Miracle-dz/UniFAR-FTUs huggingface dataset:
Genetic Determinants of Bone Mass

A genetic contribution to bone mass determination was first described in the early 70s. Elucidation of gene contribution to this has since been attempted through studies analyzing associations between bone mass acquisition and/or maintenance and polymorphic variations of several genes. The first to be described was the vitamin D receptor gene (VDR), initially claimed to contribute to almost 75% of the genetic variation in bone mineral density (BMD) in twin and general population studies. Not all of the studies published to date conclude that a clear relationship exists between polymorphic VDR alleles and BMD, and the molecular basis for the VDR gene polymorphisms influence on bone mineralization has not yet been clarified. Since then, other genes with a significant role in bone metabolism such as estradiol receptor, collagen type 1α1, TGF-β1, interleukin-6, calcitonin receptor, α2-HS-glycoprotein, osteocalcin, calcium-sensing receptor, interleukin-1 receptor antagonist, β3-adrenergic receptor, apolipoprotein E, PTH, IGF-I and glucocorticoid receptor have been analyzed. Some polymorphic variations in these genes have been associated in some works with significant differences in BMD, with even more significant contributions when associations of different gene polymorphisms were analyzed. Again, the molecular basis for the contribution of these alleles to bone mass determination has not yet been described. A different approach has been attempted by linkage analysis of loci involved in bone density in pedigrees with low BMD using BMD as a quantitative trait. Recent results do not confirm, in these families, any association with any of the previously reported genes, but rather with other as yet unidentified genes. The genetic contribution to mild variations in the general population, as a result of environmental and endogenous individual influences, probably differs completely from that providing a pathologic BMD.
Brown adipose tissue, liver, and diet-induced thermogenesis in cafeteria diet-fed rats.

Diet-induced thermogenesis (DIT) in young rats overeating a "cafeteria" (CAF) diet of palatable human foods is characterized by a chronic, propranolol-inhibitable elevation in resting metabolic rate (VO2) and is associated with various changes in brown adipose tissue (BAT) that have been taken as evidence for BAT as the effector of DIT. But direct evidence for participation of BAT in DIT has been lacking. By employing a nonocclusive cannula to sample the venous effluent of interscapular BAT (IBAT) for analysis of its O2 content and measuring tissue blood flow with microspheres, we accomplished direct determination (Fick principle) of the O2 consumption of BAT in conscious CAF rats. In comparison with normophagic controls fed chow, the CAF rats exhibited a 43% increase in metabolizable energy intake, reduced food efficiency, a 22% elevation in resting VO2 at 28 degrees C (thermoneutrality) or 24 degrees C (housing temperature), and characteristic changes in the properties of their BAT (e.g., increased mass, protein content and mitochondrial GDP binding). They also exhibited the greater metabolic response to exogenous noradrenaline characteristic of CAF rats and the near elimination by propranolol of their elevation in VO2. By the criterion of their elevated VO2, the CAF rats were exhibiting DIT at the time of the measurements of BAT blood flow and blood O2 levels. However, BAT O2 consumption was found to be no greater in the CAF rats than in the controls at either 28 or 24 degrees C. At 28 degrees C it accounted for less than 1% of whole body VO2; at 24 degrees C it increased to about 10% of overall VO2 in both diet groups. (ABSTRACT TRUNCATED AT 250 WORDS)
Position Statement. Violence and injury in ice hockey.

Ice hockey is a sport enjoyed by many men and women at the spectator and participant level. It is played with high intensity and often involves body contact. Although the women's games is far from injury free, it is the men's game that has drawn criticism for excessive violence. Much attention has been drawn to the serious injuries that have occurred in ice hockey, specifically spinal injuries, concussions, and eye injuries. Many such injuries are the result of illegal and violent acts such as checking from behind or a deliberate high stick. Because of this, some medical organizations have called for changes in the sport, such as minimum age requirements for body-checking. As a practical matter such changes are unlikely to be accepted by hockey governing boards. Many of those involved in the sport consider body-checking a fundamental component of the game. Furthermore, a distinction needs to be made between any kind of injury and a serious, catastrophic injury. For example, although a recent study found that body-checking accounted for up to 38% of ice hockey injuries, none were of the catastrophic type. With respect to catastrophic injuries such as spinal cord trauma or a blinded eye, legal body-checking accounts for significantly less than illegal body-checking (e.g., checking from behind) or violent stick work. To reduce serious injury in ice hockey, we offer 10 recommendations, key among them automatic game suspensions for certain rules violations, and recognition of the coach as the most important figure in promoting a clean, safe game.
Proteasome regulation of activation-induced T cell death.

Lactacystin, a microbial metabolite that inhibits protease activity only in the proteasome, was used to study the role of the proteasome in the activation-induced cell death (AICD) of T cells. Lactacystin induces DNA fragmentation and apoptosis in a T cell hybridoma (DO.11. 10) in a dose-dependent manner. Between 1 and 10 microM, the mildly cytotoxic lactacystin inhibited the AICD of DO.11. 10 cells cultured in anti-CD3-coated wells. Degradation of IkappaBbeta and the translocation of the NF-kappaB (p50/RelA) into the nucleus, which occurred at 1.5 hr after anti-CD3 activation, were inhibited by lactacystin. Lactacystin did not inhibit the expression of nuclear transcription factor Oct-1. The activation-induced expression of the immediate-early gene, Nur77, and the T cell death genes, CD95 (Fas) and CD95 ligand (FasL), were inhibited. Functional expression of FasL cytotoxicity and the increase of cell surface Fas were also inhibited. Lactacystin must be added within 2 hr of activation to efficiently block AICD. In addition, lactacystin failed to inhibit the killing of DO.11. 10 by FasL-expressing allo-specific cytotoxic effector cells. These observations strongly suggest a direct link between the proteasome-dependent degradation of IkappaBbeta and the AICD that occurs through activation of the FasL gene and up-regulation of the Fas gene.
Dynamics of Multiple Infection and Within‐Host Competition by the Anther‐Smut Pathogen

Infection of one host by multiple pathogen genotypes represents an important area of pathogen ecology and evolution that lacks a broad empirical foundation. Multiple infection of Silene latifolia by Microbotryum violaceum was studied under field and greenhouse conditions using the natural polymorphism for mating‐type bias as a marker. Field transmission resulted in frequent multiple infection, and each stem of the host was infected independently. Within‐host diversity of infections equaled that of nearby inoculum sources by the end of the growing season. The number of diseased stems per plant was positively correlated with multiple infection and with overwintering mortality. As a result, multiply infected plants were largely purged from the population, and there was lower within‐host pathogen diversity in the second season. However, among plants with a given number of diseased stems, multiply infected plants had a lower risk of overwintering mortality. Following simultaneous and sequential inoculation, strong competitive exclusion was demonstrated, and the first infection had a significant advantage. Dynamics of multiple infection initially included components of coinfection models for virulence evolution and then components of superinfection models after systemic colonization. Furthermore, there was evidence for an advantage of genotypes with mating‐type bias, which may contribute to maintenance of this polymorphism in natural populations.
Comparison of different protocols for 13C‐urea breath test for the diagnosis of Helicobacter pylori infection in healthy volunteers

Objective. The 13C‐urea breath test (13C‐UBT) is the most accurate non‐invasive method for diagnosis of Helicobacter pylori infection. However, several methodological issues have not been resolved yet. The aim of this study was to test different protocols of 13C‐UBT to find the optimal test drink and sampling interval. Material and methods. 13C‐UBT was performed at 3‐day intervals in 27 healthy volunteers using citric acid (test A), orange juice (B) and still water (C) as test drinks. Breath samples were collected from time 5 to 60 min. A total number of 2106 breath samples were analysed by isotope ratio mass spectrometry (cut‐off value 3.5). Results. Differences in delta values were greater than would be expected by chance (A versus B and A versus C at times 20, 25, 30, 35 and 40 min, p<0.05, Dunnett's method). There were no grey zone‐ or false‐negative results among H. pylori‐positive persons in test A at any time, but some were found in tests B and C. Optimal intervals for breath sampling are at times 20 or 25 min after 13C‐urea ingestion. Conclusions. Citric acid solution as a test drink and 20‐ or 25‐min breath sampling intervals are optimal for the 13C‐UBT in healthy volunteers.
Focal Adhesion Kinase-mediated Phosphorylation of Beclin1 Protein Suppresses Cardiomyocyte Autophagy and Initiates Hypertrophic Growth*♦

Autophagy is an evolutionarily conserved intracellular degradation/recycling system that is essential for cellular homeostasis but is dysregulated in a number of diseases, including myocardial hypertrophy. Although it is clear that limiting or accelerating autophagic flux can result in pathological cardiac remodeling, the physiological signaling pathways that fine-tune cardiac autophagy are poorly understood. Herein, we demonstrated that stimulation of cardiomyocytes with phenylephrine (PE), a well known hypertrophic agonist, suppresses autophagy and that activation of focal adhesion kinase (FAK) is necessary for PE-stimulated autophagy suppression and subsequent initiation of hypertrophic growth. Mechanistically, we showed that FAK phosphorylates Beclin1, a core autophagy protein, on Tyr-233 and that this post-translational modification limits Beclin1 association with Atg14L and reduces Beclin1-dependent autophagosome formation. Remarkably, although ectopic expression of wild-type Beclin1 promoted cardiomyocyte atrophy, expression of a Y233E phosphomimetic variant of Beclin1 failed to affect cardiomyocyte size. Moreover, genetic depletion of Beclin1 attenuated PE-mediated/FAK-dependent initiation of myocyte hypertrophy in vivo. Collectively, these findings identify FAK as a novel negative regulator of Beclin1-mediated autophagy and indicate that this pathway can facilitate the promotion of compensatory hypertrophic growth. This novel mechanism to limit Beclin1 activity has important implications for treating a variety of pathologies associated with altered autophagic flux.
Lineages of Acidophilic Archaea Revealed by Community Genomic Analysis

Novel, low-abundance microbial species can be easily overlooked in standard polymerase chain reaction (PCR)–based surveys. We used community genomic data obtained without PCR or cultivation to reconstruct DNA fragments bearing unusual 16S ribosomal RNA (rRNA) and protein-coding genes from organisms belonging to novel archaeal lineages. The organisms are minor components of all biofilms growing in pH 0.5 to 1.5 solutions within the Richmond Mine, California. Probes specific for 16S rRNA showed that the fraction less than 0.45 micrometers in diameter is dominated by these organisms. Transmission electron microscope images revealed that the cells are pleomorphic with unusual folded membrane protrusions and have apparent volumes of <0.006 cubic micrometer.
Cross hybridization to Arabidopsis thaliana array reveals cold stress responsive genes in Lepidium latifolium

Cross species hybridization is an attractive option to understand the regulatory mechanisms and transcriptional networks underlying a biological activity, particularly for a non model organism. We have used the same approach to idenitfy cold responsive differentially expressed genes (DEGs) in Lepidium latifolium using Arabidopsis thaliana cDNA array chip. In all, 1315 DEGs were discovered. Putative functions of these cold-responsive genes were explored based on annotations using TAIR database and Blast2GO. Most of the up-regulated gene products were mapped to nucleus (20%) and plastids (15%) showing higher activities as DNA binding proteins, i.e., transcription factors. In all, 45 genes encoding transcription factors were identified belonging most frequently to AP2 family proteins (Seven genes) followed by NAM domain containing proteins (Five genes). Transcription factor binding sites (TFBS) were predicted for 1,100 genes belonging to 78 clusters of co-expressed genes. Interestingly, 50% of these regulatory sites contained a microsatellite repeat. Considering, Lepidium to be a native of high altitude cold regions, the genes identified in this study can be of wide importance to agricultural biotechnologists.
Functional Identification of Three Receptor Activator of NF-κB Cytoplasmic Motifs Mediating Osteoclast Differentiation and Function*

Receptor activator of NF-κB ligand (RANKL) and its receptor activator of NF-κB (RANK) play pivotal roles in osteoclast differentiation and function. However, the structural determinants of the RANK that mediate osteoclast formation and function have not been definitively identified. To address this issue, we developed a chimeric receptor approach that permits a structure/function study of the RANK cytoplasmic domain in osteoclasts. Using this approach, we examined the role of six RANK putative tumor necrosis factor receptor-associated factor-binding motifs (PTM) (PTM1, ILLMT-REE286-293; PTM2, PSQPS349-353; PTM3, PFQEP369-373; PTM4, VYVSQTSQE537-545; PTM5, PVQEET559-564; and PTM6, PVQEQG604-609) in osteoclast formation and function. Our data revealed that the RANK cytoplasmic domain possesses three functional motifs (PFQEP369-373, PVQEET559-564, and PVQEQG604-609) capable of mediating osteoclast formation and function. Moreover, we demonstrated that these motifs play distinct roles in activating intracellular signaling. PFQEP369-373 initiates NF-κB, c-Jun N-terminal kinase, extracellular signal-regulated kinase, and p38 signaling pathways and PVQEET559-564 activates NF-κB and p38 pathways in osteoclasts, whereas PVQEQG604-609 is only capable of activating NF-κB pathway. Significantly, the revelation of these functional RANK cytoplasmic motifs has not only laid a foundation for further delineating RANK signaling pathways in osteoclasts, but, more importantly, these RANK motifs themselves represent potential therapeutic targets for bone disorders such as osteoporosis.
Energy cost of stair climbing and descending on the college alumnus questionnaire.

In calculating the physical activity index (PAI) on the college alumnus questionnaire, it is assumed that 8 kcal are expended for every 20 steps climbed. This value is equal to an energy cost of 0.40 kcal.step-1. Since it is assumed that subjects climb and descend an equal number of stairs, the total value reflects the energy cost of stepping up (estimated at 0.30 kcal.step-1) and stepping down (estimated at 0.10 kcal.step-1). However, these values appear to be based on theoretical calculations rather than empirical observation. The purpose of this study was to quantify the energy cost of stair climbing and stair descending by measuring oxygen uptake. Twenty subjects performed continuous stair-climbing and stair-descending on an escalator at a stepping rate of 70 step.min-1. Heart rate was monitored by telemetry, and oxygen uptake was measured by the Douglas bag technique from 5 to 7 min. Results showed that the gross energy cost of stair climbing is 8.6 METs, and that of stair descending is 2.9 METs. Thus, for a 70-kg person the gross caloric costs of ascending stairs (0.15 kcal.step-1) and descending stairs (0.05 kcal.step-1) are one-half of the values previously assumed. In conclusion, the algorithm for calculating PAI on the college alumnus questionnaire should be modified to reflect a total cost of 0.20 kcal for going up and down one step. Even more precise estimates can be obtained by adjusting for body weight (going up and down one flight of stairs requires 1.63 MET.min).
The effect of antiretroviral therapy on secondary transmission of HIV among men who have sex with men.

BACKGROUND Antiretroviral therapy (ART) reduces human immunodeficiency virus (HIV) RNA load and the probability of transmitting HIV to an HIV-uninfected partner. However, the potential reduction in secondary transmission associated with ART may be offset by the longer duration of infectiousness. METHODS To estimate the effects of ART on the secondary transmission of HIV among men who have sex with men, we used a previously published state-transition model of HIV disease to simulate the clinical and virologic course of HIV infection among 2 cohorts of men who have sex with men: (1) a cohort of individuals who were not receiving ART and (2) a cohort of individuals treated with US guideline-concordant ART. The model tracked the number of acts of unprotected insertive anal intercourse, transmission risk per act as determined by HIV RNA level, and the number of secondary cases generated in each cohort. RESULTS The estimated mean number of secondary transmissions from an HIV-infected individual after 10, 20, and 30 years of infection were 1.9, 2.5, and 2.5, respectively, in the untreated cohort, compared with 1.4, 1.8, and 2.3, respectively, in the treated cohort. The total number of transmissions for the treated cohort began to exceed the total number of transmissions for the untreated cohort 33 years after infection; over the entire course of infection, treatment with ART led to a 23% increase in secondary infections. All estimates of the impact of ART on secondary transmission were sensitive to changes in risk behaviors. CONCLUSIONS These results suggest that ART must be accompanied by effective HIV-related risk reduction interventions. Programs that target prevention to decrease further HIV transmission are crucial to epidemic control.
Analysis of the Allelic Diversity of the Mycobacterial Interspersed Repetitive Units in Mycobacterium tuberculosis Strains of the Beijing Family: Practical Implications and Evolutionary Considerations

ABSTRACT A study set comprised 44 Mycobacterium tuberculosis strains of the Beijing family selected for their representativeness among those previously characterized by IS6110-RFLP and spoligotyping (Northwest Russia, 1997 to 2003). In the present study, these strains were subjected to mycobacterial interspersed repetitive units (MIRU) typing to assess a discriminatory power of the 12-MIRU-loci scheme (P. Supply et al., J. Clin. Microbiol. 39:3563-3571, 2001). The 44 Russian Beijing strains were subdivided into 12 MIRU types with identical profiles: 10 unique strains and two major types shared by 10 and 24 strains. Thus, basically, two distinct sublineages appear to shape the evolution of the Beijing strains in Russia. Most of the MIRU loci were found to be (almost) monomorphic in the Russian Beijing strains; the Hunter-Gaston discriminatory index (HGDI) for all 12 loci taken together was 0.65, whereas MIRU26 (the most variable in our study) showed a moderate level of discrimination (0.49). The results were compared against all available published MIRU profiles of Beijing strains from Russia (3 strains) and other geographic areas (51 strains in total), including South Africa (38 strains), East Asia (7 strains), and the United States (4 strains). A UPGMA (unweighted pair-group method with arithmetic averages)-based tree was constructed. Interestingly, no MIRU types were shared by Russian and South African strains (the two largest samples in this analysis), whereas both major Russian types included also isolates from other locations (United States and/or East Asia). This implies the evolution of the Beijing genotype to be generally strictly clonal, although a possibility of a convergent evolution of the MIRU loci cannot be excluded. We propose a dissemination of the prevailing local Beijing clones to have started earlier in South Africa rather than in Russia since more monomorphic loci were identified in Russian samples than in South African samples (mean HGDI scores, 0.08 versus 0.17). To conclude, we suggest to use a limited number of MIRUs for preliminary subdivision of Beijing strains in Russian (loci 26 + 31), South African (10 + 26 + 39), and global settings (10 + 26 + 39).
Necrostatin‐1 protects against glutamate‐induced glutathione depletion and caspase‐independent cell death in HT‐22 cells

Glutamate, a major excitatory neurotransmitter in the CNS, plays a critical role in neurological disorders such as stroke and Parkinson’s disease. Recent studies have suggested that glutamate excess can result in a form of cell death called glutamate‐induced oxytosis. In this study, we explore the protective effects of necrostatin‐1 (Nec‐1), an inhibitor of necroptosis, on glutamate‐induced oxytosis. We show that Nec‐1 inhibits glutamate‐induced oxytosis in HT‐22 cells through a mechanism that involves an increase in cellular glutathione (GSH) levels as well as a reduction in reactive oxygen species production. However, Nec‐1 had no protective effect on free radical‐induced cell death caused by hydrogen peroxide or menadione, which suggests that Nec‐1 has no antioxidant effects. Interestingly, the protective effect of Nec‐1 was still observed when cellular GSH was depleted by buthionine sulfoximine, a specific and irreversible inhibitor of glutamylcysteine synthetase. Our study further demonstrates that Nec‐1 significantly blocks the nuclear translocation of apoptosis‐inducing factor (a marker of caspase‐independent programmed cell death) and inhibits the integration of Bcl‐2/adenovirus E1B 19 kDa‐interacting protein 3 (a pro‐death member of the Bcl‐2 family) into the mitochondrial membrane. Taken together, these results demonstrate for the first time that Nec‐1 prevents glutamate‐induced oxytosis in HT‐22 cells through GSH related as well as apoptosis‐inducing factor and Bcl‐2/adenovirus E1B 19 kDa‐interacting protein 3‐related pathways.
Molecular Typing of, and Distribution of Genetic Markers among, Burkholderia cepacia Complex Isolates from Brazil

ABSTRACT PCR tests were used to assign genomovar status to 39 non-cystic fibrosis (non-CF) and 11 CF Burkholderia cepacia complex isolates from patients in hospitals in Recife, Brazil. Non-CF isolates were assigned to genomovar IIIA (71.8%), genomovar I (15.4%), B. vietnamiensis (7.7%), and B. multivorans (5.1%). CF isolates were assigned to genomovar IIIA (18.2%), B. vietnamiensis (18.2%), and genomovar I (9.1%). Six CF isolates sharing recA PCR-restriction fragment length polymorphism (RFLP) and randomly amplified polymorphic DNA (RAPD) patterns could not be assigned to a genomovar. 16S rDNA sequence obtained from these isolates indicated a closest relationship to B. anthina, but the recA sequence was equally divergent from several genomovars. PCR screening indicated the presence of cblA in only two isolates, whereas the B. cepacia epidemic strain marker was found in 22 of 28 genomovar IIIA isolates. A type III secretion gene was detected in all but genomovar I isolates. RAPD and PCR-RFLP assays, targeting both recA and fliC, indicated a large amount of genetic variability among the isolates, with many novel patterns being observed. Nine genomovar IIIA isolates from different non-CF patients and clinical sources had identical genotypes, indicating the presence of a common clone.