Miracle-dz/UniFAR-FTUs huggingface dataset:
Functional significance of Hsp70 post-translationalmodification in prionpropagation and cellular function

The term prion (proteinaceous infectious particles) was first coined by Stanley Prusiner while naming the causative agent responsible for a group of invariably fatal neurodegenerative diseases collectively termed transmissible spongiform encephalopathies (TSE). A breakthrough in prion research came with the studies which revealed that yeast species Saccharomyces cerevisiae contains proteins that have the ability to form prions. Sup35 is a S. cerevisiae protein involved in termination of translation. In a prion state referred to as [PSI+], a significant portion of the Sup35 protein in the cell coalesces into non-functional, self-propagating, amyloid-like polymers. Thus, yeast strains that are [PSI+] show increased levels of nonsense suppression. Once present, [PSI+] propagates by recruitment of the soluble form of Sup35 into the aggregate in a manner analogous to that of mammalian prions. A search for genetic factors affecting propagation and maintenance of [PSI+] has identified an essential role for molecular chaperones, namely Hsp70 and Hsp104. The Hsp70 chaperone family and its associated co-chaperones are highly conserved from yeast to mammals. A major function of Hsp70 is to prevent the aggregation of denatured proteins by binding to exposed hydrophobic regions and preventing the accumulation of amorphous aggregates. In the model eukaryotic S. cerevisiae, to efficiently carry out such functions Hsp70 works in concert with a number of co-chaperones to regulate ATPase hydrolysis cycle of Hsp70, which in-turn dictates the peptide-binding status of Hsp70. While much data has accrued in relation to the ATPase and substrate binding cycles of Hsp70 there is a distinct lack of information regarding the regulation of this important chaperone at the post-translational level. Recent global proteomic studies have demonstrated that in vivo Hsp70 is phosphorylated. Using a simplified yeast system this study systematically assessed a variety of non-phosphorylateable and phosphomimetic Hsp70 mutants for phenotypic alterations in Hsp70 functions. It was found that alteration of Hsp70 phosphorylation status in vivo can impair prion propagation, alter both basal and acquired thermotolerance and in some cases render cells inviable. By looking at analogous mutants in closely related cytosolic Hsp70s this study identified functional similarities and differences between highly homologous Hsp70 species. This study shows a clear link between Hsp70 phosphorylation status and in vivo function. Given Hsp70s central role in a variety of important cellular metabolic pathways and the conservation of these phosphorylatable sites in higher eukaryotes, these findings have far reaching implications.
External and internal structure of Atta bisphaerica Forel (Hymenoptera: Formicidae) nests

Abstract: This work was carried out to determine the internal and external structures of Atta bisphaerica (Forel) nests. Six nests were excavated and during excavation, all data referring to chambers and tunnels were recorded. Three nests had been internally cement‐moulded, which enabled a better view of the chamber and tunnel structures. Atta bisphaerica nests presented a similar structural pattern, varying only in the number of chambers as a function of external mound area. Chambers were spherical with two communication tunnels. Internal tunnels had an elliptical section, sometimes circular, indirectly linked to chambers through ramifications and directly through short tunnels. Entrance holes were linked to the area of highest chamber concentration by tunnels from the elliptical section, which led to the nest in a radial manner. Knowledge of the colony's three‐dimensional architecture permits successful application of chemical control processes, reduces the quantity of product applied, and consequently diminishes costs and environmental damage.
Pathology of nerve cell membranes in complicated and severe human brain traumatic injuries. An electron microscopic study using cortical biopsies..

Cortical biopsies of ten patients with severe and complicated brain traumatic injuries were examined with transmission electron microscope to study the ultrastructural damage of nerve cell membranes. The nonpyramidal neurons, astrocytes and oligodendrocytes showed plasma membrane fragmentation and areas of focal necrosis, enlargement and degranulation of rough and smooth endoplasmic reticulum cisterns, Golgi complex membrane fragmentation, and irregular dilation and disasembly of nuclear envelope. The degenerated myelinated axons showed invaginations and fragmentation of axolemmal membrane, and myelin sheath vacuolization. Synaptic disassembly and disruption and disassembly of interastrocytary gap junctions were also found. Disruption of neuronal Ca2+ homeostasis, activation of phospholipases and calpain, peroxidative stress, hemoglobin cytotoxicity, glutamate cytotoxicity, and ischemia of brain parenchyma are discussed in relation with the nerve cell membrane damage.
Association entre polymorphisme de gènes de l'immunité et évènements cliniques post-transplantation rénale

Malgre les progres effectues en transplantation renale, on observe encore de nombreuses pertes de greffon sur le long terme. Mettre en evidence des polymorphismes genetiques influencant le devenir du greffon pourrait permettre d’ameliorer la prise en charge des patients greffes. Nous avons genotype 6 polymorphismes de genes de l’immunite codant l’IL-12p40, PD-1, AIF-1, Lyp, TIM-1 et -3, puis nous avons recherche une association statistique avec plusieurs evenements cliniques survenus apres la greffe. Nous avons montre que les polymorphismes des genes de l’IL-12p40, PD-1 et TIM-3 etaient associes a l’infection a CMV, que celui du gene de PD-1 influait sur la survie du greffon, et que ceux d’AIF-1 et Lyp etaient lies respectivement au cancer de la peau et a la reprise retardee de fonction du greffon. Ces resultats suggerent l’interet de stratifier genetiquement les patients afin d’en identifier certains qui beneficieraient tout particulierement d’adaptations therapeutiques.
EFFECTS OF DIFFERENT SALT CONTENTS ON SOME QUALITY CHARACTERISTICS DURING PROCESSING OF DRY-CURED TURKISH PASTIRMA

This study examined the effects of different salt contents (3, 6 and 9%) during process stages on physicochemical, lipid oxidation and microbial quality of a dry-cured meat product, pastirma, throughout 21 days of processing. Significant changes in moisture content, NaCl content, pH and water activity (aw) were observed in pastirma after the third drying and pasting stages. There were significant decreases (P 0.05) was detected on L* and a*. Salt level significantly (P < 0.05) affected thiobarbituric acid-reactive substances (TBARS) formation, which was lower in low-salt pastirma samples, while the combination of salting, drying and pressing stages increased TBARS values in high-salt pastirma samples. Higher salt content (6% and 9%) and last drying resulted in reduction of microbial count. PRACTICAL APPLICATIONS Salt (NaCl) is an important agent in inhibiting microbial growth, reducing water activity and imparting a salty taste to dry-cured meat products such as ham and pastirma. Salt content in pastirma varies from 5% to 10% in the final product and has an impact on product quality parameters. The effects of different NaCl contents (3, 6 and 9%) and processing stages on pH, water activity (aw), color parameters, lipid oxidation and microbial count were studied during processing of pastirma. Low-salt concentration had some negative impacts on pastirma characteristics, giving high aw, pH and microbial count, but low Thiobarbituric acid-reactive substances value and NaCl content. Drying, pressing and pasting with cemen mixture during pastirma processing had a positive impact on reduction of moisture, aw and microbial count.
Hydroxyl‐Ion‐Induced Subunit Dissociation of Yeast Cytoplasmic Pyruvate Decarboxylase

Cytoplasmic pyruvate decarboxylase (EC 4.1.1.1, from Saccharomyces carlsbergensis) exhibits in its circular dichroic spectrum in the 250–320-nm range a multiple two-signal band. This couplet disappears on increasing the pH up to pH 8.5. Two classes of two protons each can be quantified by these spectral changes. The first class dissociates rapidly and the apparent pK is 7.84. The thermodynamic data are ΔG= 87.7 kJ mol−1, ΔH=+ 56.0 kJ mol−1, ΔS=–108 J mol−1 K−1, very characteristic for the deprotonation of an amino-acid side chain. The second class of the protons has the following thermodynamic data: ΔG= 88.3 kJ mol−1, ΔH=–64.3 kJ mol−1, ΔS=– 520 J mol−1 K−1 which, in conjunction with kinetic reasoning and in view of enzyme stoichiometry and symmetry, suggests a conformational equilibrium exposing the second two protons. The enzyme dissociates into two dimeric subunits. This dissociation step is considered to be rate-determining for the overall process. The data are: kp= 1.4 · 10−3, ΔH≠=+ 128.3 kJ mol−1, ΔS≠=+ 136 J mol−1 K−1. If there is a conformational equilibrium, the rate constant of product formation kp will be modified by a factor β=Kc/(1 +Kc) (0 < β 1) where Kc is the conformational equilibrium constant. The subunit dissociation appears to be controlled by the enthalpy of activation indicating that a number of interactions, i.e. ionic, hydrogen and hydrophobic bridges, are to be broken. Optimal conditions for the preparation of the apo-enzyme are derived from the data.
Earnings Management and Its Impact on Accounting Earnings Quality - Experimental Study on the Jordanian Industrial Public Shareholding Companies

هدفت هذه الدراسة إلى اختبار مدى ممارسة الشركات الأردنية لإدارة الأرباح، ولمعرفة مدى تأثير ممارسات إدارة الأرباح على جودة الأرباح المحاسبية المعلن عنها. وقد اعتمدت الدراسة على عينة مكونة من (20) شركة صناعية أردنية مساهمة عامة مدرجة في بورصة عمان خلال الفترة 2005-2012، تم اختيارها بطريقة العينة الطبقية العشوائية. واستخدمت الدراسة جودة الأرباح كمتغير تابع، بينما اشتملت المتغيرات المستقلة على إدارة الأرباح بالإضافة لثلاثة متغيرات ضابطة هي حجم الشركة، ونسبة المديونية، ومعدل العائد على الأصول. وأظهرت نتائج الدراسة انخفاض جودة الأرباح لدى الشركات الصناعية الأردنية بشكل عام، كما كشفت النتائج عن ممارسة الشركات الصناعية الأردنية لإدارة الأرباح التي تستهدف تقليل الربح. أما نتائج تحليل الانحدار فقد أظهرت وجود أثر سالب ومهم إحصائيا لممارسات وأساليب إدارة الأرباح على جودة الأرباح، بينما كان لنسبة المديونية تأثير موجب وذو أهمية إحصائية على جودة الأرباح. وأوصت الدراسة بضرورة صياغة السياسات والمبادئ والمعايير المحاسبية بشكل يضمن عدم قيام الشركات باستغلال المرونة فيها للتلاعب بأرباحها، وأوصت بضرورة التطبيق الفاعل لقواعد الحاكمية المؤسسية لجميع الشركات المساهمة العامة في الأردن.
Tourism Global Value Chains and Africa

Tourism is an important driver of economic growth around the world. While Europe remains the most visited continent in the world, Asia Pacific and Africa had the highest growth rates in visitors over the decade spanning 2005–14. With a wide array of animals and picturesque landscapes, Africa has long captured the imagination of international leisure travellers. In more recent years, the growing diversity of experiences in countries such as South Africa has helped fuel a record number of visitors. While the economic importance of tourism to Africa is a central characteristic throughout the continent, there is variance in its profile at both the regional and country levels. North Africa is the most vibrant tourism destination on the continent. Southern Africa has the second largest total tourism receipts behind North Africa, with its relatively high leisure spending. Central Africa, meanwhile, has the most underdeveloped tourism industry in the world.
Verocytotoxic diarrhogenic bacteria and food and water contamination in developing countries: a challenge to the scientific and health community.

Water related issues such as water treatment and distribution have become extremely important all over the world due to population growth, growing urbanization, health and environmental pollutions. Majority of drinking water sources in Africa are still the traditional ones including dams, wells, rivers, streams and ponds which might harbor or are prone to contamination with water-borne and vector born disease agents that introduce various toxins most importantly verocytotoxins into the water bodies. These toxins are responsible for various health problems including diarrhea, hemorrhagic colitis (HC), hemolytic uremic syndrome (HUS) and thrombotic thrombocytopenic purpura (TTP). These conditions often present difficult chemotherapeutic control measures due to physiological complexity development of antimicrobial resistance among the pathogens. Poverty, inadequate portable water supply, unhygienic environments such as slums and refugee camps are predisposing factors abundant in developing countries. There is therefore the need to investigate water bodies for the prevalence of these toxin producing bacteria and their antimicrobial resistance profiles. Medicinal plant sources with potential efficacy in controlling these bacteria should also be investigated with a view to influencing policy and chemotherapy direction for effective control measures.
The InSight Mission for 2018

Spohn, H. Stone, J. Willis, J. Feldman, R. De Paula, R. Turner, S. Asmar, D. Banfield, U. Christensen, J. Clinton, V. Dehant, W. Folkner, R. Garcia, D. Giardini, M. Golombek, M. Grott, T. Hudson, C. Johnson, G. Kargl, B. Knapmeyer-Endrun, J. Maki, D. Mimoun, A. Mocquet, P. Morgan, M. Panning, W. T. Pike, C. Russell, N. Teanby, J. Tromp, R. Weber, M. Wieczorek, K. Hurst, E. Barrett, and the InSight Team. Jet Propulsion Laboratory, California Institute of Technology (bruce.banerdt@jpl.nasa.gov), Lockheed Martin Space Systems, Denver, Institut de Physique du Globe, DLR Institute for Planetology, NASA Headquarters, Marshall Space Flight Center, Cornell Univ., Max Planck Institute for Solar System Res., ETH, Zurich, Royal Observatory of Belgium, ISAE, Toulouse, Univ. British Columbia and Space Science Institute, Austrian Academy of Sciences, Vienna, Univ. Nantes, Colorado School of Mines, Univ. Florida, Gainesville, Imperial College, London, UCLA, Univ. Bristol, Princeton Univ., Marshall Space Flight Center, Obs. Côte d’Azur
The NAM-B1 transcription factor and the control of grain composition in wheat

The NAM-B1 transcription factor increases grain protein content, alters grain micronutrient content and accelerates monocarpic senescence, often without imposing a yield penalty. The aim of this thesis was to understand the mechanisms by which NAM-B1 influences nutrient remobilisation and monocarpic senescence to cause these effects. To achieve this I have examined the expression patterns of NAM-B1 and its homologues during development. I have studied the effects of NAM-B1 on nutrient transport, photosynthetic capacity and grain filling using a range of molecular biology and physiological techniques. Finally to understand the network of genes which NAM-B1 regulates I have used chromatin-immunoprecipitation followed by next-generation sequencing (ChIP-seq) to identify downstream targets, and compared these to differentially expressed genes in plants with down-regulated expression of NAM-B1 homologues (NAM RNAi plants). I have found that NAM-B1 expression increases after anthesis in both vegetative and reproductive tissues, including the grain. In stem and leaf tissues I identified that NAM genes are highly expressed in the vascular bundles, which might be important for nutrient transport. However I did not find evidence for NAM genes altering xylem or phloem transport. I found that in NAM RNAi plants, grain development was decoupled from flag leaf senescence. In RNAi plants starch synthesis enzymes were less active during the middle of grain filling than in control plants, potentially resulting in the reallocation of photosynthate to the stems as water soluble carbohydrates. Many of the putative NAM-B1 target genes identified by ChIP-seq have functions related to photosynthesis and validation of these candidate genes is ongoing. In summary I have identified putative NAM-B1 target genes and found that NAM-B1 may act in a tissue specific manner to regulate monocarpic senescence and grain filling. Furthermore I have highlighted novel functions related to carbohydrate metabolism in stems and the grain.
Analysis of the role of the X/Y homologous gene family Xmr/Slyin murine spermiogenesis

Spermatogenesis is a complex, continuous developmental process that involves the formation of highly differentiated haploid sperm from diploid spermatogonial stem cells. Deletion analysis has established that genes on the Y chromosome are essential for normal sperm production in humans, mice and Drosophila. In mice, deletions of the Y chromosome long arm (Yq) are associated with abnormal sperm head formation, reduced fertilising ability, up-regulation of spermatid-expressed sex-linked genes, and an offspring sex ratio distortion in favour of females. The severity of the testicular phenotypes correlates with the extent of the deletion, with mice lacking the Yq being sterile. It has been suggested that deficiency of a Yq-encoded multicopy genetic element (the ‘spermiogenesis factor’) is responsible for these phenotypes, and one potential candidate gene is Sly, a member of the Xlr superfamily. This family also includes Xmr, an X-linked multicopy gene found to be up-regulated (along with other X- and Y-encoded genes) in the Yq deletion models. To access the candidacy of Sly as the ‘spermiogenesis factor’, the expression of this gene was examined in the testis at the transcript and protein levels. Sly encodes a protein that is expressed in round and early elongating spermatids. SLY interacts with the acrosomal protein DKKL1, suggesting that SLY may be involved in the development or function of the acrosome, a structure that contains digestive enzymes required for fertilisation. Secondly, the role of Xmr in spermatogenesis was investigated. Xmr has been reported to encode a meiotic protein that localises to the transcriptionally silent sex body in pachytene spermatocytes. However, evidence is provided that this meiotic protein is not XMR, with the antibody used in previous studies unable to recognise XMR. Instead, Xmr is predominantly transcribed in spermatids were it encodes a cytoplasmic protein of unknown function. Next, the up-regulation of X- and Y-linked genes in spermatids from the Yq deletion mice was studied in detail. This up-regulation is due, at least in part, to increased gene transcription, and this is accompanied by changes to the epigenetic profile of the sex chromosome and centromeric heterochromatin in round spermatids. In addition, the protein levels of the up-regulated genes are also increased in the testis from Yq deletion mice, and thus the testicular phenotypes exhibited by these mice may be the result of over-expression of one or more X- and Y-encoded proteins, rather than a direct effect of Yq-linked gene deficiency. Finally, mice transgenic for Sly were generated and characterised to determine if loss of this gene alone is responsible for the spermiogenic defects observed in mice with Yq deletions. Xmr transgenic mice were also produced to examine any potential regulatory interaction between Sly and Xmr and investigate if over-expression of Xmr contributes to the phenotypes exhibited by Yq deletion mice.
Untersuchung der Spezifität von Antiterminationsproteinen in Bacillus subtilis

Regulatory systems often evolve by duplication of ancestral systems and subsequent specialization of the components of the novel signal transduction systems. In the Gram-positive bacterium Bacillus subtilis, four homologous antitermination systems control the expression of genes involved in the metabolism of glucose, sucrose and â-glucosides. Each of these systems is made up of a sensory sugar permease that also acts as phosphotransferase, an antitermination protein and a RNA switch that is composed of two mutually exclusive structures, a RNA antiterminator (RAT) and a transcriptional terminator. We have identified the essential bases in the different RAT structures that are responsible for keeping the signalling straight. Here we analysed the differences between the antitermination proteins. Since the amino acids that are involved in RNA binding are basically the same in all antitermination proteins we decided to randomly alter the sequence of the RNA-binding domain (RBD) of SacT and to screen for mutants capable of binding RAT structures normally recognized by LicT. We found that the exchange of Pro-26 to Ser completely switched the specificity of the RBD. Interestingly, positions 26 and 31 take part in RNA binding but are less conserved and not crucial. Pro-26 and Gln-31 were subjected to random mutagenesis. The mutated RBDs that were isolated during this screen showed that a change of Pro-26 to Arg, Ser or Cys is sufficient for a switch in specificity of SacT RBD. Mutations of Gln-31 to basic amino acids seem to enhance the RNA binding. Furthermore, the specificity of the interaction of the PTS components with the antiterminator proteins should be analysed. Therefore, the structures of the complexes should be solved. The complete PTS was reconstructed in vitro. We were able to show that even the isolated PRDs are still phosphorylated. Furthermore, a perfectly symmetric RAT structure was constructed for crystallography. It was shown that this RAT is still recognized by GlcT effectively in vivo and in vitro.
Invasion and molecular evolution of Daphnia pulex in Japan

We examined Daphnia pulex in Japan to clarify if they were representative of indigenous populations or colonized recently. Phylogenetic analysis of mtDNA suggests that Japanese lineages of D. pulex are immigrants from North America, and are hybrids formed with Daphnia pulicaria prior to this immigration. Based on the mtDNA sequences, the D. pulex individuals aggregated into four distinct genetic groups (JPN 1‐4) comprising a total of 21 haplotypes. Surprisingly, microsatellite analysis with 12 loci revealed only a single multilocus genotype per genetic group, suggesting that D. pulex populations in Japan are comprised of asexual individuals, derived from only four clones. According to the reported mutation rate of mtDNA, JPN 1 and 2, now widely distributed across Japan, were estimated to have invaded between 680 yr and 3400 yr ago, while JPN 3 and 4 colonized much more recently. Results also indicated that the invasion of some clones could not be attributed to recent human activities and most likely occurred by rare natural events. Since the evolutional longevity of asexual clones is thought to be limited, genetic diversity of D. pulex in Japan has the possibility of decreasing in the near future without addition of novel gene flow.