The C-terminal SH3 domain contributes to the intramolecular inhibition of Vav family proteins

Vav proteins are phosphorylation-dependent guanine nucleotide exchange factors (GEFs) that catalyze the activation of members of the Rho family of guanosine triphosphatases (GTPases). The current regulatory model holds that the nonphosphorylated, catalytically inactive state of these GEFs is maintained by intramolecular interactions among the amino-terminal domains and the central catalytic core, which block the binding of Vav proteins to GTPases. We showed that this autoinhibition is mechanistically more complex, also involving the bivalent association of the carboxyl-terminal Src homology 3 (SH3) region of Vav with its catalytic and pleckstrin homology (PH) domains. Such interactions occurred through proline-rich region-independent mechanisms. Full release from this double-locked state required synergistic weakening effects from multiple phosphorylated tyrosine residues, thus providing an optimized system to generate gradients of Vav GEF activity depending on upstream signaling inputs. This mechanism is shared by mammalian and Drosophila melanogaster Vav proteins, suggesting that it may be a common regulatory feature for this protein family.Work in the laboratory of X.R.B. has been funded by grants from the Spanish Ministry of Economy and Competitiveness (SAF2009-07172, SAF2012-3171, RD06/0020/0001, and RD12/0036/0002), the Castilla-León Autonomous Government (CSI039A12-1), and the Asociación Española Contra el Cáncer (AECC). O.L. has been supported by grants from the Spanish Ministry of Economy and Competitiveness (SAF2011-22988 and RD06/0020/1001). The salary of M.B. has been partially supported by a JAE-Predoc contract (CSIC), the AECC, and grant RD06/0020/0001. S.F. is supported by a graduate student FPI contract from the Spanish Ministry of Economy and Competitiveness (BES-2010-031386). Spanish funding is cosponsored by the European Regional Development Fund.Peer Reviewe

Modulation of the chaperone DnaK allosterism by the nucleotide exchange factor GrpE

10 p.-6 fig.Hsp70 chaperones comprise two domains, the nucleotide-binding domain (Hsp70NBD), responsible for structural and functional changes in the chaperone, and the substrate-binding domain (Hsp70SBD), involved in substrate interaction. Substrate binding and release in Hsp70 is controlled by the nucleotide state of DnaKNBD, with ATP inducing the open, substrate-receptive DnaKSBD conformation, whereas ADP forces its closure. DnaK cycles between the two conformations through interaction with two cofactors, the Hsp40 co-chaperones (DnaJ in Escherichia coli) induce the ADP state, and the nucleotide exchange factors (GrpE in E. coli) induce the ATP state. X-ray crystallography showed that the GrpE dimer is a nucleotide exchange factor that works by interaction of one of its monomers with DnaKNBD. DnaKSBD location in this complex is debated; there is evidence that it interacts with the GrpE N-terminal disordered region, far from DnaKNBD. Although we confirmed this interaction using biochemical and biophysical techniques, our EM-based three-dimensional reconstruction of the DnaK-GrpE complex located DnaKSBD near DnaKNBD. This apparent discrepancy between the functional and structural results is explained by our finding that the tail region of the GrpE dimer in the DnaK-GrpE complex bends and its tip contacts DnaKSBD, whereas the DnaKNBD-DnaKSBD linker contacts the GrpE helical region. We suggest that these interactions define a more complex role for GrpE in the control of DnaK function.This work was supported in part by Spanish Ministry of Economy and Innovation Grants BFU2013-44202 (to J. M. V.), SAF2011-22988 (to O. L.), and BFU2013-47059 (to A. M.), Madrid Regional Government Grants S2013/MIT-2807 (to J. M. V.) and S2010/BMD-2316 (to O. L.), and Basque Government Grant IT709-13 (to A. M.).Peer reviewe

Extended Floating Car Data System - Experimental Study-

IEEE Intelligent Vehicles Symposium (IV), , 06/06/2011-10/06/2011, Baden-Baden, AlemaniaThis paper presents the results of a set of extensive experiments carried out in daytime and nighttime conditions in real traffic using an enhanced or extended Floating Car Data system (xFCD) that includes a stereo vision sensor for detecting the local traffic ahead. The detection component implies the use of previously monocular approaches developed by our group in combination with new stereo vision algorithms that add robustness to the detection and increase the accuracy of the measurements corresponding to relative distance and speed. Besides the stereo pair of cameras, the vehicle is equipped with a low-cost GPS and an electronic device for CAN Bus interfacing. The xFCD system has been tested in a 198-minutes sequence recorded in real traffic scenarios with different weather and illumination conditions, which represents the main contribution of this paper. The results are promising and demonstrate that the system is ready for being used as a source of traffic state information

Molecular architecture and oligomerization of Candida glabrata Cdc13 underpin its telomeric DNA-binding and unfolding activity

The CST complex is a key player in telomere replication and stability, which in yeast comprises Cdc13, Stn1 and Ten1. While Stn1 and Ten1 are very well conserved across species, Cdc13 does not resemble its mammalian counterpart CTC1 either in sequence or domain organization, and Cdc13 but not CTC1 displays functions independently of the rest of CST. Whereas the structures of human CTC1 and CST have been determined, the molecular organization of Cdc13 remains poorly understood. Here, we dissect the molecular architecture of Candida glabrata Cdc13 and show how it regulates binding to telomeric sequences. Cdc13 forms dimers through the interaction between OB-fold 2 (OB2) domains. Dimerization stimulates binding of OB3 to telomeric sequences, resulting in the unfolding of ssDNA secondary structure. Once bound to DNA, Cdc13 prevents the refolding of ssDNA by mechanisms involving all domains. OB1 also oligomerizes, inducing higher-order complexes of Cdc13 in vitro. OB1 truncation disrupts these complexes, affects ssDNA unfolding and reduces telomere length in C. glabrata. Together, our results reveal the molecular organization of C. glabrata Cdc13 and how this regulates the binding and the structure of DNA, and suggest that yeast species evolved distinct architectures of Cdc13 that share some common principles.Agencia Estatal de Investigacion [AEI/10.13039/5011000 ´ 11 033]; Ministerio de Ciencia e Innovacion, and co-´ funded by the European Regional Development Fund(ERDF-UE) [PID2020-114429RB-I00 to O.L., PID2020-112998GB-100 to F.M.-H]; Autonomous Region of Madrid and co-funded by the European Social Fund and the European Regional Development Fund [Y2018/BIO4747 and P2018/NMT4443 to O.L. and F.M.-H.]; National Institute of Health Carlos III to CNIO; J.R.L.O. and O.N. acknowledge support from the Molecular Interactions Facility at the CIB-CSIC; N.G.-R. was supported by a Boehringer Ingelheim Fonds PhD fellowship; N.F.L. is funded by NIH [GM107287]. Funding for open access charge: Agencia Estatal de Investigacion [AEI ´ /10.13039/501100011 033]; Ministerio de Ciencia e Innovacion, co-funded by the Eu-ropean Regional Development Fund (ERDF) [PID2020-114429RB-I00].Peer reviewe

Ag-AgO nanostructures on glass substrates by solid-state dewetting: From extended to localized surface plasmons

We present here a study on the modification of morphological and plasmonic properties of Ag thin films deposited on glass substrates upon annealing in air at different temperatures. Initially, Ag films are continuous and exhibit extended surface plasmons with a resonant absorbance that depends on the film thickness. The dewetting process promotes the formation of nanoparticles with different sizes, shapes, and agglomerations states, besides a partial oxidation from Ag to AgO at surface level. The final Ag-AgO nanostructures are dependent on the annealing temperature and initial film thickness. The optical properties evolve from those typical of metallic films with high reflectivity and extended surface plasmon resonance toward localized surface plasmons characteristic of nanoparticles. The optical evolution and the final plasmonic response are evaluated according to the morphological and structural features of nanostructures. Published by AIP Publishing

Acuity, nurse staffing and workforce, missed care and patient outcomes. A cluster-unit-level descriptive comparison

Aim: To compare patient acuity, nurse staffing and workforce, missed nursing care and patient outcomes among hospital unit-clusters. Background: Relationships among acuity, nurse staffing and workforce, missed nursing care and patient outcomes, are not completely understood. Method: Descriptive design with data from four unit-clusters: medical, surgical, combined and stepdown units. Descriptive statistics were used to compare acuity, nurse staffing coverage, education and expertise, missed nursing care, and selected nurse-sensitive outcomes. Results: Patient acuity in general (medical, surgical and combined) floors is similar to step-down units, with an average of 5.6 required RN hours per patient day. In general wards, available RN hours per patient day reach only 50% of required RN hours to meet patient needs. Workforce measures are comparable among unit-clusters, and average missed nursing care is 21%. Patient outcomes vary among unit-clusters. Conclusion:Patient acuity is similar among unit-clusters, whilst nurse staffing coverage is halved in general wards. While RN education, expertise and missed care are comparable among unitclusters, mortality, skin injuries and risk of family compassion fatigue rates are higher in general wards. Implications for nursing management: Nurse managers play a pivotal role in hustling policy-makers to address structural understaffing in general wards, to maximize patient safety outcomes

Long Noncoding RNA NIHCOLE Promotes Ligation Efficiency of DNA Double-Strand Breaks in Hepatocellular Carcinoma

[Abstract] Long noncoding RNAs (lncRNA) are emerging as key players in cancer as parts of poorly understood molecular mechanisms. Here, we investigated lncRNAs that play a role in hepatocellular carcinoma (HCC) and identified NIHCOLE, a novel lncRNA induced in HCC with oncogenic potential and a role in the ligation efficiency of DNA double-stranded breaks (DSB). NIHCOLE expression was associated with poor prognosis and survival of HCC patients. Depletion of NIHCOLE from HCC cells led to impaired proliferation and increased apoptosis. NIHCOLE deficiency led to accumulation of DNA damage due to a specific decrease in the activity of the nonhomologous end-joining (NHEJ) pathway of DSB repair. DNA damage induction in NIHCOLE-depleted cells further decreased HCC cell growth. NIHCOLE was associated with DSB markers and recruited several molecules of the Ku70/Ku80 heterodimer. Further, NIHCOLE putative structural domains supported stable multimeric complexes formed by several NHEJ factors including Ku70/80, APLF, XRCC4, and DNA ligase IV. NHEJ reconstitution assays showed that NIHCOLE promoted the ligation efficiency of blunt-ended DSBs. Collectively, these data show that NIHCOLE serves as a scaffold and facilitator of NHEJ machinery and confers an advantage to HCC cells, which could be exploited as a targetable vulnerability.[Significance] This study characterizes the role of lncRNA NIHCOLE in DNA repair and cellular fitness in HCC, thus implicating it as a therapeutic target.This work was supported by the European FEDER funding (to the activities of the groups directed by P. Fortes, O. Llorca, and F. Moreno-Herrero) and grants from the Ministry of Economy and Competitiveness [SAF2015-70971-R to P. Fortes and BFU2017-83794-P (AEI/FEDER, UE) to F. Moreno-Herrero)]; MCIU/AEI/FEDER/UE (RTI2018-101759-B-I00 to P. Fortes), NIH program (CA92584 to S.P. Lees-Miller), Ligue National Contre le Cancer, Équipe Labellisée and ITMO Cancer: Consortium HETCOLI (to J. Zucman-Rossi), NIH program (P01CA092584 to G. Williams), NSERC (RGPIN-2018-04327 to G. Williams), and CFI (RCP-18-023-SEG to G. Williams), Gobierno de Navarra (33/2015 to P. Fortes), Scientific Foundation of the Spanish Association Against Cancer (AECC IDEAS20169FORT to P. Fortes); Fondo de Investigación Sanitaria (PI19/00742 to B. Sangro), financed by the National Institute of Health Carlos III and FEDER. CNIO and CIBERehd are funded by the National Institute of Health Carlos III. J.P. Unfried was a recipient of a University of Navarra's Asociación de Amigos fellowship. L. Prats-Mari is a recipient of a PFIS fellowship (FI20/00074) by the National Institute of Health Carlos III and FSE "Investing in Your Future." This work was also funded by grants from the Autonomous Region of Madrid (Tec4Bio—S2018/NMT-4443 and NanoBioCancer—Y2018/BIO-4747 to O. Llorca and F. Moreno-Herrero) and co-funded by the European Social Fund. F. Moreno-Herrero acknowledges support from the European Research Council (ERC) under the European Union Horizon 2020 Research and Innovation Program (grant agreement 681299). The GTEx Project was supported by the NIH and by NCI, NHGRI, NHLBI, NIDA, NIMH, and NINDS.Peer reviewe

Performance of non-invasive tests and histology for the prediction of clinical outcomes in patients with non-alcoholic fatty liver disease: an individual participant data meta-analysis

BackgroundHistologically assessed liver fibrosis stage has prognostic significance in patients with non-alcoholic fatty liver disease (NAFLD) and is accepted as a surrogate endpoint in clinical trials for non-cirrhotic NAFLD. Our aim was to compare the prognostic performance of non-invasive tests with liver histology in patients with NAFLD.MethodsThis was an individual participant data meta-analysis of the prognostic performance of histologically assessed fibrosis stage (F0–4), liver stiffness measured by vibration-controlled transient elastography (LSM-VCTE), fibrosis-4 index (FIB-4), and NAFLD fibrosis score (NFS) in patients with NAFLD. The literature was searched for a previously published systematic review on the diagnostic accuracy of imaging and simple non-invasive tests and updated to Jan 12, 2022 for this study. Studies were identified through PubMed/MEDLINE, EMBASE, and CENTRAL, and authors were contacted for individual participant data, including outcome data, with a minimum of 12 months of follow-up. The primary outcome was a composite endpoint of all-cause mortality, hepatocellular carcinoma, liver transplantation, or cirrhosis complications (ie, ascites, variceal bleeding, hepatic encephalopathy, or progression to a MELD score ≥15). We calculated aggregated survival curves for trichotomised groups and compared them using stratified log-rank tests (histology: F0–2 vs F3 vs F4; LSM: 2·67; NFS: 0·676), calculated areas under the time-dependent receiver operating characteristic curves (tAUC), and performed Cox proportional-hazards regression to adjust for confounding. This study was registered with PROSPERO, CRD42022312226.FindingsOf 65 eligible studies, we included data on 2518 patients with biopsy-proven NAFLD from 25 studies (1126 [44·7%] were female, median age was 54 years [IQR 44–63), and 1161 [46·1%] had type 2 diabetes). After a median follow-up of 57 months [IQR 33–91], the composite endpoint was observed in 145 (5·8%) patients. Stratified log-rank tests showed significant differences between the trichotomised patient groups (p<0·0001 for all comparisons). The tAUC at 5 years were 0·72 (95% CI 0·62–0·81) for histology, 0·76 (0·70–0·83) for LSM-VCTE, 0·74 (0·64–0·82) for FIB-4, and 0·70 (0·63–0·80) for NFS. All index tests were significant predictors of the primary outcome after adjustment for confounders in the Cox regression.InterpretationSimple non-invasive tests performed as well as histologically assessed fibrosis in predicting clinical outcomes in patients with NAFLD and could be considered as alternatives to liver biopsy in some cases

Structural insights into nonsense-mediated mRNA decay (NMD) by electron microscopy

7 pag.; 3 figs.Nonsense-mediated mRNA decay (NMD) is a pathway that detects and degrades mRNAs containing premature translation termination codons (PTCs). In humans, recognition of these aberrant mRNAs requires an exon-junction-complex (EJC) placed downstream of a PTC and the dynamic interaction of several UPF/SMG proteins, the ribosome and the EJC. These interactions promote UPF1 phosphorylation by SMG1 kinase, triggering mRNA degradation. Recent progress in our understanding of NMD has been achieved by combining cryo-electron microscopy, high-resolution structures, interaction data and functional assays. These studies uncovered a mechanism regulating SMG1 kinase as well as the architecture and functional implications of a complex containing UPF1, UPF2, UPF3 and EJC. Collectively these findings reveal the role of protein scaffolds and conformational changes in NMD regulation.This work was funded by the Spanish Government (SAF2011-22988 to O.L.), the ‘Red Tematica de Investigacion Cooperativa en Cancer(RTICC)’ (RD06/0020/1001 to O.L.) and the Human Frontiers Science Program (RGP39/2008 to O.L.). O.L. acknowledges also support by the‘Ramon Areces’ Foundation.Peer reviewe