Miracle-dz/UniFAR-FTUs huggingface dataset:
Hepatitis C virus genotypes in French blood donors

The prevalence of different hepatitis C virus (HCV) genotypes in HCV infected individuals and the relation between the HCV genotypes and the source of the infection are controversial. The aim of this study was to determine the HCV genotypes in French blood donors. Fifty‐one anti‐HCV positive blood donors were studied with detectable serum HCV RNA by nested polymerase chain reaction (PCR) using primers derived from the 5′ non‐coding region. For genotyping HCV, we used a method based on analysis of the restriction fragment length polymorphisms (RFLP) after amplification by PCR of the HCV non‐structural 5 (NS5) genome domain. Using this technique, the genotypes of 39 of the 51 blood donors (76%) were determined. Three previously described genotypes were found: 19 blood donors were infected by HCV genotype I (37%), 14 were infected by HCV genotype II (27%), 3 were infected by HCV genotype III (6%), and 3 were coinfected by two genotypes (6%). All three blood donors infected with two different genotypes were intravenous drug abusers. A past history of intravenous drug abuse was more frequent in blood donors with HCV genotype I. However, there was no difference in alanine transaminase (ALT) levels, histological lesions, and RIBA‐2 patterns in blood donors infected with either HCV genotype I or HCV genotype II. These findings indicate that most HCV genotypes isolated from French blood donors belong to HCV genotype I and HCV genotype II, and that risk factors for HCV infection may differ for different genotypes of HCV. © 1995 Wiley‐Liss, inc.
Design of a Protein-Targeting System for Lactic Acid Bacteria

ABSTRACT We designed an expression and export system that enabled the targeting of a reporter protein (the staphylococcal nuclease Nuc) to specific locations in Lactococcus lactis cells, i.e., cytoplasm, cell wall, or medium. Optimization of protein secretion and of protein cell wall anchoring was performed with L.lactis cells by modifying the signals located at the N and C termini, respectively, of the reporter protein. Efficient translocation of precursor (∼95%) is obtained using the signal peptide from the lactococcal Usp45 protein and provided that the mature protein is fused to overall anionic amino acids at its N terminus; those residues prevented interactions of Nuc with the cell envelope. Nuc could be covalently anchored to the peptidoglycan by using the cell wall anchor motif of the Streptococcus pyogenes M6 protein. However, the anchoring step proved to not be totally efficient in L. lactis, as considerable amounts of protein remained membrane associated. Our results may suggest that the defect is due to limiting sortase in the cell. The optimized expression and export vectors also allowed secretion and cell wall anchoring of Nuc in food-fermenting and commensal strains of Lactobacillus. In all strains tested, both secreted and cell wall-anchored Nuc was enzymatically active, suggesting proper enzyme folding in the different locations. These results provide the first report of a targeting system in lactic acid bacteria in which the final location of a protein is controlled and biological activity is maintained.
Ultrastructural changes in human striated muscle using three methods of training.

Abstract Skeletal muscle tissue was obtained from the vastus lateralis of six normal college male students. Two biopsies were obtained prior to, and one following the training period. Two subjects performed isotonic leg extensions, two performed isometric leg extensions, and two ran up and down stadium bleachers. All training periods lasted 8 weeks. Muscle tissue was processed immediately for electron microscope examination. The following parameters were measured from micrographs of longitudinal sections: sarcomere length, sarcomere width, A band length, I band length, intracellular fat globule quantity and diameter, mitochondria length, mitochondria quantity, and Z band width. The following parameters were measured from micrographs of cross sections: myosin fiber concentration, distance between myosin filaments, myosin filament diameter, and actin filament diameters. Observations were also made on the geometric arrangement of the filaments, glycogen, and gross myofibrillar structure. Major findings were:.
Studies on Substrate Recognition by the Budding Yeast Separase*

Sister chromatid cohesion is resolved at anaphase onset when separase, a site-specific protease, cleaves the Scc1 subunit of the chromosomal cohesin complex that is responsible for holding sister chromatids together. This mechanism to initiate anaphase is conserved in eukaryotes from budding yeast to man. Budding yeast separase recognizes and cleaves two conserved peptide motifs within Scc1. In addition, separase cleaves a similar motif in the kinetochore and spindle protein Slk19. Separase may cleave further substrate proteins to orchestrate multiple cellular events that take place during anaphase. To investigate substrate recognition by budding yeast separase we analyzed the sequence requirements at one of the Scc1 cleavage site motifs by systematic mutagenesis. We derived a cleavage site consensus motif (not(FKRWY))(ACFHILMPVWY)(DE)X(AGSV)R/X. This motif is found in 1,139 of 5,889 predicted yeast proteins. We analyzed 28 candidate proteins containing this motif as well as 35 proteins that contain a core (DE)XXR motif. We could so far not confirm new separase substrates, but we have uncovered other forms of mitotic regulation of some of the proteins. We studied whether determinants other than the cleavage site motif mediate separase-substrate interaction. When the separase active site was occupied with a peptide inhibitor covering the cleavage site motif, separase still efficiently interacted with its substrate Scc1. This suggests that separase recognizes both a cleavage site consensus sequence as well as features outside the cleavage site.
Molecular cloning of heat shock protein 10 (Hsp10) and 60 (Hsp60) cDNAs from Galeruca daurica (Coleoptera: Chrysomelidae) and their expression analysis

Abstract Galeruca daurica (Joannis) is a new outbreak pest in the Inner Mongolia grasslands in northern China. Heat shock protein 10 and 60 (Hsp10 and Hsp60) genes of G. daurica, designated as GdHsp10 and GdHsp60, were cloned by rapid amplification of cDNA ends techniques. Sequence analysis showed that GdHsp10 and GdHsp60 encoded polypeptides of 104 and 573 amino acids, respectively. Sequence alignment and phylogenetic analysis clearly revealed that the amino acids of GdHsp10 and GdHsp60 had high homology and were clustered with other Hsp10 and Hsp60 genes in insects which are highly relative with G. daurica based on morphologic taxonomy. The mRNA expression analysis by real-time PCR revealed that GdHsp10 and GdHsp60 were expressed at all development stages and in all tissues examined, but expressed highest in eggs and in adults’ abdomen; both heat and cold stresses could induce mRNA expression of GdHsp10 and GdHsp60 in the 2nd instar larvae; the two Hsp genes were expressed from high to low with the extension of treatment time in G. daurica eggs exposed to freezing point. Overall, our study provides useful information to understand temperature stress responses of Hsp60 and Hsp10 in G. daurica, and provides a basis to further study functions of Hsp60/Hsp10 relative to thermotolerance and cold hardiness mechanism.
Double-stranded microRNA mimics can induce length- and passenger strand–dependent effects in a cell type–specific manner

MicroRNAs are short (17–26) noncoding RNAs driving or modulating physiological and pathological cellular events. Overexpression of miR-155 is pathogenic in B-cell malignancy but was also reported in a number of solid tumors—in particular, in breast cancer, where its role remains unclear and often contradictory. Using representative cell line models, we sought to determine whether the discrepant miR-155 effects in breast cancer could be explained by the heterogeneity of the disease. The growth of six breast cancer cell lines transfected with several miRNA mimics was analyzed. We found MCF-7 cell growth to be inhibited by miR-155 and miR-145 mimics, both 23-nt long, but not by a number of shorter mimics, including a universal commercial negative control. Microarray and Western blot analyses revealed induction of apoptosis, associated with interferon-β after activation of the double-stranded RNA sensor pathway. 3′ Trimming of the miRNA mimics to 21 nt substantially reduced their growth-inhibitory potency. Mutating the canonical seed of the miR-155 mimic had no effect on the induced inhibition, which was abolished by mutating the miRNA seed of the artificial passenger strand. A panel of breast cancer cell lines showed a wide range of sensitivities to 23-mer mimics, broadly consistent with the sensitivity of the cell lines to Poly (I:C). We demonstrate two sources for nonspecific in vitro effects by miRNA mimics: duplex length and the artificial passenger strand. We highlight the danger of a universal 21-mer negative control and the importance of using matched seed mutants for reliable interpretation of phenotypes.
A Novel Automated Scan Chain Division Method for Shift and Capture Power Reduction in Broadside At-Speed Test

To address the excessive power during test, multiple scan divisions can be created such that not all the circuit blocks are active at the same time. While this concept has been successfully employed in the past for addressing shift power, the reported techniques for at-speed capture power reduction rely on modifications in the automatic test pattern generation (ATPG) algorithms. This paper shows how by analyzing the signal dependencies in the circuit's sequential graph, scan chain divisions can be created automatically, such that power is guaranteed to be reduced during both shift and capture when broadside test is employed. This is achieved with the existing ATPG flows and without affecting the transition fault coverage or increasing the scan time.
Abundanceand diversityofaerobic anoxygenic phototrophic bacteria in saline lakeson theTibetan plateau

Abundanceand diversityofaerobic anoxygenic phototrophic bacteria in saline lakeson theTibetan plateau Hongchen Jiang, Hailiang Dong, Bingsong Yu, Guo Lv, Shicai Deng, Yajie Wu, Minghan Dai & Nianzhi Jiao Geomicrobiology Laboratory, State Key Laboratory of Geological Processes and Mineral Resources, China University of Geosciences, Beijing, China; Department of Geology, Miami University, Oxford, OH, USA; and Key Laboratory of Marine Environmental Sciences, Xiamen University, Xiamen, China
Childhood acute lymphoblastic leukemia in the age of genomics

The recent sequencing of the human genome and technical breakthroughs now make it possible to simultaneously determine mRNA expression levels of almost all of the identified genes in the human genome. DNA “chip” or microarray technology holds great promise for the development of more refined, biologically‐based classification systems for childhood ALL, as well as the identification of new targets for novel therapy. To date gene expression profiles have been described that correlate with subtypes of ALL defined by morphology, immunophenotype, cytogenetic alterations, and response to therapy. Mechanistic insights into treatment failure have come from the definition of mRNA signatures that predict in vitro chemoresistance, as well as differences between blasts at relapse and new diagnosis. New bioinformatics tools optimize data mining, but validation of findings is essential since “over‐fitting” the data is a common danger. In the future, genomic analysis will be complemented by evaluation of the cancer proteome. © 2005 Wiley‐Liss, Inc.
Physics‐based enzyme design: Predicting binding affinity and catalytic activity

Computational enzyme design is an emerging field that has yielded promising success stories, but where numerous challenges remain. Accurate methods to rapidly evaluate possible enzyme design variants could provide significant value when combined with experimental efforts by reducing the number of variants needed to be synthesized and speeding the time to reach the desired endpoint of the design. To that end, extending our computational methods to model the fundamental physical–chemical principles that regulate activity in a protocol that is automated and accessible to a broad population of enzyme design researchers is essential. Here, we apply a physics‐based implicit solvent MM‐GBSA scoring approach to enzyme design and benchmark the computational predictions against experimentally determined activities. Specifically, we evaluate the ability of MM‐GBSA to predict changes in affinity for a steroid binder protein, catalytic turnover for a Kemp eliminase, and catalytic activity for α‐Gliadin peptidase variants. Using the enzyme design framework developed here, we accurately rank the most experimentally active enzyme variants, suggesting that this approach could provide enrichment of active variants in real‐world enzyme design applications. Proteins 2014; 82:3397–3409. © 2014 Wiley Periodicals, Inc.
Extracellular Release of the Glycosylphosphatidylinositol (GPI)-linked Leishmania Surface Metalloprotease, gp63, Is Independent of GPI Phospholipolysis

The major zinc metalloprotease ofLeishmania (gp63), an important determinant of parasite virulence, is attached to the parasite surface via a glycosylphosphatidylinositol anchor. Here we report the spontaneous release of proteolytically active gp63 from a number ofLeishmania isolates, causing cutaneous and visceral disease. To investigate the mechanism(s) of gp63 release, we transfected a gp63-deficient variant of Leishmania amazonensis with constructs expressing gp63 and various mutants thereof. Surprisingly, approximately half of wild type gp63 was found in the culture supernatant 12 h post-synthesis. Biochemical analysis of the extracellular gp63 revealed two forms of the protein, one that is released from the cell surface, and another, that apparently is directly secreted. Release of cell surface gp63 was significantly reduced when the proteolytic activity of the protein was inactivated by site-specific mutagenesis or inhibited by zinc chelation, suggesting that release involves autoproteolysis. The extracellular gp63 does not contain a glycosylphosphatidylinositol moiety or ethanolamine, indicating that phospholipolysis is not involved in the release process. Release of gp63 is also independent of glycosylation. The finding of proteolytically active, extracellular gp63 produced by multiple Leishmania isolates suggests a potential role of the extracellular enzyme in substrate degradation relevant to their survival in both the mammalian host and the insect vector.
Psychometric Properties of Turkish versions of the Leyton Obsessional Inventory-Child Version (LOI-CV) and Obsessive Beliefs Questionnaire-Child Version (OBQ-CV)

ABSTRACTObjective: Juvenile obsessive-compulsive disorder has been increasingly recognized in the literature. However, the developmentally sensitive screening tools for obsessive-compulsive disorder (OCD) in children and adolescents still lag behind psychometric tools developed for adult OCD. The Leyton Obsessional Inventory-Child Version is the most widely utilized screening tool for juvenile OCD assessment. Our aim was to assess psychometric properties of the Leyton Obsessional Inventory-Child Version (LOI-CV) and Obsessive Beliefs Questionnaire-Child Version (OBQ-CV). Method: The sample consisted of 805 children and adolescents, aged from 11 to 17 years. Mean age of the sample was 13.85 (SD±1.40) years. The LOI-CV, OBQ-CV, Obsessive Compulsive Inventory-Revised (OCI-R), State Trait Anxiety Inventory for Children (STAI-C) and Meta-Cognitions Questionnaire for Children (MCQ-C) were completed by respondents. The data were subjected to explanatory and confirmatory factor analyses. Internal consistency and t.
emm Gene Distribution among Erythromycin-Resistant and -Susceptible Italian Isolates of Streptococcus pyogenes

ABSTRACT The phenotypes and genetic determinants for macrolide resistance were determined for 167 erythromycin-resistant Streptococcus pyogenes strains. A cMLS phenotype was shown in 18% of the erythromycin-resistant strains, while inducible resistance was apparent in 31% and the M phenotype was apparent in 50%. The emm gene type of this set of resistant isolates and that of 48 erythromycin-sensitive isolates were determined. emm2 and emm48 were recorded only in the resistant strains of the M phenotype, while approximately all of the strains harboring the emm22 gene had the cMLS phenotype. More than 80% of the emm89-positive strains had the iMLS phenotype, and the same portion of emm4 strains presented the M phenotype. emm3 is recorded only among sensitive strains. The distribution of frequencies of the genetic determinant for the virulence factor M protein was significantly different both among organisms of different types of resistance and between resistant and sensitive populations of S. pyogenes under study.
Familial symptom domains in monozygotic siblings with autism

Autism is characterized by a triad of symptom domains (impaired social interaction, communication deficits, and repetitive behaviors) that vary significantly in their clinical presentation across the population. Within families with more than one affected member, however, discrepant findings exist with regard to symptom variability. Reduced intrafamily variance is of particular importance because it supports an underlying model of genetic heterogeneity in the transmission of autism, and the identification of familial clinical subtypes can be used to select more homogeneous samples for linkage analysis in the future. This study examines whether there are specific features of autism that show decreased variance within 16 families with monozygotic siblings concordant for autism. Evidence for familiality was defined as significantly decreased variance of symptom levels within monozygotic siblingships as compared to between siblingships. Using regression analysis, we demonstrated significant aggregation of symptoms within monozygotic siblingships for two of the three main symptom domains in autism: impairments in communication and social interaction showed significant familiality. Within the repetitive behavior domain, only the categories of circumscribed interests and preoccupation with part‐objects showed reduced variance within siblingships. In addition, with the exception of a negative association between the social and behavior domains, partial correlation coefficients did not reveal significant associations between the levels of different symptom domains within families, suggesting that the levels of clinical features seen in autism may be a result of mainly independent genetic traits. Because of presumed genetic heterogeneity and the wide clinical variation seen in autism and other pervasive developmental disorders, selecting probands according to specific features known to show reduced variance within families may provide more homogeneous samples for genetic analysis and strengthen the power to detect the specific genes involved in autism. © 2004 Wiley‐Liss, Inc.
THE INFLUENCE OF BODY MEASUREMENTS AND CONDITION SCORE ON PERFORMANCE RESULTS DURING THE 1998 TEVIS CUP

Body measurements and performance results were collected from 193 equids participating in the 1998 Western States Trail Ride's 100-mile endurance race, commonly known as the Tevis Cup. Age of equids (horses, mules and ponies) were 5 to 21 years and body condition scores (CS) (NRC, 1989) ranged from 2.5 to 5.5. Equids were assessed for CS 11 to 18 hours prior to the race. Rider weight and tack (RW) were weighed using a digital scale. Body weights of horses (BW) were estimated from heart girth circumference, body length and condition score data. Cannon bone circumference (CBC) was measured midway between carpal-metacarpal and metacarpal-phalangeal joints. Miles completed, times and finishing place of horses that completed the race, miles completed by horses that did not complete the race, and horses that were disqualified (identified as lame, metabolic failure, rider option or overtime) were procured from official records compiled by race management. Total ride weight (TRW) consisted of BW plus RW. BW, RW, TRW and CBC did not differ between equids that completed or did not complete the race (P>.05). The rider's weight as a proportion of the horse's body weight (RW/BW) for animals disqualified for metabolic failure was higher than those that completed the race. Animals that completed the Tevis Cup had a significantly higher CS than those equids that were disqualified for metabolic failure (4.5 vs <3.5)(P<.01). However, there was no difference between the CS of those disqualified for other reasons, including lameness.
L'utilisation des plantes de couverture dans la culture du caféier Robusta au Cameroun

Apres un bref rappel du role des plantes de couverture, l'auteur presente 5 essais realises au Cameroun avec Puerarie, Mimosa, Stylosanthes, Flemingia et Tithonia. Apres evaluation des frais d'etablissement et d'entretien des plantes de couverture, il etudie l'influence de ces plantes sur la croissance et la nutrition minerale des cafeiers, les reserves d'eau du sol, l'evolution de ce dernier, les productions. D'apres les resultats obtenus, l'auteur estime que l'utilisation d'une plante de couverture adequate constitue une pratique culturale rentable. Dans l'ouest du Cameroun, le Flemingia et le Mimosa ont augmente les rendements de 60 a 100% et meme 120% suivant les annees dans les plantations adultes. Le Flemingia avance l'entree en production des nouvelles plantations
Molecular Mechanism of Action for Allosteric Modulators and Agonists in CC-chemokine Receptor 5 (CCR5)*

The small molecule metal ion chelators bipyridine and terpyridine complexed with Zn2+ (ZnBip and ZnTerp) act as CCR5 agonists and strong positive allosteric modulators of CCL3 binding to CCR5, weak modulators of CCL4 binding, and competitors for CCL5 binding. Here we describe their binding site using computational modeling, binding, and functional studies on WT and mutated CCR5. The metal ion Zn2+ is anchored to the chemokine receptor-conserved Glu-283VII:06/7.39. Both chelators interact with aromatic residues in the transmembrane receptor domain. The additional pyridine ring of ZnTerp binds deeply in the major binding pocket and, in contrast to ZnBip, interacts directly with the Trp-248VI:13/6.48 microswitch, contributing to its 8-fold higher potency. The impact of Trp-248 was further confirmed by ZnClTerp, a chloro-substituted version of ZnTerp that showed no inherent agonism but maintained positive allosteric modulation of CCL3 binding. Despite a similar overall binding mode of all three metal ion chelator complexes, the pyridine ring of ZnClTerp blocks the conformational switch of Trp-248 required for receptor activation, thereby explaining its lack of activity. Importantly, ZnClTerp becomes agonist to the same extent as ZnTerp upon Ala mutation of Ile-116III:16/3.40, a residue that constrains the Trp-248 microswitch in its inactive conformation. Binding studies with 125I-CCL3 revealed an allosteric interface between the chemokine and the small molecule binding site, including residues Tyr-37I:07/1.39, Trp-86II:20/2.60, and Phe-109III:09/3.33. The small molecules and CCL3 approach this interface from opposite directions, with some residues being mutually exploited. This study provides new insight into the molecular mechanism of CCR5 activation and paves the way for future allosteric drugs for chemokine receptors.