Miracle-dz/UniFAR-FTUs huggingface dataset:
Changes in Signal Transducer and Activator of Transcription 3 (STAT3) Dynamics Induced by Complexation with Pharmacological Inhibitors of Src Homology 2 (SH2) Domain Dimerization*

Background: Salicylic acid-based inhibitors of signal transducer and activator of transcription 3 (STAT3) are predicted to interact with the Src homology 2 (SH2) domain, inhibiting dimerization. Results: STAT3-inhibitor interactions were interrogated by hydrogen-deuterium exchange (HDX) mass spectrometry (MS). Conclusion: HDX MS revealed local and global perturbations in STAT3 dynamics. Significance: Understanding STAT3 inhibitor interactions with the SH2 domain is critical to inhibitor development. The activity of the transcription factor signal transducer and activator of transcription 3 (STAT3) is dysregulated in a number of hematological and solid malignancies. Development of pharmacological STAT3 Src homology 2 (SH2) domain interaction inhibitors holds great promise for cancer therapy, and a novel class of salicylic acid-based STAT3 dimerization inhibitors that includes orally bioavailable drug candidates has been recently developed. The compounds SF-1-066 and BP-1-102 are predicted to bind to the STAT3 SH2 domain. However, given the highly unstructured and dynamic nature of the SH2 domain, experimental confirmation of this prediction was elusive. We have interrogated the protein-ligand interaction of STAT3 with these small molecule inhibitors by means of time-resolved electrospray ionization hydrogen-deuterium exchange mass spectrometry. Analysis of site-specific evolution of deuterium uptake induced by the complexation of STAT3 with SF-1-066 or BP-1-102 under physiological conditions enabled the mapping of the in silico predicted inhibitor binding site to the STAT3 SH2 domain. The binding of both inhibitors to the SH2 domain resulted in significant local decreases in dynamics, consistent with solvent exclusion at the inhibitor binding site and increased rigidity of the inhibitor-complexed SH2 domain. Interestingly, inhibitor binding induced hot spots of allosteric perturbations outside of the SH2 domain, manifesting mainly as increased deuterium uptake, in regions of STAT3 important for DNA binding and nuclear localization.
Colonization and dispersal in a social species, the Bechstein's bat (Myotis bechsteinii)

Metapopulation genetic models consider that colonization and dispersal are distinct behaviours. However, whether colonization and dispersal indeed reflect different biological processes in nature is unclear. One possibility to test this assumption is to assess patterns of autosomal and mitochondrial genetic structure in species with strict female philopatry, such as the communally breeding Bechstein's bat. In this species, mitochondrial DNA can spread only when females establish new colonies, and autosomal DNA is transmitted among colonies only when females mate with solitary males born in foreign colonies. Investigating the genetic structure among 37 colonies, we found that autosomal genes followed an island model on a regional scale and a model of isolation by distance on a larger geographical scale. In contrast, mitochondrial genetic structure revealed no pattern of isolation by distance at a large scale but exhibited an effect of ecological barriers on a regional scale. Our results provide strong empirical evidence that colonization and dispersal do not follow the same behavioural rules in this bat, supporting the assumption of metapopulation genetic models.
Genetic instability and the development of steroid hormone insensitivity in cultured T 47D human breast cancer cells.

The estrogen receptor (ER)-positive human breast cancer cell line T 47D exhibited genetic instability under cell culture conditions which maintained almost continuous exponential growth. This resulted in the spontaneous generation of three ER-positive sublines with a range of DNA ploidies and distinctive phenotypes. One of these sublines, T 47D-5, exhibited resistance to the growth-inhibitory effects of the synthetic nonsteroidal antiestrogen tamoxifen and the synthetic progestin ORG 2058, in marked contrast to "wild type" T 47D cells (designated T 47D-7 in this study). T 47D-5 cells were cloned by limiting dilution and 11 clonal cell lines were tested for sensitivity to tamoxifen. Although all clones of T 47D-5 were significantly less sensitive than T 47D-7 cells, a spectrum of sensitivities was observed. Three clones, T 47D-5-13, T 47D-5-21, and T 47D-5-23, were further characterized by measuring the concentrations of receptors for estrogen, progesterone, growth hormone, and epidermal growth factor and responses to estradiol, tamoxifen, and progestin, in terms of both induction of specific proteins and effects on cellular proliferation. Although the T 47D-5 subline and clone T 47D-5-23 were insensitive to both the growth-stimulatory effects of estradiol and the inhibitory effects of tamoxifen, this was not related to the concentration of ER or its ability to induce progesterone receptor. Estrogen receptor levels were similar in resistant and sensitive clones of T 47D-5 [70,000-81,000 sites/cell] and were 2.5-fold greater than in the sensitive T 47D-7 line [32,600 +/- 5,000 (SEM) sites/cell]. Northern blots showed no difference in the size of ER mRNA transcripts between sensitive and resistant clones. Estradiol treatment increased progesterone receptor (PR) levels in all cell lines but the magnitude and sensitivity of this response were unrelated to growth responses indicating a divergence in estrogenic control of cellular proliferation and specific protein synthesis within these clones. T 47D-5, T 47D-5-13, T 47D-5-21, and T 47D-5-23 were all insensitive to the growth-inhibitory effects of ORG 2058. The progestin was also unable to increase lactogenic and epidermal growth factor receptor concentrations in these four lines in contrast to the response in T 47D-7 cells. The insensitivity to progestin in the T 47D-5 subline and its three clonal cell lines could be accounted for, in part, by a 75-80% reduction in PR levels when compared with T 47D-7 cells. (ABSTRACT TRUNCATED AT 400 WORDS)
Identification of Human microRNA Targets From Isolated Argonaute Protein Complexes

MicroRNAs (miRNAs) constitute a class of small non-coding RNAs that regulate gene expression on the level of translation and/or mRNA stability. Mammalian miRNAs associate with members of the Argonaute (Ago) protein family and bind to partially complementary sequences in the 3’ untranslated region (UTR) of specific target mRNAs. Computer algorithms based on factors such as free binding energy or sequence conservation have been used to predict miRNA target mRNAs. Based on such predictions, up to one third of all mammalian mRNAs seem to be under miRNA regulation. However, due to the low degree of complementarity between the miRNA and its target, such computer programs are often imprecise and therefore not very reliable. Here we report the first biochemical identification approach of miRNA targets from human cells. Using highly specific monoclonal antibodies against members of the Ago protein family, we co-immunoprecipitate Ago-bound mRNAs and identify them by cloning. Interestingly, most of the identified targets are also predicted by different computer programs. Moreover, we randomly analyzed six different target candidates and were able to experimentally validate five as miRNA targets. Our data clearly indicate that miRNA targets can be experimentally identified from Ago complexes and therefore provide a new tool to directly analyze miRNA function.
Structural determinants of the substrate specificities of xylanases from different glycoside hydrolase families

Xylanases are of widespread importance in several food and non-food biotechnological applications. They degrade heteroxylans, a structurally heterogeneous group of plant cell wall polysaccharides, and other important components in various industrial processes. Because of the highly complex structures of heteroxylans, efficient utilization of xylanases in these processes requires an in-depth knowledge of their substrate specificity. A significant number of studies on the three-dimensional structures of xylanases from different glycoside hydrolase (GH) families in complex with the substrate provided insight into the different mechanisms and strategies by which xylanases bind and hydrolyze structurally different heteroxylans and xylo-oligosaccharides (XOS). Combined with reports on the hydrolytic activities of xylanases on decorated XOS and heteroxylans, major advances have been made in our understanding of the link between the three-dimensional structures and the substrate specificities of these enzymes. In this review, authors gave a concise overview of the structure–function relationship of xylanases from GH5, 8, 10, and 11. The structural basis for inter- and intrafamily variation in xylanase substrate specificity was discussed as are the implications for heteroxylan degradation.
The CLIP‐CHIP Oligonucleotide Microarray: Dedicated Array for Analysis of All Protease, Nonproteolytic Homolog, and Inhibitor Gene Transcripts in Human and Mouse

The CLIP‐CHIP oligonucleotide microarray allows the analysis of mRNA transcript levels in a tissue sample for all proteases, nonproteolytic homologs, and protease inhibitors of the human and mouse genome. In the protocol presented in this unit, total RNA is extracted from a tissue, and the resulting mRNA is reverse transcribed into cDNA and dsDNA and then amplified in an in vitro transcription reaction. The amplified antisense RNA is labeled with a fluorescent dye and hybridized to the CLIP‐CHIP, which contains unique oligonucleotides that are specifically designed for the protease, nonproteolytic homologs, protease inhibitors, and control samples. After hybridization, the fluorescence intensity of each spot is measured, thus identifying mRNA transcripts that are expressed and allowing basic quantification of expressed transcripts. Curr. Protoc. Protein Sci. 56:21.19. 1‐21.19. 16. © 2009 by John Wiley & Sons, Inc.
Hydrogen Peroxide Production from Glycerol Metabolism Is Dispensable for Virulence of Mycoplasma gallisepticum in the Tracheas of Chickens

ABSTRACT Hydrogen peroxide (H2O2) is a by-product of glycerol metabolism in mycoplasmas and has been shown to cause cytotoxicity for cocultured eukaryotic cells. There appears to be selective pressure for mycoplasmas to retain the genes needed for glycerol metabolism. This has generated interest and speculation as to their function during infection. However, the actual effects of glycerol metabolism and H2O2 production on virulence in vivo have never been assessed in any Mycoplasma species. To this end, we determined that the wild-type (WT) Rlow strain of the avian pathogen Mycoplasma gallisepticum is capable of producing H2O2 when grown in glycerol and is cytotoxic to eukaryotic cells in culture. Transposon mutants with mutations in the genes present in the glycerol transport and utilization pathway, namely, glpO, glpK, and glpF, were identified. All mutants assessed were incapable of producing H2O2 and were not cytotoxic when grown in glycerol. We also determined that vaccine strains ts-11 and 6/85 produce little to no H2O2 when grown in glycerol, while the naturally attenuated F strain does produce H2O2. Chickens were infected with one of two glpO mutants, a glpK mutant, Rlow, or growth medium, and tracheal mucosal thickness and lesion scores were assessed. Interestingly, all glp mutants were reproducibly virulent in the respiratory tracts of the chickens. Thus, there appears to be no link between glycerol metabolism/H2O2 production/cytotoxicity and virulence for this Mycoplasma species in its natural host. However, it is possible that glycerol metabolism is required by M. gallisepticum in a niche that we have yet to study.
Chlorhexidine gluconate to cleanse patients in a medical intensive care unit: the effectiveness of source control to reduce the bioburden of vancomycin-resistant enterococci.

BACKGROUND Historically, methods of interrupting pathogen transmission have focused on improving health care workers' adherence to recommended infection control practices. An adjunctive approach may be to use source control (eg, to decontaminate patients' skin). METHODS We performed a prospective sequential-group single-arm clinical trial in a teaching hospital's medical intensive care unit from October 2002 to December 2003. We bathed or cleansed 1787 patients and assessed them for acquisition of vancomycin-resistant enterococci (VRE). We performed a nested study of 86 patients with VRE colonization and obtained culture specimens from 758 environmental surfaces and 529 health care workers' hands. All patients were cleansed daily with the procedure specific to the study period as follows: period 1, soap and water baths; period 2, cleansing with cloths saturated with 2% chlorhexidine gluconate; and period 3, cloth cleansing without chlorhexidine. We measured colonization of patient skin by VRE, health care worker hand or environmental surface contamination by VRE, and patient acquisition of VRE rectal colonization. RESULTS Compared with soap and water baths, cleansing patients with chlorhexidine-saturated cloths resulted in 2.5 log(10) less colonies of VRE on patients' skin and less VRE contamination of health care workers' hands (risk ratio [RR], 0.6; 95% confidence interval [CI], 0.4-0.8) and environmental surfaces (RR, 0.3; 95% CI, 0.2-0.5). The incidence of VRE acquisition decreased from 26 colonizations per 1000 patient-days to 9 per 1000 patient-days (RR, 0.4; 95% CI, 0.1-0.9). For all measures, effectiveness of cleansing with nonmedicated cloths was similar to that of soap and water baths. CONCLUSION Cleansing patients with chlorhexidine-saturated cloths is a simple, effective strategy to reduce VRE contamination of patients' skin, the environment, and health care workers' hands and to decrease patient acquisition of VRE.
Invited Commentary Invited Commentary: How Big Is That Interaction (in My Community)—and in Which Direction?

In an accompanying article, Turner et al. (Am J Epidemiol. 2014;180(12):1145–1149) compare the joint effects of smoking and air pollution to make inferences about the reduction in lung cancer mortality achieved when reducing each exposure separately and when reducing both together. In this commentary, we use first principles to quantify the difference between the risk or mortality reduction obtained from reducing each of 2 exposures together and the sum of the risk differences obtained from reducing the 2 exposures separately. Metrics of the impact of joint effects or comparisons of joint effects presented in units of absolute risk, such as Rothman’s I, can provide more meaningful quantitative measures of public health impact than unitless metrics (e.g., ratios) and standardized metrics (e.g., the population attributable fraction) of potential interventions for reducing smoking and air pollution exposure. In particular, the venerable attributable community risk metric can provide an estimate of the community impact of such interventions in units of absolute risk. A spreadsheet we provide demonstrates the calculation of the various metrics for hypothetical data similar to those reported by Turner et al. Using algebra, graphics, and examples, we show that positive interaction, or synergy, on the additive scale implies that the impact on risk reduction from a program that applies both interventions will be lesser than the sum of the impacts of the separate interventions.
Fiscal federalism and regional performance in Russia

Sound regional policies are essential for balanced and sustained economic growth. The interaction of federal and regional policies with cross-regional structural differences affects human and physical capital formation, the business climate, private investment, market depth, and competition. This paper summarizes the main elements of Russia’s fiscal federalism, describes the channels through which it operates, and assesses the effectiveness of regional transfers in reducing regional disparities. The results suggest that federal transfers to regions contributed to reducing disparities arising from heterogeneous regional tax bases and fiscal revenues. This allowed regions with initially lower per capita income to increase human and physical capital at higher rates. There is little evidence for transfers contributing to increased cross-regional growth synchronization. The results also suggest that federal transfers did not significantly improve regional fiscal sustainability, a conclusion that is supported by the lack of convergence in per capita real income across Russian regions in the last 15 years.
The Spine Service Line: Optimizing Patient-Centered Spine Care

Study Design. Literature review and expert opinion on the delivery of spine care. Objective. Our objective was to describe the goals of a spine service line and encourage the implementation of a systems-based approach to spine care. The benefits to patients and institutions are discussed. Summary of Background Data. Spine care delivery and its associated costs are rising rapidly. There exists tremendous variability in the rate at which it is delivered. With so many options for spine care, patients are subject to decisions of providers with disparate backgrounds and expertise. This leads to inefficiencies in diagnosis and delivery of care. All these factors lead to increased costs of care of uncertain benefit and increased burden to society. Methods. The literature on systems-based approaches to spine care was reviewed. Those relating to health care policy and recent clinical trials were emphasized. How these data work in a systems-based approach was described. Additionally, the authors’ experiences working in and within a structured spine care system were related and included. Results. We describe 3 spine care episodes and where each possesses particular inefficiencies that lead to increased costs without added value to the delivery of spine care. The primary episode is the start of the patient’s painful incident. We propose a more uniform guidelines-based approach using appropriate (and similar) diagnostic testing and education. The secondary phase of care can be costly as more sophisticated diagnostic and treatment methods are instituted. Within an institution or spine care practice, matching the level of providers with the patients at this phase of care would lead to better utilization of resources. Additionally, benefits to the institution would be greater if managed properly. The third phase of care focuses on intervention with long-term benefits. We discuss the use of registry like data and analysis of outcomes on these patients. Agreement within a group or institution on operative indications would allow for more uniform analysis of these outcomes. Alternative revenue streams are also discussed. Conclusions. The patient with spinal disease is in need of high-quality, proven, and efficient care. Using a systems-based approach, we can minimize escalating costs associated with inefficient health care and delivery. Cooperation between physicians and institutions is critical to this process.
IT support for communities of practice in organizational settings

Communities of Practice (CoPs) are increasingly being seen as innovative and creative value adding entities in organisations. Their contributions in the sharing of perspectives and context, support of learning processes and creating a social and communal identity, yield invaluable knowledge exchanges. With the advent of internetworking, the boundaries of organisational settings are broadened. This is particularly significant to CoPs as they can continue their ways of working, work practices, social engagement and connectivity in these settings, harnessing Information Technology (IT). This paper reports on early findings from an ongoing investigation into ways in which IT can support practices and knowledge exchange processes of CoPs in organisational settings.
U24, a novel intron-encoded small nucleolar RNA with two 12 nt long, phylogenetically conserved complementarities to 28S rRNA.

Following computer searches of sequence banks, we have positively identified a novel intronic snoRNA, U24, encoded in the ribosomal protein L7a gene in humans and chicken. Like previously reported intronic snoRNAs, U24 is devoid of a 5'-trimethyl-cap. U24 is immunoprecipitated by an antifibrillarin antibody and displays an exclusively nucleolar localization by fluorescence microscopy after in situ hybridization with antisense oligonucleotides. In vertebrates, U24 is a 76 nt long conserved RNA which is metabolically stable, present at approximately 14,000 molecules per human HeLa cell. U24 exhibits a 5'-3' terminal stem-box C-box D structure, typical for several snoRNAs, and contains two 12 nt long conserved sequences complementary to 28S rRNA. It is, therefore, strikingly related to U14, U20 and U21 snoRNAs which also possess long sequences complementary to conserved sequences of mature 18S or 28S rRNAs. In 28S rRNA the two tracts complementary to U24 are adjacent to each other, they involve several methylated nucleotides and are surprisingly close, within the rRNA secondary structure, to complementarities to snoRNAs U18 and U21. Identification of the yeast Saccharomyces cerevisiae U24 gene directly confirms the outstanding conservation of the complementarity to 28S rRNA during evolution, suggesting a key role of U24 pairing to pre-rRNA during ribosome biogenesis, possible in the control of pre-rRNA folding. Yeast S.cerevisiae U24 is also intron-encoded but not in the same host-gene as in humans or chicken.
Prolonged Apoptotic Cell Accumulation in Germinal Centers of Mer-Deficient Mice Causes Elevated B Cell and CD4+ Th Cell Responses Leading to Autoantibody Production

Mer receptor tyrosine kinase is a member of the Tyro-3/Axl/Mer (TAM) subfamily of receptor tyrosine kinases, and its expression on phagocytes facilitates their clearance of apoptotic cells (ACs). Mer expression in germinal centers (GCs) occurs predominantly on tingible body macrophages. B and T cells do not express Mer. In this study, we show that Mer deficiency ((Mer−/−) resulted in the long-term accumulation of ACs primarily in GCs and not in the T cell zone, marginal zone, or red pulp areas of the spleen. AC accumulation in GCs led to augmented Ab-forming cell, GC, and IgG2 Ab responses in Mer−/− mice, which were sustained for at least 80 d. Enhanced responses in Mer−/− mice were due to increased activation and proliferation of B cells and CD4+ Th cells, including follicular helper T cells, which resulted in high titers of anti-nuclear Abs in Mer−/− mice compared with wild-type controls. Secondary IgG-producing Ab-forming cell, total IgG, and IgG2 Ab responses were also increased in Mer−/− mice. Finally, compared with wild-type controls, Mer−/− mice had increased percentage of IFN-γ–producing CD4+ Th cells and elevated levels of Th1 (i.e., IL-2 and IFN-γ) and proinflammatory (i.e., TNF and IL-6) cytokines, consistent with elevated levels of Th1-biased IgG2 Abs in Mer−/− mice. Together, our results demonstrate that Mer deficiency induces prolonged accumulation of ACs in GCs, resulting in dysregulation of GC B cell and CD4+ Th cell responses and Th1 cytokine production, leading to alteration of B cell tolerance and the development of autoantibodies.