Miracle-dz/UniFAR-FTUs huggingface dataset:
On the reproductive biology of the western Atlantic bluefin tuna, Thunnus thynnus

The Atlantic bluefin tuna, Thunnus thynnus, is a highly migratory species capable of traversing great distances throughout the North Atlantic Ocean, but spawning is known to occur only in the Mediterranean Sea and the Gulf of Mexico/Straits of Florida. The regulatory body charged with managing Atlantic bluefin tuna, the International Commission for the Conservation of Atlantic Tunas (ICCAT), currently recognizes two spawning stocks, eastern and western, separated by a management line at 45° W. The eastern stock spawns from May through July in the Mediterranean Sea with an age at first maturity of 3--4 years. Due in part to a moratorium on fishing for bluefin tuna in the Gulf of Mexico, considerably less research has been conducted on the western spawning stock, and, subsequently, knowledge about basic biological characteristics of this stock is lacking. The age at maturity for western bluefin tuna has been reported as 5--16 years and is a topic of debate among fisheries managers. For stock assessment and management, ICCAT assumes an age at maturity for western bluefin tuna of 9 years. While only two spawning grounds are known, fish of reproductively mature size routinely do not return to either of these two locations during the presumed spawning season indicating additional spawning grounds may exist. Atlantic bluefin tuna were sampled on and off the known spawning grounds, and maturity status was determined for male and female fish. All fish sampled on the spawning grounds (n=250) had mature gonads, and the spawning season in the north/central Gulf of Mexico was defined as April--June. Histological analyses showed a peak in oocyte maturation, and thus spawning activity, in May in the Gulf of Mexico sampling region. Actively spawning fish from the Mediterranean Sea were compared with those from the Gulf of Mexico. Realized fecundity and spawning periodicity were found to be similar for both stocks, but the western spawning stock sampled in the north/central Gulf of Mexico spawns one month earlier than the eastern stock. Fish sampled far from the known spawning grounds provided further information about the reproductive condition of western bluefin tuna. The youngest female and male to show signs of maturity had estimated ages of 6 years and 5 years, respectively. About one quarter of all females sampled contained vitellogenic or early atretic oocytes, and based on rates of atresia, it is unlikely these fish spawned in the Gulf of Mexico. These results provide more extensive information about the reproductive biology of western Atlantic bluefin tuna and revise the age at maturity for the western spawning stock. This lower size and age at maturity, coupled with new results from endocrinology and electronic tagging data, suggests alternative spawning grounds exist, and more comprehensive spatial and temporal sampling is necessary to understand the reproductive biology of Atlantic bluefin tuna.
Improving the nutritional value of soybean meal through fermentation using newly isolated bacteria

ii ACKNOWLEDGEMENTS . iii LIST OF FIGURES . vii LIST OF TABLES . viii LIST OF ABBREVIATIONS.ix 1.0 INTRODUCTION: LITERATURE REVIEW . 1 1.1 Challenges faced by piglets . 1 1.1.1 Physiological factors . 1 1.1.2 Social factors . 3 1.1.3 Diet composition . 3 1.2 Soybeans . 4 1.2. 1 Positive factors of soybeans . 4 1.2. 2 Negative factors of soybeans . 7 1.3 Current applications used to improve soybean . 19 1.3. 1 Processing . 19 1.3. 2 Biotechnology and selective breeding strategies . 20 1.3. 3 Addition of enzymes . 21 1.3. 4 Microbial fermentation . 22 1.4 Summary and rationale . 26
DEVELOPMENT OF GENOMIC RESOURCES FOR THE EVALUATION OF RED SNAPPER, AN EMERGING SPECIES CANDIDATE FOR MARINE AQUACULTURE AND STOCK ENHANCEMENT

ii ACKNOWLEDGMENTS iv DEDICATION vi LIST OF TABLES xi LIST OF ILLUSTRATIONS xii CHAPTER I – INTRODUCTION 1 CHAPTER II – DEVELOPMENT AND CHARACTERIZATION OF HOMOLOGOUS MICROSATELLITE MARKERS 10 Introduction 10 Materials and Methods 13 Microsatellite Discovery 13 Candidate Microsatellite Evaluation and Selection 14 Multiplex Assay Optimization 16 Results 16 Discussion 18 CHAPTER III – DEVELOPMENT AND CHARACTERIZATION OF GENOMIC RESOURCES FOR RED SNAPPER: HIGH-DENSITY LINKAGE MAPPING, ANCHORING OF A FIRST DRAFT GENOME ASSEMBLY AND COMPARATIVE GENOMIC ANALYSIS 20
Constraints-Based Modeling to Identify Gene Targets for Overproduction of Ethanol by Escherichia coli: The Effect of Glucose Phosphorylation Reaction

Copyright: © 2015 Desai T, et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Constraints-Based Modeling to Identify Gene Targets for Overproduction of Ethanol by Escherichia coli: The Effect of Glucose Phosphorylation Reaction
Antibacterial Activity and Phytochemical Analysis of Selected Bryophytes against Penicillin Resiatant Bacterial Pathogens

Resistance to Penicillin drugs is a global concern. Medicinal plant products provide unlimited opportunities for new drug leads because of the unmatched availability of chemical diversity. There is a continuous and urgent need to discover new antimicrobial compounds from the lower plant forms like bryophytes against new and re-emerging drug resistant infectious diseases. In this study, the collected epiphytic bryophytes Pogonatum microstomum (Schwaegr.) Brid, Fissidens brevinervis (Broth.) and Pallavicinia lyelli (Hook) were tested against Penicillin resistant bacterial pathogens. They were extracted by percolation method using various solvents like acetone, ethyl acetate and distilled water. The antimicrobial activity was evaluated against the different penicillin resistant pathogenic bacterial strains using agar well diffusion method. The bryophyte extracts showed remarkable inhibitory activity against bacterial pathogens. The extracts were further screened for phytochemical studies and they revealed the presence of alkaloids, flavonoids, phenol, proteins and amino acids, resins, saponins, steroids, tannins, xanthoproteins and sugars. The antimicrobial activities of bryophytes may be due to the presence of various secondary metabolites, which may enhance at the high altitudes.
Effect of a continuous hot water treatment tubers on seed-borne fungal pathogens of potato

Summary The viability of five pathogens was decreased by treatment with hot water when tested in ~ itro. Polyscvtalum pustulans was most sensitive and Rhizoctonia solani least sensiti~e. Potato tubers were exposed to 55 ~ for 5 rain in a commercial continuous hot water treatment plant using naturally contaminated seed tubers and tubers which had been inoculated by dipping in comminuted cultures. The frequency of eyes colonised by P. pu.wulans, Helminthosporium solanL and R. solani was reduced to virtually zero and the effect persisted on tubers st, bsequent ly stored at 4 ~ and at 15 ~ for up to 16 wk. Results with Colletotrichum coccodes ~ere inconclusive. Treatment suppressed Penicillium spp. which, however, rapidly rccolonised the eyes during storage, leading to higher contamination levels in the treated than in the untrealed tubers. \Vith tubers inoculated with Phomafoveata, good control was achieved when the incubation period before treatment was 10 d but not when the period was 42 d.
How to build a healty colony: age structure and immune strategies in bumblebees

In social insects, the worker turnover rate (its ‘pace’) shows considerable variation between colonies. This has epidemiological consequences for parasites because in `fast-paced` colonies, with short-lived workers, the time of residence in a given host will be reduced. Here we investigate whether differences in colony pace reflect a life-history strategy against parasite transmission. We infected bumblebees (Bombus terrestris) with the infectious gut parasite Crithidia bombi and experimentally manipulated birth and death rates to mimic slow and fast pace. Fewer workers and, importantly, fewer last generation workers were infected in colonies with a higher turnover rate. This suggests increased fitness in “fast-paced colonies, as daughter queens exposed to few infective cells are less likely to be infected and have a higher chance of founding their own colonies. We therefore propose that a high worker turnover rate acts as a strategy of defence against a spreading disease; parasitism therefore likely drives the variation in worker lifespan commonly observed in social insects. § A version of this Chapter is in preparation as S. D. Buechel & P. Schmid-Hempel.
Patterns of reproductive effort in Arabidopsis thaliana: Confounding effects of size and developmental stage

AbstractWe demonstrate for the annual Arabidopsis thaliana, that reproductive effort (RE) varies with plant size but is affected more directly by developmental stage; i.e. RE is “stage-dependent”. We evaluated plant size and RE under a constant environment with two harvest criteria, and under a variable environment (a range of densities) with one harvest criterion. Plants of 10 genotypes were grown singly and harvested either at maturity of the first fruit (early) or at complete senescence (late). Plants from a subset of 3 genotypes were grown at 6 additional densities and harvested at maturity of the first fruit. For plants grown singly, later harvest resulted in significantly higher RE (seed biomass / total remaining above ground biomass) and larger plant size than early harvest. Conversely, RE decreased with increasing size for plants grown under a range of densities and harvested at maturity of the first fruit. We argue that these apparently contradictory relationships between RE and size are a conseq.
Unusual clockwise loop migration lengthens travel distances and increases potential risks for a central Asian, long distance, trans-equatorial migrant, the Red-footed Falcon Falco vespertinus

ABSTRACT Capsule: Red-footed Falcons Falco vespertinus migrating from northern Kazakhstan proceed west before heading south to Africa; their northbound travel follows a different route with passage close to shooting hotspots in the Mediterranean. Aim: To use tracking and ringing data to document for the first time the migration of globally threatened Red-footed Falcons from northern Kazakhstan. Methods: Light-level geolocators were deployed on breeding adults in Kazakhstan and recovered one year later. Ringing and observational data from more than 100 years of Russian-language and other literature were summarized and mapped alongside the geolocator data. Results: Geolocator, ringing and observational data together demonstrate that Red-footed Falcons from northern Kazakhstan have a clockwise loop migration that begins with a long and unusual westward trek around eastern Europe’s large inland seas before continuing to extreme southern Africa. Return migration is farther west and requires crossing two major migratory barriers: the Sahara and the Mediterranean. Conclusion: The loop migration we describe requires an extensive longitudinal movement, exposes central Asian Red-footed Falcons to multiple desert, mountain and marine crossings, and, at outbound and return Mediterranean bottlenecks, crosses sites where raptor shooting is common.
DR. BABLU BHATTACHARYYA: A JOURNEY OF FOUR DECADES WITH TUBULIN

Dr. Bhabatarak Bhattacharyya, a chemist turned biologist, is an eminent and distinguished scientist in the field of biophysical chemistry. He devoted his entire life in understanding a very interesting cytoskeletal protein, tubulin that polymerizes to form microtubules. He discovered a novel chaperone activity of tubulin and elucidated the folding/unfolding pathways of tubulin. He characterized the binding of different anticancer drugs to tubulin and most importantly contributed in unfolding the mystery of colchicine binding to tubulin. His contribution towards the scientific community will always be cherished and appreciated.
Características químicas bromatológicas de plantas remanescentes a cultura do mini milho

The objective of this study was evaluate the nutritional value, histological sections and in vitro digestibility of maize plants harvested at the stage 90 days after planting. The treatments comprised five maize plant types: a hybrid AG1051 and four open-pollinated cultivars, and two harvest approaches: whole maize plants and maize plants without cobs. The maize varieties used were: Alagoano, Branquinha, St. Louis and Vicosence. The treatments were fitted into a randomized block design with three replicates in a split plot scheme, with maize varieties as main plots and harvest approaches as subplots. Among the varieties selected, those that had higher values for CP in maize plants without cobs were the Alagoano and Vicosence cultivars. For NDT in maize plants without cobs the varieties that had best results (P<0.05) were the AG1051, Branquinha and Vicosence. These varieties presented the greatest potential for forage production. For NDF and IVNDFD in maize plants without cobs the variety that had higher values (P<0.05) was the Alagoano. It can be concluded that, under the nutritional value and harvest stage, all the varieties studied in the trial can be used for ruminant feeding, with or without cobs.
Growing on the Edge: Hydraulic Architecture of Mangroves: Ecological Plasticity and Functional Significance of Water Conducting Tissue in Rhizophora mucronata and Avicennia marina

Background and aims Although mangroves are extensively studied, little is known about their ecological wood anatomy. This investigation examined the potential use of the vessel density as a proxy for soil water salinity in the mangrove species Rhizophora mucronata (Rhizophoraceae) from Kenya. Methods In a time-standardized approach, 50 wood discs from trees growing in six salinity categories were investigated. Vessel densities, tangential and radial diameters of rainy and dry season wood of one distinct year, at three positions on the stem disks, were measured. A repeated measures ANOVA with the prevailing salinity was performed. Key results Vessel density showed a significant increase with salinity supporting it as a prospective measure of salinity. Interestingly, the negative salinity response of the radial diameter of vessels was less striking, and tangential diameter was constant under the varying environmental conditions. An effect of age, growth rate or the presence of a vessel-dimorphism could be excluded as the cause of the lacking ecological trend. Conclusions The clear trend in vessel density with salinity, together with the absence of a growth rate and age effect validates its potential as an environmental proxy. However, it can only be used as a relative measure of salinity since other environmental variables such as inundation frequency have an additional influence on the vessel density. In view of a reliable, absolute proxy future research should focus on finding wood anatomical features correlated exclusively with soil water salinity or inundation frequency. The plasticity in vessel density with differing salinity suggests a role in the establishment of a safe water transport system. To confirm this hypothesis the role of the inter-vessel pits, their relation to the rather constant vessel diameter and the underlying physiology and cell biology needs to be examined.
Timing of Light Exposure During Incubation to Improve Hatchability, Chick Quality and Post-Hatch Well-Being in Broiler Chickens: 21 or 18 Days

Providing light during incubation has been shown to hatchability and post hatch development; however, the optimal timing of this light is still not known. To determine if there is an effect of exposing embryos to light for the first 18 d of incubation or the entire 21 d of incubation, we incubated broiler chicken eggs (N = 3096) for either 18 d (18DL), 21 d (21DL) or not at all (DARK). Embryo mortality, chick weight, proportion of cull or dirty chicks, or those with leg or other abnormalities was not affected by incubation conditions (p>0.05). The DARK broilers had a lower hatch rate, a lower proportion of unhealed navels and no defect chicks than both the 18DL and the 21DL (p<0.05) broilers. There was no effect of incubation condition (p>0.05) on 45 d weight gain or 45 d feed conversion. The DARK broilers vocalized more during isolation and had longer latency to right during tonic immobility than both the 18DL and the 21DL (p<0.05) broilers. The DARK broilers had higher composite asymmetry scores and corticosterone concentrations than both the 18DL and the 21DL (p<0.05) broilers. There were no differences observed between the lighting treatments in any measure (p>0.05). Hatchability, chick quality, fear response and stress susceptibility were all improved with lighted incubation irrespective if the lighting occurred for 18 or 21 days. Providing light during the first 18 d of incubation can improve production and bird welfare.
The Relation Between the Electrolytic Solution Pressures of the Metals and Their Toxicity to the Stickleback (Gasterosteus Aculeatus L.)

1. Lethal concentration limits have been determined for the hydrogen ion and the ions of eighteen metals. The three-spined stickleback ( Gasterosteus aculeatus L.) has been employed as test animal. 2. According to their lethal concentration limits on a mg. /l. basis their order of increasing toxicity is: Sr Ca Na Ba Mg K Mn'' Co'' Cr''' Ni'' Au''' Zn Cd'' Pb'' Al Cu'' H Hg'' Ag. 3. On a molar concentration basis the order is as follows: Na Ca Sr Mg Ba K Mn'' Co'' Cr''' Ni'' H Zn Al Au''' Cd'' Pb'' Cu'' Hg'' Ag. 4. All these ions, with the exception of the first six (the metals of the alkalis and alkaline earths), bring about the death of fish by precipitating the gill secretions, thus causing asphyxiation. The alkali and alkaline earth metals appear to enter the body and act as true internal poisons. 5. The position of iron is uncertain. The toxicity of solutions of iron salts appears to be due, mainly if not entirely, to their acidity. 6. On a mg. /l. or molar concentration basis there is a marked relationship between the toxicity of the metals and their solution pressures. The metals of very low solution pressure (Ag, Cu, etc.), i.e. those whose ions are most ready to part with their charges and enter into combination with other ions or compounds, are the most toxic as they precipitate the gill secretions and bring about asphyxiation with extreme rapidity. Metals of somewhat higher solution pressure (Zn, Pb, Cd) act in the same way but more slowly. Manganese, which of all the heavy metals has the highest solution pressure, takes effect very slowly and the ions of the alkali and alkaline earth metals, which have a high affinity for their charges, do not precipitate the gill secretions at all. 7. In the case of all the ions other than those of the alkali and alkaline earth metals the reactions responsible for the death of the fish take place outside the body. Thus their speed of action does not depend on their penetrating power and the permeability factor does not enter. This is probably responsible in great measure for the good agreement observed between their toxicity and their affinity for their electrical charges.
The Polycistronic miRNA Cluster miR-17-92 Is Over-Expressed in Early Phase Chronic Myeloid Leukemia (CML) CD34+ Cells.

Micro RNAs (miRNAs) are small non-coding, single-stranded RNAs regulating gene expression by hybridization to complementary sequences in target mRNAs. Aberrant miRNA expression has been found in a variety of human malignancies including B-cell leukemias and lymphomas. The polycistronic miR-17–92 cluster, which includes seven miRNAs (miR-17-5p, miR-17-3p, miR-18a, miR-19a, miR-20a, miR-19b-1, miR-92-1), resides in intron 3 of the C13orf25 gene located on human chromosome 13 and has recently been described to harbor oncogenic potential in a murine transplantation model. In addition, expression of the polycistron can be regulated by c-myc, which is also activated by the Bcr-Abl oncogene product. To study miRNA expression in CML, K562 cells were analyzed by microarray analysis (miCHIP) for normalized expression of 244 miRNAs following treatment either with imatinib to inhibit Bcr-Abl kinase activity or with specific anti bcr-abl shRNA to knock-down gene expression. Both of these treatment strategies led to a 2–4-fold reduction of six mature miRNAs (miR-17-5p, miR-17-3p, miR-18a, miR-20a miR-19b-1, miR-92–1) as compared to untreated control cells. The reduction of the miR-17–92 miRNA cluster expression was confirmed for each individual mature miRNA species encoded in the cluster by real-time RT-PCR. Treatment with either imatinib or anti-bcr-abl shRNA also down-regulates expression of mature miRNA miR-19a (>3-fold) in K562 cells as quantified by real-time RT-PCR. We next used PCR based quantification to analyze miR-17–92 expression in purified normal (n=4) and CML CD34+ cells harvested at diagnosis of chronic phase disease (n=16). Individual mature miRNAs of the cluster were up-regulated (2–6-fold) in CML as compared to normal CD34+ cells. Additionally, the pri-miRNA for the miR-17–92 cluster was up-regulated in 70% (7/10) of CML samples. Interestingly, retrovirus-mediated over-expression of the miR-17-19b-1 cluster in K562 cells mediates enhanced colony-formation of transduced cells. Furthermore, K562 cells expressing high levels of the miR-17-19b-1 cluster are more resistant to proliferation inhibition induced by specific anti-myc RNAi, indicating some functional role of the miR-17-92 cluster on proliferation and survival in this model. In summary, the polycistronic miR-17–92 cluster is up-regulated in early chronic phase CML CD34+ cells and may contribute to cellular transformation by the Bcr-Abl oncogene product.
IDENTIFICACIÓN Y ANÁLISIS NUTRICIONAL DE ESPECIES FORRAJERAS EN SISTEMAS DE VEGETACIÓN NATURAL DEL PIEDEMONTE AMAZÓNICO

En la Amazonia colombiana, el establecimiento de las praderas como monocultivo para la alimentacion animal se ha realizado de manera tradicional a partir de la tumba y quema del bosque; las cuales son practicas destructivas que han desencadenado problemas ecologicos, ambientales sociales y economicos. La presente investigacion objetivo reconocer el potencial forrajero de las especies nativas, presentes en areas de vegetacion natural en el piedemonte amazonico, como alternativa sostenible para la alimentacion animal. El area de estudio se centro en los municipios de El Doncello, Florencia y Belen de los Andaquies. A partir de pruebas de cafeteria con bovinos y un indicador de selectividad (IS) fueron identificadas especies de plantas con diferentes niveles de selectividad, cuyo calculo se elaboro en funcion del consumo y la abundancia de la especie consumida. Para el analisis nutricional fue determinada a digestibilidad in vitro de la materia seca (DIVMS), proteina cruda (PC), fenoles totales y fibra en detergente neutra (FDN) y en detergente acida (FDA). En total fueron seleccionadas 16 especies en funcion de su calidad nutricional y el indice de selectividad. Las especies Clibadium sp. , Aegiphila integrifolia, Acalypha diversifolia, Piper sp. y Marsypiantes sp. fueron caracterizadas por presentar niveles de PC, DIVMS y selectividad animal sobresalientes, indicando su potencial para ser implementadas y utilizadas en sistemas de alimentacion animal.