Miracle-dz/UniFAR-FTUs huggingface dataset:
160 A dynamic model for the linker histone

Linker histones play an important role in the packing of chromatin. This family of proteins generally consists of a short, unstructured N-terminal domain, a central globular domain, and a C-terminal domain (CTD). The CTD, which makes up roughly half of the protein, is intrinsically disordered in solution but adopts a specific fold upon interaction with DNA (Fang et al., 2012). While the globular domain structure is well characterized, the structure of the CTD remains unknown. Sequence alignment alone does not reveal any significant homologs for this region of the protein. Construction of a model thus requires additional information. For example, the atomic model for the rat histone H1d CTD, proposed over a decade ago, used novel bioinformatics tools and biochemical data (Bharath et al., 2002). New fluorescence resonance energy transfer (FRET) studies of the folding of the CTD in the presence of linear DNA, single nucleosomes, and oligonucleosomal arrays (Caterino et al., 2011; Fang et al., 2012) have stimulated our interest in constructing a dynamic model of the protein. We have obtained preliminary information about the structure and dynamics of the linker histone CTD through ab initio folding simulations using the Rosetta modeling package (Rohl et al., 2004). By analyzing a large number of conformations sampled through a Monte Carlo procedure, we get a clearer picture of the preferred states of the protein and its dynamics. Our results show that the CTD may frequently adopt a structure with 3–5 helices and helix-turn-helix motifs in specific regions. Some of the best scoring structures show high similarity with the HMG-box-containing proteins previously used as templates by Bharath et al. Further clustering analysis of our results hints of a preferred set of conformations for the CTD of the linker histone. Comparison of these models with distances measured by FRET may help account for the distinct structures of the CTD observed upon binding to different macromolecular partners.
Alcohol-induced Bone Loss and Quality during Adolescence is Improved by Green Tea Polyphenols

Our previous studies have shown significant osteo-protective effects of green tea polyphenols (GTP, green tea extract) in various bone loss models. To test the hypothesis that green tea supplementation would protect against binge alcohol-induced deterioration of bone quality in adolescent drinkers, we used a similar approach with green tea supplementation in drinking water. Using a six week, 2 × 3 factorial design of treatment × dose in male Sprague Dawley (SD) adolescent rats, bone parameters [femoral and lumbar vertebrae-4 (LV-4) area (BMA), bone mineral content (BMC), bone mineral density (BMD)], bone turnover biomarkers [serum osteocalcein (OC) and tartrateresistant acid phosphatase-5b (TRAP-5b)] and blood chemistry were measured. The blood chemistry results showed that alcohol administration significantly decreased albumin, glucose, alkaline phosphatase, and amylase levels; increased globulin, phosphorus, creatine kinase, cholesterol, and potassium levels; and had no effect on protein, calcium, blood urea nitrogen, creatinine, aspartate aminotransferase, alanine aminotransferase, sodium, and chloride. GTP supplementation significantly suppressed alkaline phosphatase levels and had no impact on other blood chemistry parameters. Alcohol administration lowered BMA, BMC, and BMD of the femur and LV-4, as well as serum TRAP-5b, but had no impact on serum OC. Supplementation of GTP into the drinking water increased BMD for the femur and BMC for the LV-4. GTP had no effect on scanned BMA or serum OC concentration. There was an interaction between the alcohol administration and GTP dosage in serum TRAP-5b and several parameters of bone strength, which reduced the negative effect on alcohol-induced bone modeling. In summary, our results show that a 6-week binge alcohol administration lowered bone mineral content, density, and strength in femura, reduced proximal tibial trabecular bone volume and lumbar vertebrae, and decreased cortical thickness at the tibial middiaphysis. Supplementation of GTP into the drinking water increased femoral bone mineral density and tibial cortical thickness at the mid-diaphysis. Importantly, GTP supplementation into drinking water improved overall bone quality in young binge-alcohol treated male rats through suppressing bone turnover rate.
Seasonal patterns of nonstructural carbohydrates of apple (Malus pumila Mill.) fruits: Relationship with relative growth rates and contribution to solute potential

SummaryThe seasonal dry-weight accumulation of midseason (cv. Cox’s Orange Pippin) and late-maturing (cv. Golden Delicious) apple (Malus pumila Mill.) fruits, followed the characteristic sigmoid growth pattern. Similar to patterns reported for peach fruits, apple fruit relative growth rates of dry-matter accumulation, calculated on a degree-day basis, declined rapidly in an exponential fashion early in the season, then decreased slowly taking an asymptotic course later in the season. Unlike peach, the relative growth rate curve of apple fruits did not exhibit a distinct phase shift between two physiological phases of growth. However, seasonal changes of the relative nonstructural carbohydrate composition of apple fleshy tissue, in particular, the rapid increase of sucrose later in the season, indicated that there may be two phases of fruit sink activity in both cultivars. Seasonal patterns of nonstructural carbohydrates of the two apple cultivars were different if expressed on a dry weight basis. In ‘Cox’.
Crystallization and polymorphic behavior of enzymatically produced sunflower oil based cocoa butter equivalents

A multi-methodological approach was used to study the isothermal crystallization of cocoa butter (CB) in the presence of sunflower oil based cocoa butter equivalents (CBEs). pNMR, DSC, oscillatory rheology, XRD, and PLM were used for this purpose. All the techniques confirmed that at 20 degrees C isothermal crystallization of all the blends is a two-step process with formation of alpha crystals in the first step and formation of beta' crystals in the second step. The blends with high amount of CBEs contained more high-melting triacylglycerols (TAGs) and diacylglycerol (DAG) in compare with CB acting as seed crystals enhancing the formation of alpha- crystals in the first crystallization step. Therefore, the induction time of the first crystallization step was inversely related to the amount of CBE. In contrast, the subsequent polymorphic transition was delayed by the presence of the CBE due to their low-melting TAGs. However, adding up to 5% CBE did not change the Foubert's parameters for isothermal crystallization significantly. All the blends (except 5% HOSO CBE), had alpha mediated beta' crystallization. Picturing of the microstructure showed that for the CB and the blends up to 50% large microstructures, indicative of the beta(V) polymorph developed during storage. At 100%, a dense network of spherulites was formed at the beginning of the crystallization period, but upon further storage, no large morphological changes were observed.
Estudios sobre genética del síndrome metabólico y obesidad en un modelo de primates no humanos: potencial relevancia para la investigación clínica y biomédica

This paper summarizes current research performed in a large pedigreed colony (N > 2000) of baboons housed at the Southwest Foundation for Biomedical Research in San Antonio, Texas, USA. It integrates a database currently in progress, which includes the collection of extensive phenotypic data. The long-term goal of this project is to identify genes that could influence Revista de Endocrinologia y Nutricion 2003;11(3):120-128 MG 121 edigraphic.com adiposity-related phenotypes and to test the hypothesis that the pleiotropic effects of such genes affect other phenotypes related to an increased risk of developing common diseases, mainly coronary heart disease and type 2 diabetes. Rodents are the most common animal model for research in obesity, coronary artery disease and type 2 diabetes. However, there are strong physiological and developmental differences between rodents and humans resulting from the evolutionary divergence that occurred approximately 65 to 75 million years ago. The physiological and developmental traits of humans and baboons are much more similar and it is easier to collect data under well controlled situations in these animals than in a human population. For these reasons, the baboon is a highly valuable nonhuman primate model in the study of obesity and the metabolic syndrome. To date, we have obtained several adipose-specific endocrine measures, adipose tissue biopsies, and estimates of body composition on a large portion of our pedigreed colony. Our results seem to demonstrate that the pattern of adipose tissue accumulation closely parallels the pattern observed in humans. We have also been able to detect significant additive genetic heritabilities for these obesity-related phenotypes.
Nitrogen fertilisation of durum wheat: a case study in Mediterranean area during transition to conservation agriculture

Nitrogen (N) nutrition plays a key role for high yields and quality in durum wheat ( Triticum turgidum L. subsp. durum (Desf.) Husn); in Mediterranean environments, data regarding N fertilisation management during the transition phase to conservation agriculture (CA) are limited. The aim of this work was to study the effects of N fertiliser forms and rates on yield and some quality traits of durum wheat, during the transition period to CA in Mediterranean areas; moreover, indication on the recommendable N form/rate combinations have been given. Field trials were carried out in south of Italy, during the first two years of transition to CA (from 2010 to 2012) in a durum wheat-based rotation. Following a split-plot design arranged on a randomised complete blocks with three replications, two N forms (main plots) - urea and calcium nitrate - and four N rates (sub-plots) - 50, 100, 150 and 200 kg N ha –1 - plus an un-fertilised Control, were compared. The following parameters were analysed: grain yield, N-input efficiency, grains protein concentration (GPC), total gluten, gluten fractions and minerals concentration in kernels. Calcium nitrate gave the highest yield (4.48 t ha–1), as predicted by the quadratic model, at 146 kg N ha –1 , on average. This was particularly noticeable in 2012, when the distribution of rainfall and temperatures regimes as well as residues’ status could have favoured such N-form. These results were confirmed by the observed higher values of all indices describing N-input efficiency. High GPC values (14.8%) were predicted at slightly higher N-rates (173 kg N ha –1 , averaging both N forms). In particular, gluten proteins and glutenin/gliadin ratio accrued as the N doses increased, reaching the highest values at 150 kg N ha –1 , also positively affecting the quality of durum wheat flour. Iron and zinc concentrations were noticeably increased (38% and 37% on average) by N supply, probably due to the enhanced water use efficiency under CA systems. Principal component analysis summarised properly the obtained results: analysing the N-rates at 150 kg N ha –1 , it was confirmed that yields and quality characteristics of durum wheat were optimised in the wettest year (2011) with calcium nitrate. Moreover, the scarce amount of residues characterising the transition phase to CA, requires N application rates not lower than 150 kg ha–1 in order to ensure stable yields and important quality traits. These N rates should be modulated as the accumulation of crop residues increases over time, thanks to long-term effects of CA on soil chemical, physical and biological properties.
GENETIC AND NON-GENETIC PARAMETER ESTIMATES OF DAIRY CATTLE IN ETHIOPIA: A REVIEW

Ethiopia is endowed with diverse ecosystems inhabited by an abundant diversity of animal, plant and microbial genetic resources due to the availability of diverse agro-ecology. The productivity of any species depends largely on their reproductive performance. Reproduction is an indicator of reproductive efficiency and the rate of genetic progress in both selection and crossbreeding programs. Reproductive performance does not usually refer to a single trait, but to a combination of many traits and is an indicator of reproductive efficiency and the rate of genetic progress. The main indicators of reproductive performance those are reported by many authors are age at first service, age at first calving, calving interval, days open and number of services per conception. The non-genetic factors like sex of calf, season, year, and parity had significant effect on reproductive performance traits. Knowledge on these factors and their influence on cattle performance are important in management and selection decisions. Development of breeding objectives and effective genetic improvement programs require knowledge of the genetic variation among economically important traits and accurate estimates of heritability, repeatability and genetic correlations of these traits. The estimates of genetic parameters are helpful in determining the method of selection to predict direct and correlated response to selection, choosing a breeding system to be adopted for future improvement as well as genetic gains. The reproductive performance of Ethiopian indigenous and exotic breeds producing in the country is low due to various environmental factors and absence of integrated record on the sector that leads a biased result and recommendations of the genetic parameter estimates. Selection and designing of breeding programs for improving the production and productivity of indigenous breed through keeping their native potentials should be based on the results obtained from accurate genetic parameter estimates like heritability, repeatability and correlation between traits.
Conserving the Ecological Services Provided by Insects

American Entomologist • Volume 54, Number 2 In the case of many insects and other invertebrates, basic biology and life history information are unknown. Before protecting a species under the law, we must have, at a minimum, information on the biology, distribution, and threats to the species, not to mention clear documentation of its decline. In the long run, more funding should be allocated to invertebrate survey, systematics, taxonomy, and population ecology so that these species can be identified and cataloged and their life histories understood. ESA members are vital to this effort.
Adaptive neurocomputation with spiking semiconductor neurons

In this thesis, we study the neurocomputation by implementing two different neuron models. One is a semi magnetic micro p-n wire that emulates nerve fibres and supports the electrical propagation and regeneration. The other is a silicon neuron based on Hodgkin-Huxley conductance model that can generate spatiotemporal spiking patterns. The former model focuses on the spatial propagation of electrical pulses along a transmission line and presents the thesis that action potentials may be represented by solitary waves. The later model focuses on the dynamical properties such as how the output patterns of the active networks adapt to external stimulus. To demonstrate the dynamical properties of spiking networks, we present a central pattern generator (CPG) network with winnerless competition architecture. The CPG consists of three silicon neurons which are connected via reciprocally inhibitory synapses. The network of three neurons was stimulated with current steps possessing different time delays and that the voltage oscillations of the three neurons were recorded as a function of the strengths of inhibitory synaptic interconnections and internal parameters of neurons, such as voltage thresholds, time delays, etc. The architecture of the network is robust and sensitively depends on the stimulus. Stimulus dependent rhythms can be generated by the CPG network. The stimulus-dependent sequential switching between collective modes of oscillations in the network can explain the fundamental contradiction between sensitivity and robustness to external stimulus and the mechanism of pattern memorization. We successfully apply the CPG in modulating the heart rate of animal models (rats). The CPG was stimulated with respiratory signals and generated tri-phasic patterns corresponding to the respiratory cycles. The tri-phasic stimulus from the CPG was used to synchronize the heart rate with respiration. In this way, we artificially induce the respiratory sinus arrhythmia (RSA), which refers to the heart rate fluctuation in synchrony with respiration. RSA is lost in heart failure. Our CPG paves to way to novel medical devices that can provide a therapy for heart failure.
Implication des microARNs dans la conversion des adipocytes blancs en adipocytes thermogéniques

La decouverte recente d'adipocytes bruns fonctionnels chez les humains adultes a conduit a envisager leur utilisation afin d’augmenter la depense energetique dans de potentiels traitements contre l'obesite et les maladies associees. Par ailleurs, des ilots d’adipocytes bruns, appeles adipocytes "brite" (brown in white), emergent dans le tissu adipeux blanc apres une exposition au froid ou une stimulation des recepteurs β3-adrenergiques. En utilisant les cellules hMADS, nous avons identifie plusieurs miARNs regules pendant le « britening ». miR-125b et let-7i ont des niveaux d’expression plus bas dans les adipocytes « brites ». Des analyses fonctionnelles utilisant un « mimic » de miR-125b ou un inhibiteur ont revele que miR-125b agit comme un frein sur le « brunissage » des cellules hMADS en alterant leur respiration ainsi que leur contenu mitochondrial. In vivo, nous avons montre que miR-125b et let-7i sont moins exprimes dans le tissu adipeux brun par rapport au tissu adipeux blanc. La stimulation des recepteurs β3-adrenergiques ou l'exposition au froid induit une diminution d’expression des miARNs dans les deux tissus et est associee a l'activation du tissu adipeux brun et au recrutement des adipocytes « brites ». Nous avons constate que l’injection de miR-125b ou let-7i dans le tissu adipeux blanc sous-cutane inhibait l’expression de genes du « brunissage » induite par la stimulation de la voie β3-adrenergique. En conclusion, nos observations ont montre que miR-125b et let-7i jouaient un role important dans la modulation des adipocytes « brites » et des adipocytes « bruns » en ciblant l’expression de genes mitochondriaux et en diminuant la biogenese mitochondriale.
Effect of commercial Bacillus thuringiensis toxins on Tyrophagus putrescentiae (Schrank) fed on wolfberry (Lycium barbarum L.)

ABSTRACT A laboratory study was conducted at the Traditional Chinese Medicine Center in Huazhong Agricultural University, Wuhan, China. Two commercial Bacillus thuringiensis (Bt) toxins (var. israelensis and tenebrionis) were used in this study at six concentrations (0, 2, 4, 8, 16 and 32 mg kg−1). We evaluated the growth and some biological properties of Tyrophagus putrescentiae (Schrank) fed on one Chinese herb (wolfberry) in the dark at 25°C and 80% relative humidity (RH). Mortalities of T. putrescentiae on wolfberry were examined after 1, 2, 3 and 4 weeks. The results indicated that the chosen Bt toxins had similar governing effects on the growth of T. putrescentiae and its biology. Increase of Bt toxin concentrations caused marked decreases in fecundity and longevity of T. putrescentiae. Development time and mortality of T. putrescentiae also increased with Bt dosage. The highest mortalities (81.22% and 90.91%) of T. putrescentiae adults were recorded due to the use of Bt toxins (Bt1 and Bt2) at the rates of 32 mg kg−1 after 4 weeks, so this dosage might be the best for controlling T. putrescentiae and maintaining quality of dried wolfberry fruits.
Differences between microbial communities in worm guts and the soils they inhabit

The composition of a soil microbial community and the services provided are dependent on soil conditions: pH moisture and oxygen content and nutrient levels. In this study, we examined the biodiversity of a soil under two orchard production management systems, organic and integrated fruit production, looking at the bulk soil and the soil contents of the earthworm, Lumbricus terrestris. Nucleic acids were extracted from the soil; relative gene levels of 16S rRNA for various microbial groups and functional genes of nitrogen metabolism were determined by qPCR. At the DNA level there was no difference between the two bulk soils, and the main difference between soil and gut was an increase in fungi and a decrease in nitrate reductase in the integrated soil. Microbial group composition at the RNA level the bulk soils were again similar, however differences between the bulk and gut soils were greater. Functional genes varied greatly, suggesting that organic soil within the midgut processes more nitrite by dissimilatory reduction than by denitrification, minimising nitrous oxide emissions.
Forced expression of Nanog in hematopoietic stem cells results in a γδT-cell disorder

Nanog is a key molecule involved in the maintenance of the self-renewal of undifferentiated ES cells. In this work we investigate whether Nanog has the ability to enhance self-renewal in hematopoietic stem cells. Contrary to our expectation, no positive effect of Nanog transduction was detected in bone marrow reconstitution assays. However, recipients of nanog -transduced (Nanog o ) HSC invariantly develop a unique disorder typified by an atrophic thymus occupied by Nanog-expressing γδ TCR + cells (Nanog o T cells). All thymi are eventually occupied by Nanog o T cells with CD25 + CD44 + surface phenotype, home selectively to the thymus upon transfer, and suppress normal thymocyte development, which is partly ascribed to destruction of the microenvironment in the thymus cortex. Moreover, this initial disorder invariantly develops to a lymphoproliferative disorder, in which Nanog o T cells undergo unlimited proliferation in the peripheral lymphoid tissues and eventually kill the host. This invariable end-result suggests that Nanog is a candidate oncogene for γδ T cell malignancy. worthwhile to determine if the molecules involved in the self-renewal of ES cells can enhance that of HPC. The initial aim of this work was to evaluate the effect of ectopic expression of Nanog on the behavior of hematopoietic stem cells. While this expectation was not the case, we report here that Nanog overexpression induces an unusual γδ TCR + cell type that destroys the microenvironment of the thymus and eventually develops to a malignant lymphoproliferative disorder. cell of the Nanog-induced of into the process of lymphoproliferative disorder of T cells.