MMP-2 and MMP-9 in normal mucosa are independently associated with outcome of colorectal cancer patients.

BackgroundUpregulation of the matrix metalloproteinases MMP-2 and MMP-9 in various cancers has been associated with worse survival of the patients.MethodsWe assessed MMP-2 and MMP-9 levels in normal colorectal mucosa from colorectal cancer patients in relation to the course of the disease.ResultsA high protein expression of MMP-2 as well as MMP-9 in normal mucosa was found to be correlated with worse 5-year survival. The combination of both parameters was an even stronger prognostic factor. These protein levels were found not to be related to the corresponding single nucleotide polymorphisms of MMP-2 (-1306C>T) and MMP-9 (-1562C>T). Multivariate analyses indicated that the MMP-2 and MMP-9 levels in normal mucosa are prognostic for survival, independent of TNM classification.ConclusionMMP-2 and MMP-9 levels in normal mucosa are indicative of the course of disease in colorectal cancer patients

Potential regulatory interactions of Escherichia coli RraA protein with DEAD-box helicases.

Members of the DEAD-box family of RNA helicases contribute to virtually every aspect of RNA metabolism, in organisms from all domains of life. Many of these helicases are constituents of multicomponent assemblies, and their interactions with partner proteins within the complexes underpin their activities and biological function. In Escherichia coli the DEAD-box helicase RhlB is a component of the multienzyme RNA degradosome assembly, and its interaction with the core ribonuclease RNase E boosts the ATP-dependent activity of the helicase. Earlier studies have identified the regulator of ribonuclease activity A (RraA) as a potential interaction partner of both RNase E and RhlB. We present structural and biochemical evidence showing how RraA can bind to, and modulate the activity of RhlB and another E. coli DEAD-box enzyme, SrmB. Crystallographic structures are presented of RraA in complex with a portion of the natively unstructured C-terminal tail of RhlB at 2.8-Å resolution, and in complex with the C-terminal RecA-like domain of SrmB at 2.9 Å. The models suggest two distinct mechanisms by which RraA might modulate the activity of these and potentially other helicases

Crystal structure of Caulobacter crescentus polynucleotide phosphorylase reveals a mechanism of RNA substrate channelling and RNA degradosome assembly

Polynucleotide phosphorylase (PNPase) is an exoribonuclease that cleaves single-stranded RNA substrates with 3′–5′ directionality and processive behaviour. Its ring-like, trimeric architecture creates a central channel where phosphorolytic active sites reside. One face of the ring is decorated with RNA-binding K-homology (KH) and S1 domains, but exactly how these domains help to direct the 3′ end of single-stranded RNA substrates towards the active sites is an unsolved puzzle. Insight into this process is provided by our crystal structures of RNA-bound and apo Caulobacter crescentus PNPase. In the RNA-free form, the S1 domains adopt a ‘splayed’ conformation that may facilitate capture of RNA substrates. In the RNA-bound structure, the three KH domains collectively close upon the RNA and direct the 3′ end towards a constricted aperture at the entrance of the central channel. The KH domains make non-equivalent interactions with the RNA, and there is a marked asymmetry within the catalytic core of the enzyme. On the basis of these data, we propose that structural non-equivalence, induced upon RNA binding, helps to channel substrate to the active sites through mechanical ratcheting. Structural and biochemical analyses also reveal the basis for PNPase association with RNase E in the multi-enzyme RNA degradosome assembly of the α-proteobacteria

Web-based multimodal graphs for visually impaired people

This paper describes the development and evaluation of Web-based multimodal graphs designed for visually impaired and blind people. The information in the graphs is conveyed to visually impaired people through haptic and audio channels. The motivation of this work is to address problems faced by visually impaired people in accessing graphical information on the Internet, particularly the common types of graphs for data visualization. In our work, line graphs, bar charts and pie charts are accessible through a force feedback device, the Logitech WingMan Force Feedback Mouse. Pre-recorded sound files are used to represent graph contents to users. In order to test the usability of the developed Web graphs, an evaluation was conducted with bar charts as the experimental platform. The results showed that the participants could successfully use the haptic and audio features to extract information from the Web graphs

CryoEM structures of human CMG-ATPγS-DNA and CMG-AND-1 complexes.

DNA unwinding in eukaryotic replication is performed by the Cdc45-MCM-GINS (CMG) helicase. Although the CMG architecture has been elucidated, its mechanism of DNA unwinding and replisome interactions remain poorly understood. Here we report the cryoEM structure at 3.3 Å of human CMG bound to fork DNA and the ATP-analogue ATPγS. Eleven nucleotides of single-stranded (ss) DNA are bound within the C-tier of MCM2-7 AAA+ ATPase domains. All MCM subunits contact DNA, from MCM2 at the 5'-end to MCM5 at the 3'-end of the DNA spiral, but only MCM6, 4, 7 and 3 make a full set of interactions. DNA binding correlates with nucleotide occupancy: five MCM subunits are bound to either ATPγS or ADP, whereas the apo MCM2-5 interface remains open. We further report the cryoEM structure of human CMG bound to the replisome hub AND-1 (CMGA). The AND-1 trimer uses one β-propeller domain of its trimerisation region to dock onto the side of the helicase assembly formed by Cdc45 and GINS. In the resulting CMGA architecture, the AND-1 trimer is closely positioned to the fork DNA while its CIP (Ctf4-interacting peptide)-binding helical domains remain available to recruit partner proteins

Knowledge of pelvic floor problems: a study of third trimester, primiparous women

INTRODUCTION AND HYPOTHESIS: Pelvic floor problems in women (urinary incontinence, faecal incontinence, uterovaginal prolapse) are common, and have an adverse effect on quality of life. We hypothesized that there is low knowledge of these problems amongst primiparous women in their third trimester of pregnancy. METHODS: We conducted a cross-sectional study in antenatal clinics of three hospitals in London, UK, from 2011 to 2013. Primiparous women aged ≥18 years and in the third trimester of pregnancy answered questions on pelvic floor problems. Knowledge scores were calculated based on the proportion of questions answered correctly. RESULTS: A total of 249 women completed the question set. The average knowledge score across all domains was low at 45 %. Scores were lowest for the less common problems of faecal incontinence (35 %) and prolapse (36 %). The score for urinary incontinence was higher at 63 %, but low when questions explored more detailed levels of knowledge (41 %). Knowledge scores were positively associated with both education to tertiary level and the use of books as the information source on pregnancy and delivery. Only 35 % of women cited antenatal classes as a source. CONCLUSIONS: Knowledge of pelvic floor problems is low amongst third-trimester, primiparous women in this London-based population. Adequate knowledge of these problems is important for women to be able to make informed choices about their antenatal care and to seek help if problems arise. The data suggest scope for health-care professionals to raise these issues early during pregnancy, and to help women access accurate sources of information

Antiapoptotic herpesvirus Bcl-2 homologs escape caspase-mediated conversion to proapoptotic proteins

The antiapoptotic Bcl-2 and Bcl-x(L) proteins of mammals are converted into potent proapoptotic factors when they are cleaved by caspases, a family of apoptosis-inducing proteases (E. H.-Y. Cheng, D. G. Kirsch, R. J. Clem, R. Ravi, M. B. Kastan, A. Bedi, K. Ueno, and J. M. Hardwick, Science 278:1966-1968, 1997; R. J. Clem, E. H.-Y. Cheng, C. L. Karp, D. G. Kirsch, K. Ueno, A. Takahashi, M. B. Kastan, D. E. Griffin, W. C. Earnshaw, M. A. Veliuona, and J. M. Hardwick, Proc. Natl. Acad. Sci. USA 95:554-559, 1998). Gamma herpesviruses also encode homologs of the Bcl-2 family. All tested herpesvirus Bcl-2 homologs possess antiapoptotic activity, including the more distantly related homologs encoded by murine gammaherpesvirus 68 (gammaHV68) and bovine herpesvirus 4 (BHV4), as described here. To determine if viral Bcl-2 proteins can be converted into death factors, similar to their cellular counterparts, five herpesvirus Bcl-2 homologs from five different viruses were tested for their susceptibility to caspases. Only the viral Bcl-2 protein encoded by gammaHV68 was susceptible to caspase digestion. However, unlike the caspase cleavage products of cellular Bcl-2, Bcl-x(L), and Bid, which are potent inducers of apoptosis, the cleavage product of gammaHV68 Bcl-2 lacked proapoptotic activity. KSBcl-2, encoded by the Kaposi's sarcoma-associated herpesvirus, was the only viral Bcl-2 homolog that was capable of killing cells when expressed as an N-terminal truncation. However, because KSBcl-2 was not cleavable by caspases, the latent proapoptotic activity of KSBcl-2 apparently cannot be released. The Bcl-2 homologs encoded by herpesvirus saimiri, Epstein-Barr virus, and BHV4 were not cleaved by apoptotic cell extracts and did not possess latent proapoptotic activities. Thus, herpesvirus Bcl-2 homologs escape negative regulation by retaining their antiapoptotic activities and/or failing to be converted into proapoptotic proteins by caspases during programmed cell death

Local group star formation in warm and self-interacting dark matter cosmologies

The nature of the dark matter can affect the collapse time of dark matter haloes, and can therefore be imprinted in observables such as the stellar population ages and star formation histories of dwarf galaxies. In this paper, we use high-resolution hydrodynamical simulations of Local Group-analogue (LG) volumes in cold dark matter (CDM), sterile neutrino warm dark matter (WDM) and self-interacting dark matter (SIDM) models with the EAGLE galaxy formation code to study how galaxy formation times change with dark matter model. We are able to identify the same haloes in different simulations, since they share the same initial density field phases. We find that the stellar mass of galaxies depends systematically on resolution, and can differ by as much as a factor of 2 in haloes of a given dark matter mass. The evolution of the stellar populations in SIDM is largely identical to that of CDM, but in WDM early star formation is instead suppressed. The time at which LG haloes can begin to form stars through atomic cooling is delayed by ∼200 Myr in WDM models compared to CDM. It will be necessary to measure stellar ages of old populations to a precision of better than 100 Myr, and to address degeneracies with the redshift of reionization – and potentially other baryonic processes – in order to use these observables to distinguish between dark matter models