Using Amino Acid Correlation and Community Detection Algorithms to Identify Functional Determinants in Protein Families

Correlated mutation analysis has a long history of interesting applications, mostly in the detection of contact pairs in protein structures. Based on previous observations that, if properly assessed, amino acid correlation data can also provide insights about functional sub-classes in a protein family, we provide a complete framework devoted to this purpose. An amino acid specific correlation measure is proposed, which can be used to build networks summarizing all correlation and anti-correlation patterns in a protein family. These networks can be submitted to community structure detection algorithms, resulting in subsets of correlated amino acids which can be further assessed by specific parameters and procedures that provide insight into the relationship between different communities, the individual importance of community members and the adherence of a given amino acid sequence to a given community. By applying this framework to three protein families with contrasting characteristics (the Fe/Mn-superoxide dismutases, the peroxidase-catalase family and the C-type lysozyme/α-lactalbumin family), we show how our method and the proposed parameters and procedures are related to biological characteristics observed in these protein families, highlighting their potential use in protein characterization and gene annotation

Bewertung der Adaptivität von Geschossbauten für den städtischen Raum

Demografische Veränderungen, ein sich wandelnder Arbeitsmarkt und konjunkturelle Schwankungen mit unterschiedlich dominierenden Gewerbezweigen erfordern Gebäude, die sich an verändernde Nutzeranforderungen anpassen können. Zur Erhöhung der Ressourceneffizienz sind Gebäude nicht nur hinsichtlich des Materialeinsatzes und Energieverbrauchs zu optimieren, sondern darüber hinaus für einen langen Nutzungshorizont auszulegen. Um die Anpassungsfähigkeit von Geschossbauten an verschiedene Nutzungsformen bewerten zu können, wurde im Rahmen des Innovationsprogramms „Zukunft Bau“ das Forschungsprojekt „Adaptive Gebäudestrukturen zur Erhöhung der Ressourceneffizienz von Geschossbauten im städtischen Raum“ durchgeführt. Im folgenden Beitrag werden die Motivation zum Forschungsprojekt, eine Übersicht zu wesentlichen Fragestellungen und die Ergebnisse in einer zusammenfassenden Darstellung vorgestellt.Demographic changes, a transforming labour market and economic volatility with different dominant industries require buildings that can adapt to changing user requirements. In order to increase resource efficiency, buildings must not only be optimised in terms of material use and energy consumption, but also designed for a long horizon of use. In order to be able to evaluate the adaptability of multi-storey buildings to different forms of use, the research project “Adaptive building structures to increase the resource efficiency of multi-storey buildings in urban areas” was carried out within the framework of the „Zukunft Bau“ research initiative. In the following article, the motivation for the research project, an overview of the main aspects and the results are presented in a summarising form

Old World megadroughts and pluvials during the Common Era

Climate model projections suggest widespread drying in the Mediterranean Basin and wetting in Fennoscandia in the coming decades largely as a consequence of greenhouse gas forcing of climate. To place these and other “Old World” climate projections into historical perspective based on more complete estimates of natural hydroclimatic variability, we have developed the “Old World Drought Atlas” (OWDA), a set of year-to-year maps of tree-ring reconstructed summer wetness and dryness over Europe and the Mediterranean Basin during the Common Era. The OWDA matches historical accounts of severe drought and wetness with a spatial completeness not previously available. In addition, megadroughts reconstructed over north-central Europe in the 11th and mid-15th centuries reinforce other evidence from North America and Asia that droughts were more severe, extensive, and prolonged over Northern Hemisphere land areas before the 20th century, with an inadequate understanding of their causes. The OWDA provides new data to determine the causes of Old World drought and wetness and attribute past climate variability to forced and/or internal variability

The Involvement of SMILE/TMTC3 in Endoplasmic Reticulum Stress Response

The state of operational tolerance has been detected sporadically in some renal transplanted patients that stopped immunosuppressive drugs, demonstrating that allograft tolerance might exist in humans. Several years ago, a study by Brouard et al. identified a molecular signature of several genes that were significantly differentially expressed in the blood of such patients compared with patients with other clinical situations. The aim of the present study is to analyze the role of one of these molecules over-expressed in the blood of operationally tolerant patients, SMILE or TMTC3, a protein whose function is still unknown.We first confirmed that SMILE mRNA is differentially expressed in the blood of operationally tolerant patients with drug-free long term graft function compared to stable and rejecting patients. Using a yeast two-hybrid approach and a colocalization study by confocal microscopy we furthermore report an interaction of SMILE with PDIA3, a molecule resident in the endoplasmic reticulum (ER). In accordance with this observation, SMILE silencing in HeLa cells correlated with the modulation of several transcripts involved in proteolysis and a decrease in proteasome activity. Finally, SMILE silencing increased HeLa cell sensitivity to the proteasome inhibitor Bortezomib, a drug that induces ER stress via protein overload, and increased transcript expression of a stress response protein, XBP-1, in HeLa cells and keratinocytes.In this study we showed that SMILE is involved in the endoplasmic reticulum stress response, by modulating proteasome activity and XBP-1 transcript expression. This function of SMILE may influence immune cell behavior in the context of transplantation, and the analysis of endoplasmic reticulum stress in transplantation may reveal new pathways of regulation in long-term graft acceptance thereby increasing our understanding of tolerance

Higher Creatinine Concentrations in Ethyl Glucuronide-Positive Urine Specimens Collected from Subjects in a Controlled Alcohol Abstinence Program: Is Serum Creatinine a Good Marker of Renal Function in Drinkers?

Creatinine is higher in ethyl glucuronide-positive urines of drivers under controlled alcohol abstinence program, accounting for a late antidiuretic effect of alcohol. The consequent temporary decrease in serum creatinine may account for its negative trend at the increase in alcohol intake observed in epidemiological studies.AbstractAims The aim of this study was to examine urine creatinine concentrations in drivers submitted to controlled alcohol abstinence programs.Methods Urine samples (n = 32,210) were screened for ethyl glucuronide (EtG) by immunoassay during a 2-year period. Non-negatives underwent EtG and ethyl sulfate (EtS) confirmation by coupled-column Liquid Chromatography-Tandem Mass Spectrometry. Urine samples were tested for dilution by the analysis of creatinine content with <0.2 g/l indicating a dilute specimen.Results The mean urine creatinine was significantly higher in EtG positives compared to negatives (1.47 0.98 vs. 1.17 +/- 0.79 g/l). The difference between positives and negatives was consistent within genders and age groups (<45; 45). The higher urinary creatinine in EtG positives is explained by a late antidiuretic effect of alcohol.Conclusion Attempts to dilute urine specimens by drinking water or other liquids before voiding are less effective for EtG/EtS compared with illicit drugs excreted in urine. If the temporary decrease in serum creatinine as a consequence of the late antidiuretic effect of alcohol is confirmed by controlled studies, serum creatinine as an indicator of kidney function should be reconsidered in drinkers

Disparities in the Local Management of Breast Cancer in the US according to Health Insurance Status.

Although standard practice guidelines for breast cancer are clear, the interplay between insurance and practice patterns for the US is poorly defined. This study was performed to test for associations between patient insurance status and presentation of breast cancer as well as local therapy patterns in the US, via a large national dataset. We queried the NCI Surveillance, Epidemiology, and End Results data base for breast cancer cases diagnosed from 2007 to 2011 in women aged 18-64 with nonmetastatic ductal/lobular cancers, treated surgically. We tested for associations between insurance status (insured/Medicaid/uninsured) and choice of surgical procedure (mastectomy/breast conserving surgery [BCS]), omission of radiotherapy (RT) following BCS, and administration of post-mastectomy radiation (PMRT). There were 129,565 patients with localized breast cancer analyzed. The health insurance classification included insured (84.5%), Medicaid (11.5%), uninsured (2.1%) and unknown (1.9%). Medicaid or uninsured status was associated with large, node positive tumors, black race, and low income. The BCS rate varied by insurance status: insured (52.2%), uninsured (47.7%), and Medicaid (45.2%), p \u3c 0.001. In multivariable analysis, Medicaid insurance remained significantly associated with receipt of mastectomy (OR [95% CI] = 1.07 [1.03-1.11]), while RT was more frequently omitted after BCS in both Medicaid (OR [95% CI] = 1.14 [1.07-1.21]) and uninsured (OR [95% CI] = 1.29 [1.14-1.47]) patients. Insurance status was associated with significant variations in breast cancer care in the US. Although patient choice cannot be determined from this dataset, departure from standard of care is associated with specific types of insurance coverage. Further investigation into the reasons for these departures is strongly suggested

Benefits versus drawbacks of delaying surgery due to additional consultations in older patients with breast cancer

Abstract Background Additional evaluations, including second opinions, before breast cancer surgery may improve care, but may cause detrimental treatment delays that could allow disease progression. Aims We investigate the timing of surgical delays that are associated with survival benefits conferred by preoperative encounters versus the timing that are associated with potential harm. Methods and results We investigated survival outcomes of SEER Medicare patients with stage 1–3 breast cancer using propensity score‐based weighting. We examined interactions between the number of preoperative evaluation components and time from biopsy to definitive surgery. Components include new patient visits, unique surgeons, medical oncologists, or radiation oncologists consulted, established patient encounters, biopsies, and imaging studies. We identified 116 050 cases of whom 99% were female and had an average age of 75.0 (SD = 6.2). We found that new patient visits have a protective association with respect to breast cancer mortality if they occur quickly after diagnosis with breast cancer mortality subdistribution Hazard Ratios [sHRs] = 0.87 (95% Confidence Interval [CI] 0.76–1.00) for 2, 0.71 (CI 0.55–0.92) for 3, and 0.63 (CI 0.37–1.07) for 4+ visits at minimal delay. New patient visits predict worsened mortality compared with no visits if the surgical delay is greater than 33 days (CI 14–53) for 2, 33 days (CI 17–49) for 3, and 44 days (CI 12–75) for 4+. Medical oncologist visits predict worse outcomes if the surgical delay is greater than 29 days (CI 20–39) for 1 and 38 days (CI 12–65) for 2+ visits. Similarly, surgeon encounters switch from a positive to a negative association if the surgical delay exceeds 29 days (CI 17–41) for 1 visit, but the positive estimate persists over time for 3+ surgeon visits. Conclusion Preoperative visits that cause substantial delays may be associated with increased mortality in older patients with breast cancer