Phylogenetic analysis and protein structure modelling identifies distinct Ca2+/Cation antiporters and conservation of gene family structure within Arabidopsis and rice species

BACKGROUND: The Ca(2+)/Cation Antiporter (CaCA) superfamily is an ancient and widespread family of ion-coupled cation transporters found in nearly all kingdoms of life. In animals, K(+)-dependent and K(+)-indendent Na(+)/Ca(2+) exchangers (NCKX and NCX) are important CaCA members. Recently it was proposed that all rice and Arabidopsis CaCA proteins should be classified as NCX proteins. Here we performed phylogenetic analysis of CaCA genes and protein structure homology modelling to further characterise members of this transporter superfamily. FINDINGS: Phylogenetic analysis of rice and Arabidopsis CaCAs in comparison with selected CaCA members from non-plant species demonstrated that these genes form clearly distinct families, with the H(+)/Cation exchanger (CAX) and cation/Ca(2+) exchanger (CCX) families dominant in higher plants but the NCKX and NCX families absent. NCX-related Mg(2+)/H(+) exchanger (MHX) and CAX-related Na(+)/Ca(2+) exchanger-like (NCL) proteins are instead present. Analysis of genomes of ten closely-related rice species and four Arabidopsis-related species found that CaCA gene family structures are highly conserved within related plants, apart from minor variation. Protein structures were modelled for OsCAX1a and OsMHX1. Despite exhibiting broad structural conservation, there are clear structural differences observed between the different CaCA types. CONCLUSIONS: Members of the CaCA superfamily form clearly distinct families with different phylogenetic, structural and functional characteristics, and therefore should not be simply classified as NCX proteins, which should remain as a separate gene family. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12284-016-0075-8) contains supplementary material, which is available to authorized users

Protein Phylogenetic Analysis of Ca2+/cation Antiporters and Insights into their Evolution in Plants

Cation transport is a critical process in all organisms and is essential for mineral nutrition, ion stress tolerance, and signal transduction. Transporters that are members of the Ca2+/cation antiporter (CaCA) superfamily are involved in the transport of Ca2+ and/or other cations using the counter exchange of another ion such as H+ or Na+. The CaCA superfamily has been previously divided into five transporter families: the YRBG, Na+/Ca2+ exchanger (NCX), Na+/Ca2+, K+ exchanger (NCKX), H+/cation exchanger (CAX), and cation/Ca2+ exchanger (CCX) families, which include the well-characterized NCX and CAX transporters. To examine the evolution of CaCA transporters within higher plants and the green plant lineage, CaCA genes were identified from the genomes of sequenced flowering plants, a bryophyte, lycophyte, and freshwater and marine algae, and compared with those from non-plant species. We found evidence of the expansion and increased diversity of flowering plant genes within the CAX and CCX families. Genes related to the NCX family are present in land plant though they encode distinct MHX homologs which probably have an altered transport function. In contrast, the NCX and NCKX genes which are absent in land plants have been retained in many species of algae, especially the marine algae, indicating that these organisms may share “animal-like” characteristics of Ca2+ homeostasis and signaling. A group of genes encoding novel CAX-like proteins containing an EF-hand domain were identified from plants and selected algae but appeared to be lacking in any other species. Lack of functional data for most of the CaCA proteins make it impossible to reliably predict substrate specificity and function for many of the groups or individual proteins. The abundance and diversity of CaCA genes throughout all branches of life indicates the importance of this class of cation transporter, and that many transporters with novel functions are waiting to be discovered

The Ubiquitin Proteasome System Acutely Regulates Presynaptic Protein Turnover and Synaptic Efficacy

AbstractBackground: The ubiquitin proteasome system (UPS) mediates regulated protein degradation and provides a mechanism for closely controling protein abundance in spatially restricted domains within cells. We hypothesized that the UPS may acutely determine the local concentration of key regulatory proteins at neuronal synapses as a means for locally modulating synaptic efficacy and the strength of neurotransmission communication.Results: We investigated this hypothesis at the Drosophila neuromuscular synapse by using an array of genetic and pharmacological tools. This study demonstrates that UPS components are present in presynaptic boutons and that the UPS functions locally in the presynaptic compartment to rapidly eliminate a conditional transgenic reporter of proteasome activity. We assayed a panel of synaptic proteins to determine whether the UPS acutely regulates the local abundance of native synaptic targets. Both acute pharmacological inhibition of the proteasome (<1 hr) and targeted genetic perturbation of proteasome function in the presynaptic neuron cause the specific accumulation of the essential synaptic vesicle-priming protein DUNC-13. Most importantly, acute pharmacological inhibition of the proteasome (<1 hr) causes a rapid strengthening of neurotransmission (an approximately 50% increase in evoked amplitude) because of increased presynaptic efficacy. The proteasome-dependent regulation of presynaptic protein abundance, both of the exogenous reporter and native DUNC-13, and the modulation of presynaptic neurotransmitter release occur on an intermediate, rapid (tens of minutes) timescale.Conclusions: Taken together, these studies demonstrate that the UPS functions locally within synaptic boutons to acutely control levels of presynaptic protein and that the rate of UPS-dependent protein degradation is a primary determinant of neurotransmission strength

Design and qualification of an absolute thickness measuring machine

Thesis (S.M.)--Massachusetts Institute of Technology, Dept. of Mechanical Engineering, 2004.Includes bibliographical references (leaf 68).The target fabrication group at Lawrence Livermore National Laboratory develops various high energy density physics targets, which are used to study the interaction of materials when shot with high energy lasers. These targets consist of many different types of materials glued together including low density foams, plastics, and metals. To verify models, the physicists need to know the exact thickness of the targets and target components to [plus-minus] 1.0 [mu]m. The target components are typically 3-5 mm in diameter and 200-300 [mu]m thick and may have features such as moguls or two-dimensional sine waves machined onto them. As of yet, no commercial thickness measuring machine exists on the market capable of measuring thicknesses to [plus-minus] 1.0 [mu]m. To solve this problem, an absolute thickness measuring machine was developed that uses a precision air-bearing XY stage to scan a target between two confocal displacement lasers that measure the profile of each side of the target. A NIST traceable gage block of known thickness is used to calculate the thickness of the target. This paper describes the design and qualification of the absolute thickness measuring machine. It focuses on the error budget and tests performed to qualify the machine. Without compensation factors, the absolute thickness measuring machine was able to measure the thickness of a gage block to 0.5 [mu]m.by Darcy K. Kelly.S.M

Reducing restrictive practices across health, education and criminal justice settings

In many institutions in the UK, when an adult or child is distressed or agitated, staff may use techniques such as physical restraint and/or being locked in a seclusion room to contain the situation. These ‘restrictive practices’ can be physically harmful and cause psychological trauma. We systematically reviewed interventions to reduce the use of restrictive practices in institutional settings and found the most effective interventions combined techniques from a common pool. Health, education and criminal justice sectors should be encouraged to prioritise evidence backed interventions to prevent harm, reduce associated costs, and improve care

Chimpanzees demonstrate individual differences in social information use

Studies of transmission biases in social learning have greatly informed our understanding of how behaviour patterns may diffuse through animal populations, yet within-species inter-individual variation in social information use has received little attention and remains poorly understood. We have addressed this question by examining individual performances across multiple experiments with the same population of primates. We compiled a dataset spanning 16 social learning studies (26 experimental conditions) carried out at the same study site over a 12-year period, incorporating a total of 167 chimpanzees. We applied a binary scoring system to code each participant’s performance in each study according to whether they demonstrated evidence of using social information from conspecifics to solve the experimental task or not (Social Information Score—‘SIS’). Bayesian binomial mixed effects models were then used to estimate the extent to which individual differences influenced SIS, together with any effects of sex, rearing history, age, prior involvement in research and task type on SIS. An estimate of repeatability found that approximately half of the variance in SIS was accounted for by individual identity, indicating that individual differences play a critical role in the social learning behaviour of chimpanzees. According to the model that best fit the data, females were, depending on their rearing history, 15–24% more likely to use social information to solve experimental tasks than males. However, there was no strong evidence of an effect of age or research experience, and pedigree records indicated that SIS was not a strongly heritable trait. Our study offers a novel, transferable method for the study of individual differences in social learning

A qualitative systematic review of published work on disclosure and help-seeking for domestic violence and abuse among women from ethnic minority populations in the UK

Introduction: Domestic violence and abuse has been recognised as an international public health problem. However, the pervasiveness of the problem is unknown due in part to underreporting, especially among women from ethnic minority populations. In relation to this group, this review seeks to explore: (1) the barriers to disclosure; (2) the facilitators of help-seeking; and (3) self-perceived impacts of domestic violence. Design: We systematically identified published qualitative studies conducted among women from ethnic minority populations in the UK. Data analysis was completed using thematic analysis approach. Result: 562 papers were identified and eight papers from four studies conducted among women from ethnic minority populations in the UK met the inclusion criteria and were reviewed. Barriers to disclosure include: Immigration status, community influences, problems with language and interpretation, and unsupportive attitudes of staff within mainstream services. Facilitators of help-seeking were: escalation of abuse and safety of children. Self-perceived impact of abuse includes: shame, denial, loss of identity and lack of choice. Conclusion: There is an on-going need for staff from domestic violence services to be aware of the complexities within which women from ethnic minority populations experience domestic violence and abuse

The distribution of neuraminidase among the cytoplasmic membranes of HeLa cells infected with an influenza virus

1. The post-mitochondrial fraction of HeLa cells infected with influenza virus was sub-fractionated by density gradient flotation centrifugation.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/41681/1/705_2005_Article_BF01254167.pd

Swine Influenza A Outbreak, Fort Dix, New Jersey, 1976

Published literature and events surrounding the outbreak are reviewed

Human Cardiomyocytes Prior to Birth by Integrationâ Free Reprogramming of Amniotic Fluid Cells

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/135525/1/Supplemental_Information.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/135525/2/sct320165121595.pd