Miracle-dz/UniFAR-FTUs huggingface dataset:
The role of vicariance and dispersal on New Zealand's estuarine biodiversity: the case of Paracorophium (Crustacea: Amphipoda)

To investigate the role of vicariance and dispersal on New Zealand’s estuarine biodiversity, we examined variability in mitochondrial cytochrome c oxidase subunit I (COI) gene sequences for the amphipod genus Paracorophium. Individuals from the two nominate endemic species (Paracorophium excavatum and Paracorophium lucasi) were collected from sites throughout the North and South Islands. Sequence divergences of 12.8% were detected among the species. However, divergences of up to 11.7% were also observed between well supported clades, suggesting the possibility of cryptic species. Nested clade analyses identified four distinct lineages from within both P. excavatum and P. lucasi, with boundaries between clades corresponding to topographical features (e.g. Cook Straight, North and East Cape). Sequence divergences of 3.7–4.9% were also observed within geographic regions (e.g. east and west coasts of the upper North Island). Genetic structure in Paracorophium appears to represent prolonged isolation and allopatric evolutionary processes dating back to the Upper Miocene and continuing through the Pliocene and early Pleistocene. On the basis of molecular clock estimates from sequence divergences and reconstructions of New Zealand’s geological past, we suggest that sea level and landmass changes during the early Pleistocene (2 Mya) resulted in the isolation of previously contiguous populations leading to the present-day patterns. COI genetic structure was largely congruent with previously observed allozyme patterns and highlights the utility of COI as an appropriate marker for phylogeographic studies of the New Zealand estuarine fauna. © 2011 The Linnean Society of London, Biological Journal of the Linnean Society, 2011, 103, 863–874.
Analysis of the Role of Astral Rays in Pronuclear Migration in Sand Dollar Eggs by the Colcemid‐UV Method

The formation and migration of the sperm aster, and the migration of male and female pronuclei during fertilization were investigated in the eggs of the sand dollar, Clypeaster japonicus using the Colcemid‐UV method. When an egg in Colcemid sea water was irradiated locally with UV light (about 365 nm wavelength) at a limited region containing sperm head, a sperm aster formed in this region, and migrated to the center of the UV‐irradiated region during its formation. When the UV‐irradiated region was displaced or its shape was changed after the formation of the sperm aster, the aster migrated to the center of the new UV‐irradiated region. The direction of the migration of the sperm aster coincided with the direction of the longest astral rays. Direct contact between astral rays and the egg surface was not essential for sperm aster migration. When a region containing both the sperm centrosome and the female pronucleus was irradiated with UV light, the female pronucleus migrated toward the center of the sperm aster after they were connected by astral rays. The migration was suppressed when UV light was shaded over the region between the aster and the female pronucleus. These results suggest that the female pronucleus migrates to the sperm aster by attractive force between them.
Molecular phylogeography and evolutionary history of Picea likiangensis in the Qinghai–Tibetan Plateau inferred from mitochondrial and chloroplast DNA sequence variation

Abstract The aim of the present study was to examine the phylogeographic and evolutionary history of Picea likiangensis, a dominant species of the conifer forests in the eastern declivity of the Qinghai–Tibetan Plateau. We collected 422 individuals from 42 natural populations of three major varieties classified under this species. In conifers, mitochondrial (mt) DNA and chloroplast (cp) DNA dispersed by seeds or pollen experience very different levels of gene flow. To this end, we examined the sequence variation of two mtDNA fragments (nad5 intron 1 and nad1 intron b/c) and three cpDNA fragments (trnL–trnF, trnS–trnG and nadhK/C). We found that cpDNA probably introgressed from P. purpurea into remote populations of P. likiangensis through long‐distance dispersal. Multiple refugia seem to have been maintained for P. likiangensis during the Last Glacial Maximum because the cpDNA and mtDNA haplotypes recovered were fixed in the different regions. Postglacial expansions were only detected at the distributional edges of this species where a single cpDNA or mtDNA haplotype was fixed in adjacent populations. However, genetic imprints of postglacial expansions from these two sets of markers were different in the western and southeastern regions, which may result from the long‐distance dispersal of the cpDNA, as well as its fast lineage sorting during intraspecific divergences. Analysis of molecular variance further suggested that genetic differentiation between the three varieties is higher at cpDNA markers than at mtDNA markers, which supports the previous viewpoint that cpDNA markers with a high rate of gene flow may be more effective in delimitating closely related taxa. Together, the results of the present study highlight the evolutionary complexity of a widely distributed species owing to interactions among local and edge expansion, long‐distance dispersal, and intraspecific divergences at two sets of DNA genomes with different rates of gene flow.
Tyrex: Size-Based Resource Allocation in MapReduce Frameworks

Many large-scale data analytics infrastructures are employed for a wide variety of jobs, ranging from short interactive queries to large data analysis jobs that may take hours or even days to complete. As a consequence, data-processing frameworks like MapReduce may have workloads consisting of jobs with heavy-tailed processing requirements. With such workloads, short jobs may experience slowdowns that are an order of magnitude larger than large jobs do, while the users may expect slowdowns that are more in proportion with the job sizes. To address this problem of large job slowdown variability in MapReduce frameworks, we design a scheduling system called TYREX that is inspired by the well-known TAGS task assignment policy in distributed-server systems. In particular, TYREX partitions the resources of a MapReduce framework, allowing any job running in any partition to read data stored on any machine, imposes runtime limits in the partitions, and successively executes parts of jobs in a work-conserving way in these partitions until they can run to completion. We develop a statistical model for dynamically setting the runtime limits that achieves near optimal job slowdown performance, and we empirically evaluate TYREX on a cluster system with workloads consisting of both synthetic and real-world benchmarks. We find that TYREX cuts in half the job slowdown variability while preserving the median job slowdown when compared to state-of-the-art MapReduce schedulers such as FIFO and FAIR. Furthermore, TYREX reduces the job slowdown at the 95th percentile by more than 50% when compared to FIFO and by 20-40% when compared to FAIR.
Novel Gluconeogenesis Regulators for Anti-diabetic Drug Repurposing using Transgenic Zebrafish pck1 Reporters

Phosphoenolpyruvate carboxykinase is an enzyme that catalyzes the rate-limiting step of gluconeogenesis and is encoded by the pck1 gene. High levels of pck1 gene expression are associated with type 2 diabetes. The main goal of the present study is to identify compounds that can modulate pck1 expression. Furthermore, the knowledge gained from this study can streamline the process of identifying regulators by high-throughput screening in the future. A luminescent zebrafish reporter Tg(pck1:luc2) was used to screen the NIH Clinical Collections library containing 727 small molecules. Four leads were identified and validated using the fluorescence reporters Tg(pck1:Venus) and Tg(pck1:eGFP) as well as endogenous pck1 expression using quantitative PCR, where they down-regulated pck1 expression in larval zebrafish. One of the validated compounds (levofloxacin) altered glucose metabolism in adult zebrafish as determined by glucose tolerance tests. Methods were also established for efficient screening of future chemical libraries to identify novel anti-diabetic therapeutics.
Functional genomics of photoperiodic bulb initiation in onion (Allium cepa)

Bulb initiation is a process which is photoperiodically driven, drawing parallels with flowering. Photoperiodic flowering is well characterised at molecular and genetic levels and occurs when photoreceptors interact with the circadian clock, regulating the expression of CONSTANS (CO), which itself regulates the expression of floral pathway integrating genes such as FLOWERING LOCUS T (FT), leading to floral initiation. Two genes which regulate CO transcription are FLAVIN-BINDING, KELCH REPEAT, F-BOX (FKF1) and GIGANTEA (GI). The onion genome is very large with a high level of duplication, presenting challenges for any molecular-based study. The aim of this study was to test the hypothesis that genes controlling daylength response are conserved between the model plant Arabidopsis and onion and hence between the different end-processes bulbing and flowering. Bulbing ratios were used to measure the response of onion plants to long day (LD) and short day (SD) conditions and the reversibility of the bulbing process. It was shown that bulbing is reversible, with a delay when plants are transferred from SDs to LDs, suggesting the accumulation of an inhibitor. Diurnal expression patterns of onion genes homologous to Arabidopsis flowering time genes were examined using quantitative RT-PCR. Phylogenetic analyses were conducted to validate the identity of the homologues. Molecular and phylogenetic data suggests that an onion GIGANTEA (GI) homologue was isolated. Peaks of expression of ZT10 in LDs and ZT7 in SDs mirror the expression of Arabidopsis GI. Homologues of FKF1 and the circadian clock gene ZEITLUPE (ZTL) were also characterised. The putative FKF1 homologue showed different expression patterns in varieties exhibiting different daylength responses. These differences may contribute to the different daylength responses. A CO-like gene, which is closely related to Arabidopsis COL4, and three FT-like genes were also characterised. It appears that many of the genes controlling daylength response are conserved in onion.
Characterization of an α‐amylase from sorghum (Sorghum bicolor) obtained under optimized conditions

Sorghum malt α-amylase can compete with bacterial α-amylase in industrial applications, if sufficiently stable and produced in a large enough quantity. Conditions for maximal α-amylase production in sorghum malt and the physico-chemical properties of the α-amylase so produced are reported in this study. Sorghum grains were steeped in buffers with varying pH (4.0–8.0) for 24 h, at room temperature, and germinated for another 48 h to obtain the green malt. The buffer that induced the highest quantity of α-amylase was chosen as the optimal pH and served as the medium for further steeping experiments conducted at different temperatures (10, 20, 30, 40, 50 and 60°C). The α-amylase activity in the extract was determined in order to obtain the optimum temperature for α-amylase induction at this particular pH. For the purpose of comparison, the α-amylase produced at the optimum pH and temperature was purified to apparent homogeneity by a combination of ion-exchange and size-exclusion chromatography, and further characterized. Eight-fold higher α-amylase activity was induced in pH 6.5 buffer at 20°C compared with water, the traditional steeping medium. The Km and Vmax were estimated to be 1.092 ± 0.05 mg mL−1 and 3516 ± 1.981 units min−1, respectively. The activation energy of the purified amylase for starch hydrolysis was 6.2 kcal K−1 mol−1. Chlorides of calcium and manganese served as good activators, whereas CuSO4 inhibited the enzyme with a 42% loss in activity at 312 mm salt concentration. Copyright © 2012 The Institute of Brewing & Distilling
The Effects of Black Cumin, Black Caraway Extracts and Their Combination on Shelf Life Extension of Silver Carp (Hypophthalmichthys molitrix) during Refrigerated Storage

This study aimed to determine the antioxidant and the antibacterial activities of Nigella sativa L. (Cu) and Bunium persicum Boiss (Ca) extracts on the shelf life of silver carp, which is stored at 4 ± 1C for 15 days. In order to evaluate the quality of fish samples, some tests such as microbiological total viable count (TVC) and psychrotrophic count, chemical peroxide value, thiobarbituric acid reactive substances, and total volatile base nitrogen and sensory characteristics were analyzed over a period of 15 days. The results indicated that the lipid oxidation and spoilage of the samples have been delayed in three treatments of the extracts significantly (P < 0.05) in comparison with the control. Also, the psychotropic bacteria and TVC remained lower than the proposed acceptable limit (7 log10 colony-forming unit/g). According to the sensory analysis results, the treatment of Cu extract had high quality and enhanced the beneficial effects on sensory characteristics. Results show that the B. persicum Boiss and N. sativa L. extracts have significant effect on extension of the shelf life of fresh silver carp up to 6–9 days at refrigerated storage condition. Practical Applications The consumers tend to eat fresh fishes rather than processed or frozen ones, while the shelf life of refrigerated fish, as a highly perishable food, is normally short. The main reason for the deterioration of fish is chemical and bacteriological activities that lead to loss of quality and subsequent spoilage. So, using different methods in order to extend the shelf life of fish is an important issue. Black caraway and black cumin are consumed widely as spices and traditional flavorings in food. These spices, regarding to their antioxidant and antibacterial properties, can be used in order to extend the shelf life and freshness quality of fishes during refrigerated storage. Results show that the Bunium persicum Boiss and Nigella sativa L. extracts have significant effect on the extension of shelf life of fresh silver carp up to 6–9 days at refrigerated storage condition.
Prediction of fertility based on frozen-thawed seminal traits in Sahiwal bulls

The present investigation was carried out to predict the fertility of bulls on the basis of post-thawed seminal traits and in vitro fertility tests using deep frozen semen straws and conception rate of Sahiwal bulls maintained at the institute. The overall least squares means for post-thaw motility, non-eosinophilic sperms, abnormal sperms, hypo-osmotic swelling reacted sperms and acrosomal integrity were 56.47p0. 48, 57.60p0. 93, 12.13pO. 14, 52.66p0. 79, and 55.79p0. 85, respectively. The overall least squares means for computer assisted semen analysis parameters like per cent motility (%), straight line velocity (µ/sec), curvilinear velocity (µ/sec), mean linearity (%), lateral head displacement (µ) and velocity of average path (µ/sec) were 60.17p1. 24,42.03p1. 05, 92.74p2. 51, 59.39p1. 50, 6.99p0. 24 and 64.84p1. 50, respectively. The effect of bull was significant on post-thaw motility, abnormal sperms, noneosinophilic sperms, per cent motility, hypo-osmotic swelling reacted sperms, acrosomal integrity, curvilinear velocity and velocity of ayerage path. The mean conception rate was 44.67%. The multiple linear regression equation based of seminal traits on conception rate showed a high R2 value (90%). The actual,and predicted fertility rate of bulls did not differ significantly. Therefore, fertility rate of breeding bulls could easily be predicted with high accuracy by using the in vitro frozen thawed seminal traits of bulls prior to extensive use through artificial insemination.
The ecological consequences of hybridization between native westslope cutthroat trout (Oncorhynchus Clarkii Lewisi) and introduced rainbow trout (O. Mykiss) in south western Alberta

Species introductions are legitimate, modern threats to native ecosystems worldwide. While the commonly recognized mechanisms of impact (predation, competition, disease transmission and habitat manipulation) remain valid, hybridization, introgressive and otherwise, has been recognized as the most significant threat to certain ecosystems. Specifically, the introduction of rainbow trout (Oncorhynchus mykiss) has been identified as a main factor in the extinction, extirpation and genetic pollution of multiple cutthroat subpopulations, namely the westslope cutthroat trout (Oncorhynchus clarkii lewisi) (Behnke 2002). This thesis offers a perspective on this situations that is strongly based on the differing glacial refugia occupied by these sister taxa during the Wisconsin Glaciation. While O. clarkii lewisi and several other salmonid species (bull trout, Salvelinus confluentus; lake trout Salvelinus namaycush; white fish, Coregonus clupeaformis and Prosopium williamsoni) sought refuge in proglacial lakes, O. mykiss and other anadromous pacific salmon typically sought refuge in the Pacific Ocean through their anadromous forms. I hypothesize that having more recently derived from an anadromous form O. mykiss will possess characteristics more typical of a highly migratory species, than the more
Dynamique des génomes et évolution du métabolisme lipidique chez les levures du clade Yarrowia

Yarrowia lipolytica appartient a un groupe de levures qui a diverge tres tot dans l'arbre des hemiascomycetes. Cette levure est capable d'utiliser, comme seule source de carbone, des substrats hydrophobes tres varies et est capable de synthetiser de nouveaux acides gras libres a partir de composes non hydrophobes. Ces caracteristiques font de Y. lipolytica un modele de levure hemiascomycete pour l'etude du metabolisme des lipides. Sa capacite oleagineuse est facilitee par l'expansion de familles de proteines ayant eu lieu au cours de l'evolution apres la divergence du clade Yarrowia. En effet, parmi les 204 genes impliques dans le metabolisme des lipides dans Y. lipolytica, plus de 67% sont regroupes dans 30 familles multigeniques avec un maximum de 16 membres pour la famille de la lipase. Le recent sequencage de genomes 5 dans le clade Yarrowia a permis de comparer leur contenu genetique. L'etude des familles de genes du metabolisme des lipides a permis de mettre en evidence les mecanismes impliques dans l'evolution de ce clade. Toutes les fonctions necessaires pour le metabolisme des lipides sont presentes dans toutes les especes etudiees, avec au moins un gene par famille, meme pour les especes qui ont de 500 a 1000 moins de genes que Y. lipolytica. Ces especes se sont d'ailleurs revelees etre toutes oleagineuses, grâce a des etudes physiologiques. Les familles de genes observees proviennent de multiples duplications de genes dont chaque exemplaire evolue independamment par differents processus de sub- ou neofonctionalisations, fixations, pseudogenisations ou pertes. Les contractions et expansions de familles de proteines, l'expression des genes, la syntenie et la localisation relative des genes dans le genome ont ete etudies. Plus particulierement, la pression de selection agissant sur ces familles de genes a ete comparee a celles agissant sur le reste du genome. La combinaison de ces approches, physiologie, genomique et transcriptomique, a permis d'ameliorer la comprehension du metabolisme lipidique, de son evolution et de la regulation des genes dans un clade des levures oleagineuses.
ANTIBIOGRAM AND SUSCEPTIBILITY PATTERN OF METHICILLIN-RESISTANT STAPHYLOCOCCUS AUREUS COLLECTED FROM VARIOUS CLINICAL SAMPLES IN BENGALURU

Methicillin-resistant Staphylococcus aureus (MRSA) is a major cause of nosocomial and community infections. A total of 671 clinical specimens were collected and subjected to standard microbiological screening methods for S. aureus. Subsequently, the antibiotic sensitivity test was performed for the confirmed MRSA isolates. Out of 323 (48.14%) strains of S. aureus isolated from clinical samples, 97 (30%) were found to be MRSA. The prevalence rate of MRSA was higher in clinical samples collected from males (58.8%) when compared to MRSA strains isolated from samples collected from females (41.2%). The highest number of MRSA isolates of 78.4% of MRSA strains were obtained from wound pus samples, 3.1% from urine, 4.1% from sputum, 5.2% from eye swab, and 1.0% from ear swab. The percentage of MRSA stains isolated among the age group 21-30 years is 3.5-fold higher than the strains isolated from the group aged between 61 and 70 years (6.19%). Almost all clinical MRSA strains (100%) were resistant to oxacillin, 90% resistant to ampicillin, 84.5% to penicillin-G, 76.2% erythromycin, 71% to cephalexin, and 40.2% to cotrimoxazole. However, here we reported 7.22% MRSA strains resistance to linezolid and 28.87% to vancomycin. The higher percentage of intermediate resistance was noted against antibiotics such as gentamycin and ciprofloxacin. Keywords: Staphylococcus aureus, Methicillin resistance, Nosocomial infections, Vancomycin, Linezolid.
Methods of Genome Analysis in Plants

Part 1: genome analysis - a prologue, P.P. Jauhar chromosome pairing as a tool in genome analysis - merits and limitations, P.P. Jauhar and L.R. Joppa chromosome banding and genome analysis in diploid and cultivated polyploid wheats, B. Friebe and B.S. Gill numerical meiotic models for the inference of genomic affinity in polyploids, C.F. Crane limitations and pitfalls in the use of quantitative polyploid meiotic models for genome analysis, J. Sybenga molecular-meiotic analysis of cotton, D.M. Stelly et al. Part 2 Characteristics of nuclear DNA and genome analysis: analysis of plant DNA content by feulgen microspectrophotometry and flow cytometry, H.J. Price and J.S. Johnston genome analysis of polyploid species employing variation in repeated nucleotide sequences, J. Dvorak and J. Dubcovsky development and application of simple sequence repeat (SSR) loci for plant genome analysis, S.M. Brown et al. Part 3 "In situ" hybridization and genomic painting: genomic southern and "in situ" hybridization for plant genome analysis, J.S. Heslop-Harrison and T. Schwarzacher multicolour fluorescence "in situ" hybridization - a new tool for genome analysis, Y. Mukai. Part 4 Isozyme and molecular markers in genome analysis: genome analysis in the triticeae using isozymes, G. Hart genome analysis in polyploids using molecular markers, J.A. G. da Silva and M.E. Sorrells barley genome mapping and its applications, P.M. Hayes et al RAPD analysis of plant genomes, G. Penner. Part 5 Cytoplasmic genome analysis - phylogenetic inferences: plasmon analysis as the counterpart of genome analysis, K. Tsunewaki chloroplast DNA analysis of the monogenomic triticeae - phylogenetic implications and genome-specific markers, R.J. Mason-Gamer and E.A. Kellogg chromosome microdissection and microcloning - application to genome analysis, F. -T. Kao numerical taxonomy and genome analysis, B.R. Baum and P.K. Gupta. Part 6 Genomic constitution of an important crop plant as revealed by these different techniques: genomic constitution of bread wheat - current status, Y. Yen et al.
Effect of feeding wet mash on the performance of broilers

In the experiment water was mixed @ OTl' 400T2" 500T3' 600T4' 700Ts and 800T6 g/kg diet and offered to chicks ad lib. from 3-6 weeks of age. The initial body weight, final body weight and weight gain did not differ significantly among the groups. The average feed consumption in Tl' T2" T3 and T4 groups was not statistically different, however birds in Tsand T6 groups consulned significantly less feed than other groups. Feed conversion ratio in Tl' T:2 and T3 groups did not differ significantly, however in Ts group it was superior to all other groups. This difference in FeR was significant from Tl' T2 and T3 groups but not fronl T4 and T6. The cost benefit analysis revealed 12.99% saving of feed in T5 group as con1pared to control.