Conformational Selection and Substrate Binding Regulate the Monomer/Dimer Equilibrium of the C-terminal domain of Escherichia coli Enzyme I

The bacterial phosphotransferase system (PTS) is a signal transduction pathway that couples phosphoryl transfer to active sugar transport across the cell membrane. The PTS is initiated by the binding of phosphoenolpyruvate (PEP) to the C-terminal domain (EIC) of enzyme I (EI), a highly conserved protein that is common to all sugar branches of the PTS. EIC exists in a dynamic monomer/dimer equilibrium that is modulated by ligand binding and is thought to regulate the overall PTS. Isolation of EIC has proven challenging, and conformational dynamics within the EIC domain during the catalytic cycle are still largely unknown. Here, we present a robust protocol for expression and purification of recombinant EIC from Escherichia coli and show that isolated EIC is capable of hydrolyzing PEP. NMR analysis and residual dipolar coupling measurements indicate that the isolated EIC domain in solution adopts a stable tertiary fold and quaternary structure that is consistent with previously reported crystallographic data. NMR relaxation dispersion measurements indicate that residues around the PEP binding site and in the β3α3 turn (residues 333-366), which is located at the dimer interface, undergo a rapid transition on the sub-millisecond time scale (with an exchange rate constant of ～1500 s(-1)) between major open (～97%) and minor closed (～3%) conformations. Upon PEP binding, the β3α3 turn is effectively locked in the closed state by the formation of salt bridges between the phosphate group of PEP and the side chains of Lys(340) and Arg(358), thereby stabilizing the dimer.     

Protein carbonylation and adipocyte mitochondrial function

Carbonylation is the covalent, non-reversible modification of the side chains of cysteine, histidine, and lysine residues by lipid peroxidation end products such as 4-hydroxy- and 4-oxononenal. In adipose tissue the effects of such modifications are associated with increased oxidative stress and metabolic dysregulation centered on mitochondrial energy metabolism. To address the role of protein carbonylation in the pathogenesis of mitochondrial dysfunction, quantitative proteomics was employed to identify specific targets of carbonylation in GSTA4-silenced or overexpressing 3T3-L1 adipocytes. GSTA4-silenced adipocytes displayed elevated carbonylation of several key mitochondrial proteins including the phosphate carrier protein, NADH dehydrogenase 1α subcomplexes 2 and 3, translocase of inner mitochondrial membrane 50, and valyl-tRNA synthetase. Elevated protein carbonylation is accompanied by diminished complex I activity, impaired respiration, increased superoxide production, and a reduction in membrane potential without changes in mitochondrial number, area, or density. Silencing of the phosphate carrier or NADH dehydrogenase 1α subcomplexes 2 or 3 in 3T3-L1 cells results in decreased basal and maximal respiration. These results suggest that protein carbonylation plays a major instigating role in cytokine-dependent mitochondrial dysfunction and may be linked to the development of insulin resistance in the adipocyte.     

Mapping ultra-weak protein-protein interactions between heme transporters of Staphylococcus aureus

Iron is an essential nutrient for the proliferation of Staphylococcus aureus during bacterial infections. The iron-regulated surface determinant (Isd) system of S. aureus transports and metabolizes iron porphyrin (heme) captured from the host organism. Transportation of heme across the thick cell wall of this bacterium requires multiple relay points. The mechanism by which heme is physically transferred between Isd transporters is largely unknown because of the transient nature of the interactions involved. Herein, we show that the IsdC transporter not only passes heme ligand to another class of Isd transporter, as previously known, but can also perform self-transfer reactions. IsdA shows a similar ability. A genetically encoded photoreactive probe was used to survey the regions of IsdC involved in self-dimerization. We propose an updated model that explicitly considers self-transfer reactions to explain heme delivery across the cell wall. An analogous photo-cross-linking strategy was employed to map transient interactions between IsdC and IsdE transporters. These experiments identified a key structural element involved in the rapid and specific transfer of heme from IsdC to IsdE. The resulting structural model was validated with a chimeric version of the homologous transporter IsdA. Overall, our results show that the ultra-weak interactions between Isd transporters are governed by bona fide protein structural motifs.     

Age and sexual assault during robberies

We use data from the National Incident-Based Reporting System to examine the effects of offender and victim age on whether male offenders commit sexual assault while robbing women. Restricting analyses to robberies reveals the offenders' age preferences since it allows one to control for the effects of opportunity. We find that robbers of all ages are most likely to sexually assault women at ages 15-29 years, ages when their reproductive potential is highest. However, in contrast to the idea that rape is a direct adaptation, victims are no more likely to be raped than sexually assaulted at these ages. The age of the offender is also a strong predictor of sexual assault. The likelihood that a robber commits a sexual assault increases from age 12 years until he reaches his early thirties when it begins to decline. This age pattern corresponds, to some extent, to age differences in the male sex drive.     

Effects of Global Positioning System Collar Weight on Zebra Behavior and Location Error

ABSTRACT Global Positioning System (GPS) collars are increasingly being used to study fine-scale patterns of animal behavior. Previous studies on GPS collars have tried to determine the causes of location error without attempting to investigate whether the accuracy of fixes provides a correspondingly accurate measure of the animal's natural behavior. When comparing 2 types of GPS collar, we found a significant effect of collar weight and fit on the rate of travel of plains zebra (Equus burchelli antiquorum) females in the Makgadikgadi, Botswana. Although both types of collar were well within accepted norms of collar weight, the slightly heavier collars (0.6% of total body mass [TBM]) reduced rate of travel by >50% when foraging compared with the collar that was 0.4% of TBM. Collar effect was activity specific, particularly interfering with grazing behavior; the effect was less noticeable when zebras crossed larger interpatch distances. We highlight that small differences in collar weight or fit can affect specific behaviors, limiting the extrapolation of fine-scaled GPS data. This has important implications for wildlife biologists, who hitherto have assumed that collars within accepted weight limits have little or no effect on animal movement parameters.     

系统理论指导下辩证思维模式与抗休克决策

休克是由于有效循环血量不足引发的微循环障碍而表现一系列症候群,作为一种系统性疾病,病因十分复杂多样,诊疗过程中的临床决策应全面而富有针对性,并充分考虑到救治措施的协调一致和互相配合。系统论主张整体大于部分之和强调的就是措施之间的整体化效果,充分考虑到患者个体间差异,辩证分析不同类型休克、不同个体间不同表现,在系统理论指导下的富有针对性措施间协调一致的决策模式才是较为完整的休克救治临床决策模式。     

IMGT-Kaleidoscope, the formal IMGT-ONTOLOGY paradigm

IMGT, the international ImMunoGeneTics information system (http://imgt.cines.fr), is the reference in immunogenetics and immunoinformatics. IMGT standardizes and manages the complex immunogenetic data which include the immunoglobulins (IG) or antibodies, the T cell receptors (TR), the major histocompatibility complex (MHC) and the related proteins of the immune system (RPI) which belong to the immunoglobulin superfamily (IgSF) and the MHC superfamily (MhcSF). The accuracy and consistency of IMGT data and the coherence between the different IMGT components (databases, tools and Web resources) are based on IMGT-ONTOLOGY, the first ontology for immunogenetics and immunoinformatics. IMGT-ONTOLOGY manages the immunogenetics knowledge through diverse facets relying on seven axioms, "IDENTIFICATION", "DESCRIPTION", "CLASSIFICATION", "NUMEROTATION", "LOCALIZATION", "ORIENTATION" and "OBTENTION", that postulate that objects, processes and relations have to be identified, described, classified, numerotated, localized, orientated, and that the way they are obtained has to be determined. These axioms constitute the Formal IMGT-ONTOLOGY, also designated as IMGT-Kaleidoscope. Through the example of the IG molecular synthesis, the concepts generated from the "IDENTIFICATION", "DESCRIPTION", "CLASSIFICATION" and "NUMEROTATION" axioms are detailed with their main instances and semantic relations. The axioms have been essential for the conceptualization of the molecular immunogenetics knowledge and can be used to generate concepts for multi scale approaches at the molecule, cell, tissue, organ, organism or population level, emphasizing the generalization of the application domain. In that way the Formal IMGT-ONTOLOGY represents a paradigm for the elaboration of ontologies in system biology.     

Imprint cytology of vacuum-assisted breast biopsy specimens: a rapid diagnostic tool in non-palpable solid lesions

Objective:  Imprint cytology provides a rapid preliminary diagnosis shortly after the completion of breast biopsy. This study aims to assess the validity of imprint cytology for the pre-operative diagnosis of non-palpable mammographic solid lesions excised by vacuum-assisted breast biopsy (VABB).
Methods:  Seventy-two women with non-palpable Breast Imaging Reporting and Data System 3 and 4 mammographic solid lesions without microcalcifications underwent VABB on the stereotactic Fischer's table with 11-G Mammotome vacuum probes. Imprint samples were examined (Diff-Quick stain, modified Papanicolaou stain and May-Grünwald–Giemsa). The cores were dipped into a CytoRich Red Collection fluid for a few seconds in order to obtain samples with the use of the specimen wash. After the completion of cytological procedures, the core was prepared for routine pathological study. The pathologist was blind to the preliminary cytological results. The cytological and pathological diagnoses were comparatively evaluated.
Results:  The sensitivity of the cytological imprints for cancer was 90%. The specificity of the method for cancer diagnosis was 100%. Two precursor lesions were present in the material: one case of atypical ductal hyperplasia, which was successfully detected, and one case of lobular neoplasia, which escaped detection. The cytological imprints were inadequate in four out of 72 cases (5.6%), but none of them were included within the malignant subgroup.
Conclusions:  Imprint cytology seems to be an important adjunctive tool in the management of patients with non-palpable mammographic solid lesions. Its very satisfactory sensitivity and optimal specificity could establish its use in general clinical practice.     

混合蛋白质体系中魟鱼和海兔肝铁蛋白释放铁的动力学研究

分别制备含有魟鱼肝铁蛋白(1iver ferritin of Dasyatis akajei,DALF)和海兔肝铁蛋白(Liver ferritin of Aplysia,ALF)的混合蛋白质体系。选用电子光谱技术和不同电子供体,研究在混合蛋白质体系中,DALF和ALF释放铁的动力学过程和规律。实验结果表明,采用Na2S2O4作为还原剂时,DALF以两相行为进行释放铁的反应;而选用抗坏血酸作为还原剂时,DALF却以一级反应动力学方式进行释放铁的反应,简化释放铁的过程。在混合蛋白质体系中且以抗坏血酸和Na2S2O4为电子供体时,ALF均以一级反应动力学过程进行释放铁的反应,认为某些蛋白质参与协助ALF释放铁反应,从而简化释放铁的过程。     

Platform-basin transect of a middle to late Jurassic large-scale carbonate platform system (Shotori mountains,Tabas area,east-central Iran)

Summary Following a phase of predominantly siliciclastic sedimentation in the Early and Middle Jurassic, a large-scale, low-latitude carbonate depositional system was established in the northern part of the Tabas Block, part of the central-east Iranian microplate, during the Callovian and persisted until the latest Oxfordian/Early Kimmeridgian. Running parallel to the present eastern block margin, a NNW/SSE-trending carbonate platform developed in an area characterized by reduced subsidence rates (Shotori Swell). The growth of this rimmed, flat-topped barrier platform strongly influenced the Upper Jurassic facies pattern and sedimentary history of the Tabas Block. The platform sediments, represented by the predominantly fine-grained carbonates of the Esfandiar Limestone Formation, pass eastward into slope to basin sediments of the Qal'eh Dokhtar Limestone Formation (platform-derived allochthonites, microbialites, and peri-platform muds). Towards the west, they interfinger with bedded limestones and marlstones (Kamar-e-Mehdi Formation), which were deposited in an extensive shelf lagoon. In a N−S direction, the Esfandiar Platform can be traced for about 170 km, in an E-W direction, the platform extended for at least 35–40 km. The width of the eastern slope of the platform is estimated at 10–15 km, the width of the western shelf lagoon varied considerably (>20–80 km). During the Late Callovian to Middle Oxfordian, the Esfandiar Platform flourished under arid climatic conditions and supplied the slope and basinal areas with large amounts of carbonates (suspended peri-platform muds and gravitational sediments). Export pulses of platform material, e.g. ooids and aggregate grains, into the slope and basinal system are interpreted as highstand shedding related to relative sealevel variations. The high-productivity phase was terminated in the Late Oxfordian when the eastern platform areas drowned and homogeneous deep water marls of the Upper Oxfordian to Kimmeridgian Korond Formation onlapped both the Qal'eh Dokhtar Limestone Formation and the drowned Esfandiar Limestone Formation. Tectonic instability, probably caused by faulting at the margins of the Tabas Block in connection with rotational movements of the east-central Iranian block assemblage, was responsible for the partial drowning of the eastern platform areas. In some areas, relicts of the platform persisted to produce shallow-water sediments into the Kimmeridgian.