry weight and seed yield kg ha -1 ) increased significantly with increasing N rates from 0 to 100 kg N ha -1 . The growth and yield parameters per plant decreased significantly with increasing plant populations from 40 000 to 16 000 plants ha -1 , but the seed yield (kg ha -1 ) obtained at 80 000 plants ha -1 was significantly higher than all the other plant populations. The interactions of N x plant population confounded the main effect of each factor on the growth and yield of sunflower. The seed yield (3425 kg ha -1 ) obtained from the use of 100 kg N ha -1 at 80 000 plants ha -1 was significantly higher than those obtained from all other combinations of N x population and out-yielded the main effects of 100 kg N ha -1 and 80 000 plants ha -1 by 18 % and 25 %, respectively. The use of 100 kg N ha -1 at 80 000 plants ha -1 is therefore recommended for maximum yield of sunflower in Bauchi.
Rate of Germination and Seedling Growth of Perennial Ryegrass Seed following Osmoconditioning

This study evaluates the effects of seed osmoconditioning on germination and seedling growth of perennial ryegrass (Lolium perenne L.). Seeds were osmoconditioned in polyethylene glycol 8000 with water potentials ranging from 0 to -1-4 MPa for 48 hours. Osmoconditioning for this crop at -1-1 MPa resulted in a 35% germination increase after 48 hours under optimum (15/25C) germination conditions. This promotive effect was observed until 104 hours for percentage germination and root growth and 118 hours for shoot growth (.)
MMEJ-based Precision Gene Editing for applications in Gene Therapy and Functional Genomics

Experiments in gene editing commonly elicit error-prone non-homologous end joining for DNA double-strand break (DSB) repair. Microhomology-mediated end joining (MMEJ) can generate more predictable outcomes for functional genomic and somatic therapeutic applications. MENTHU is a computational tool that predicts nuclease-targetable sites likely to result in MMEJ-repaired, homogeneous genotypes (PreMAs) in zebrafish. We deployed MENTHU on 5,885 distinct Cas9-mediated DSBs in mouse embryonic stem cells, and compared the predictions to those by inDelphi, another DSB repair predictive algorithm. MENTHU correctly identified 46% of all PreMAs available, doubling the sensitivity of inDelphi. We also introduce MENTHU@4, an MENTHU update trained on this large dataset. We trained two MENTHU-based algorithms on this larger dataset and validated them against each other, MENTHU, and inDelphi. Finally, we estimated the frequency and distribution of SpCas9-targetable PreMAs in vertebrate coding regions to evaluate MMEJ-based targeting for gene discovery. 44 out of 54 genes (81%) contained at least one early out-of-frame PreMA and 48 out of 54 (89%) did so when also considering Cas12a. We suggest that MMEJ can be deployed at scale for reverse genetics screenings and with sufficient intra-gene density rates to be viable for nearly all loss-of-function based gene editing therapeutic applications.
Interactive diagnostic game for time perception : Timo's adventure game

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Bacterial Community of Koumiss from Mongolia Investigated by Culture and Culture-Independent Methods

The bacterial community of fermented horse milk (koumiss) from Mongolia was studied using three methods: cultivation, direct identification by 16S rRNA clone library and denaturing gradient gel electrophoresis (DGGE). Ninety-eight strains were isolated by traditional cultivation and 61 of those were randomly selected for further identification by 16S rRNA gene sequencing. The strains were dominated by lactic acid bacteria (LAB; six different lactobacilli), Acinetobacter, Bacillus and Psychrobacter. Construction of the clone library analysis revealed that 16S sequences of 220 clones, genus Lactobacillus was dominant, but Streptococcus thermophilus, Acetobacter pasteurianus and uncultured clones were also detected. Ten unique bands were sequenced from the DGGE and revealed: Lactococcus lactis, Lactococcus lactis subsp. lactis, Clostridium acidurici, Acinetobacter johnsonii, Dickeya sp. , Enterobacter sp. , Pseudomonas sp. , Raoultella sp. , and Ruminococcus sp. In vitro growth inhibition of three human pathogens, Escherichia coli, Enterobacter sakazakii and Staphylococcus aureus by 14 culturable bacteria displayed that only three of the isolates tested inhibit growth of E. sakazakii while most of the other bacteria delayed growth of the target bacteria.
Elasmoid scales of fishes as model in biomedical bone research

Summary With growing incidence of bone disorders (such as osteoporosis), the demand for fast and reliable alternatives to existing screens based on mammalian bone is increasing. Cell culture-based models that currently are being used, have limited value in the study of cell-cell and cell-matrix interactions. The dermal bone of fish scales offers an unprecedented and attractive model to study bone physiology, both in vivo and in vitro. The elasmoid scale of teleost fishes is of particular interest as it could stand as a model for direct bone formation as found in mammals and it has many advantageous traits: scales carry both bone-forming and bone-degrading cell populations, attached on their natural substrate, such that interactions between cell populations remain intact. The scale contains a collagen type-I matrix impregnated with apatites. Scales come in the hundreds per fish, are easily harvested and can be exposed in vitro for direct study of bone regulatory compounds. Scales are transparent allowing real-time visualization of cellular activities on either side of the scale. Removed scales are replaced quickly and the regeneration process strongly resembles osteogenesis as seen in early bone development. These advantages warrant more fundamental research on scales as models in biomedical bone research. We here address the state-of-the-art on development, structure and physiology of fish scales.
Correlation of Total Phenolic and Flavonoid Contents of Brazilian Honeys with Colour and Antioxidant Capacity

Sixty Brazilian honey samples were analysed for their total phenolic content with the Folin-Denis reagent, total flavonoid content by aluminium chloride method, and antioxidant activity by reaction with 2,2-diphenyl-1-picrylhydrazyl radical. Colour was also classified according to visual analysis and Pfund scale. Linear relationships were observed between colour and flavonoid content, total phenolics and antioxidant capacity, and total flavonoid and phenolic contents. The white-coloured Citrus honey showed the lowest antioxidant activity, while the light ambar Verbenaceae honey showed the highest total phenolics and antioxidant activity. Dark-coloured and polyfloral honeys, though less popularized among consumers, showed average to high antioxidant capacity.
Changes in growth rate of wild-type and PDC1 mutant Saccharomyces cerevisiae in response to caffeine

Saccharomyces cerevisiae is one of the most studied organisms and can provide vital insight into human physiology. With caffeine the most common drug used by humans, the objective of this experiment was to study how varying caffeine concentrations affected the cell counts of wild-type and mutant strains of S. cerevisiae over time. We prepared three treatments of caffeine concentrations: 100 mM, 150 mM, and 0 mM with three replicates for each treatment. The response of average cell growth rate was measured from 0 to 6 hours of incubation by counting the number of cells using a haemocytometer. We found a significant difference in growth rate between the wild-type and mutant strains of S. cerevisiae using a two-way ANOVA test (p=0.030). This is attributed to the deletion of the PDC1 gene in the mutant, resulting in decreased cell growth due to impaired glucose fermentation. Furthermore, there was a significant difference in the growth rate of S. cerevisiae at different caffeine concentrations (p=2.5x10 -6 ). There was also a significant difference between the caffeine effect on wild-type compared to its effect on mutant S. cerevisiae (p=0.0099). We interpret this to be a result of the mutant already functioning with less pyruvate decarboxylase enzyme, so it will be less affected by the presence of caffeine. From our data, we can therefore conclude that mutant S. cerevisiae has greater resistance to caffeine than wild-type S. cerevisiae .
Genetic and phenotypic profiles of endangered Andalusian sheep and goat breeds

The Grazalema Merino and Lebrija Churro Sheep and the Andalusian White and Andalusian Black goat breeds, previously chosen as priority breeds in need of conservation, were considered as having priority for this study. In order to define the genetic as well as the phenotypic profiles the following characters were used: head profile, ear size, ear orientation, ear consistency, horns, pigmentation of mucous, hoofs, udder, nneness of fur, hair or wool, length of hair or wool, presence of wattles and goatee bear, supernumerary nipples. , udder shape, orientation and pigmentation of nipple, and peculiarities of coat. The allelic frequencies for each system were calculated to obtain the genetic profiles of each breed. In the two goat breeds and in the Grazalema Merino breed, the majority of the loci were genetically in Hardy-Weinberg equilibrium, but this was not true of the Lebrijan Churro breed which seems to indicate that the latter was either subjected to natural or artificial selection for these genes or crosses with outside breeds had taken place. The profiles of the breeds were compared with foreign breeds considered traditional or unmodified by man. The profile of the Andalusian White has already been studied by Rodero and they reached the conclusion that this breed can be considered traditional, completing the studies made on other breeds from the Mediterranean area. The data on the Andalusian Black seems to indicate that this breed might be considered traditional or subtraditional with strong polymorphism in most of its characters. Although less markedly than in the latter breed, the same is true of the Lebrijan Churro. In this breed the denning characters of Archaism fit well within those common to an archaic breed. The Grazalema Merino is more standardised than the above mentioned not as nxed than the precocious ones.
Volatile Compounds in Crumb of Whole-Meal Wheat Bread Fermented with Different Yeast Levels and Fermentation Temperatures

The influence of fermentation temperatures (8, 16, and 32°C) and yeast levels (2, 4, and 6%) on the formation of volatile compounds in the crumb of whole-meal wheat bread was investigated. Volatile compounds were extracted by dynamic headspace extraction and analyzed by gas chromatography–mass spectrometry. Results were evaluated with multivariate data analysis and ANOVA. Bread fermented at a high temperature (32°C) had higher peak areas of the Maillard reaction products 2-furancarboxaldehyde, 2-acetylfuran, 2-methylpyrazine, and phenylacetaldehyde compared with bread fermented at lower fermentation temperatures. Bread fermented at low temperatures (8 and 16°C) was characterized by having higher peak areas of the fermentation products 3-methylbutanal, 2-methylbutanal, ethyl acetate, ethyl hexanoate, ethyl propanoate, and 3-methylbutanol. Fermentation of bread with 6% yeast resulted in a higher peak area of the important fermentation product 2-phenylethanol. It also reduced the peak areas of important lipi.
Genome-Wide Proteomics and Quantitative Analyses on Halophilic Archaea

The aerobic, haloalkaliphilic archaeon Natronomonas pharaonis is able to survive in salt-saturated lakes of pH 11. With genome-wide shotgun proteomics, 886 soluble proteins (929 proteins in total) of the theoretical Natronomonas pharaonis soluble proteome consisting of 2187 proteins have been confidentially identified by MS/MS. By comparing the identified proteins of Natronomonas pharaonis with homologues of other organisms, both extreme diversity between halophiles and occasional extraordinary sequence conservation to proteins from unrelated species were observed, substantiating genetic exchange between organisms that are evolutionary nearly unrelated to cope with several extreme conditions. Alternative and largely overlapping open reading frames (called overprinting) could not be identified in the genome of neither Natronomonas pharaonis nor Halobacterium salinarum, leading to the conclusion that in halophiles, not more than one protein can be produced from the same genomic sequence stretch. In the second part of this work, analyses on both the transcriptional and translational level have been performed on the halophilic archaeon Halobacterium salinarum, to gain insights into its lifestyle changes leading to cell response when challenged by heat shock. Thereby, quantitative proteomic data obtained from two different approaches regarding the labeling method (ICPL; SILAC), the fractionation of the protein or peptide mixtures (2DE; 1DE-LC), the mass spectrometric analysis (MALDI-TOF/TOF; ESI Q-TOF), and the choice of the growth medium (complex; synthetic) were integrated with data from whole-genome DNA microarrays, real-time quantitative PCR (RTqPCR), and Northern analyses. A number of genes congruently displayed substantial induction after heat shock on both the transcript and protein level as in the case of the thermosome, two AAA-type ATPases, a Dps-like ferritin protein (DpsA), a hsp5-type molecular chaperone, and the transcription initiation factor tfbB. In contrast, the dnaK operon (hsp70) did not exhibit any significant upregulation in either of the approaches. Some genes encoding enzymes of the TCA cycle, of pathways flowing into the latter, and of pathways leading to pyrimidine synthesis, were only translationally induced. Finally, differential transcriptional induction of the transcription initiation factors tfbB and tfbA, determined by RTqPCR, led to the conclusion that they may regulate genes by reciprocal action. The multiplicity of proteomics and transcriptomics methods are complementing one another, covering a bigger area on the one hand, but also confirming some unexpected findings.