A quantitative literature-curated gold standard for kinase-substrate pairs

We describe the Yeast Kinase Interaction Database (KID, http://www.moseslab.csb.utoronto.ca/KID/), which contains high- and low-throughput data relevant to phosphorylation events. KID includes 6,225 low-throughput and 21,990 high-throughput interactions, from greater than 35,000 experiments. By quantitatively integrating these data, we identified 517 high-confidence kinase-substrate pairs that we consider a gold standard. We show that this gold standard can be used to assess published high-throughput datasets, suggesting that it will enable similar rigorous assessments in the future

Overall and sex-specific associations between fetal adversity and child development at age 1 year : evidence from Brazil

A growing body of epigenetic research suggests that in-utero adaptations to environmental changes display important sex-specific variation. We tested this heterogeneous adaptation hypothesis using data from 900 children born at the University Hospital in São Paulo, Brazil, between October 2013 and April 2014. Crude and adjusting linear models were used to quantify the associations between prematurity, being small for gestational age, and children's physical and mental development at 12 months of age. Prematurity was negatively associated with neuropsychological development in final models (z score difference, -0.42, 95% confidence intervals: -0.71, -0.14), but associations did not vary significantly by sex. For being small for gestational age, associations with height-for-age, weight-for-age, and neuropsychological development were also negative, but they were systematically larger for male than for female infants (P < 0.05 for all). These results suggest that male fetuses may be more vulnerable to intrauterine adversity than female fetuses. Further research will be needed to better understand the mechanisms underlying these sex-specific associations

RNA-binding proteins ZFP36L1 and ZFP36L2 promote cell quiescence.

Progression through the stages of lymphocyte development requires coordination of the cell cycle. Such coordination ensures genomic integrity while cells somatically rearrange their antigen receptor genes [in a process called variable-diversity-joining (VDJ) recombination] and, upon successful rearrangement, expands the pools of progenitor lymphocytes. Here we show that in developing B lymphocytes, the RNA-binding proteins (RBPs) ZFP36L1 and ZFP36L2 are critical for maintaining quiescence before precursor B cell receptor (pre-BCR) expression and for reestablishing quiescence after pre-BCR-induced expansion. These RBPs suppress an evolutionarily conserved posttranscriptional regulon consisting of messenger RNAs whose protein products cooperatively promote transition into the S phase of the cell cycle. This mechanism promotes VDJ recombination and effective selection of cells expressing immunoglobulin-μ at the pre-BCR checkpoint.This work was funded by the Biotechnology and Biological Sciences Research Council, a Medical Research Council CASE studentship with GSK, an MRC centenary award (A.G) and project grants from Bloodwise. DJH was supported by a Medical Research Council Clinician Scientist FellowshipThis is the author accepted manuscript. The final version is available from the American Association for the Advancement of Science via http://dx.doi.org/10.1126/science.aad597

OSBP-related protein-2 (ORP2) : a novel Akt effector that controls cellular energy metabolism

ORP2 is a ubiquitously expressed OSBP-related protein previously implicated in endoplasmic reticulum (ER)lipid droplet (LD) contacts, triacylglycerol (TG) metabolism, cholesterol transport, adrenocortical steroidogenesis, and actin-dependent cell dynamics. Here, we characterize the role of ORP2 in carbohydrate and lipid metabolism by employing ORP2-knockout (KO) hepatoma cells (HuH7) generated by CRISPR-Cas9 gene editing. The ORP2-KO and control HuH7 cells were subjected to RNA sequencing, analyses of Akt signaling, carbohydrate and TG metabolism, the extracellular acidification rate, and the lipidome, as well as to transmission electron microscopy. The loss of ORP2 resulted in a marked reduction of active phosphorylated Akt(Ser473) and its target Glycogen synthase kinase 3(Ser9), consistent with defective Akt signaling. ORP2 was found to form a physical complex with the key controllers of Akt activity, Cdc37, and Hsp90, and to co-localize with Cdc37 and active Akt(Ser473) at lamellipodial plasma membrane regions, in addition to the previously reported ER-LD localization. ORP2-KO reduced glucose uptake, glycogen synthesis, glycolysis, mRNA-encoding glycolytic enzymes, and SREBP-1 target gene expression, and led to defective TG synthesis and storage. ORP2-KO did not reduce but rather increased ER-LD contacts under basal culture conditions and interfered with their expansion upon fatty acid loading. Together with our recently published work (Kentala et al. in FASEB J 32:1281-1295, 2018), this study identifies ORP2 as a new regulatory nexus of Akt signaling, cellular energy metabolism, actin cytoskeletal function, cell migration, and proliferation.Peer reviewe

A computational platform for high-throughput analysis of RNA sequences and modifications by mass spectrometry

Abstract: The field of epitranscriptomics continues to reveal how post-transcriptional modification of RNA affects a wide variety of biological phenomena. A pivotal challenge in this area is the identification of modified RNA residues within their sequence contexts. Mass spectrometry (MS) offers a comprehensive solution by using analogous approaches to shotgun proteomics. However, software support for the analysis of RNA MS data is inadequate at present and does not allow high-throughput processing. Existing software solutions lack the raw performance and statistical grounding to efficiently handle the numerous modifications found on RNA. We present a free and open-source database search engine for RNA MS data, called NucleicAcidSearchEngine (NASE), that addresses these shortcomings. We demonstrate the capability of NASE to reliably identify a wide range of modified RNA sequences in four original datasets of varying complexity. In human tRNA, we characterize over 20 different modification types simultaneously and find many cases of incomplete modification

A computational platform for high-throughput analysis of RNA sequences and modifications by mass spectrometry

Abstract: The field of epitranscriptomics continues to reveal how post-transcriptional modification of RNA affects a wide variety of biological phenomena. A pivotal challenge in this area is the identification of modified RNA residues within their sequence contexts. Mass spectrometry (MS) offers a comprehensive solution by using analogous approaches to shotgun proteomics. However, software support for the analysis of RNA MS data is inadequate at present and does not allow high-throughput processing. Existing software solutions lack the raw performance and statistical grounding to efficiently handle the numerous modifications found on RNA. We present a free and open-source database search engine for RNA MS data, called NucleicAcidSearchEngine (NASE), that addresses these shortcomings. We demonstrate the capability of NASE to reliably identify a wide range of modified RNA sequences in four original datasets of varying complexity. In human tRNA, we characterize over 20 different modification types simultaneously and find many cases of incomplete modification

Contemporary Tendencies in Mediation

Editors: Humberto dalla Bernardina de Pinho, Juliana Loss de AndradePresentation / Humberto Dalla Bernardina de Pinho, Juliana Loss de Andrade. -- Mediation in England / Neil Andrews. -- Un Reto para la Mediación: el Diseño de su Código Deontológico / Nuria Belloso Martín. -- Alternative Dispute Resolution and Aboriginal-Crown Reconciliation in Canada / Roshan Danesh, Jessica Dickson. -- A False ‘Prince Charming’ Keeps ‘Sleeping Beauty’ in a Coma: On Voluntary Mediation Being the True Oxymoron of Dispute Resolution Policy / Giuseppe De Palo. -- Programa de Derivación Judicial en Puerto Rico Desde la Perspectiva de la Mediación / Jacqueline N. Font-Guzmán. -- Mediation in Switzerland / Isabelle Hering. -- Reconocimiento y eficacia de los acuerdos de mediación mercantil internacional / Juliana Loss de Andrade. -- The Uses of Mediation / Lela P. Love, Joseph B. Stulberg. -- Multi-Dimensional Mediation / Paul E. Mason. -- “Italy Is Doing It – Should We Be?” Civil and Commercial Mediation in Italy / Giovanni Matteucci. -- Limites dos Meios Alternativos de Conflito / José Marinho Paulo Junior. -- New Perspectives of Civil and Commercial Mediation in Brazil / Humberto Dalla Bernardina de Pinho. -- Practical Impacts of Theoretical Lenses / Elton Simoes, Andrea Maia. -- Development and Resistance in South Europe Justice Systems to Restorative Justice / Helena Soleto Muño

Escalada terapêutica: uma possibilidade de intervenção para crianças com paralisia cerebral

A escalada terapêutica, uma adaptação da “Escalada Esportiva”, pode promover melhoria da coordenação motora, do equilíbrio e resistência muscular. Objetivo: Avaliar o efeito dessa intervenção na força de preensão manual, controle postural, mobilidade funcional e controle da espasticidade de crianças com paralisia cerebral. Método: Estudo do tipo série de casos, descritivo, com 7 pacientes com idade de 9,6 ± 3,7 anos, que passaram por sessões de escalada terapêutica, 1 hora/sessão, duas vezes/semana. Resultados: Após 19 sessões foi verificado aumento de força na mão direita (p = 0,022) e melhoria do equilíbrio estático e da marcha (p = 0,007). Observou-se também melhora da mobilidade funcional (p = 0,014). O escore na escala Ashworth modificada mostrou controle eficiente da espasticidade, ainda que a diferença não tenha atingido significância estatística. Conclusão: A escalada terapêutica melhorou a força de preensão manual, o controle postural e a mobilidade funcional dos pacientes.Therapeutic climbing, an adaptation of sport climbing, can promote improvements in motor coordination, balance, and muscle endurance. Objective: The aim of this study was to evaluate the effects of this intervention on handgrip strength, postural control, functional mobility, and the spasticity control of children with cerebral palsy. Method: Case series study with 7 patients with a mean age of 9.6 ± 3.7 years, who took part in 1-hour sessions of therapeutic climbing twice a week. Results: After 19 sessions, there was an increase in handgrip strength of the right hand (p = 0.022) and improvement in static balance and gait (p = 0.007). Functional mobility also improved significantly (p = 0.014). The score on the Ashworth modified scale showed an efficient control of spasticity, although the difference has not reached statistical significance. Conclusion: Therapeutic climbing improved the handgrip strength, postural control, and functional mobility of patients