Miracle-dz/UniFAR-FTUs huggingface dataset:
Shifting Dynamics of Intestinal Macrophages during Simian Immunodeficiency Virus Infection in Adult Rhesus Macaques

Key Points Lamina propria macrophages are short-lived and destroyed after SIV infection. Intestinal submucosa macrophages are long-lived and may become SIV/HIV reservoirs. Gut biopsies are insufficient for monitoring submucosal long-lived macrophages. The intestinal tract is a primary barrier to invading pathogens and contains immune cells, including lymphocytes and macrophages. We previously reported that CD163+CD206− (single-positive [SP]) interstitial macrophages of the lung are short-lived and succumb early to SIV infection. Conversely, CD163+CD206+ (double-positive [DP]) alveolar macrophages are long-lived, survive after SIV infection, and may contribute to the virus reservoir. This report characterizes analogous populations of macrophages in the intestinal tract of rhesus macaques (Macaca mulatta) with SIV/AIDS. By flow cytometry analysis, immunofluorescence staining, and confocal microscopy, CD163+CD206+ DP macrophages predominated in the lamina propria of uninfected animals, compared with CD163+CD206− SP macrophages, which predominated in the lamina propria in animals with SIV infection that were exhibiting AIDS. In submucosal areas, CD163+CD206+ DP macrophages predominated in both SIV-infected and uninfected macaques. Furthermore, BrdU-labeled CD163+CD206+ DP and CD163+CD206− SP macrophages recently arriving in the colon, which are both presumed to be shorter-lived, were observed to localize only in the lamina propria. Conversely, longer-lived CD163+CD206+ DP macrophages that retained dextran at least 2 mo after in vivo administration localized exclusively in the submucosa. This suggests that CD163+CD206+ DP intestinal macrophages of the lamina propria were destroyed after SIV infection and replaced by immature CD163+CD206− SP macrophages, whereas longer-lived CD163+CD206+ DP macrophages remained in the submucosa, supporting their potential role as an SIV/HIV tissue reservoir. Moreover, the DP macrophages in the submucosa, which differ from lamina propria DP macrophages, may be missed from pinch biopsy sampling, which may preclude detecting virus reservoirs for monitoring HIV cure.
4E‐BP1 and 4E‐BP2 double knockout mice are protected from aging‐associated sarcopenia

Sarcopenia is the loss of muscle mass/function that occurs during the aging process. The links between mechanistic target of rapamycin (mTOR) activity and muscle development are largely documented, but the role of its downstream targets in the development of sarcopenia is poorly understood. Eukaryotic initiation factor 4E‐binding proteins (4E‐BPs) are targets of mTOR that repress mRNA translation initiation and are involved in the control of several physiological processes. However, their role in skeletal muscle is still poorly understood. The goal of this study was to assess how loss of 4E‐BP1 and 4E‐BP2 expression impacts skeletal muscle function and homeostasis in aged mice and to characterize the associated metabolic changes by metabolomic and lipidomic profiling.
Morphological growth curves for locally adapted swine in Brazil

Growth curves were determined for four breeds of Brazilian locally adapted swine (Moura, Piau, Nilo and Monteiro) using nonlinear models. Data was collected on 13 morphological measurements of 220 animals of both sexes from 30 days of age to adult stages. Curves were fitted using nonlinear regression equations (Gompertz, Weibull, Logistic, Brody, Von Bertalanffy and Richards). The best curve was selected by the highest R2 and lowest root mean squared error. The Weibull function was the most suitable for all breeds and genders. In general, females reached their adult size earlier, but males were larger. On the one hand, the Moura breed is the most similar to industrial breeds one, possibly because it is reared in fattening systems. On the other hand, the Monteiro breed was a later-developing one. Brazilian pig breeds have different growth patterns, associated with the genetic origin of the breed and its adaptations to environment.
Nocturnal asthma is affected by genetic interactions between RORA and 
NPSR1

Neuropeptide S Receptor 1 ( NPSR1) and Retinoid Acid Receptor‐Related Orphan Receptor Alpha (RORA ) interact biologically, are both known candidate genes for asthma, and are involved in controlling circadian rhythm. Thus, we assessed (1) whether interactions between RORA and NPSR1 specifically affect the nocturnal asthma phenotype and (2) how this may differ from other asthma phenotypes.
Landscape-level perceptual abilities in white-footed mice : perceptual range and the detection of forested habitat

We define perceptual range as the distance from which an animal can perceive key landscape elements, such as distant patches of forested habitat. We argue that perceptual range should be a determinant of not only dispersal success in unfamiliar or hostile landscapes, but also of several landscape-level ecological processes influencing population dynamics. To redress the absence of empirical information on perceptual ranges, we simulated the dispersal of forest-dwelling white-footed mice (Peromyscus leucopus) across an agricultural landscape by releasing mice into unfamiliar, hostile agricultural habitat at various distances from fragments of forested habitat. We found that these forest mice have a remarkably low perceptual range with regard to detecting their forested (core) habitat. Mice released into bare fields failed to even orient towards forested habitat as little as 30 m distant, while mice in crop fields appeared unable to locate forest habitat as little as 10 m distant. These mice seemed to locate forested habitat by vision, despite the availability of non-visual cues. Future work will undoubtedly demonstrate vast differences in landscape-level perceptual abilities among animals, and show clearly that the ecological effects of a given landscape configuration will be influenced by the behavioral attributes of the species in question.
TrkB-Shc Signaling Protects against Hippocampal Injury Following Status Epilepticus

Temporal lobe epilepsy (TLE) is a common and commonly devastating form of human epilepsy for which only symptomatic therapy is available. One cause of TLE is an episode of de novo prolonged seizures [status epilepticus (SE)]. Understanding the molecular signaling mechanisms by which SE transforms a brain from normal to epileptic may reveal novel targets for preventive and disease-modifying therapies. SE-induced activation of the BDNF receptor tyrosine kinase, TrkB, is one signaling pathway by which SE induces TLE. Although activation of TrkB signaling promotes development of epilepsy in this context, it also reduces SE-induced neuronal death. This led us to hypothesize that distinct signaling pathways downstream of TrkB mediate the desirable (neuroprotective) and undesirable (epileptogenesis) consequences. We subsequently demonstrated that TrkB-mediated activation of phospholipase Cγ1 is required for epileptogenesis. Here we tested the hypothesis that the TrkB-Shc-Akt signaling pathway mediates the neuroprotective consequences of TrkB activation following SE. We studied measures of molecular signaling and cell death in a model of SE in mice of both sexes, including wild-type and TrkBShc/Shc mutant mice in which a point mutation (Y515F) of TrkB prevents the binding of Shc to activated TrkB kinase. Genetic disruption of TrkB-Shc signaling had no effect on severity of SE yet partially inhibited activation of the prosurvival adaptor protein Akt. Importantly, genetic disruption of TrkB-Shc signaling exacerbated hippocampal neuronal death induced by SE. We conclude that therapies targeting TrkB signaling for preventing epilepsy should spare TrkB-Shc-Akt signaling and thereby preserve the neuroprotective benefits. SIGNIFICANCE STATEMENT Temporal lobe epilepsy (TLE) is a common and devastating form of human epilepsy that lacks preventive therapies. Understanding the molecular signaling mechanisms underlying the development of TLE may identify novel therapeutic targets. BDNF signaling thru TrkB receptor tyrosine kinase is one molecular mechanism promoting TLE. We previously discovered that TrkB-mediated activation of phospholipase Cγ1 promotes epileptogenesis. Here we reveal that TrkB-mediated activation of Akt protects against hippocampal neuronal death in vivo following status epilepticus. These findings strengthen the evidence that desirable and undesirable consequences of status epilepticus-induced TrkB activation are mediated by distinct signaling pathways downstream of this receptor. These results provide a strong rationale for a novel therapeutic strategy selectively targeting individual signaling pathways downstream of TrkB for preventing epilepsy.
Biotechnology and Bioengineering

Funding information Danish Council for Independent Research – Denmark for her postdoctoral grant, Grant/ Award Number: 5054‐00062B; Aarhus University Research Foundation, Grant/Award Number: AUFF‐E‐2015‐FLS‐9‐12 Abstract Surface charge engineering has received considerable interest from the scientific and industrial community in the last few decades. Although it was previously hypothesized that the surface charge–charge interactions were not a fundamental force to determine protein folding and stability, many studies today show that surface charge plays a key role determining protein structure and activity. This review aims to (a) highlight the value of surface charged engineering of proteins to improve enzyme stability and activity in aqueous media and in the presence of ionic liquids (ILs) and organic solvents, (b) describe the existing approaches (genetic engineering or chemical modifications) for surface charged engineering, and (c) demonstrate the applicability of these surface charged enzymes in biocatalysis. The review provides a new foundation for the scientific and research community to exploit the surface engineering of protein concept for the development of new enzymes that are more active and stable in the presence of ILs and organic solvents, thereby offering new opportunities for industrial biocatalysis. Furthermore, this review is a useful tool for researchers to decide the best available technology to improve their enzyme system/ process.
Role of Arabidopsis receptor for activated C-protein kinase 1 in plant growth, development and abscisic acid responses

ii TABLE OF CONTENTS . iv LIST OF TABLES. viii LIST OF FIGURES . ix LIST OF ABBREVIATIONS . xi ACKNOWLEDGEMENTS. xii CO-AUTHORSHIP STATEMENT . xiv CHAPTER 1 GENERAL INTRODUCTION . 1 1.1 Abscisic Acid Signaling . 2 1.1.1 The physiological function of ABA . 2 1.1.2 ABA function in other organisms. 5 1.1. 3 The ABA receptors . 5 1.2 RACK1, a Versatile Scaffold Protein in Plants? 7 1.2.
An NMR study into the structure and interactions of the transmembrane domains of Neu and PDGFβ receptor tyrosine kinases

Receptor tyrosine kinases (RTKs) form a medically important class of membrane proteins whose malfunction as signalling entities has been reported as the cause of a large number of diseases. The structure and dynamics of the transmembrane domain (TM) of these receptors is central to their role in cellular signalling. However, this structure–function relationship is poorly understood. This is largely due to the problems associated with the production of these proteins for analyses in vitro and the fact that they are hydrophobic and require membrane mimetics to solubilise them, which in turn often means loss of structural integrity. This study aimed at using solution- and solid- state NMR to probe the structure and interactions of two biologically important RTK-TMs for which no high resolution structures exist. For the oncogenic Neu receptor tyrosine kinase transmembrane domain, it was sought to understand which amino acids are involved in stabilising the helical dimer. Synthetic peptides were reconstituted into liposomes and then analysed using solid-state NMR. The platelet-derived growth factor β receptor transmembrane domain was another RTK-TM whose structure and interactions with E5 protein were studied using solution-state NMR. A detailed protocol for the expression, purification and reconstitution of PDGFβR-TM into membrane mimetics was devised in order to perform the stated NMR analyses.
Field evaluation of the resistance of transgenic rice expressing CpTI or CpTI+ Bt to lepidopterous pests

The results showed that the transgenic rice expressing CpTI or CpTI+ Bt had high or moderate resistance to lepidopterous pests in the whole growing season. The control effic acies of the transgenic rice against stem borers, including Chilo suppressalis , Tryporyza incertalas, and Sesamia inferens, were up to 69.80%-96. 40% at tillerin g stage and 83.40%-93.30% at filling stage, while percentage of “dead heart” at tillering stage and percentage of “white head” at filling stage were above 10 % for corresponding non-transgenic rice. The field investigation also indicated that the transgenic rice could control the population of Cnaphalo crocis medinulsis in paddy fields effectively. The average leaf damage indexes of the transgenic rice ranged from 0.37 to 4.05, in comparison with 23.52 for the corresponding n on-transgenic rice. However, there was no significant difference in resistance to Nilaparvata lugens, Reiclia dorsalis and Nephotettix cincticeps betwe e n the transgenic rice and their corresponding non-transgenic rice.
Seasonal and interannual variability of zooplankton vertical distribution and biomass size spectra off Ubatuba, Brazil

The analysis of plankton size distributions in response to physical and biological forcing is relevant to the understanding of marine ecological processes. In this study, we evaluated the influence of seasonal intrusions of the South Atlantic Central Water (SACW) on zooplankton vertical distribution and normalized biomass size spectra (NBSS) on the inner shelf off subtropical Brazil. Monthly sampling was performed at a fixed station for 5 years and zooplankton samples were analyzed with a ZooScan system. SACW intrusions led to increases in nitrate, chlorophyll and zooplankton biomass in different depth strata. NBSS slopes and intercepts varied between SACW intrusion and retraction phases and stratification was a key factor explaining seasonal fluctuations in NBSS parameters. The zooplankton interannual variability was related to the changing strength of SACW intrusions during the time series, as indicated by surfacing 18 and 208C isotherms in certain years and intrusion phases, indicative of transient upwelling. We conclude that the temporal components of zooplankton variability in this subtropical coastal ecosystem were governed by SACW intrusions, affecting the vertical distribution of zooplankton biomass and size structure.
Utilizing Early Generation Stability Characteristic to Breed Restorer Line of Hybrid Rice

Screening elite restorer lines is one of the key points to improve the grain yield and rice quality in hybrid rice breeding.The traditional method of the restorer line breeding is characterized by time-consuming and low efficiency,and it should take 5 to 8 years to get a restorer line.By crossing the early generation stability rice with an important restorer line Shuhui 527,three stable lines(2371,409 and 2441) were obtained in F2 populations.Meanwhile,the restoration of the two lines(2371 and 409) were confirmed by molecular marker assisted selection(MAS). It was found that line 2371 had strong restoration ability and its two hybrid combinations showed obvious heterosis.The method by utilization of early generation stability characteristic and MAS showed time-saving(1-2 years) and high efficiency for breeding a new restorer line.
International Review of Research in Open and Distributed Learning Co-Construction Concept Through Cloud-Based Social Network Platform Design, Implementation, and Evaluation

Today’s learners can easily share their thoughts on their social networks, and this movement, undoubtedly, has been affecting their learning. However, learners in such an ad hoc social network environment need a deliberate design to support their idea sharing and concept exchange. Gaining insights into how to stimulate concept sharing in a social network helps learners learn. To this end, this study examined how to design a cloud-based concept construction platform, and analyzed the users’ interaction behaviours on the platform. A cloud-based platform named CoCoing.info was implemented to achieve the aim. The platform has three major functions: (a) co-construction concept building, (b) social network organization, and (c) concept circulation among social networks. Seven hundred and twenty-six accounts registered on the platform. Users constructed 2,121 concepts using 20,049 nodes, and 1,618 files were established. The access statistics results indicated that the platform was used throughout the day, in which the ratio of in-class to after-class access was 0.59:0.41. Among the interactions, 31.24% belonged to concept construction and 68.76% were user responses. Meanwhile, the key player social networking analysis results indicated that teachers appear to play a crucial role in initiating concept construction and triggering social interaction within the type of concept construction social network.
ALLOZYME VARIATION THROUGH A CLINAL HYBRID ZONE BETWEEN THE TOADS BUFO AMERICANUS AND B. HEMIOPHRYS IN SOUTHEASTERN MANITOBA

Enzyme variation was assayed among toads along a transect through the hybrid zone between Bufo hemiophrys and B. americanus in southeastern Manitoba. Thirteen of 26 loci exhibited polymorphism, and clines in allele frequencies through the zone were noted at five loci. The mid-point of the hybrid zone appears to be further to the west by about 11 to 12 km, when compared with that described in a previous morphological study (Cook, 1978). High levels of heterozygosity were found, yet deficiencies in observed numbers of heterozygotes compared to expected numbers were recorded in some samples. Populations of toads within the hybrid zone are composed mainly of intermediates, apparently interbreeding without hindrance. Introgression is asymmetrical with evident gene flow from B. hemiophrys into B. americanus. This zone has features typical of stable "allopatric" (sensu Woodruff, 1973) hybrid zones and is coincident with an ecotone between western prairie and eastern forest habitats. These two species probably met in secondary contact after the retreat of glacial Lake Agassiz up to 8000 yr ago. The stability of this zone is ensured by the continuing reproduction of the intermediate individuals in the ecotone, in concordance with a hypothesis of hybrid superiority in a narrow, clinal hybrid zone.
Bio-efficacy of Some Newer Acaro-insecticides against Yellow Mite (Polyphagotarsonemus latus (Banks)) and Thrips (Scirtothrips dorsalis Hood) in Chilli

Field experiments conducted at ICAR-Indian Institute of Vegetable Research, Varanasi during 2011–14 to evaluate the efficacy of different newer molecules against yellow mite (Polyphagotarsonemus latus Banks) and thrips (Scirtothrips dorsalis Hood) infesting chilli revealed that maximum reduction in mite population was obtained in treatment with chlorfenapyr @ 1.5 mL L−1 (69.95%) followed by spiromesifen @ 0.6 mL L−1 (57.43%) and fipronil @ 0.35 g L−1 (57.29%). In case of thrips, maximum reduction was achieved with fipronil (75.41%) followed by spiromesifen (58.29%). Significantly higher green chilli yield (121.43 q ha−1) was obtained from chlorfenapyr treated plots followed by fipronil (110.14 q ha−1), spiromesifen (109.65 q ha−1) and fenazaquin (108.67 q ha−1) indicating superiority of these newer molecules over the conventional ones. However, the maximum cost benefit ratio was recorded in dimethoate 30 EC followed by dicofol 18.5 EC and chlorfenapyr 10 SC. Chlorfenapyr 10 SC was found to be the most effective and yielded the highest among all the treatments but showed lower C: B ratio of 1: 8.36 due to its relatively high cost.
Effect of alfalfa saponins on cholesterol metabolism and its molecular mechanisms

To investigate the effects of alfalfa saponins on cholesterol metabolism and its molecular mechanism,32healthy male Sprague Dawley(SD)rats were randomly divided into four groups:normal control group,alfalfa saponins group,hyperlipidemia model group,hyperlipidemia model+alfalfa saponins group.The first four weeks were the hyperlipidemia model establishment period:rats in the normal control group and in the alfalfa saponin group were fed with a basal diet while the other two groups were fed with a high fat diet.The last four weeks were the alfalfa saponins treatment period,alfalfa saponins(240mg/kg)were administrated to both the alfalfa saponin group and to the hyperlipidemia model+alfalfa saponins group by gavage.The body weight,liver index,serum lipid level,total cholesterol and total bile acids in liver and faeces of the rats were measured.The mRNA expression of CYP7a1and ABCG5/ABCG8were measured by real-time PCR.Alfalfa saponins significantly reduced the body weight,liver index and the serum cholesterol level but increased the accumulation of cholesterol in liver and the excretion of cholesterol and bile acids in faeces in hyperlipidemia rats and significantly increased the cholesterol excretion in faeces of normal rats.The mRNA expression of CYP7a1 and ABCG5/ABCG8were multiplied in the alfalfa saponins treated groups.The results indicated that alfalfa saponins could adjust the distribution of cholesterol in rats and had a significant effect on the decrease of serum lipid.This effect could result from the increasing mRNA expression of CYP7a1and ABCG5/ABCG8in liver.
Effect of dietary nitrogen source and crude protein content on nitrogen balance and lactating performance of dairy cows

The aim of the present study was to evaluate the effect of two crude protein contents (CP) and two main nitrogen sources in the diet of dairy cows, using sugarcane as forage, on intake, total apparent digestibility, milk yield and composition, and nitrogen balance. Twelve Holstein cows in late lactation were assigned in three contemporary square, in a Latin Square design 4 × 4, with 2 × 2 factorial treatment arrangement, in 21-day trial by period, 14 for diet adaptation and the last seven for sampling and analysis. Cows were housed in individual stalls and fed a total mixed ration (TMR) "ad libitum" composed of two main nitrogen sources (cottonseed meal or whole raw soybean grain) and two levels of CP (130g or 148g/kg dry matter DM) in the diet. In the present study, there was an interaction effect between nitrogen source and crude protein on DM intake (DMI). Cows fed whole raw soybean had higher DMI when the CP content of the diet was 130 g CP/kg DM, while cows fed cottonseed meal had higher DMI when the CP content of the diet was 148 g CP/kg DM. A similar result of DMI was observed for organic matter intake, whereas there was no interaction effect between dietary nitrogen source and crude protein content on intake of other nutrients. Total apparent digestibility of NDF and TDN was higher when soybean was used as the main diet nitrogen source; whereas the digestibility of dietary CP was not changed by the nitrogen sources. Although there were changes in the DMI and the apparent digestibility coefficient, in the current study, there was no effect of dietary crude protein content and nitrogen source on milk yield. In conclusion, the use of low dietetic concentrations of crude protein (130 g/Kg of DM) does not change the lactating performance of dairy cows and may reduce diet cost, while the choice between whole raw soybean grain or cottonseed meal as a protein ingredient may depends only on the availability and/or price, as both ingredients result in similar performance.