Miracle-dz/UniFAR-FTUs huggingface dataset:
Identifying novel mechanisms of genome maintenance in Saccharomyces cerevisiae using the DNA damage- inducibility of ribonucleotide reductase

The identification of genome maintenance genes in Saccharomyces cerevisiae has been limited to loss-of-function screens that ignore the consequences of gene overexpression. Here, I assay expression of the DNA damage-inducible gene, RNR3, using reporter synthetic genetic array (RSGA) methodology to identify genes that result in genome instability when overexpressed. I find 41 of ~5100 genes screened result in increased RNR3 expression, including known DNA repair genes, transcriptional regulators of RNR3, and a subset of genes exhibiting elevated levels of spontaneous DNA damage as determined by the presence of Rad52 foci. 61% of genes identified had no reported connection to genome stability when compared to previous overexpression studies, leaving 25 novel putative genome maintenance genes for follow-up. Finally, I show that induction of RNR3 in known genome instability mutants is not always dependent on the upstream checkpoint kinase Dun1, suggesting a non-canonical Dun1-independent pathway for RNR3 up-regulation following checkpoint activation.
Scientific and technical assistance concerning the survival, establishment and spread of Batrachochytrium salamandrivorans (Bsal) in the EU

Abstract A new fungus, Batrachochytrium salamandrivorans (Bsal), was identified in wild populations of salamanders in the Netherlands and Belgium, and in kept salamander populations in Germany and the United Kingdom. EFSA assessed the potential of Bsal to affect the health of wild and kept salamanders in the EU, the effectiveness and feasibility of a movement ban of traded salamanders, the validity, reliability and robustness of available diagnostic methods for Bsal detection, and possible alternative methods and feasible risk mitigation measures to ensure safe international and EU trade of salamanders and their products. Bsal was isolated and characterised in 2013 from a declining fire salamander (Salamandra salamandra) population in the Netherlands. Based on the available evidence, it is likely that Bsal is a sufficient cause for the death of S. salamandra both in the laboratory and in the wild. Despite small sample sizes, the available experimental evidence indicates that Bsal is associated with disease and death in individuals of 12 European and 3 Asian salamander species, and with high mortality rate outbreaks in kept salamanders. Bsal experimental infection was detected in individuals of at least one species pertaining to the families Salamandridae, Plethodontidae, Hynobiidae and Sirenidae. Movement bans constitute key risk mitigation measures to prevent pathogen spread into naïve areas and populations. The effectiveness of a movement ban is mainly dependent on the import volumes, possibility of Bsal to remain viable outside susceptible/tolerant species, and the capacity to limit illegal movements. Duplex real‐time PCR can be used to detect Bsal DNA, but has not been fully validated. Quarantining salamanders, enacting legislation that requires testing of animals to demonstrate freedom from Bsal, before movement can take place, restricting salamander movements, tracking all traded species, hygienic procedures/biosecurity measures before and during movements, and increasing public awareness are relevant measures for ensuring safe intra‐EU and international trade of salamanders.
GONADAL DEVELOPMENT AND SPAWNING FREQUENCY OF TILAPIA (Oreochromis niloticus) THAT FEEDED BY VITAMIN E SUPPLEMENTATION [Perkembangan Gonad dan Performa Pemijahan Induk Ikan Nila (Oreochromis Niloticus) yang diberi Pakan dengan Penambahan Vitamin E Suplementasi]

Vitamin E merupakan salah satu mikronutrien penting yang berpengaruh terhadap performa reproduksi ikan. Penelitian penambahan vitamin E dalam pakan induk ikan nila (Oreochromis niloticus) bertujuan untuk mengetahui pengaruh vitamin E terhadap perkembangan gonad dan performa pemijahan induk ikan nila. Pakan uji yang digunakan adalah pakan formula dengan kadar protein 35% dan lemak 10% ditambahkan vitamin E (tingkat kemurnian 50%) dengan dosis A) 0, B) 75, C) 150, D) 225, E) 300 and F) 375 mg/kg pakan (kontrol). Induk ikan nila umur 6-7 bulan sebanyak 180 ekor dipelihara dalam 6 jaring ukuran 3x3x1,5m yang diletakkan dalam kolam 6000 m2 dengan kedalaman air 80 cm. Masing-masing jaring diisi dengan 20 ekor induk betina dan 10 ekor induk jantan dan dipelihara selama 13 minggu pada bulan September sampai dengan November 2011. Hasil penelitian menunjukkan bahwa penambahan vitamin E pada pakan induk ikan nila memberikan nilai indeks gonad somatik lebih tinggi dibandingkan yang kontrol. Penambahan vitamin E sebanyak 225 mg/kg pakan memberikan nilai persentase induk matang gonad yang tertinggi (80%) dan frekuensi pemijahan yang terbanyak yaitu 22 kali selama masa pemeliharaan 13 minggu. Berdasarkan hasil penelitian yang diperoleh dapat disimpulkan bahwa penambahan vitamin E sebanyak 225 mg/kg pakan dapat meningkatkan perkembangan gonad, jumlah induk betina yang matang gonad, persentase total pemijahan dan frekuensi pemijahan pada induk ikan nila.
Comparisons of Canyon Grassland Vegetation and Seed Banks along an Early Successional Gradient

Abstract The seed bank represents the future trajectory of plant communities following disturbance and is vital to their regeneration. Worldwide, grassland seed banks have been well studied. However, there are no examinations of the seed bank for the Pacific Northwest Bunchgrass Prairie system found in the Pacific Northwest of the United States. This absence may arise from the limited amount of intact grasslands in this type following decades of agricultural development and cultivation. In this study, we examined the seed bank from grasslands sites along an early successional gradient to evaluate how they relate to above ground vegetation, successional stage, and historical cultivation. We found that similarities between above ground vegetation and the seed bank were the strongest in the earliest successional stages, when annual grasses dominate. Surprisingly, this relationship was driven by the presence of a relatively new introduced annual grass, Ventenata dubia. Finally, the seed bank within cultivated sites had significantly (p < 0.05) more introduced species than noncultivated reference sites, especially seeds of introduced annual grasses. Overall, our results suggest that these sites are native seed limited and could potentially shift to invasive species dominance with further disturbance, especially on historically cultivated areas. These results have important implications for management given the conservation concern for these remaining intact grasslands. In addition, they add to the growing literature regarding the Pacific Northwest Bunchgrass Prairie and seed banks within the grassland biome.
Lactic Acidosis : A Poorly Understood Concept

Lactic acidosis is a condition commonly encountered in the hospital setting particularly in critically ill patients and is very often used as a diagnostic adjunct when encountering cases of ischaemia or other hypoperfusion states. Despite its use many clinicians have long forgotten the biochemical mechanisms that give rise to hyperlactataemia. One reason for this is because the basic science regarding lactate metabolism is taught in the early years of the medical undergraduate course, and unless one specialises in metabolic medicine, is unlikely to encounter it again. In this article we aim to elucidate the basic mechanisms of lactate metabolism and the accompanying acidosis, and illustrate various clinical settings that give rise to this biochemical abnormality. DOI : 10.14302/issn.2572-5424.jgm-16-1066 Corresponding Author: Sanjay Harrison, Northern Deanery, UK, Email: quibit21@hotmail.com.
The Evolution of Gene Function in Caenorhabditis spp.

The Evolution of Gene Function in Caenorhabditis spp. Adrian Verster Doctor of Philosophy Graduate Department of Molecular Genetics University of Toronto 2014 The sequence of the genome gradually evolves, and such changes can affect the function of the genes encoded within. Here I try to understand the causes and consequences of changes in gene function between related species, particularly in Caenorhabditis nematodes. The goal of the first section of my thesis is to compare biological gene function of 1-1 orthologs by using loss of function phenotypes in C. elegans and C. briggsae. I did this by constructing and screening an RNA interference (RNAi) library in C. briggsae and comparing these RNAi phenotypes to those in C. elegans. This approach found 91 examples of orthologs with different in vivo functions, around 7% of the genes screened. For one of these examples, sac-1, I was able to explain the different biological function by a difference in molecular function, in this case by a difference in gene expression. Given the extremely high phenotypic similarity of these two species I hypothesize that many of these examples of different RNAi phenotypes likely represent cases of changes in gene function which have preserved the developmental phenotypes of the animal due to high levels of stabilizing selection, a model known as Developmental System Drift. In support of this, I found several cases where a phenotype is not present in the C. briggsae copy of an ortholog, but it is present in another related family member, suggesting that this related gene has taken over the function of the original gene in C. briggsae. I also found that recently evolved genes are enriched for having different RNAi phenotypes, which led me to consider what could explain their rapid rate of evolution of in
Seasonal Movement Patterns and Habitat Use of Brook Trout Salvelinus fontinalis and Brown Trout Salmo trutta in North Central Pennsylvania

The eastern Brook Trout Salvelinus fontinalis faces a variety of threats largely due to anthropogenic alterations to the landscape and climate change. However, one threat that has implications for Brook Trout population management is the introduction of non-native Brown Trout Salmo trutta, as potential negative impacts of Brown Trout on Brook Trout populations have been documented. For resource management agencies, understanding the temporal and spatial movement patterns and habitat requirements of any species is essential for conserving existing populations and restoring habitats that once supported self-sustaining populations. I employed radio biotelemetry to quantify movement and habitat use of Brook Trout and Brown Trout from September 2012 through February 2013. I equipped 55 Brook Trout and 45 Brown Trout, distributed among five interconnected streams in North Central Pennsylvania, with radiotransmitters. To identify potential relationships between movement and covariates, I used generalized additive mixed models. Thalweg profiles of the streams were also surveyed to quantify available residual pool habitat and I used discrete choice models with random effects to evaluate Brook and Brown Trout habitat use. To corroborate observations in Brook Trout movement made through radio-tracking, Brook Trout fin clips were taken for microsatellite analysis. Average total movement was greater for Brown Trout (2,924 ± 4,187 m) than for Brook Trout (1,769 ± 2,194 m). Maximum net movement was 10,317 m and 11,273 m completed by a Brook Trout and Brown Trout, respectively. Results indicated a large amount of among-fish variability in movement of both species with the majority of movement coinciding with the onset of the spawning season and increases in stream flow. Microsatellite analysis revealed consistent findings to those in radio-tracking, indicating a moderate to high degree gene flow among study populations. There was an overall preference for pool versus non-pool habitats; however, habitat use of pools was non-linear over time. Brook Trout displayed a greater preference for deep (0.33-1.5 m deep) pool habitats over shallow (0.1-0.32 m deep) pool and non-pool habitats. Conversely, Brown Trout selected for all pool habitat categories similarly. Habitat use of both species was found to be scale dependent. At smaller spatial scales (50 m), habitat use was primarily related to time of year and fish size. However, at larger spatial scales
Optimizing mungbean productivity and irrigation water use efficiency through the use of low water-consumption during plant growth stages

This research was conducted during 2014/2015 and 2015/2016 seasonsin the Agricultural Research Station, King Abdulaziz University at Hada Al-Sham region, Saudi Arabia to produce mungbean as a new legume crop in Saudi Arabia using low water consumption through maximizing crop yield with optimizing irrigation water use efficiency under drought stress during vegetative and flowering growth stages.No significant differences were found between the yield and yield components when practicing water stress during vegetative stage compared with full irrigation treatment in the two seasons. MN96 cv. was significantly dominated over NMf cv. in all studied traits except flowering date.The highest IWUE and seed yield/ha were obtained from the MN96 cv. under full irrigation and water stress during vegetative stage without significantly differences between them in the two seasons.
Behavioural evidence for magnetic orientation in rodents

Magnetoreception in rodents was studied in this Ph.D. thesis. Behavioural evidence for compass magnetic orientation was found in two subterranean African rodents: the social giant mole-rat (Fukomys mechowii) and solitary silvery mole-rat (Heliophobius argenteocinereus) and epigeic rodent bank vole (Clethrionomys glareolus). The study is also focused on the role of magnetic orientation in solving the orientation task in Morris water maze in bank vole.
Description of the acoustical interaction and synchronization between duetters of the Large-footed Finch (Pezopetes capitalis)

Abstract Duets are highly coordinated acoustical displays produced by two individuals. Studying the structure of duet songs and its causes is essential to understand the ecological role and evolution of this form of communication. Our goals in this study were to describe the structure of the duet of the Large-footed Finch, the temporal synchronization of each individual, and to test the effect of provoked (playback) duets. We recorded birds at Cerro de la Muerte, Costa Rica and simulated territory intrusions using playback trials. The duet of this species consisted of overlapping notes between both members of a mated pair, which were emitted either randomly or periodically. Temporal synchronization was similar between both individuals in a mated pair. Both partners adjust the silent intervals between notes in response to the duration of its partner’s note. The high frequency of the second part of the duet of this species decreased with time and the second individual, in duetting this part, not only synchronized its notes temporally with the first individual, but also synchronized the high frequency. The high frequency of the first note the second individual sung was a bit lower than the previous note sung by the first individual. Finally, birds responding to provoked duets produced duets with higher frequency and higher rate of notes compared to unprovoked duets. Our results provide information on the temporal and frequency synchronization in duets of an endemic emberizid and provide new information about a less reported vocal behaviour in bird duets, the acoustic frequency coordination.
Optimum extent of barley grain processing and barley silage proportion in feedlot cattle diets: Growth, feed efficiency, and fecal characteristics

Koenig, K. M. and Beauchemin, K. A. 2011. Optimum extent of barley grain processing and barley silage proportion in feedlot cattle diets: Growth, feed efficiency and fecal characteristics. Can. J. Anim. Sci. 91: 411-422. A study was conducted to evaluate the effects of forage proportion and extent of processing of barley grain on growth, intake, feed conversion efficiency, and fecal characteristics of feedlot cattle. Crossbred steers (120; 407±31 kg) were housed individually and assigned to 10 diets (n=12): two degrees of temper rolling of barley grain [processing index (PI) of 82% (standard) or 87% (coarse)] were combined with five levels of barley silage [3, 6, 9, 12, and 15% of dietary dry matter (DM)]. The PI was determined as the weight of grain after processing expressed as a percentage of the weight before processing. Cattle were slaughtered after 104-109 d on feed, at a final weight of 576 kg, SEM = 5.1. There were very few interactions between grain processing and silage proportion for the variables measured. Grain processing had no effect (P>0.05) on average daily gain (1.59 kg d-1, SEM = 0.057) or final weight. Feeding PI-87% barley tended to increase dry matter intake (DMI) over the experiment (7.63 vs. 7.34 kg d-1, SEM = 0.123, P=0.10) compared with feeding PI-82% barley. Higher DMI of cattle fed PI-87% barley corresponded to lower estimated starch digestibility, as a result of increased appearance of whole kernels and grain fragments in feces. Consequently, gain:feed ratio tended (0.210 vs. 0.219, SEM = 0.0035, P=0.06) to decrease by 4% with PI-87% versus PI-82% barley. Similarly, silage proportion had no effect on gain but DMI increased (P=0.05) linearly from 7.19 to 7.75 kg d-1 (SEM = 0.194) with increasing proportion of silage. Consequently, gain:feed ratio decreased linearly from 0.225 to 0.202 (SEM = 0.0056) with increasing silage proportion. Optimum proportion of barley silage to maximize feed conversion efficiency was 3 to 6% of DM. Decreasing the extent of barley processing or increasing the silage proportion may reduce the risk of acidosis, but feed conversion efficiency is lowered. Formulating diets to reduce the incidence of digestive disorders may decrease the cost of mortalities and treatment of sick animals, thereby improving animal health and welfare, but these costs are unlikely to offset the increased cost of gain in commercial feedlots.
Phenotypic diversity and relationships among Chilean Choclero maize (Zea mays L. mays) landraces

Abstract Choclero is a Chilean traditional floury maize, consumed as a vegetable, with large economic and cultural value due to its culinary properties that give unique characteristics to the traditional local cuisine. Market diversification demands new materials with different ear and kernel characteristics, which are at present not fulfilled by breeders due to lack of genetic diversity. At present, the Instituto de Investigaciones Agropecuarias has a Choclero germplasm collection composed of 96 accessions, which can supply this lack of diversity, or increase the gene pool. In the present study, 34 selected Chilean Choclero landraces were characterized for 41 agromorphological traits. Phenotypic evaluation in three environments representative of the core production area revealed significant genetic variability for most of the evaluated traits, leading to the identification of several promising accessions. The greater contribution of genotype in most phenological plant, ear and kernel traits suggest their potential usefulness for breeding purposes. Principal component analysis explained over 75% of the total variation for 29 quantitative agromorphological traits. Cluster analysis separated accessions into four major groups, differentiated mainly by plant phenology and ear trait. These findings indicate a number of useful traits at an intra-racial level and a wide range of phenotypic variation that provides a good source of diversity for use in the development of new Choclero varieties.
Influence of Spacing and Pruning on Growth Characteristics, Yield and Economics of Tomato (Solanum lycopersicum L.) Grown Under Protected Environment

Tomato (Solanum lycopersicum L.) is one of the most important vegetable crops grown under the protected environment in India. Area of this crop under the protected environment is increasing day by day due to higher as well as quality returns from inside environment as compared to the open field conditions. Tomato belongs to family Solanaceae with diploid chromosome number (2n=24) and is a typical self-pollinated day neutral plant (Yadav et al., 2017). Vegetable production, profits are greatly dependent on the quantity and quality of the yield of the crop. Under the polyhouse conditions plant geometry is an important factor for optimum crop stand and to get maximum return per unit area and time. Pruning of leaves and side shoots also reported to enhance the ultimate yield in various ways. Training maximizes the plant's ability to obtain the sunlight needed for growth and development (Gou et al., 1991). It is also important to maintain adequate air movement around the plant to reduce risk of fungus and insect problems. A dense canopy of leaves shades the fruits, causing them to be pale (Herbert, 1998). Relatively high perishability has made tomato plants to be more vulnerable to intensive crop International Journal of Current Microbiology and Applied Sciences ISSN: 2319-7706 Volume 6 Number 9 (2017) pp. 1833-1838 Journal homepage: http://www.ijcmas. com
Phylogeny of the hyper‐diverse rove beetle subtribe Philonthina with implications for classification of the tribe Staphylinini (Coleoptera: Staphylinidae)

With 71 genera and over 2700 described species, Philonthina is the most speciose subtribe of rove beetle tribe Staphylinini and forms a major component of the largest remaining higher systematics challenge in Staphylinini, the ‘Staphylinini propria’ clade. A related systematics issue concerns the position of the genus Holisus (Hyptiomina), which was recovered within the Neotropical philonthine lineage in several recent analyses of morphology. With the aims of resolving the phylogeny of Philonthina and the position and, thus, validity of Hyptiomina, we performed phylogenetic analyses of the tribe Staphylinini based on molecular (six genes, 4471 bp) and morphological (113 characters) data including 138 taxa from all relevant lineages of Staphylinini. We found that ‘Staphylinini propria’ is a monophylum consisting of six lineages: current subtribes Anisolinina, Philonthina, Staphylinina and Xanthopygina; and two new subtribes, Algonina Schillhammer and Brunke and Philothalpina Chatzimanolis and Brunke. While the previously hypothesized Neotropical lineage of Philonthina was corroborated, Holisus was recovered as a separate subtribe, outside of Philonthina, within an informal ‘Southern Hemisphere clade’. Based on our analyses, we propose tentative new concepts of the polyphyletic genera Belonuchus and Philonthus. We propose the following taxonomic changes: synonymy of the subtribes Staphylinina Latreille (valid name) and Eucibdelina Sharp; resurrection of genera Barypalpus Cameron and Trapeziderus Motschulsky from synonymy with Rientis Sharp and Belonuchus Nordmann, respectively; transfer of 38 Belonuchus species, 16 Hesperus Fauvel species and one Philonthus Stephens species to Trapeziderus as new combinations; transfer of two Hesperus species to Eccoptolonthus Bernhauer as new combinations; transfer of one Belonuchus species to Paederomimus Sharp as a new combination; and transfer of Pridonius Blackwelder new status from its position as a subgenus of Quedius (subtribe Quediina) to Philonthina as a genus, and new combinations for its two described species.