Miracle-dz/UniFAR-FTUs huggingface dataset:
Coupled structure change of SecA and SecG revealed by the synthetic lethality of the secAcsR11 and ΔsecG::kan double mutant

An Escherichia coli strain carrying either the secAcsR11 or ΔsecG::kan mutation is unable to grow at low temperature owing to cold‐sensitive protein translocation but grows normally at 37°C. However, introduction of the two mutations into the same cells caused a severe defect in protein translocation and the cells were unable to grow at any temperature examined, indicating that secG is essential for the secAcsR11 mutant. The mutant SecA (csSecA) was found to possess a single amino acid substitution in the precursor‐binding region and was defective in the interaction with the precursor protein. Furthermore, the membrane insertion of SecA and the membrane topology inversion of SecG, both of which took place upon the initiation of protein translocation, were significantly retarded even at 37°C, when csSecA was used instead of the wild‐type SecA. The insertion of the wild‐type SecA was also significantly defective when SecG‐depleted membrane vesicles were used in place of SecG‐containing ones. No insertion of csSecA occurred into SecG‐depleted membrane vesicles. Examination of in vitro protein translocation at 37°C revealed that SecG is essential for csSecA‐dependent protein translocation. We conclude that SecG and SecA undergo a coupled structure change, that is critical for efficient protein translocation.
Structure et fonctionnement des aquifères karstiques : caractérisation par la géochimie des eaux

Depuis 1991, le brgm a lance, en association avec le cnrs, un programme de recherche sur la connaissance de la structure et du fonctionnement des karsts en vue de leur exploitation. Dans un premier temps, une synthese des methodes d'evaluation de la ressource du karst d'un point de vue hydrodynamique a ete effectuee (these b. Marsaud, 1996). Dans le prolongement de ces travaux, une caracterisation hydrogeochimique des ecoulements souterrains d'origine karstique a ete realisee. 1. Dans un premier temps, une systhese des concepts et methodes de l'hydrogeochimie des eaux souterraines en milieu carbonate a ete realisee. Les informations apportees par les differents traceurs geochimiques ont ete identifiees ainsi que l'ensemble des methodes mises en oeuvre pour exploiter les donnees hydrogeochimiques et interpreter les variations du chimisme des eaux aux exutoires karstiques. 2. Dans un second temps, une etude a ete appliquee aux karsts du larzac. Elle a permis d'analyser les reponses geochimiques de plusieurs differents et d'en extraire les informations relatives au fonctionnement et a la structure de ces aquiferes. Ceux-ci ont fait l'objet d'un suivi hydrodynamique et hydrogeochimique pendant plusieurs cycles hydrologiques (2 a 5 cycles). Cette etude vise d'une part a ameliorer la connaissance de ces karsts d'un point de vue applique, mais surtout, cette analyse a pour objectif d'aborder certains aspects fondamentaux du fonctionnement des karsts. A travers l'exemple du larzac, ce sont les variations du chimisme dans les aquiferes karstiques en general que nous avons cherche a comprendre. 3. Afin d'obtenir une vision d'ensemble de l'hydrogeochimie en milieu karstique, les resultats obtenus sur le larzac ont ete compares a ceux issus d'autres systemes karstiques. Puis, une methodologie d'etude hydrogeochimique des karsts a ete proposee en fonction des donnees disponibles et des informations recherchees.
Aeromedical evacuation-relevant hypobaria worsens axonal and neurologic injury in rats after underbody blast-induced hyperacceleration

BACKGROUND Occupants of military vehicles targeted by explosive devices often suffer from traumatic brain injury (TBI) and are typically transported by the aeromedical evacuation (AE) system to a military medical center within a few days. This study tested the hypothesis that exposure of rats to AE-relevant hypobaria worsens cerebral axonal injury and neurologic impairment caused by underbody blasts. METHODS Anesthetized adult male rats were secured within cylinders attached to a metal plate, simulating the hull of an armored vehicle. An explosive located under the plate was detonated, resulting in a peak vertical acceleration force on the plate and occupant rats of 100G. Rats remained under normobaria or were exposed to hypobaria equal to 8,000 feet in an altitude chamber for 6 hours, starting at 6 hours to 6 days after blast. At 7 days, rats were tested for vestibulomotor function using the balance beam walking task and euthanized by perfusion. The brains were then analyzed for axonal fiber injury. RESULTS The number of internal capsule silver-stained axonal fibers was greater in animals exposed to 100G blast than in shams. Animals exposed to hypobaria starting at 6 hours to 6 days after blast exhibited more silver-stained fibers than those not exposed to hypobaria. Rats exposed to 100% oxygen (O2) during hypobaria at 24 hours postblast displayed greater silver staining and more balance beam foot-faults, in comparison with rats exposed to hypobaria under 21% O2. CONCLUSION Exposure of rats to blast-induced acceleration of 100G increases cerebral axonal injury, which is significantly exacerbated by exposure to hypobaria as early as 6 hours and as late as 6 days postblast. Rats exposed to underbody blasts and then to hypobaria under 100% O2 exhibit increased axonal damage and impaired motor function compared to those subjected to blast and hypobaria under 21% O2. These findings raise concern about the effects of AE-related hypobaria on TBI victims, the timing of AE after TBI, and whether these effects can be mitigated by supplemental oxygen.
Mother-Specific Signature in the Maternal Transcriptome Composition of Mature, Unfertilized Zebrafish Eggs

Maternal mRNA present in mature oocytes plays an important role in the proper development of the early embryo. As the composition of the maternal transcriptome in general has been studied with pooled mature eggs, potential differences between individual eggs are unknown. Here we present a transcriptome study on individual zebrafish eggs from clutches of five mothers in which we focus on the differences in maternal mRNA abundance per gene between and within clutches. To minimize technical interference, we used mature, unfertilized eggs from siblings. About half of the number of analyzed genes was found to be expressed as maternal RNA. The expressed and non-expressed genes showed that maternal mRNA accumulation is a non-random process, as it is related to specific biological pathways and processes relevant in early embryogenesis. Moreover, it turned out that overall the composition of the maternal transcriptome is tightly regulated as about half of the expressed genes display a less than twofold expression range between the observed minimum and maximum expression values of a gene in the experiment. Even more, the maximum gene-expression difference within clutches is for 88% of the expressed genes lower than twofold. This means that expression differences observed in maternally expressed genes are primarily caused by differences between mothers, with only limited variability between eggs from the same mother. This was underlined by the fact that 99% of the expressed genes were found to be differentially expressed between any of the mothers in an ANOVA test. Furthermore, linking chromosome location, transcription factor binding sites, and miRNA target sites of the genes in clusters of distinct and unique mother-specific gene-expression, suggest biological relevance of the mother-specific signatures in the maternal transcriptome composition. Altogether, the maternal transcriptome composition of mature zebrafish oocytes seems to be tightly regulated with a distinct mother-specific signature.
Unexpected effect of urate on hydrogen peroxide-induced oxidative damage in embryonic chicken cardiac cells

Abstract Uric acid (UA) is a potent scavenger of oxidants in most mammalian and avian species. The aim of this study was to obtain more comprehensive information regarding the relationship between different concentrations of UA and oxidative balance in chicken cardiac cells. First, oxidative damage parameters were measured in chicken cardiac cells treated with different concentrations of UA. UA concentrations within the normal physiological range had no effect, while treatment with a high level of UA, i.e. 1200 μM, increased the malondialdehyde (MDA) and protein carbonyl contents, decreased the superoxide dismutase (SOD) and catalase (CAT) activities, and had no effect on glutathione (GSH) in cardiac muscle cells. In addition, the nuclear factor erythroid 2-related factor 2 (Nrf2) pathway was stimulated in cells treated with 1200 μM UA. Next, the role of UA in protecting cells from oxidative damage was investigated in hydrogen peroxide (H2O2)-damaged chicken cardiac cells. Treatment with UA within the normal physiological range reduced the increased MDA and protein carbonyl contents and SOD enzymatic activity induced by H2O2 exposure to some extent and inhibited reactive oxygen species (ROS) formation, presumably as a result of the Nrf2 pathway activation in H2O2-damaged cells. By contrast, the MDA and protein carbonyl contents were increased, SOD enzymatic activity was depressed, and the Nrf2 pathway was further down-regulated in H2O2-damaged cells treated with 1200 μM UA. In conclusion, the results indicated that physiological UA concentration partially alleviated oxidative stress in chicken cardiac muscle cells treated with H2O2. However, supraphysiological UA concentrations promoted oxidative damages directly in primary cultured chicken cardiac muscle cells and aggravated oxidative stress in H2O2-damaged cells.
A novel role of the chromokinesin Kif4A in DNA damage response

Chromokinesins are microtubule-motor molecules that possess chromatin binding activity and are important for mitotic and meiotic regulation. The chromokinesin-member Kif4A is unique in that it localizes to nucleus during interphase of the cell cycle. Kif4A deletion by gene targeting in mouse embryonic cells was known to associate with DNA damage response. However, its precise role in DNA damage or repair pathway is not clear. Here we report that Kif4A associates with BRCA2 in a biochemical identification and that the interaction is mediated by the Kif4A C-terminal cargo-binding domain and BRCA2 C-terminal conserved region. Upon nucleus-specific laser micro-irradiation, Kif4A was rapidly recruited to sites of DNA damage. Significantly, the depletion of Kif4A from cells by shRNA impaired the ionizing-radiation induced foci (IRIF) formation of Rad51, both quantitatively and qualitatively. In contrast, the IRIF of γ-H2AX or NBS1 was largely intact. Moreover, Kif4A knockdown rendered cells hypersensitive to ionizing radiation in a colonogenic survival assay. We further demonstrated that Kif4A deficiency led to significantly decreased homologous recombination in an I-SceI endonuclease induced in vivo recombination assay. Together, our results suggest a novel role for a chromokinesin family member in the DNA damage response by modulating the BRCA2/Rad51 pathway.
The arbovirus vector Culex torrentium is more prevalent than Culex pipiens in northern and central Europe

Two species of arbovirus vector, Culex torrentium and Culex pipiens (Diptera: Culicidae), occur in several European countries, but difficulties in their accurate identification and discrimination have hampered both detailed and large‐scale distribution and abundance studies. Using a molecular identification method, we identified to species 2559 larvae of Cx. pipiens/torrentium collected from 138 sites in 13 European countries ranging from Scandinavia to the Mediterranean coast. In addition, samples of 1712 males of Cx. pipiens/torrentium collected at several sites in the Czech Republic were identified to species based on the morphology of their hypopygia. We found that the two species occur together in large areas of Europe, and that Cx. torrentium dominates in northern Europe and Cx. pipiens dominates south of the Alps. The transition in dominance occurs in central Europe, where both species are roughly equally common. There was a strong correlation between the length of the growing season at different sites and occurrences of the two species. As the growing season increases, the proportion and detection of Cx. torrentium decrease, whereas those of Cx. pipiens increase. The present findings have important consequences for the interpretation of the results of studies on major enzootic and link‐vectors of mosquito‐borne bird‐associated viruses (i.e. Sindbis, West Nile and Usutu viruses), especially in central Europe and Scandinavia.
The Evolution of Polymorphic Hybrid Incompatibilities in House Mice

Reproductive barriers are often assumed to arise from fixed genetic differences between species, despite frequent individual variation in the strength of reproductive isolation between populations. Larson et al. report polymorphism. Resolving the mechanistic and genetic bases of reproductive barriers between species is essential to understanding the evolutionary forces that shape speciation. Intrinsic hybrid incompatibilities are often treated as fixed between species, yet there can be considerable variation in the strength of reproductive isolation between populations. The extent and causes of this variation remain poorly understood in most systems. We investigated the genetic basis of variable hybrid male sterility (HMS) between two recently diverged subspecies of house mice, Mus musculus domesticus and Mus musculus musculus. We found that polymorphic HMS has a surprisingly complex genetic basis, with contributions from at least five autosomal loci segregating between two closely related wild-derived strains of M. m. musculus. One of the HMS-linked regions on chromosome 4 also showed extensive introgression among inbred laboratory strains and transmission ratio distortion (TRD) in hybrid crosses. Using additional crosses and whole genome sequencing of sperm pools, we showed that TRD was limited to hybrid crosses and was not due to differences in sperm motility between M. m. musculus strains. Based on these results, we argue that TRD likely reflects additional incompatibilities that reduce hybrid embryonic viability. In some common inbred strains of mice, selection against deleterious interactions appears to have unexpectedly driven introgression at loci involved in epistatic hybrid incompatibilities. The highly variable genetic basis to F1 hybrid incompatibilities between closely related mouse lineages argues that a thorough dissection of reproductive isolation will require much more extensive sampling of natural variation than has been commonly utilized in mice and other model systems.
Influence of Multiple Blood Meals on Gonotrophic Dissociation and Fecundity in Aedes albopictus

Abstract Gonotrophic dissociation and fecundity in adult female Aedes albopictus affect the transmission of arbovirus and mosquito population dynamics. Female Ae. albopictus bloodfed on guinea pig and human hosts produced significantly (P < 0.05) higher number of eggs (80 and 82/female, respectively) than females fed on chicken (67 eggs/female). Fecundity in mosquitoes that took a double blood meal (chicken and guinea pig), a triple blood meal (3 separate guinea pigs), or mixed blood meals (chicken, guinea pig, and human) was significantly (P < 0.001) higher than in females fed on a single chicken or on 2 separate chickens (refeeding). Gonotrophic dissociation in laboratory colony of Ae. albopictus was first observed and its frequency decreased with multiple blood meals with triple feeding or mixed feeding (3 meals on 3 host types). Blood meal source did not significantly influence gonotrophic dissociation in Ae. albopictus.
Dominant-Negative Effects of a Novel Mutated Ins2 Allele Causes Early-Onset Diabetes and Severe β-Cell Loss in Munich Ins2C95S Mutant Mice

The novel diabetic mouse model Munich Ins2C95S was discovered within the Munich N-ethyl-N-nitrosourea mouse mutagenesis screen. These mice exhibit a T→A transversion in the insulin 2 (Ins2) gene at nucleotide position 1903 in exon 3, which leads to the amino acid exchange C95S and loss of the A6-A11 intrachain disulfide bond. From 1 month of age onwards, blood glucose levels of heterozygous Munich Ins2C95S mutant mice were significantly increased compared with controls. The fasted and postprandial serum insulin levels of the heterozygous mutants were indistinguishable from those of wild-type littermates. However, serum insulin levels after glucose challenge, pancreatic insulin content, and homeostasis model assessment (HOMA) β-cell indices of heterozygous mutants were significantly lower than those of wild-type littermates. The initial blood glucose decrease during an insulin tolerance test was lower and HOMA insulin resistance indices were significantly higher in mutant mice, indicating the development of insulin resistance in mutant mice. The total islet volume, the volume density of β-cells in the islets, and the total β-cell volume of heterozygous male mutants was significantly reduced compared with wild-type mice. Electron microscopy of the β-cells of male mutants showed virtually no secretory insulin granules, the endoplasmic reticulum was severely enlarged, and mitochondria appeared swollen. Thus, Munich Ins2C95S mutant mice are considered a valuable model to study the mechanisms of β-cell dysfunction and death during the development of diabetes.
Towards a metabolic and isotopic steady state in CHO batch cultures for reliable isotope‐based metabolic profiling

Attaining metabolic and isotopic balanced growth is one critical condition for physiological studies using isotope‐labeled tracers, but is very difficult to obtain in batch culture due to the extensive metabolite exchange with the surrounding medium and related physiological changes. In the present study, we investigated metabolic and isotopic behavior of CHO cells in differently designed media. We observed that the assumption of balanced cell growth cannot be justified in batch culture of CHO cells directly using conventional, commercially available media. By systematically redesigning media composition and characterizing metabolic steady state based on mass balances and measurement of labeling dynamics, we achieved balanced cell growth for the main cellular substrates in CHO cells. This was done in a step‐by‐step analysis of growth and primary metabolism of CHO cells with the use of [U‐13C]glucose feeding and adjusting concentrations of amino acids in the growth medium. The optimized media obtained at the end of the study provide balanced growth and isotopic steady state or at least asymptotic steady state. As a result, we established a platform to conduct isotope‐based physiological studies of mammalian systems more reliably and therefore well suited for later use in metabolic profiling of mammalian systems such as 13C‐labeled metabolic flux analysis.
Insights into the function of the human P-TEFb component CDK9 in the regulation of chromatin modifications and co-transcriptional mRNA processing

Cyclin-dependent kinase-9 (CDK9) was originally characterized as a transcription elongation factor which regulates RNA Polymerase II (RNAPII) activity following transcriptional initiation. However, recent evidence from a number of studies have shown that CDK9 plays an important role in regulating not only RNAPII activity but also co-transcriptional histone modification and mRNA processing events such as splicing and 3' end processing. Importantly, our previous work and the work presented here demonstrate that CDK9 functions to guide a complex network of chromatin modifications including histone H2B monoubiquitination (H2Bub1), H3 lysine 4 trimethylation (H3K4me3) and H3K36me3. This function appears to be dependent upon not only the phosphorylation of the RNA Polymerase II C-terminal domain but also upon other CDK9 targets such as the Suppressor of Ty Homolog-5 (SUPT5H), Negative Elongation Factor-E (NELF-E) and probably the human Rad6 homolog UBE2A. We provide a working model by which CDK9 may control co-transcriptional replication-dependent histone mRNA 3' end processing in an H2Bub1 and H3K4me3-dependent manner and uncover new and important differences between the functions of human CDK9 and its yeast counterparts Ctk1 and Bur1.
AgNOR cut-point to distinguish mild and moderate epithelial dysplasia.

BACKGROUND Distinguishing mild and moderate epithelial dysplasia is difficult and controversial. We demonstrated earlier that silver-stainable nucleolar organizer region (AgNOR) is a simple, inexpensive and quantifiable method which can standardize this distinction reliably. OBJECTIVE To establish a cut-point mean AgNOR count for epithelial dysplasia validated by bootstrapping. METHODS One hundred oral leukoplakia biopsies at Dr R. Ahmed Dental College, Kolkata, India, examined for epithelial dysplasia using standard method (gold standard) were assessed for their mean AgNOR counts. A cut-point was selected employing receiver operating characteristic (ROC) curve. This estimate was stabilized by 10 000 resamples (with replacement) using parametric and non-parametric bootstrap, a Monte Carlo statistical method, corrected for bias to estimate standard errors (SE) of cut-point. RESULTS Area under the curve (AUC) was 74%; non-parametric method suggested mean AgNOR cut-point = 2.42 AgNORs/nucleus; parametric method suggested cut-point = 2.57. The cut-point 95% confidence intervals (CIs) (bias corrected and accelerated) from parametric method (2.31; 2.66) was lower than non-parametric (2.43; 2.82). CONCLUSION Applying a conservative paradigm, taking the lowest of all bootstrap 95% CIs, we suggest that mean AgNOR count of 2.3 be used as a cut-point for distinguishing between mild and moderate dysplasia. This strategy will provide an inexpensive, meaningful, definitive, reproducible and consistent diagnostic test for epithelial dysplasia.
Pregnancy and birth rates among HIV-infected women in the United States: the confounding effects of illicit drug use

Objective To determine the effect of HIV infection on pregnancy and birth rates and assess the potentially confounding effect of illicit drug use. Design A retrospective record review of matched cohorts examining pregnancy outcomes for HIV-positive women and two HIV-negative comparison groups (one matched by drug use). Methods Ninety HIV-positive women who gave birth in a US city between 1989 and 1993 were matched to HIV-negative women by race, age, parity and date of index birth (group 1, N = 180) and also by the type of illicit drug used (group 2, N = 90). Data were abstracted on tubal ligations and pregnancies occurring before April 1996. Results A total of 63% of HIV-positive women used cocaine during the index pregnancy and 26% also used opiates. HIV-positive women had fewer tubal ligations than group 1 (38.9% versus 51.1%, P = 0.058), but there was no difference when matching included drug use (38.9% in group 2). HIV infection was associated with a decrease in the number of pregnancies; this decrease was most marked when matching included drug use (18.0 versus 32.1 pregnancies per 100 woman-years, P < 0.01). There were no significant differences in spontaneous or therapeutic terminations. Poisson regression analysis demonstrated that HIV infection and older age were associated with fewer pregnancies, and cocaine use with an increased pregnancy rate. Conclusion This study confirms that HIV infection is associated with a decrease in the number of pregnancies, but also illustrates the confounding effects of illicit drug use among women in the United States.