Human long intrinsically disordered protein regions are frequent targets of positive selection

Intrinsically disordered regions occur frequently in proteins and are characterized by a lack of a well-defined three-dimensional structure. Although these regions do not show a higher-order of structural organization, they are known to be functionally important. Disordered regions are rapidly evolving, largely attributed to relaxed purifying selection and an increased role of genetic drift. It has also been suggested that positive selection might contribute to their rapid diversification. However, for our own species it is currently unknown whether positive selection has played a role during the evolution of these protein regions. Here we address this question by investigating the evolutionary pattern of more than 6,600 human proteins with intrinsically disordered regions and their ordered counterparts. Our comparative approach with data from more than 90 mammalian genomes uses a-priori knowledge of disordered protein regions and we show that this increases the power to detect positive selection by an order of magnitude. We can confirm that human intrinsically disordered regions evolve more rapidly, not only within humans but also across the entire mammalian phylogeny. They have, however, experienced substantial evolutionary constraint, hinting at their fundamental functional importance. We find compelling evidence that disordered protein regions are frequent targets of positive selection and estimate that the relative rate of adaptive substitutions differs 4-fold between disordered and ordered protein regions in humans. Our results suggest that disordered protein regions are important targets of genetic innovation and that the contribution of positive selection in these regions is more pronounced than in other protein parts

Welcome to the family: Identification of the nad+ transporter of animal mitochondria as member of the solute carrier family slc25

Subcellular compartmentation is a fundamental property of eukaryotic cells. Communication and metabolic and regulatory interconnectivity between organelles require that solutes can be transported across their surrounding membranes. Indeed, in mammals, there are hundreds of genes encoding solute carriers (SLCs) which mediate the selective transport of molecules such as nucleotides, amino acids, and sugars across biological membranes. Research over many years has identified the localization and preferred substrates of a large variety of SLCs. Of particular interest has been the SLC25 family, which includes carriers embedded in the inner membrane of mitochondria to secure the supply of these organelles with major metabolic intermediates and coen-zymes. The substrate specificity of many of these carriers has been established in the past. However, the route by which animal mitochondria are supplied with NAD+ had long remained obscure. Only just recently, the existence of a human mitochondrial NAD+ carrier was firmly established. With the realization that SLC25A51 (or MCART1) represents the major mitochondrial NAD+ carrier in mammals, a long-standing mystery in NAD+ biology has been resolved. Here, we summarize the functional importance and structural features of this carrier as well as the key observations leading to its discovery

Social dynamics of obesity

We explain the recent increases in obesity in the United States with a model involving falling food prices, endogenous social body weight norms, and heterogeneous human metabolism. Calibrating an analytical choice model to American women in the 30-to 60-yr-old age bracket, we compare the predicted weight distributions to National Health and Nutrition Examination survey data spanning (intermittently) the years 1976-2000. The model, the first to describe explicitly complete weight distribution dynamics for this group, predicts average weights and obesity rates with considerable accuracy and captures a significant portion of the recent growth in upper quantile weights. (JEL D11, I12, Z13

A New Experimental Polytrauma Model in Rats: Molecular Characterization of the Early Inflammatory Response

Background. The molecular mechanisms of the immune response after polytrauma are highly complex and far from fully understood. In this paper, we characterize a new standardized polytrauma model in rats based on the early molecular inflammatory and apoptotic response. Methods. Male Wistar rats (250 g, 6–10/group) were anesthetized and exposed to chest trauma (ChT), closed head injury (CHI), or Tib/Fib fracture including a soft tissue trauma (Fx + STT) or to the following combination of injuries: (1) ChT; (2) ChT + Fx + STT; (3) ChT + CHI; (4) CHI; (5) polytrauma (PT = ChT + CHI + Fx + STT). Sham-operated rats served as negative controls. The inflammatory response was quantified at 2 hours and 4 hours after trauma by analysis of “key” inflammatory mediators, including selected cytokines and complement components, in serum and bronchoalveolar (BAL) fluid samples. Results. Polytraumatized (PT) rats showed a significant systemic and intrapulmonary release of cytokines, chemokines, and complement anaphylatoxins, compared to rats with isolated injuries or selected combinations of injuries. Conclusion. This new rat model appears to closely mimic the early immunological response of polytrauma observed in humans and may provide a valid basis for evaluation of the complex pathophysiology and future therapeutic immune modulatory approaches in experimental polytrauma

Combined Perfusion and Permeability Imaging Reveals Different Pathophysiologic Tissue Responses After Successful Thrombectomy.

Despite successful recanalization of large-vessel occlusions in acute ischemic stroke, individual patients profit to a varying degree. Dynamic susceptibility-weighted perfusion and dynamic T1-weighted contrast-enhanced blood-brain barrier permeability imaging may help to determine secondary stroke injury and predict clinical outcome. We prospectively performed perfusion and permeability imaging in 38 patients within 24 h after successful mechanical thrombectomy of an occlusion of the middle cerebral artery M1 segment. Perfusion alterations were evaluated on cerebral blood flow maps, blood-brain barrier disruption (BBBD) visually and quantitatively on ktrans maps and hemorrhagic transformation on susceptibility-weighted images. Visual BBBD within the DWI lesion corresponded to a median ktrans elevation (IQR) of 0.77 (0.41-1.4) min-1 and was found in all 7 cases of hypoperfusion (100%), in 10 of 16 cases of hyperperfusion (63%), and in only three of 13 cases with unaffected perfusion (23%). BBBD was significantly associated with hemorrhagic transformation (p < 0.001). While BBBD alone was not a predictor of clinical outcome at 3 months (positive predictive value (PPV) = 0.8 [0.56-0.94]), hypoperfusion occurred more often in patients with unfavorable clinical outcome (PPV = 0.43 [0.10-0.82]) compared to hyperperfusion (PPV = 0.93 [0.68-1.0]) or unaffected perfusion (PPV = 1.0 [0.75-1.0]). We show that combined perfusion and permeability imaging reveals distinct infarct signatures after recanalization, indicating the severity of prior ischemic damage. It assists in predicting clinical outcome and may identify patients at risk of stroke progression

Bowel Preparation for Colonoscopy with Sodium Phosphate Solution versus Polyethylene Glycol-Based Lavage: A Multicenter Trial

Background: Adequate bowel preparation is essential for accurate colonoscopy. Both oral sodium phosphate (NaP) and polyethylene glycol-based lavage (PEG-ELS) are used predominantly as bowel cleansing modalities. NaP has gained popularity due to low drinking volume and lower costs. The purpose of this randomized multicenter observer blinded study was to compare three groups of cleansing (NaP, NaP + sennosides, PEG-ELS + sennosides) in reference to tolerability, acceptance, and cleanliness. Patient and Methods: 355 outpatients between 18 and 75 years were randomized into three groups (A, B, C) receiving NaP = A, NaP, and sennosides = B or PEG-ELS and sennosides = C. Gastroenterologists performing colonoscopies were blinded to the type of preparation. All patients documented tolerance and adverse events. Vital signs, premedication, completeness, discomfort, and complications were recorded. A quality score (0–4) of cleanliness was generated. Results: The three groups were similar with regard to age, sex, BMI, indication for colonoscopy, and comorbidity. Drinking volumes (L) (A = 4.33 + 1.2, B = 4.56 + 1.18, C = 4.93 + 1.71) were in favor of NaP (P = .005). Discomfort from ingested fluid was recorded in A = 39.8% (versus C: P = .015), B = 46.6% (versus C: P = .147), and C = 54.6%. Differences in tolerability and acceptance between the three groups were statistically not significant. No differences in adverse events and the cleanliness effects occurred in the three groups (P = .113). The cleanliness quality scores 0–2 were calculated in A: 77.7%, B: 86.7%, and C: 85.2%. Conclusions: These data fail to demonstrate significant differences in tolerability, acceptance, and preparation quality between the three types of bowel preparation for colonoscopy. Cleansing with NaP was not superior to PEG-ELS

Micro-mechanical response of ultrafine grain and nanocrystalline tantalum

In order to investigate the effect of grain boundaries on the mechanical response in the micrometer and submicrometer levels, complementary experiments and molecular dynamics simulations were conducted on a model bcc metal, tantalum. Microscale pillar experiments (diameters of 1 and 2 μm) with a grain size of ~100–200 nm revealed a mechanical response characterized by a yield stress of ~1500 MPa. The hardening of the structure is reflected in the increase in the flow stress to 1700 MPa at a strain of ~0.35. Molecular dynamics simulations were conducted for nanocrystalline tantalum with grain sizes in the range of 20–50 nm and pillar diameters in the same range. The yield stress was approximately 6000 MPa for all specimens and the maximum of the stress–strain curves occurred at a strain of 0.07. Beyond that strain, the material softened because of its inability to store dislocations. The experimental results did not show a significant size dependence of yield stress on pillar diameter (equal to 1 and 2 um), which is attributed to the high ratio between pillar diameter and grain size (~10–20). This behavior is quite different from that in monocrystalline specimens where dislocation ‘starvation’ leads to a significant size dependence of strength. The ultrafine grains exhibit clear ‘pancaking’ upon being plastically deformed, with an increase in dislocation density. The plastic deformation is much more localized for the single crystals than for the nanocrystalline specimens, an observation made in both modeling and experiments. In the molecular dynamics simulations, the ratio of pillar diameter (20–50 nm) to grain size was in the range 0.2–2, and a much greater dependence of yield stress to pillar diameter was observed. A critical result from this work is the demonstration that the important parameter in establishing the overall deformation is the ratio between the grain size and pillar diameter; it governs the deformation mode, as well as surface sources and sinks, which are only important when the grain size is of the same order as the pillar diameter

Micro-mechanical response of ultrafine grain and nanocrystalline tantalum

In order to investigate the effect of grain boundaries on the mechanical response in the micrometer and submicrometer levels, complementary experiments and molecular dynamics simulations were conducted on a model bcc metal, tantalum. Microscale pillar experiments (diameters of 1 and 2 μm) with a grain size of ~100-200 nm revealed a mechanical response characterized by a yield stress of ~1500 MPa. The hardening of the structure is reflected in the increase in the flow stress to 1700 MPa at a strain of ~0.35. Molecular dynamics simulations were conducted for nanocrystalline tantalum with grain sizes in the range of 20-50 nm and pillar diameters in the same range. The yield stress was approximately 6000 MPa for all specimens and the maximum of the stress-strain curves occurred at a strain of 0.07. Beyond that strain, the material softened because of its inability to store dislocations. The experimental results did not show a significant size dependence of yield stress on pillar diameter (equal to 1 and 2 um), which is attributed to the high ratio between pillar diameter and grain size (~10-20). This behavior is quite different from that in monocrystalline specimens where dislocation 'starvation' leads to a significant size dependence of strength. The ultrafine grains exhibit clear 'pancaking' upon being plastically deformed, with an increase in dislocation density. The plastic deformation is much more localized for the single crystals than for the nanocrystalline specimens, an observation made in both modeling and experiments. In the molecular dynamics simulations, the ratio of pillar diameter (20-50 nm) to grain size was in the range 0.2-2, and a much greater dependence of yield stress to pillar diameter was observed. A critical result from this work is the demonstration that the important parameter in establishing the overall deformation is the ratio between the grain size and pillar diameter; it governs the deformation mode, as well as surface sources and sinks, which are only important when the grain size is of the same order as the pillar diameter.Fil: Yang, Wen. University of California at San Diego; Estados UnidosFil: Ruestes, Carlos Javier. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Mendoza. Instituto Interdisciplinario de Ciencias Básicas. - Universidad Nacional de Cuyo. Instituto Interdisciplinario de Ciencias Básicas; ArgentinaFil: Li, Zezhou. University of California at San Diego; Estados UnidosFil: Abad, Oscar Torrents. Leibniz Institute for New Materials; AlemaniaFil: Langdon, Terence G.. University of Southern California; Estados UnidosFil: Heiland, Birgit. Leibniz Institute for New Materials; AlemaniaFil: Koch, Marcus. Leibniz Institute for New Materials; AlemaniaFil: Arzt, Eduard. Leibniz Institute for New Materials; Alemania. Universitat Saarland; AlemaniaFil: Meyers, Marc A.. University of California at San Diego; Estados Unido