bluuebunny/crossref_metadata_2025 huggingface dataset:
Integrative view on how erythropoietin signaling controls transcription patterns in erythroid cells
Authors: Perreault Andrea A. , Venters Bryan J.
Published: February 2018

Purpose of review

Erythropoietin (EPO) is necessary and sufficient to trigger dynamic transcriptional patterns that drive the differentiation of erythroid precursor cells into mature, enucleated red cells. Because the molecular cloning and Food and Drug Administration approval for the therapeutic use of EPO over 30 years ago, a detailed understanding of how EPO works has advanced substantially. Yet, the precise epigenetic and transcriptional mechanisms by which EPO signaling controls erythroid expression patterns remains poorly understood. This review focuses on the current state of erythroid biology in regards to EPO signaling from human genetics and functional genomics perspectives.

Recent findings

The goal of this review is to provide an integrative view of the gene regulatory underpinnings for erythroid expression patterns that are dynamically shaped during erythroid differentiation. Here, we highlight vignettes connecting recent insights into a genome-wide association study linking an EPO mutation to anemia, a study linking EPO-signaling to signal transducer and activator of transcription 5 (STAT5) chromatin occupancy and enhancers, and studies that examine the molecular mechanisms driving topological chromatin organization in erythroid cells.

The genetic, epigenetic, and gene regulatory mechanisms underlying how hormone signal transduction influences erythroid gene expression remains only partly understood. A detailed understanding of these molecular pathways and how they intersect with one another will provide the basis for novel strategies to treat anemia and potentially other hematological diseases. As new regulators and signal transducers of EPO-signaling continue to emerge, new clinically relevant targets may be identified that improve the specificity and effectiveness of EPO therapy.
Familial hypercholesterolemia: experience from France
Authors: Rabès Jean-Pierre , Béliard Sophie , Carrié Alain
Published: February 2018

Purpose of review

We provide an overview of molecular diagnosis for familial hypercholesterolemia in France including descriptions of the mutational spectrum, polygenic susceptibility and perspectives for improvement in familial hypercholesterolemia diagnosis.

Recent findings

Molecular testing for familial hypercholesterolemia is recommended for patients with a LDL-cholesterol level above 190 mg/dl (adults) associated with criteria related to personal and family history of hypercholesterolemia and premature cardiovascular disease. Among the 3381 index cases included with these characteristics in the French registry for familial hypercholesterolemia, 2054 underwent molecular diagnosis and 1150 (56%) were found to have mutations (93.5% in LDL Receptor (LDLR), 4.7% in apolipoprotein B and 1.8% in Proprotein convertase subtilisin/kexin type 9). A total of 416 different pathogenic variants were found in the LDLR gene. Based on gene score calculation, a polygenic origin may be suggested in 36% of nonmutated patients. Involvement of genetic counselors and education of healthcare professionals for genetics of familial hypercholesterolemia are underway with the aim of improving the efficiency of the diagnosis.

Genetic cascade screening for familial hypercholesterolemia is currently implemented in France with the complexity to address the diversity of its molecular cause in index cases. Optimization of patient care pathways is critical to improve both the rate of diagnosis and the management of familial hypercholesterolemia patients.
Survey on the Adherence to the 2009 NASPGHAN‐ESPGHAN Gastroesophageal Reflux Guidelines by Brazilian Paediatricians
Authors: Vieira Sarah Cristina Fontes , Gurgel Flavia Matos , Leão Maria Zuleide , Costa‐Silva Tiê Emídio , Barreto Ikaro Daniel de Carvalho , Martins‐Filho Paulo Ricardo Saquete , Vieira Mário César , Gurgel Ricardo Queiroz
Published: February 2018

Objective:

The aim of the study was to evaluate the management of gastroesophageal reflux in children among Brazilian pediatricians and adherence to the 2009 North American Society of Pediatric Gastroenterology, Hepatology, and Nutrition (NASPGHAN), and European Society of Gastroenterology, Hepatology, and Nutrition (ESPGHAN) Guideline in Brazil.

Methods:

An observational cross‐sectional study was conducted, applying a standard questionnaire with 12 questions about gastroesophageal reflux (GER) and gastroesophageal reflux disease (GERD) management in infants, children, and adolescents to the pediatricians during the 37th Brazilian Pediatrics Congress in October, 2015. Adherence to the 2009 NASPGHAN‐ESPGHAN Guideline was verified through analyses of interviewees’ answers. Pediatricians’ demographic and professional characteristics were screened.

Results:

A total of 390 Brazilian pediatricians answered the questionnaire. None showed complete adherence to Guideline recommendations. GERD diagnosis by history alone was reported by 67%, irrespective of the child's age. The mean score for diagnostic adherence to the guidelines was 0.94 ± 0.86 (range 0–4). Working in public health services (P = 0.026) was the only variable retained as a significant predictor of poor adherence for GER/GERD diagnosis after multivariate logistic regression analysis. No significant statistical differences were found between Brazilian regions on total score (P = 0.774). Proton pump inhibitors were prescribed by 28.4% of the pediatricians independent of child's age, and 59% use proton pump inhibitors to treat babies with unexplained crying and/or distressed behavior.

Conclusions:

2009 NASPGHAN‐ESPGHAN Guideline recommendations had poor adherence by Brazilian pediatricians. Studies evaluating the reasons for the poor adherence to NASPGHAN/ESPGHAN guidelines are urgently needed.
Impact of Relational Coordination on Nurse Job Satisfaction, Work Engagement and Burnout
Authors: Havens Donna Sullivan , Gittell Jody Hoffer , Vasey Joseph
Published: February 2018

AIM

To explore how relational coordination, known to enhance quality and efficiency outcomes for patients and hospitals, impacts direct care nurse outcomes such as burnout, work engagement, and job satisfaction, addressing the “Quadruple Aim,” to improve the experience of providing care.

BACKGROUND

Hospitals are complex organizations in which multiple providers work interdependently, under conditions of uncertainty and time constraints, to deliver safe quality care despite differences in specialization, training, and status. Relational coordination—communicating and relating for the purpose of task integration—is known to improve quality, safety, and efficiency under these conditions, but less is known about its impact on the well-being of direct care providers themselves.

METHODS

Surveys measuring relational coordination among nurses and other types of providers as well as job-related outcomes in 5 acute care community hospitals were completed by direct care RNs.

RESULTS

Relational coordination was significantly related to increased job satisfaction, increased work engagement, and reduced burnout.

CONCLUSIONS

Relational coordination contributes to the well-being of direct care nurses, addressing the Quadruple Aim by improving the experience of providing care.
Psychological Stress and Mitochondria: A Conceptual Framework
Authors: Picard Martin , McEwen Bruce S.
Published: February 2018

Background

The integration of biological, psychological, and social factors in medicine has benefited from increasingly precise stress response biomarkers. Mitochondria, a subcellular organelle with its own genome, produce the energy required for life and generate signals that enable stress adaptation. An emerging concept proposes that mitochondria sense, integrate, and transduce psychosocial and behavioral factors into cellular and molecular modifications. Mitochondrial signaling might in turn contribute to the biological embedding of psychological states.

Methods

A narrative literature review was conducted to evaluate evidence supporting this model implicating mitochondria in the stress response, and its implementation in behavioral and psychosomatic medicine.

Results

Chronically, psychological stress induces metabolic and neuroendocrine mediators that cause structural and functional recalibrations of mitochondria, which constitutes mitochondrial allostatic load. Clinically, primary mitochondrial defects affect the brain, the endocrine system, and the immune systems that play a role in psychosomatic processes, suggesting a shared underlying mechanistic basis. Mitochondrial function and dysfunction also contribute to systemic physiological regulation through the release of mitokines and other metabolites. At the cellular level, mitochondrial signaling influences gene expression and epigenetic modifications, and modulates the rate of cellular aging.

Conclusions

This evidence suggests that mitochondrial allostatic load represents a potential subcellular mechanism for transducing psychosocial experiences and the resulting emotional responses—both adverse and positive—into clinically meaningful biological and physiological changes. The associated article in this issue of Psychosomatic Medicine presents a systematic review of the effects of psychological stress on mitochondria. Integrating mitochondria into biobehavioral and psychosomatic research opens new possibilities to investigate how psychosocial factors influence human health and well-being across the life-span.
Uncomplicated 90Y Selective Internal Radio Therapy in a Patient With Hepatocellular Carcinoma After Arterial and Portal Vein Embolizations
Authors: van der Pol Jochem , de Vos-Geelen Judith , Bucerius Jan , Mitea Cristina , van der Leij Christiaan
Published: February 2018

Selective internal radio therapy (SIRT) with 90Y-glass microspheres was performed in a cirrhotic patient with hepatocellular carcinoma (Barcelona Clinic Liver Cancer stage C) after arterial coil embolization for treatment of intratumoral hemorrhage and planned preoperative right portal vein embolization. Three technetium 99mTc macro-albumin-aggregate injections were needed to optimize intralesional uptake without extrahepatic deposition. The consecutive SIRT treatment was uncomplicated with a remarkable result.
Metabolic Changes in Central Poststroke Pain Following Thalamic Intracerebral Hemorrhage
Authors: Kim Na Young , Lee Sang Chul , An Young-sil , Shin Ji-Cheol , Kim Yong Wook
Published: February 2018

Purpose

Central poststroke pain (CPSP) is one of the most refractory neuropathic pains following stroke. Injury in the spinothalamic pathway appears crucial for the development of CPSP, but changes in activity in multiple brain regions may also be related. We investigated brain metabolic changes in patients with CPSP following thalamic intracerebral hemorrhage (ICH).

Methods

Forty-three patients with thalamic ICH were examined. Overall brain metabolism was measured with 18F-FDG PET. Images were analyzed with statistical parametric mapping (SPM12). Patients with CPSP (n = 20) were compared with patients without CPSP (n = 23). In addition, the association between regional brain metabolism and the severity of CPSP was investigated.

Results

In comparison to patients in the non-CPSP group, the CPSP group exhibited significant hypometabolism in the ipsilesional precentral, postcentral gyri, and the contralesional cuneus (P
uncorrected < 0.001), whereas significant hypermetabolism was found in the medial dorsal nucleus of the contralesional thalamus (P
uncorrected < 0.001). In addition, brain metabolism in the ipsilesional Crus I and Crus II of the cerebellum was positively correlated to pain intensity ratings (P
uncorrected < 0.001).

Conclusion

Our findings suggested that an altered state of resting brain metabolism in various brain regions related to sensory processing and cognitive functioning may be involved in the underlying mechanism of CPSP following thalamic ICH.
Safety and Efficacy of Rituximab: Experience of a Single Multiple Sclerosis Center
Authors: Alldredge Brett , Jordan Allison , Imitola Jaime , Racke Michael K.
Published: February 2018

Objectives

Multiple sclerosis (MS) is an immune-mediated disease of the central nervous system. B cells play an important pathogenic role in MS. Rituximab (RTX), a B-cell depleting drug, has been used to treat MS and neuromyelitis optica (NMO). Patient characteristics, safety, and efficacy measures are reviewed to ascertain the therapeutic benefit and safety of RTX in a real-world setting with long-term follow-up.

Methods

This is a retrospective chart review of patients who received RTX at The Ohio State University's MS clinic from January 2005 to October 2016.

Results

Of the 64 patient charts reviewed, 23 had a relapsing remitting MS, 17 had primary progressive MS (PPMS), and 24 had NMO. In the relapsing remitting MS cohort, there was an annual relapse rate of 0.005 and 87% were reported as clinically stable at the end of the chart review period. In the primary progressive MS cohort, 47% were reported as clinically stable at the end of the chart review period. In the NMO cohort, there was an annual relapse rate of 0.0074 and 79% were reported as clinically stable at the end of the chart review period. A total of 29 infusion reactions were reported in 21 patients. None were serious and only 1 patient elected to stop RTX due to an adverse event.

Conclusions

Rituximab demonstrated good tolerability and efficacy in cases of both relapsing and progressive forms of MS and NMO.
Molecular determinants of Yellow Fever Virus pathogenicity in Syrian Golden Hamsters: one mutation away from virulence
Authors: Klitting Raphaëlle , Roth Laura , Rey Félix A. , de Lamballerie Xavier
Published: February 2018

Yellow fever virus (Flavivirusgenus) is an arthropod-borne pathogen which can infect humans, causing a severe viscerotropic disease with a high mortality rate. Adapted viral strains allow the reproduction of yellow fever disease in hamsters with features similar to the human disease. Here, we used the Infectious Subgenomic Amplicons reverse genetics method to produce an equivalent to the hamster-virulent strain, Yellow FeverAp7, by introducing a set of 4 synonymous and 6 non-synonymous mutations into a single subgenomic amplicon, derived from the sequence of theAsibistrain. The resulting strain, Yellow FeverAp7M, induced a disease similar to that described forAp7in terms of symptoms, weight evolution, viral loads in the liver and lethality. Using the same methodology, we produced mutant strains derived from eitherAp7MorAsibiviruses and investigated the role of each ofAp7Mnon-synonymous mutations in itsin vivophenotype. This allowed identifying key components of the virulence mechanism in hamsters. InAp7Mvirus, the reversion of either E/Q27H or E/D155A mutations, led to an important reduction of both virulence andin vivoreplicative fitness. In addition, the introduction of the single D155AAp7Mmutation within the E protein of theAsibivirus was sufficient to drastically modify its phenotype in hamsters towards both a greater replication efficiency and virulence. Finally, inspection of theAsibistrain E protein structure combined toin vivotesting revealed the importance of an exposed α-helix in domain I, containing residues 154 and 155, forAp7Mvirulence in hamsters.
Next generation CRISPR/Cas9 transcriptional activation inDrosophilausing flySAM
Authors: Jia Yu , Xu Rong-Gang , Ren Xingjie , Ewen-Campen Ben , Rajakumar Rajendhran , Zirin Jonathan , Yang-Zhou Donghui , Zhu Ruibao , Wang Fang , Mao Decai , Peng Ping , Qiao Huan-Huan , Wang Xia , Liu Lu-Ping , Xu Bowen , Ji Jun-Yuan , Liu Qingfei , Sun Jin , Perrimon Norbert , Ni Jian-Quan
Published: February 2018

CRISPR/Cas9-based transcriptional activation (CRISPRa) has recently emerged as a powerful and scalable technique for systematic over-expression genetic analysis inDrosophila melanogaster.We present flySAM, a potent new tool forin vivoCRISPRa, which offers a major improvement over existing strategies in terms of effectiveness, scalability, and ease-of-use. flySAM outperforms existingin vivoCRISPRa strategies, and approximates phenotypes obtained using traditional Gal4-UAS over-expression. Further, because flySAM typically only requires a single sgRNA, it dramatically improves scalability. We use flySAM to demonstrate multiplexed CRISPRa, which has not been previously shownin vivo.In addition, we have simplified the experimental usage of flySAM by creating a single vector encoding both the UAS:Cas9-activator and the sgRNA, allowing for inducible CRISPRa in a single genetic cross. flySAM will thus replace previous CRISPRa strategies as the basis of our growing genome-wide transgenic over-expression resource, TRiP-OE.
A Gender-Dependent Molecular Switch of Inflammation via MyD88/Estrogen Receptor-alpha Interaction
Authors: El Sabeh Rana , Bonnet Mélanie , Le Corf Katy , Lang Kevin , Kfoury Alain , Badran Bassam , Hussein Nader , Virard François , Treilleux Isabelle , Le Romancer Muriel , Lebecque Serge , Manié Serge , Coste Isabelle , Renno Toufic
Published: February 2018

Most Toll-like receptors and IL-1/IL-18 receptors activate a signaling cascade via the adaptor molecule MyD88, resulting in NF-κB activation and inflammatory cytokine and chemokine production. Females are less susceptible than males to inflammatory conditions, presumably due to protection by estrogen. Here we show that MyD88 interacts with a methylated, cytoplasmic form of estrogen receptor-alpha (methER-α). This interaction is required for NF-κB transcriptional activity and pro-inflammatory cytokine production, and is dissociated by estrogen. Importantly, we show a strong gender segregation in gametogenic reproductive organs, with MyD88/methER-α interactions found in testicular tissues and in ovarian tissues from menopausal women, but not in ovaries from women age 49 and less -suggesting a role for estrogen in disrupting this complex in situ. Collectively, our results indicate that the formation of MyD88/methER-α complexes during inflammatory signaling and their disruption by estrogen may represent a mechanism that contributes to gender bias in inflammatory responses.
Cross-type Biomedical Named Entity Recognition with Deep Multi-Task Learning
Authors: Wang Xuan , Zhang Yu , Ren Xiang , Zhang Yuhao , Zitnik Marinka , Shang Jingbo , Langlotz Curtis , Han Jiawei
Published: February 2018

Motivation

State-of-the-art biomedical named entity recognition (BioNER) systems often require handcrafted features specific to each entity type, such as genes, chemicals and diseases. Although recent studies explored using neural network models for BioNER to free experts from manual feature engineering, the performance remains limited by the available training data for each entity type.

Results

We propose a multi-task learning framework for BioNER to collectively use the training data of different types of entities and improve the performance on each of them. In experiments on 15 benchmark BioNER datasets, our multi-task model achieves substantially better performance compared with state-of-the-art BioNER systems and baseline neural sequence labeling models. Further analysis shows that the large performance gains come from sharing character- and word-level information among relevant biomedical entities across differently labeled corpora.

Availability

Our source code is available athttps://github.com/yuzhimanhua/lm-lstm-crf.

Contact

xwang174@illinois.edu,xiangren@usc.edu.
Exploratory re-encoding of Yellow Fever Virus genome: new insights for the design of live-attenuated viruses
Authors: Klitting R. , Riziki T. , Moureau G. , Piorkowski G. , Gould E. A. , de Lamballerie X.
Published: February 2018

Virus attenuation by genome re-encoding is a pioneering approach for generating effective live-attenuated vaccine candidates. Its core principle is to introduce a large number of synonymous substitutions into the viral genome to produce stable attenuation of the targeted virus. Introduction of large numbers of mutations has also been shown to maintain stability of the attenuated phenotype by lowering the risk of reversion and recombination of re-encoded genomes. Identifying mutations with low fitness cost is pivotal as this increases the number that can be introduced and generates more stable and attenuated viruses. Here, we sought to identify mutations with low deleterious impact on thein vivoreplication and virulence of yellow fever virus (YFV). Following comparative bioinformatic analyses of flaviviral genomes, we categorized synonymous transition mutations according to their impact on CpG/UpA composition and secondary RNA structures. We then designed 17 re-encoded viruses with 100-400 synonymous mutations in the NS2A-to-NS4B coding region of YFVAsibiandAp7M(hamster-adapted) genomes. Each virus contained a panel of synonymous mutations designed according to the above categorisation criteria. The replication and fitness characteristics of parent and re-encoded viruses were comparedin vitrousing cell culture competition experiments.In vivolaboratory hamster models were also used to compare relative virulence and immunogenicity characteristics. Most of the re-encoded strains showed no decrease in replicative fitnessin vitro. However, they showed reduced virulence and, in some instances, decreased replicative fitnessin vivo. Importantly, the most attenuated of the re-encoded strains induced robust, protective immunity in hamsters following challenge withAp7M, a virulent virus. Overall, the introduction of transitions with no or a marginal increase in the number of CpG/UpA dinucleotides had the mildest impact on YFV replication and virulencein vivo. Thus, this strategy can be incorporated in procedures for the finely tuned creation of substantially re-encoded viral genomes.
Ethical Shades of Gray: Questionable Research Practices in Health Professions Education
Authors: Artino Anthony R. , Driessen Erik W. , Maggio Lauren A.
Published: February 2018

Purpose

To maintain scientific integrity and engender public confidence, research must be conducted responsibly. Whereas scientific misconduct, like data fabrication, is clearly irresponsible and unethical, other behaviors—often referred to as questionable research practices (QRPs)—exploit the ethical shades of gray that color acceptable practice. This study aimed to measure the frequency of self-reported QRPs in a diverse, international sample of health professions education (HPE) researchers.

Method

In 2017, the authors conducted an anonymous, cross-sectional survey study. The web-based survey contained 43 QRP items that asked respondents to rate how often they had engaged in various forms of scientific misconduct. The items were adapted from two previously published surveys.

Results

In total, 590 HPE researchers took the survey. The mean age was 46 years (SD=11.6), and the majority of participants were from the United States (26.4%), Europe (23.2%), and Canada (15.3%). The three most frequently reported QRPs were adding authors to a paper who did not qualify for authorship (60.6%), citing articles that were not read (49.5%), and selectively citing papers to please editors or reviewers (49.4%). Additionally, respondents reported misrepresenting a participant’s words (6.7%), plagiarizing (5.5%), inappropriately modifying results (5.3%), deleting data without disclosure (3.4%), and fabricating data (2.4%). Overall, 533 (90.3%) respondents reported at least one QRP.

Conclusions

Notwithstanding the methodological limitations of survey research, these findings indicate that a substantial proportion of HPE researchers report a range of QRPs. In light of these results, reforms are needed to improve the credibility and integrity of the HPE research enterprise.

“Researchers should practice research responsibly. Unfortunately, some do not.” –Nicholas H. Steneck, 20061
KLF6 and STAT3 co-occupy regulatory DNA and functionally synergize to promote axon growth in CNS neurons
Authors: Wang Zimei , Mehra Vatsal , Simpson Matthew.T. , Maunze Brian , Holan Lyndsey , Eastwood Erik , Blackmore Murray G. , Venkatesh Ishwariya
Published: February 2018

Members of the KLF family of transcription factors can exert both positive and negative effects on axon regeneration in the central nervous system, but the underlying mechanisms are unclear. KLF6 and −7 share nearly identical DNA binding domains and stand out as the only known growth-promoting family members. Here we confirm that similar to KLF7, expression of KLF6 declines during postnatal cortical development and that forced re-expression of KLF6 in corticospinal tract neurons of adult female mice enhances axon regeneration after cervical spinal injury. Unlike KLF7, however, these effects were achieved with wildtype KLF6, as opposed constitutively active mutants, thus simplifying the interpretation of mechanistic studies. To clarify the molecular basis of growth promotion, RNA sequencing identified 454 genes whose expression changed upon forced KLF6 expression in cortical neurons. Network analysis of these genes revealed sub-networks of downregulated genes that were highly enriched for synaptic functions, and sub-networks of upregulated genes with functions relevant to axon extension including cytoskeleton remodeling, lipid synthesis and transport, and bioenergetics. The promoter regions of KLF6-sensitive genes showed enrichment for the binding sequence of STAT3, a previously identified regeneration-associated gene. Notably, co-expression of constitutively active STAT3 along with KLF6 in cortical neurons produced synergistic increases in neurite length. Finally, genome-wide ATAC-seq footprinting detected frequent co-binding by the two factors in pro-growth gene networks, indicating co-occupancy as an underlying mechanism for the observed synergy. These findings advance understanding of KLF-stimulated axon growth and indicate functional synergy of KLF6 transcriptional effects with those of STAT3.

SIGNIFICANCE STATEMENT

The failure of axon regeneration in the CNS limits recovery from damage and disease. These findings show the transcription factor KLF6 to be a potent promoter of axon growth after spinal injury, and more importantly clarify the underlying transcriptional changes. In addition, bioinformatics analysis predicted a functional interaction between KLF6 and a second transcription factor, STAT3, and genome-wide footprinting confirmed frequent co-occupancy. Co-expression of the two factors yielded synergistic elevation of neurite growth in primary neurons. These data point the way toward novel transcriptional interventions to promote CNS regeneration.
Human POMC processing in vitro and in vivo revealed by quantitative peptidomics
Authors: Kirwan Peter , Kay Richard , Brouwers Bas , Herranz-Perez Vicente , Jura Magdalena , Larraufie Pierre , Pembroke Jason , Bartels Theresa , White Anne , Gribble Fiona , Reimann Frank , Farooqi I. Sadaf , O’Rahilly Stephen , Merkle Florian T.
Published: February 2018

Human obesity can result from the aberrant production or processing of proopiomelanocortin (POMC) in hypothalamic neurons, but it is unclear which human POMC-derived peptides are most relevant to body weight regulation. To address this question, we analysed both hypothalamic neurons derived from human pluripotent stem cells (hPSCs) and primary human hypothalamic tissue using quantitative liquid chromatography tandem mass spectroscopy (LC-MS/MS). In both in vitro- and in vivo-derived samples, we found that POMC was processed into β-melanocyte stimulating hormone (β-MSH), whose existence in the human brain has been controversial. β-MSH and desacetyl α-MSH (d-α-MSH) were produced at roughly equimolar concentrations and in vast excess to acetylated α-MSH (5-to 200-fold), suggesting that the importance of both d-α-MSH and β-MSH to human obesity has been underestimated. Since body weight is sensitive to changes in MSH concentration, we asked whether hPSC-derived hypothalamic neurons could provide mechanistic insights into the processing and secretion of MSH peptides. We found that cultured human hypothalamic neurons appropriately trafficked POMC and its derivatives, and robustly (P<0.0001) secreted them when depolarised. Furthermore, the adipocyte-derived hormone leptin significantly (P<0.01) promoted their production of both d-α-MSH and β-MSH. These results establish hPSC-derived hypothalamic neurons as a model system for studying human-specific aspects of POMC processing that might be therapeutically harnessed to treat obesity.
Fragile X mental retardation protein is a size-dependent translational activator
Authors: Greenblatt Ethan J. , Spradling Allan C.
Published: February 2018

FMR1 enhances translation of large neural/oocyte proteins

Mutations in the highly conservedFragile X mental retardation gene (Fmr1)cause the most common inherited human intellectual disability/autism spectrum disorder.Fmr1is also needed for ovarian follicle development, and lesions are the largest genetic cause of premature ovarian failure (POF). FMR1 associates with ribosomes and is thought to repress translation, but identifying functional targets has been difficult. We analyzed FMR1’s role in quiescentDrosophilaoocytes stored prior to ovulation, cells that depend entirely on translation of stored mRNA. Ribosome profiling revealed that in quiescent oocytes FMR1 stimulates the translation of large proteins, including at least twelve proteins whose human homologs are associated with dominant intellectual disability disorders, and 25 others associated with neural dysfunction. Knockdown of Fmr1 in unstored oocytes did not affect embryo development, but more than 50% of embryos derived from stored oocytes lacking FMR1 developed severe neural defects. Fmr1’s previously unappreciated role promoting the translation of large proteins from stored mRNAs in oocytes and neurons may underlie POF as well as multiple aspects of neural dysfunction.
Rbfox splicing factors maintain skeletal muscle mass by regulating calpain3 and proteostasis
Authors: Singh Ravi K. , Kolonin Arseniy M. , Fiorotto Marta L. , Cooper Thomas A.
Published: February 2018

Alternative splicing promotes proteomic diversity important for cellular differentiation and cell fate determination. Here, we show that deletion of the highly conserved Rbfox1 and Rbfox2 alternative splicing regulators in adult mouse skeletal muscle causes rapid, severe loss of muscle mass. Homeostasis of skeletal muscle tissue requires a dynamic balance between protein synthesis and degradation (proteostasis) but the mechanisms that regulate this balance are not well understood. Rbfox deletion did not cause reduced global protein synthesis, but resulted in reduced autophagy flux and altered splicing of hundreds of transcripts including Capn3, which produced an active form of calpain3 protease. The results indicate Rbfox proteins regulate proteostasis in skeletal muscle tissue by control of calpain and autophagy-lysosome pathways.

Highlights

Proteostasis in adult skeletal muscle is post-transcriptionally regulated, in part by alternative splicing via Rbfox1/2

Rbfox1/2 regulate hundreds of targets in skeletal muscle, including Calpn3, to maintain muscle mass in adult mice

Autophagy flux is markedly decreased in muscle lacking Rbfox1/2

As for neurons, altered proteostasis is detrimental to adult muscle
Ferroptosis-like signaling facilitates a potent innate defense againstPlasmodiuminfection
Authors: Kain Heather S. , Arang Nadia , Glennon Elizabeth K. , Douglass Alyse N. , Dudgeon Denali R. , Johnson Jarrod S. , Aderem Alan , Kaushansky Alexis
Published: February 2018

The facets of host control duringPlasmodiumliver infection remain largely unknown and conventional innate regulatory pathways are only minimally effective at eliminating parasites1-3. Ferroptosis, a recently described form of iron-dependent cell death that drives accumulation of reactive oxygen species and lipid peroxides, but has not yet been shown to function as an innate immune response4,5. Inducing ferroptosis with pharmacologicals or by genetic perturbation of its negative regulators, GPX4 and SLC7a11, dramatically reduces survival of thePlasmodiumLiver Stage. In contrast, knockdown or knockout of NOX1 or knockdown of TFR1, which are required for ferroptosis, increases the number of Liver Stage parasites. Moreover, we demonstrate that blocking ferroptosis renders parasite-infected hepatocytes resistant to P53-mediated hepatocyte death. Our work establishes that ferroptotic signaling serves to controlPlasmodiuminfection in the liver and raises the possibility that ferroptosis operates as an axis of the innate immune system to defend against intracellular pathogens.
DNA Topoisomerase I differentially modulates R-loops across the human genome
Authors: Manzo Stefano Giustino , Hartono Stella Regina , Sanz Lionel A. , De Biasi Sara , Cossarizza Andrea , Capranico Giovanni , Chedin Frederic
Published: February 2018

Background

Co-transcriptional R-loops are abundant non-B DNA structures in mammalian genomes. DNA Topoisomerase I (Top1) is often thought to regulate R-loop formation owing to its ability to resolve both positive and negative supercoils. How Top1 regulates R-loop structures at a global level is unknown.

Results

Here, we performed high-resolution strand-specific R-loop mapping in human cells depleted for Top 1 and found that Top1 depletion resulted in both R-loop gains and losses at thousands of transcribed loci, delineating two distinct gene classes. R-loop gains were characteristic for long, highly transcribed, genes located in gene-poor regions anchored to Lamin B1 domains and in proximity to H3K9me3-marked heterochromatic patches. R-loop losses, by contrast, occurred in gene-rich regions overlapping H3K27me3-marked active replication initiation regions. Interestingly, Top1 depletion coincided with a block of the cell cycle in G0/G1 phase and a trend towards replication delay.

Conclusions

Our findings reveal new properties of Top1 in regulating R-loop homeostasis and suggest a potential role for Top1 in controlling replication initiation via R-loop formation.
Structural and histone binding studies of the chromo barrel domain of TIP60
Authors: Zhang Yuzhe , Lei Ming , Liang Xiao , Loppnau Peter , Li Yanjun , Min Jinrong , Liu Yanli
Published: February 2018

TIP60 consists of an N-terminal chromo barrel domain (TIP60-CB) and a C-terminal acetyltransferase domain and acetylates histone and non-histone proteins within diverse cellular processes. Whereas the TIP60-CB is thought to recognize histone tails, molecular details of this interaction remain unclear. Here we attempted a quantitative analysis of the interaction between the TIP60-CB and histone peptides, but did not observe any binding through either fluorescence polarization or isothermal titration calorimetry. We solved a crystal structure of the TIP60-CB alone. Analysis of the crystal structure demonstrates a putative peptide binding site that may be occluded by the basic side chain of a residue in a unique β hairpin between the two N-terminal strands of the β barrel.
CALISTA: Clustering and Lineage Inference in Single-Cell Transcriptional Analysis
Authors: Gao Nan Papili , Hartmann Thomas , Fang Tao , Gunawan Rudiyanto
Published: February 2018

We present CALISTA (Clustering and Lineage Inference in Single-Cell Transcriptional Analysis), a numerically efficient and highly scalable toolbox for an end-to-end analysis of single-cell transcriptomic profiles. CALISTA includes four essential single-cell analyses for cell differentiation studies, including single-cell clustering, reconstruction of cell lineage specification, transition gene identification, and pseudotemporal cell ordering. In these analyses, we employ a likelihood-based approach where single-cell mRNA counts are described by a probabilistic distribution function associated with stochastic gene transcriptional bursts and random technical dropout events. We evaluated the performance of CALISTA by analyzing single-cell gene expression datasets from in silico simulations and various single-cell transcriptional profiling technologies, comprising a few hundreds to tens of thousands of cells. A comparison with existing single-cell expression analyses, including MONOCLE 2 and SCANPY, demonstrated the superiority of CALISTA in reconstructing cell lineage progression and ordering cells along cell differentiation paths. CALISTA is freely available on https://www.cabselab.com/calista.
cisTEM: User-friendly software for single-particle image processing
Authors: Grant Tim , Rohou Alexis , Grigorieff Nikolaus
Published: February 2018

We have developed new open-source software called cisTEM (computational imaging system for transmission electron microscopy) for the processing of data for high-resolution electron cryo-microscopy and single-particle averaging. cisTEM features a graphical user interface that is used to submit jobs, monitor their progress, and display results. It implements a full processing pipeline including movie processing, image defocus determination, automatic particle picking, 2D classification, ab-initio 3D map generation from random parameters, 3D classification, and high-resolution refinement and reconstruction. Some of these steps implement newly-developed algorithms; others were adapted from previously published algorithms. The software is optimized to enable processing of typical datasets (2000 micrographs, 200k - 300k particles) on a high-end, CPU-based workstation in half a day or less, comparable to GPU-accelerated processing. Jobs can also be scheduled on large computer clusters using flexible run profiles that can be adapted for most computing environments. cisTEM is available for download from cistem.org.
An Investigation of Detection Biases in the Unattended Periphery During Simulated Driving
Authors: Kingsley Li Musen , Lau Hakwan , Odegaard Brian
Published: February 2018

While people often think they veridically perceive much of the visual surround, recent findings indicate that when asked to detect targets such as gratings embedded in visual noise, observers make more false alarms in the unattended periphery. Do these results from psychophysics studies generalize to naturalistic settings? We used a modern game engine to create a simulated driving environment where participants (as drivers) had to make judgments about the colors of pedestrians’ clothing in the periphery. Confirming our hypothesis based on previous psychophysics studies, we found that subjects showed liberal biases for unattended locations when detecting specific colors of pedestrians’ clothing. A second experiment showed that this finding was not simply due to a confirmation bias in decision-making when subjects were uncertain. Together, these results support the idea that in everyday visual experience, there is subjective inflation of experienced detail in the periphery, which may happen at the decisional level.
Partially Overlapping Brain Networks for Singing and Cello Playing
Authors: Segado Melanie , Hollinger Avrum , Thibodeau Joseph , Penhune Virginia , Zatorre Robert J.
Published: February 2018

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This research uses an MR-Compatible cello to compare functional brain activation during singing and cello playing within the same individuals to determine the extent to which arbitrary auditory-motor associations, like those required to play the cello, co-opt functional brain networks that evolved for singing. Musical instrument playing and singing both require highly specific associations between sounds and movements. However, vocal motor control is an evolutionarily old human trait and the auditory-motor associations used for singing are also used for speech and nonspeech vocalizations. This sets it apart from the arbitrary auditory-motor associations required to play musical instruments. The pitch range of the cello is similar to that of the human voice, but cello playing is completely independent of the vocal apparatus and can therefore be used to dissociate the auditory-vocal network from that of the auditory-motor network. While in the MR-Scanner, 11 expert cellists listened to and subsequently produced individual tones either by singing or cello playing. All participants were able to sing and play the target tones in tune (within 50Cents). We found that brain activity during cello playing directly overlaps with brain activity during singing in many areas within the auditory-vocal network. These include primary motor, dorsal pre-motor, and supplementary motor cortices, the primary and periprimary auditory cortices within the superior temporal gyrus including Heschl’s gyrus, anterior insula, anterior cingulate cortex, and intraparietal sulcus, and cerebellum but, notably, exclude the periaqueductal grey and basal ganglia. Second, we found that activity within the overlapping areas is positively correlated with, and therefore likely contributing to, both singing and playing in tune determined with performance measures. Third, we found that activity in auditory areas is functionally connected with activity in dorsal motor and pre-motor areas, and that the connectivity between them is positively correlated with good performance on this task. This functional connectivity suggests that the brain areas are working together to contribute to task performance and not just coincidently active. Last, our findings showed that cello playing may directly co-opt vocal areas (including larynx area of motor cortex), especially if musical training begins before age 7.
Protein synthesis controls phosphate homeostasis
Authors: Pontes Mauricio H. , Groisman Eduardo A.
Published: February 2018

Phosphorus is an essential element assimilated largely as orthophosphate (Pi). Cells respond to Pi starvation by importing Pi from their surroundings. We now report that impaired protein synthesis alone triggers a Pi starvation response even when Pi is plentiful in the extracellular milieu. In the bacteriumSalmonella entericaserovar Typhimurium,this response entails phosphorylation of the regulatory protein PhoB and transcription of PhoB-dependent Pi transporter genes and is eliminated upon stimulation of adenosine triphosphate (ATP) hydrolysis. When protein synthesis is impaired due to low cytoplasmic magnesium (Mg2+),Salmonellatriggers the Pi starvation response because ribosomes are destabilized, which reduces ATP consumption and thus free cytoplasmic Pi. This response is transient because low cytoplasmic Mg2+promotes an uptake in Mg2+and a decrease in ATP levels, which stabilizes ribosomes, resulting in ATP consumption and Pi increase, thus ending the response. Notably, pharmacological inhibition of protein synthesis also elicited a Pi starvation response in the bacteriumEscherichia coliand the yeastSaccharomyces cerevisiae. Our findings identify a regulatory connection between protein synthesis and Pi homeostasis that is widespread in nature.
Genetic Interaction Score (S-Score) Calculation, Clustering, and Visualization of Genetic Interaction Profiles for Yeast
Authors: Roguev Assen , Ryan Colm J. , Xu Jiewei , Colson Isabelle , Hartsuiker Edgar , Krogan Nevan
Published: February 2018

This protocol describes computational analysis of genetic interaction screens, ranging from data capture (plate imaging) to downstream analyses. Plate imaging approaches using both digital camera and office flatbed scanners are included, along with a protocol for the extraction of colony size measurements from the resulting images. A commonly used genetic interaction scoring method, calculation of the S-score, is discussed. These methods require minimal computer skills, but some familiarity with MATLAB and Linux/Unix is a plus. Finally, an outline for using clustering and visualization software for analysis of resulting data sets is provided.
Complement-Dependent Cytotoxicity Assay
Authors: Duensing Thomas D. , Watson Susan R.
Published: February 2018

A useful feature of therapeutic antibodies is the ability to kill the cells to which they bind. Antibodies are capable of mediating cell killing in a variety of ways. Apoptosis, complement-mediated mechanisms, and antibody-dependent cellular cytotoxicity are all effects that can be assayed to characterize lead antibody candidates. Extensive, multidose characterizations of a series of candidates can be performed in a short amount of time using assays developed for high-throughput flow cytometry systems. Antibodies that contain the Fc portion of the human IgG1 can activate complement-mediated cell death. One way in which they do this is via direct complement killing of tumor cells by the membrane attack complex, a process usually called complement-dependent cytotoxicity.
Preparation of Antisense Oligonucleotides to Inhibit miRNA Function
Authors: Li Chengjian , Zamore Phillip D.
Published: February 2018

This protocol is used to design antisense oligonucleotides (ASOs) for specific inhibition of miRNA function in cultured cells. The incorporation of 2′-O-methyl-modifications in ASOs enhances their potency and resistance to degradation, whereas 3′-terminal cholesterol-conjugation facilitates delivery of ASOs into cells.
Inhibiting miRNA Function by Antisense Oligonucleotides in Cultured Mammalian Cells
Authors: Li Chengjian , Zamore Phillip D.
Published: February 2018

Methods for transfecting antisense oligonucleotides (ASOs) into mammalian cells for suppression of miRNA function are described in this protocol. The effects of ASOs on the miRNA are evaluated by measuring the protein level of the putative miRNA target or the activity of a reporter bearing a 3′ untranslated region (3′ UTR) derived from the putative miRNA target.
Maximum-likelihood determination of anomalous substructures
Authors: Read Randy J. , McCoy Airlie J.
Published: February 2018

A fast Fourier transform (FFT) method is described for determining the substructure of anomalously scattering atoms in macromolecular crystals that allows successful structure determination by X-ray single-wavelength anomalous diffraction (SAD). This method is based on the maximum-likelihood SAD phasing function, which accounts for measurement errors and for correlations between the observed and calculated Bijvoet mates. Proof of principle is shown that this method can improve determination of the anomalously scattering substructure in challenging cases where the anomalous scattering from the substructure is weak but the substructure also constitutes a significant fraction of the real scattering. The method is deterministic and can be fast compared with existing multi-trial dual-space methods for SAD substructure determination.
Distributed computing for macromolecular crystallography
Authors: Krissinel Evgeny , Uski Ville , Lebedev Andrey , Winn Martyn , Ballard Charles
Published: February 2018

Modern crystallographic computing is characterized by the growing role of automated structure-solution pipelines, which represent complex expert systems utilizing a number of program components, decision makers and databases. They also require considerable computational resources and regular database maintenance, which is increasingly more difficult to provide at the level of individual desktop-basedCCP4 setups. On the other hand, there is a significant growth in data processed in the field, which brings up the issue of centralized facilities for keeping both the data collected and structure-solution projects. The paradigm of distributed computing and data management offers a convenient approach to tackling these problems, which has become more attractive in recent years owing to the popularity of mobile devices such as tablets and ultra-portable laptops. In this article, an overview is given of developments by CCP4 aimed at bringing distributed crystallographic computations to a wide crystallographic community.
Unleashing apprenticeship: from onboarding to professional development
Authors: Moon Hanna
Published: February 2018

Purpose

The purpose of this paper is to explore the process and activities of apprenticeship from onboarding to professional development.

Design/methodology/approach

Literature was reviewed to highlight the important characteristics of cognitive and collaborative apprenticeship, onboarding and professional development.

Findings

The conceptual model was developed to identify the specific activities of apprenticeship at the onboarding, developmental and proficient phases.

Originality/value

This study enlightens the aspects of the way in which apprentices can make adjustments to their organizations and become proficient workforces.