Genetic analysis of DNA repair in the hyperthermophilic archaeon, Thermococcus kodakaraensis

Extensive biochemical and structural analyses have been performed on the putative DNA repair proteins of hyperthermophilic archaea, in contrast to the few genetic analyses of the genes encoding these proteins. Accordingly, little is known about the repair pathways used by archaeal cells at high temperature. Here, we attempted to disrupt the genes encoding the potential repair proteins in the genome of the hyperthermophilic archaeon Thermococcus kodakaraensis. We succeeded in isolating null mutants of the hjc, hef, hjm, xpb, and xpd genes, but not the radA, rad50, mre11, herA, nurA, and xpg/fen1 genes. Phenotypic analyses of the gene-disrupted strains showed that the xpb and xpd null mutants are only slightly sensitive to ultraviolet (UV) irradiation, methyl methanesulfonate (MMS) and mitomycin C (MMC), as compared with the wild-type strain. The hjm null mutant showed sensitivity specifically to mitomycin C. On the other hand, the null mutants of the hjc gene lacked increasing sensitivity to any type of DNA damage. The Hef protein is particularly important for maintaining genome homeostasis, by functioning in the repair of a wide variety of DNA damage in T. kodakaraensis cells. Deletion of the entire hef gene or of the segments encoding either its nuclease or helicase domain produced similar phenotypes. The high sensitivity of the Δhef mutants to MMC suggests that Hef performs a critical function in the repair process of DNA interstrand cross-links. These damage-sensitivity profiles suggest that the archaeal DNA repair system has processes depending on repair-related proteins different from those of eukaryotic and bacterial DNA repair systems using homologous repair proteins analyzed here.     

MyDas,an Extensible Java DAS Server

A large number of diverse, complex, and distributed data resources are currently available in the Bioinformatics domain. The pace of discovery and the diversity of information means that centralised reference databases like UniProt and Ensembl cannot integrate all potentially relevant information sources. From a user perspective however, centralised access to all relevant information concerning a specific query is essential. The Distributed Annotation System (DAS) defines a communication protocol to exchange annotations on genomic and protein sequences; this standardisation enables clients to retrieve data from a myriad of sources, thus offering centralised access to end-users.We introduce MyDas, a web server that facilitates the publishing of biological annotations according to the DAS specification. It deals with the common functionality requirements of making data available, while also providing an extension mechanism in order to implement the specifics of data store interaction. MyDas allows the user to define where the required information is located along with its structure, and is then responsible for the communication protocol details.     

Metabolite-sensitive, ATP-dependent, protein kinase-catalyzed phosphorylation of HPr, a phosphocarrier protein of the phosphotransferase system in gram-positive bacteria

In this review article we summarize the recent information available concerning important mechanistic and physiological aspects of the protein kinase-mediated phosphorylation of seryl residue-46 in HPr, a phosphocarrier protein of the phosphoenolpyruvate: sugar phosphotransferase system in Gram-positive bacteria. Emphasis is placed upon the information recently obtained in two laboratories through the use of site-specific mutants of the HPr protein. The results show that (i) in contrast to eukaryotic protein kinases, the HPr(ser) kinase recognizes the tertiary structure of HPr rather than a restricted part of the primary sequence of the protein; (ii) like seryl protein kinases of eukaryotes, the HPr(ser) kinase can phosphorylate a threonyl residue, but not a tyrosyl residue when such a residue replaces the regulatory seryl residue in position-46 of the protein; (iii) the regulatory consequences of seryl phosphorylation are due to the introduction of a negative charge at position-46 in the protein rather than the bulky phosphate group; and (iv) PTS protein-HPr interactions influence the conformation of HPr, thereby retarding or stimulating the rate of kinase-catalyzed seryl-46 phosphorylation. The physiological consequences of HPr(ser) phosphorylation in vivo are still a matter of debate.     

Protein tyrosine phosphatases in osteoclast differentiation, adhesion, and bone resorption

Osteoclasts are large cells derived from the monocyte-macrophage hematopoietic cell lineage. Their primary function is to degrade bone in various physiological contexts. Osteoclasts adhere to bone via podosomes, specialized adhesion structures whose structure and subcellular organization are affected by mechanical contact of the cell with bone matrix. Ample evidence indicates that reversible tyrosine phosphorylation of podosomal proteins plays a major role in determining the organization and dynamics of podosomes. Although roles of several tyrosine kinases are known in detail in this respect, little is known concerning the roles of protein tyrosine phosphatases (PTPs) in regulating osteoclast adhesion. Here we summarize available information concerning the known and hypothesized roles of the best-researched PTPs in osteoclasts - PTPRO, PTP epsilon, SHP-1, and PTP-PEST. Of these, PTPRO, PTP epsilon, and PTP-PEST appear to support osteoclast activity while SHP-1 inhibits it. Additional studies are required to provide full molecular details of the roles of these PTPs in regulating osteoclast adhesion, and to uncover additional PTPs that participate in this process.     

Mechanical regulation of mitogen-activated protein kinase signaling in articular cartilage

Articular chondrocytes respond to mechanical forces by alterations in gene expression, proliferative status, and metabolic functions. Little is known concerning the cell signaling systems that receive, transduce, and convey mechanical information to the chondrocyte interior. Here, we show that ex vivo cartilage compression stimulates the phosphorylation of ERK1/2, p38 MAPK, and SAPK/ERK kinase-1 (SEK1) of the JNK pathway. Mechanical compression induced a phased phosphorylation of ERK consisting of a rapid induction of ERK1/2 phosphorylation at 10 min, a rapid decay, and a sustained level of ERK2 phosphorylation that persisted for at least 24 h. Mechanical compression also induced the phosphorylation of p38 MAPK in strictly a transient fashion, with maximal phosphorylation occurring at 10 min. Mechanical compression stimulated SEK1 phosphorylation, with a maximum at the relatively delayed time point of 1 h and with a higher amplitude than ERK1/2 and p38 MAPK phosphorylation. These data demonstrate that mechanical compression alone activates MAPK signaling in intact cartilage. In addition, these data demonstrate distinct temporal patterns of MAPK signaling in response to mechanical loading and to the anabolic insulin-like growth factor-I. Finally, the data indicate that compression coactivates distinct signaling pathways that may help define the nature of mechanotransduction in cartilage.     

Prediction of Protein Phosphorylation Sites by Using the Composition of k-Spaced Amino Acid Pairs

As one of the most widespread protein post-translational modifications, phosphorylation is involved in many biological processes such as cell cycle, apoptosis. Identification of phosphorylated substrates and their corresponding sites will facilitate the understanding of the molecular mechanism of phosphorylation. Comparing with the labor-intensive and time-consuming experiment approaches, computational prediction of phosphorylation sites is much desirable due to their convenience and fast speed. In this paper, a new bioinformatics tool named CKSAAP_PhSite was developed that ignored the kinase information and only used the primary sequence information to predict protein phosphorylation sites. The highlight of CKSAAP_PhSite was to utilize the composition of k-spaced amino acid pairs as the encoding scheme, and then the support vector machine was used as the predictor. The performance of CKSAAP_PhSite was measured with a sensitivity of 84.81%, a specificity of 86.07% and an accuracy of 85.43% for serine, a sensitivity of 78.59%, a specificity of 82.26% and an accuracy of 80.31% for threonine as well as a sensitivity of 74.44%, a specificity of 78.03% and an accuracy of 76.21% for tyrosine. Experimental results obtained from cross validation and independent benchmark suggested that our method was very promising to predict phosphorylation sites and can be served as a useful supplement tool to the community. For public access, CKSAAP_PhSite is available at http://59.73.198.144/cksaap_phsite/.     

Proteins of the synaptic membrane

The purpose of this communication is to provide a survey of contempory information concerning the composition, disposition, and functional significance of proteins in or on synaptic membranes derived from rat brain synaptosomes. Special emphasis is placed on their content of glycoproteins, fibrous proteins, proteins susceptible to rapid phosphorylation and dephosphorylation, and receptors for various putative neurotransmitters. Their nature, localization, possible interactions, and potential function in synaptic transmission are discussed.     

PhosphoBase, a database of phosphorylation sites: release 2.0.

PhosphoBase contains information about phosphorylated residues in proteins and data about peptide phosphorylation by a variety of protein kinases. The data are collected from literature and compiled into a common format. The current release of PhosphoBase (October 1998, version 2.0) comprises 414 phosphoprotein entries covering 1052 phosphorylatable serine, threonine and tyrosine residues. The kinetic data from peptide phosphorylation assays for approximately 330 oligopeptides is also included. The database entries are cross-referenced to the corresponding records in the Swiss-Prot protein database and literature references are linked to MedLine records. PhosphoBase is available via the WWW at http://www.cbs.dtu. dk/databases/PhosphoBase/     

Binding of HTm4 to cyclin-dependent kinase (Cdk)-associated phosphatase (KAP).Cdk2.cyclin A complex enhances the phosphatase activity of KAP, dissociates cyclin A, and facilitates KAP dephosphorylation of Cdk2

Cyclin-dependent kinase 2 (cdk2) activation requires phosphorylation of Thr160 and dissociation from cyclin A. The T-loop of cdk2 contains a regulatory phosphorylation site at Thr160. An interaction between cdc-associated phosphatase (KAP) and cdk2 compromises the interaction between cdk2 and cyclin A, which permits access of KAP, a Thr160-directed phosphatase, to its substrate, cdk2. We have reported that KAP is bound and activated by a nuclear membrane protein, HTm4. Here, we present in vitro data showing the direct interaction between the HTm4 C terminus and KAP Tyr141. We show that this interaction not only facilitates access of KAP to Thr160 and accelerates KAP kinetics, but also forces exclusion of cyclin A from the KAP.cdk2 complex.     

Web-based consumer health information: public access, digital division, and remainders

Public access Internet portals and decreasing costs of personal computers have created a growing consensus that unequal access to information, or a "digital divide," has largely disappeared for US consumers. A series of technology initiatives in the late 1990s were believed to have largely eliminated the divide. For healthcare patients, access to information is an essential part of the consumer-centric framework outlined in the recently proposed national health information initiative. Data from a recent study of health information-seeking behaviors on the Internet suggest that a "digitally underserved group" persists, effectively limiting the planned national health information infrastructure to wealthier Americans.     

Improving Access to Emergency Contraception Pills through Strengthening Service Delivery and Demand Generation: A Systematic Review of Current Evidence in Low and Middle-Income Countries

Objectives

Emergency contraception pills (ECP) are among the 13 essential commodities in the framework for action established by the UN Commission on Life-Saving Commodities for Women and Children. Despite having been on the market for nearly 20 years, a number of barriers still limit women''s access to ECP in low- and middle-income countries (LMIC) including limited consumer knowledge and poor availability. This paper reports the results of a review to synthesise the current evidence on service delivery strategies to improve access to ECP.

Methods

A narrative synthesis methodology was used to examine peer reviewed research literature (2003 to 2013) from diverse methodological traditions to provide critical insights into strategies to improve access from a service delivery perspective. The studies were appraised using established scoring systems and the findings of included papers thematically analysed and patterns mapped across all findings using concept mapping.

Findings

Ten papers were included in the review. Despite limited research of adequate quality, promising strategies to improve access were identified including: advance provision of ECP; task shifting and sharing; intersectoral collaboration for sexual assault; m-health for information provision; and scale up through national family planning programs.

Conclusion

There are a number of gaps in the research concerning service delivery and ECP in LMIC. These include a lack of knowledge concerning private/commercial sector contributions to improving access, the needs of vulnerable groups of women, approaches to enhancing intersectoral collaboration, evidence for social marketing models and investment cases for ECP.     

Comparative anatomy, homologies and evolution of the pectoral muscles of bony fish and tetrapods: a new insight

The Osteichthyes, including bony fishes and tetrapods, is a highly speciose group of vertebrates, comprising more than 42,000 living species. The anatomy of osteichthyans has been the subject of numerous comparative studies, but most of these studies concern osteological structures; much less attention has been paid to muscles. The most detailed comparative analyses of osteichthyan pectoral muscles that were actually based on a direct observation of representatives of various major actinopterygian and sarcopterygian groups were provided several decades ago by authors such as Howell and Romer. Despite the quality of their work, these authors did not have access to much information that is now available. In the present work, an updated discussion on the homologies and evolution of the osteichthyan pectoral muscles is provided, based on the authors' own analyses and on a survey of the literature, both old and recent. It is stressed that much caution should be taken when the results obtained in molecular and developmental studies concerning the pectoral muscles of model actinopterygians such as the teleostean zebrafish are discussed and compared with the results obtained in studies concerning model sarcopterygians from clades such as the Amphibia and/or the Amniota. This is because, as shown here, as a result of the different evolutionary routes followed within the actinopterygian and the sarcopterygian clades none of the individual muscles found, for example, in derived actinopterygians such as teleosts is found in derived sarcopterygians such as tetrapods. It is hoped that the information provided in the present work may help in paving the way for future analyses of the pectoral muscles in taxa from different osteichthyan groups and for a proper comparison between these muscles in those taxa.     

Data‐driven modeling reconciles kinetics of ERK phosphorylation,localization, and activity states

The extracellular signal‐regulated kinase (ERK) signaling pathway controls cell proliferation and differentiation in metazoans. Two hallmarks of its dynamics are adaptation of ERK phosphorylation, which has been linked to negative feedback, and nucleocytoplasmic shuttling, which allows active ERK to phosphorylate protein substrates in the nucleus and cytosol. To integrate these complex features, we acquired quantitative biochemical and live‐cell microscopy data to reconcile phosphorylation, localization, and activity states of ERK. While maximal growth factor stimulation elicits transient ERK phosphorylation and nuclear translocation responses, ERK activities available to phosphorylate substrates in the cytosol and nuclei show relatively little or no adaptation. Free ERK activity in the nucleus temporally lags the peak in nuclear translocation, indicating a slow process. Additional experiments, guided by kinetic modeling, show that this process is consistent with ERK's modification of and release from nuclear substrate anchors. Thus, adaptation of whole‐cell ERK phosphorylation is a by‐product of transient protection from phosphatases. Consistent with this interpretation, predictions concerning the dose‐dependence of the pathway response and its interruption by inhibition of MEK were experimentally confirmed.     

Specific tyrosine phosphorylation induced in Schistosoma mansoni miracidia by haemolymph from schistosome susceptible, but not resistant, Biomphalaria glabrata

Molecular interplay during snail-schistosome interactions is poorly understood and there is much to discover concerning the effect of snail host molecules on molecular processes in schistosomes. Using the Biomphalaria glabrata - Schistosoma mansoni host-parasite system, the effects of exposure to haemolymph, derived from schistosome-resistant and susceptible snail strains, on protein tyrosine phosphorylation in miracidia have been investigated. Western blotting revealed several tyrosine phosphorylated proteins in this larval stage. Exposure of miracidia to haemolymph from susceptible snails for 60 min resulted in a striking, 5-fold, increase in the tyrosine phosphorylation of a 56 kDa (p56) S. mansoni protein. In contrast, haemolymph from resistant snails had little effect on protein tyrosine phosphorylation levels in miracidia. Confocal microscopy revealed that tyrosine phosphorylation was predominantly associated with proteins present in the tegument. Finally, treatment of miracidia with the tyrosine kinase inhibitor genistein significantly impaired their development into primary sporocysts. The results open avenues for research that focus on the potential importance of phospho-p56 to the outcome of schistosome infection in snails, and the significance of protein tyrosine kinase-mediated signalling events to the transformation of S. mansoni larvae.     

Connexins,gap junctional intercellular communication and kinases

A number of kinases and signal transduction pathways are known to affect gap junctional intercellular communication and/or phosphorylation of connexins. Most of the information is available for protein kinase A, protein kinase C, mitogen-activated protein kinase, and the tyrosine kinase Src. Much less is known for protein kinase G, Ca(2+)-calmodulin dependent protein kinase, and casein kinase. However, the present lack of knowledge is not necessarily synonymous with lack of importance in the regulation of intercellular communication and phosphorylation of connexins. Kinases and the phosphorylation of connexins may be involved in the regulation of gap junctional intercellular communication at all levels ranging from the expression of connexin genes to the degradation of the gap junction channels. The exact role of the phosphorylation depends both on the kinase and the connexin involved, as well as the cellular context.     

Profiling the Trypanosoma cruzi phosphoproteome

Protein phosphorylation is a reversible post-translational modification essential for the regulation of several signal transduction pathways and biological processes in the living cell. Therefore, the identification of protein phosphorylation sites is crucial to understand cell signaling control at the molecular level. Based on mass spectrometry, recent studies have reported the large-scale mapping of phosphorylation sites in various eukaryotes and prokaryotes. However, little is known about the impact of phosphorylation in protozoan parasites. To in depth characterize the phosphoproteome of Trypanosoma cruzi, a parasite of the Kinetoplastida class, protein samples from cells at different phases of the metacyclogenesis--differentiation process of the parasites from non-infective epimastigotes to infective metacyclic trypomastigotes--were enriched for phosphopeptides using TiO(2) chromatography and analyzed on an LTQ-Orbitrap mass spectrometer. In total, 1,671 proteins were identified, including 753 phosphoproteins, containing a total of 2,572 phosphorylation sites. The distribution of phosphorylated residues was 2,162 (84.1%) on serine, 384 (14.9%) on threonine and 26 (1.0%) on tyrosine. Here, we also report several consensus phosphorylation sequence motifs and as some of these conserved groups have enriched biological functions, we can infer the regulation by protein kinases of this functions. To our knowledge, our phosphoproteome is the most comprehensive dataset identified until now for Kinetoplastida species. Here we also were able to extract biological information and infer groups of sites phosphorylated by the same protein kinase. To make our data accessible to the scientific community, we uploaded our study to the data repositories PHOSIDA, Proteome Commons and TriTrypDB enabling researchers to access information about the phosphorylation sites identified here.     

Protein kinase C (PKC) isozyme-specific substrates and their design

Protein kinase C (PKC), a phospholipid-dependent serine/threonine kinase, appears to be involved in the signal transduction response to many hormones and growth factors; there are 11 different PKC isozymes. Because PKC isozymes directly and/or indirectly participate in signal transduction pathways of normal and transformed cells through phosphorylation of target proteins, it is critical to understand the diversity of the intracellular signaling pathways regulated by each PKC isozyme. Thus, PKC isozyme-specific substrates are useful to understand the characterization of the intracellular signaling pathways for each PKC isozyme. Consensus sequences and sequence information obtained from PKC target proteins are very important to design PKC isozyme-specific peptide substrates. Moreover, computational prediction programs of phosphorylation sites using a library of peptide substrates aid in the fast design of PKC isozyme-specific peptide substrates. Although a large number of target proteins and synthetic peptides for PKCs are known, only two peptide substrates (peptide 422–426 of murine elongation factor-1α and Alphatomega peptide) have been reported as PKC isozyme-specific peptide substrates. This discussion will review the literature concerning these native and synthetic PKC isozyme-specific peptide substrates and their design.     

Survival curves, reproductive life span and age-related pathology of Mus caroli.

Although Mus caroli is being used in a number of laboratories as an experimental animal, basic information concerning its life span, reproductive ability, and age-related pathologies has been unavailable. Here we present this basic information, and discuss the similarities to and differences from the laboratory mouse, Mus musculus domesticus [strains A/StTrWo and (A/StTrWo x C57BL/6NNia)F1] and, from published data, wild-type Mus musculus.