Miracle-dz/UniFAR-FTUs huggingface dataset:
Blocking CD27-CD70 Costimulatory Pathway Suppresses Experimental Colitis1

The pathogenesis of human inflammatory bowel disease (IBD) and most experimental models of IBD is dependent on the activation and expansion of CD4+ T cells via interaction with mucosal APCs. The costimulatory receptor CD70 is transiently expressed on the surface of conventional dendritic cells, but is constitutively expressed by a unique APC population in the intestinal lamina propria. We used two experimental IBD models to evaluate whether interfering the interaction between CD70 and its T cell ligand CD27 would affect the development of colitis. Adoptive transfer of naive CD27-deficient CD45RBhigh CD4+ T cells into Rag-1−/− mice resulted in significantly less disease than when wild-type CD45RBhighCD4+ T cells were used. Moreover, a monoclonal anti-CD70 Ab prevented the disease caused by the transfer of wild-type CD45RBhigh CD4+ T cells into Rag-1−/− mice and the same Ab also ameliorated an established disease. The colitis associated proinflammatory cytokines IL-6, TNF-α and IFN-γ were significantly reduced after anti-CD70 Ab treatment, suggesting an overall reduction in inflammation due to blockade of pathogenic T cell expansion. Anti-CD70 Ab treatment also suppressed trinitrobenzene sulfonic acid-induced colitis in SJL/J mice. Because anti-CD70 Ab treatment suppressed multiple proinflammatory cytokines, this may be a more potent therapeutic approach for IBD than blockade of individual cytokines.
Characterization of Schizosaccharomyces pombe his1 and his5 cDNAs

We have isolated Schizosaccharomyces pombe cDNAs corresponding to the genes his1+ and his5+. The his1 cDNA was isolated by functional complementation of the His− phenotype in a his1‐29 gcn3 Saccharomyces cerevisiae strain, while the his5 cDNA was isolated as a suppressor of the 3‐amino‐1,2,4‐triazole (3‐AT) sensitivity in a gcn3 S. cerevisiae strain. his1 and his5 are each present in single copy in haploid S. pombe. As is the case with S. cerevisiae, we have found that the growth of wild‐type strains of S. pombe is sensitive to 3‐AT, an inhibitor of imidazoleglycerol‐phosphate dehydratase. This enzyme is encoded by the HIS3 gene in S. cerevisiae and the his5+ gene in S. pombe. Treatment of S. pombe cells with 3‐AT leads to a small increase in the level of the his5 transcript, but no effect is seen on the level of the his1 transcript. This is in contrast to larger increases in transcription of amino acid biosynthetic genes, regulated by the general amino acid control, seen previously in similarly treated cultures of S. cerevisiae. These results suggest that there are likely to be some differences in the regulation of amino acid biosynthesis between these two yeasts.
Healthy obesity and objective physical activity

Background: Disease risk is lower in metabolically healthy obese adults than in their unhealthy obese counterparts. Studies considering physical activity as a modifiable determinant of healthy obesity have relied on self-reported measures, which are prone to inaccuracies and do not capture all movements that contribute to health. Objective: We aimed to examine differences in total and moderateto-vigorous physical activity between healthy and unhealthy obese groups by using both self-report and wrist-worn accelerometer assessments. Design: Cross-sectional analyses were based on 3457 adults aged 60–82 y (77% male) participating in the British Whitehall II cohort study in 2012–2013. Normal-weight, overweight, and obese adults were considered “healthy” if they had ,2 of the following risk factors: low HDL cholesterol, hypertension, high blood glucose, high triacylglycerol, and insulin resistance. Differences across groups in total physical activity, based on questionnaire and wrist-worn triaxial accelerometer assessments (GENEActiv), were examined by using linear regression. The likelihood of meeting 2010 World Health Organization recommendations for moderate-to-vigorous activity ($2.5 h/wk) was compared by using prevalence ratios. Results: Of 3457 adults, 616 were obese [body mass index (in kg/ m) $30]; 161 (26%) of those were healthy obese. Obese adults were less physically active than were normal-weight adults, regardless of metabolic health status or method of physical activity assessment. Healthy obese adults had higher total physical activity than did unhealthy obese adults only when assessed by accelerometer (P = 0.002). Healthy obese adults were less likely to meet recommendations for moderate-to-vigorous physical activity than were healthy normal-weight adults based on accelerometer assessment (prevalence ratio: 0.59; 95% CI: 0.43, 0.79) but were not more likely to meet these recommendations than were unhealthy obese adults (prevalence ratio: 1.26; 95% CI: 0.89, 1.80). Conclusions: Higher total physical activity in healthy than in unhealthy obese adults is evident only when measured objectively, which suggests that physical activity has a greater role in promoting health among obese populations than previously thought. Am J Clin Nutr 2015;102:268–75.
Fission yeast Cut2 required for anaphase has two destruction boxes

The fission yeast Schizosaccharomyces pombe cut2+ gene is essential for sister chromatid separation. Cut2 protein, which locates in the interphase nucleus and along the metaphase spindle, disappears in anaphase with the same timing as mitotic cyclin destruction. This proteolysis depends on the APC (Anaphase‐Promoting Complex)–cyclosome which contains ubiquitin ligase activity. The N‐terminus of Cut2 contains two stretches similar to the mitotic cyclin destruction box. We show that both sequences (33RAPLGSTKQ and 52RTVLGGKST) serve as destruction boxes and are required for in vitro polyubiquitination and proteolysis. Cut2 with doubly mutated destruction boxes inhibits anaphase, whereas Cut2 with singly mutated boxes can suppress cut2 mutations. Strong expression of the N‐terminal 73 residues containing the destruction boxes leads to the accumulation of endogenous cyclin and Cut2, and arrests cells in metaphase, whereas the same fragment with the mutated boxes does not. Cut2 proteolysis occurs in vitro using Xenopus mitotic extracts in the presence of functional destruction boxes. Furthermore, Cut2 is polyubiquitinated in an in vitro system using HeLa extracts, and this polyubiquitination requires the destruction boxes.
Analysis of expression of toxin-coregulated pili in classical and El Tor Vibrio cholerae O1 in vitro and in vivo

The expression of toxin-coregulated pili (TCP) and their structural subunit TcpA was compared in 20 strains of Vibrio cholerae of the classical and El Tor biotypes. Bacteria were isolated from the intestines of rabbits with experimental cholera and compared with the same strains grown under optimal TCP expression conditions in vitro. Immunoblotting revealed that TcpA production was induced in both biotypes after vibrios entered the intestinal milieu; TcpA-negative inocula gave rise to TcpA-positive vibrios after multiplication in the gut. The levels of TcpA expressed during growth in the intestine were, for most strains, comparable to those attained under optimal growth conditions in vitro. Of 11 classical strains tested, 10 expressed TCP antigen on the bacterial surface at levels comparable to or exceeding those seen after growth in vitro as determined by an inhibition enzyme-linked immunosorbent assay. In contrast, only one of the nine El Tor strains studied produced detectable amounts of TCP surface antigen in vivo and no fimbriae or surface antigen reacting with anti-TCP serum was found on El Tor vibrios from human cholera stools. Distinct TCP fimbriae were observed by immunoelectron microscopy on classical-biotype vibrios grown either in rabbit intestines or in vitro but were not detected on El Tor vibrios. The results show that TCP is expressed on V. cholerae O1 of the classical biotype but not on V. cholerae O1 of the El Tor biotype in the intestines of rabbits with experimental cholera infection.
Efficacy of piperine, an alkaloidal constituent from Piper nigrum on erythrocyte antioxidant status in high fat diet and antithyroid drug induced hyperlipidemic rats

The main aim of this study was to investigate the effect of piperine on erythrocyte antioxidant status in high fat diet (HFD) and antithyroid drug induced hyperlipidemic rats. Male Wistar rats were divided into eight groups. The first four groups were fed a control diet and in addition were given respectively 1% carboxymethyl cellulose (CMC); 10 mg/kg body weight carbimazole (CM); 10 mg CM + 40 mg/kg body weight piperine and 10 mg CM + 2 mg/kg body weight atorvastatin (ATV). A similar pattern was followed for the next four groups except that they were all fed HFD instead of the control diet. Erythrocyte osmotic fragility, total cholesterol, phospholipids, lipid peroxidation products, enzymic and non‐enzymic antioxidant status were studied in all experimental groups. Significantly increased osmotic fragility, total cholesterol/phospholipid ratio, thiobarbituric acid reactive substances and lipid hydroperoxides were observed in the plasma and erythrocytes of HFD fed and CM treated rats compared to the control. Superoxide dismutase, catalase, glutathione peroxidase, vitamin E and reduced glutathione in erythrocytes and vitamin C in the plasma were also significantly lowered in HFD fed, antithyroid drug treated rats compared to control animals. Concurrent piperine supplementation along with HFD and antithyroid drug administration normalized erythrocyte osmotic fragility, reduced lipid peroxidation, and improved the enzymic and non‐enzymic antioxidant status compared to those rats that did not receive piperine. Thus, our results indicate that piperine supplementation markedly protects erythrocytes from oxidative stress by improving the antioxidant status in HFD fed antithyroid drug treated rats. Copyright © 2006 John Wiley & Sons, Ltd.
Stress pendant la période d'abattage chez les bovins : rôles de la réactivité émotionnelle et des facteurs environnementaux

La periode d’abattage est complexe car elle se compose d’une succession de situations associees a une multitude de facteurs de stress. L’animal est generalement prive d’alimentation et est ensuite confronte a un environnement changeant et contraignant qui demande en permanence des adaptations comportementales et physiologiques affectant son etat emotionnel. Les objectifs de cette these sont (i) de mieux comprendre l’origine des reactions des bovins au cours de la periode d’abattage, et (ii) d’evaluer leur stress d’un point de vue comportemental et physiologique a l’aide d’etudes menees a la fois en abattoir industriel et dans des conditions experimentales.Nos travaux sur le terrain mettent en evidence la necessite de tenir compte de toutes les procedures d’abattage, y compris les plus courtes, ainsi que des contraintes organisationnelles des abattoirs car elles influencent l’etat de stress des bovins. Pendant la periode d’elevage, la caracterisation des bovins selon leur reactivite emotionnelle,qui depend en partie de leur experience anterieure et de leur race, permet d’identifier les animaux susceptibles de reagir plus fortement aux procedures d’abattage. Elle permet egalement de determiner les facteurs de stress preponderants associes a ces procedures. Ainsi, la nouveaute et la separation sociale expliquent en partie les reactions de stress a l’abattage chez les vaches. Chez les taurillons, les reactions de stress a l’abattage sont liees a leur reactivite cardiaque a la soudainete et a l’Homme. De plus, les bovins reagissent plus fortement a differents facteurs de stress lorsqu’ils sont prives de nourriture. L’etat physiologique des bovins influence donc leurs reactions de stress a l’abattage, probablement en modulant leur perception de la situation. Afin de reduire le niveau de stress des bovins pendant la periode d’abattage, nos travaux montrent qu’il est possible d’agir sur l’environnement en limitant les sources de stress directes et indirectes. Il est egalement possible d’agir au niveau de l’animal par le biais de son experience anterieure et de sa genetique.
An Investigation Into the Temperature Stability of a Guided Wave Structural Health Monitoring System Using Permanently Attached Sensors

When testing complex structures using a deployable guided wave system, the measured signals are often far too complex to directly interpret without a priori knowledge of the geometry of the structure. However, in a structural health monitoring (SHM) scenario, the sensors are permanently attached to the structure and so changes in the system can be monitored by comparison to an earlier baseline measurement, taken when the structure was undamaged. This paper investigates such a system for the SHM of plate-like structures using guided waves. The basis of the system is a distributed array of permanently attached piezoelectric guided wave transducers where pairs of transducers are used in pitch-catch configuration allowing the detection and localization of damage in the plate. It has been observed that the use of a single baseline measurement suffers in the medium to long-term due to the variation of environmental conditions. A key parameter in the instability is the change in the temperature of the test structure. A method of using a database of baselines, termed optimal baseline subtraction (OBS), is described and applied to an experimental SHM system. The objective of this paper is to investigate the suitability and robustness of OBS under varying rates of temperature change and its use in the localization of damage. Results have shown that through the OBS an improvement of up to 20 dB in signal-to-coherent noise ratio may be achieved compared with single baseline subtraction
The Effects of Neonatal Dorsal Root Section on the Survival and Dendritic Development of Lumbar Motoneurons in the Rat

Peripheral nerve crush during the early neonatal period results in the death of a large proportion of affected motoneurons and abnormal dendritic development in those which survive. The present study reports the effects of neonatal dorsal root section on motoneurons supplying the extensor digitorum longus muscle of the rat. This lesion did not result in motoneuron death, but did disrupt subsequent dendritic development. In cells retrogradely labelled with cholera toxin subunit B conjugated to horseradish peroxidase, there was little change in adult dendritic morphology in the transverse plane, where abnormalities associated with loss of efferent contact and cell death have been found. However, there was a caudal expansion of the dendritic field, an effect seen following nerve crush but not after blockade of neuromuscular transmission alone. The results show that disruption of dorsal root sensory inputs alone can affect the dendritic development of motoneurons but does not cause their death. In conjunction with our earlier findings, it is clear that both afferent and efferent connections are required for normal dendritic development, and disruption of either has a characteristic effect on survival and dendritic morphology.
Structural Properties of a Multifunctional T-Shaped RNA Domain That Mediate Efficient Tomato Bushy Stunt Virus RNA Replication

ABSTRACT In positive-strand RNA viruses, 5′ untranslated regions (5′ UTRs) mediate many essential viral processes, including genome replication. Previously, we proposed that the 5′-terminal portion of the genomic leader sequence of Tomato bushy stunt virus (TBSV) forms an RNA structure containing a 3-helix junction, termed the T-shaped domain (TSD). In the present study, we have carried out structure-function analysis of the proposed TSD and have confirmed an important role for this domain in mediating efficient viral RNA amplification. Using a model TBSV defective interfering RNA replicon and a protoplast system, we demonstrated that various TSD subelements contribute to the efficiency of viral RNA replication. In particular, the stabilities of all three stems (S1, S2, and S4) forming the 3-helix junction are important, while stem-loop 3—a terminal extension of S2—is largely dispensable. Additionally, some of the sequences forming the 3-helix junction are required in an identity-dependent manner. Thus, both secondary structure and nucleotide identity are important for TSD-mediated viral RNA replication. Importantly, these results are fully consistent with the dual functions we defined previously for the sequences corresponding to loops 3 and 4, respectively, in facilitating 5′ cap- and 3′ poly(A) tail-independent translation of the genome by forming a loop-loop interaction with the 3′-proximal translational enhancer and in mediating viral RNA replication through formation of a pseudoknot with the adjacent downstream RNA domain. Also, since comparable TSDs and associated interactions are predicted in the 5′ UTRs of all sequenced Aureusvirus genomes, members of at least one other genus in the family Tombusviridae appear to utilize this type of multifunctional RNA domain.
Firefly luciferase gene: structure and expression in mammalian cells

The nucleotide sequence of the luciferase gene from the firefly Photinus pyralis was determined from the analysis of cDNA and genomic clones. The gene contains six introns, all less than 60 bases in length. The 5' end of the luciferase mRNA was determined by both S1 nuclease analysis and primer extension. Although the luciferase cDNA clone lacked the six N-terminal codons of the open reading frame, we were able to reconstruct the equivalent of a full-length cDNA using the genomic clone as a source of the missing 5' sequence. The full-length, intronless luciferase gene was inserted into mammalian expression vectors and introduced into monkey (CV-1) cells in which enzymatically active firefly luciferase was transiently expressed. In addition, cell lines stably expressing firefly luciferase were isolated. Deleting a portion of the 5'-untranslated region of the luciferase gene removed an upstream initiation (AUG) codon and resulted in a twofold increase in the level of luciferase expression. The ability of the full-length luciferase gene to activate cryptic or enhancerless promoters was also greatly reduced or eliminated by this 5' deletion. Assaying the expression of luciferase provides a rapid and inexpensive method for monitoring promoter activity. Depending on the instrumentation employed to detect luciferase activity, we estimate this assay to be from 30- to 1,000-fold more sensitive than assaying chloramphenicol acetyltransferase expression.
Environmental change, shifting distributions, and habitat conservation plans: A case study of the California gnatcatcher

Abstract Many species have already experienced distributional shifts due to changing environmental conditions, and analyzing past shifts can help us to understand the influence of environmental stressors on a species as well as to analyze the effectiveness of conservation strategies. We aimed to (1) quantify regional habitat associations of the California gnatcatcher (Polioptila californica); (2) describe changes in environmental variables and gnatcatcher distributions through time; (3) identify environmental drivers associated with habitat suitability changes; and (4) relate habitat suitability changes through time to habitat conservation plans. Southern California's Western Riverside County (WRC), an approximately 4,675 km2 conservation planning area. We assessed environmental correlates of distributional shifts of the federally threatened California gnatcatcher (hereafter, gnatcatcher) using partitioned Mahalanobis D 2 niche modeling for three time periods: 1980–1997, 1998–2003, and 2004–2012, corresponding to distinct periods in habitat conservation planning. Highly suitable gnatcatcher habitat was consistently warmer and drier and occurred at a lower elevation than less suitable habitat and consistently had more CSS, less agriculture, and less chaparral. However, its relationship to development changed among periods, mainly due to the rapid change in this variable. Likewise, other aspects of highly suitable habitat changed among time periods, which became cooler and higher in elevation. The gnatcatcher lost 11.7% and 40.6% of highly suitable habitat within WRC between 1980–1997 to 1998–2003, and 1998–2003 to 2004–2012, respectively. Unprotected landscapes lost relatively more suitable habitat (−64.3%) than protected landscapes (30.5%). Over the past four decades, suitable habitat loss within WRC, especially between the second and third time periods, was associated with temperature‐related factors coupled with landscape development across coastal sage scrub habitat; however, development appears to be driving change more rapidly than climate change. Our study demonstrates the importance of providing protected lands for potential suitable habitat in future scenarios.
Compressing the free energy range of substructure stabilities in iso‐1‐cytochrome c

Evolutionary conservation of substructure architecture between yeast iso‐1‐cytochrome c and the well‐characterized horse cytochrome c is studied with limited proteolysis, the alkaline conformational transition and global unfolding with guanidine‐HCl. Mass spectral analysis of limited proteolysis cleavage products for iso‐1‐cytochrome c show that its least stable substructure is the same as horse cytochrome c. The limited proteolysis data yield a free energy of 3.8 ± 0.4 kcal mol−1 to unfold the least stable substructure compared with 5.05 ± 0.30 kcal mol−1 for global unfolding of iso‐1‐cytochrome c. Thus, substructure stabilities of iso‐1‐cytochrome c span only ∼1.2 kcal mol−1 compared with ∼8 kcal mol−1 for horse cytochrome c. Consistent with the less cooperative folding thus expected for the horse protein, the guanidine‐HCl m‐values are ∼3 kcal mol−1M−1 versus ∼4.5 kcal mol−1M−1 for horse versus yeast cytochrome c. The tight free energy spacing of the yeast cytochrome c substructures suggests that its folding has more branch points than for horse cytochrome c. Studies on a variant of iso‐1‐cytochrome c with an H26N mutation indicate that the least and most stable substructures unfold sequentially and the two least stable substructures unfold independently as for horse cytochrome c. Thus, important aspects of the substructure architecture of horse cytochrome c, albeit compressed energetically, are preserved evolutionally in yeast iso‐1‐cytochrome c.
An unstable beta 2-microglobulin: major histocompatibility complex class I heavy chain intermediate dissociates from calnexin and then is stabilized by binding peptide

Proper assembly of the class I heavy chain (HC), beta 2-microglobulin (beta 2m), and peptide must occur in the endoplasmic reticulum (ER) in order for MHC class I molecules to be expressed on the cell surface. Newly synthesized class I HC bind calnexin, an ER resident chaperone. These calnexin-associated class I HC appeared to lack the stable association with beta 2m in peptide transporter-deficient T2 cells since beta 2m-unassociated class I HC-specific HC10 antibody, but not beta 2m-associated class I HC-specific W6/32 antibody, coimmunoprecipitated calnexin. To determine the precursor-product relationship of the pool of HC that bind peptide, class I-restricted peptides were added to lysates of T2 cells in vitro. These peptides stabilized preexisting beta 2m-associated HC complexes (beta 2m+:HC:pep- ), but had no significant effect on the preexisting pool of calnexin- associated HC that lack beta 2m. Release of HC from calnexin appeared to be controlled by the binding of beta 2m, since beta 2m-deficient FO- 1 cells showed a prolonged association of class I HC with calnexin, while beta 2m-transfected FO-1 cells displayed a more rapid dissociation of class I HC from calnexin. Consistent with this result, the dissociation of class I HC from calnexin did not appear to be dependent on peptide binding since the dissociation rates were similar in peptide transporter-deficient T2 cells and in wild-type T1 cells. From these observations, we speculate that in the stepwise assembly of class I molecules, calnexin may mediate dimerization of class I HC with beta 2m, and that the unstable beta 2m+:HC:pep- complexes, after dissociation from calnexin, subsequently bind peptide to complete the assembly.