bluuebunny/crossref_metadata_2025 huggingface dataset:
Videography in Pediatric Emergency Research
Authors: Kerrey Benjamin T. , O'Connell Karen J. , Myers Sage R. , Rinderknecht Andrea S. , Frey Mary E. , Dyas Jenna R. , Boyd Stephanie , Mak Allison L. , Cochrane Niall , Donoghue Aaron J.
Published: August 2018

Objectives

High-quality clinical research of resuscitations in a pediatric emergency department is challenging because of the limitations of traditional methods of data collection (chart review, self-report) and the low frequency of cases in a single center. To facilitate valid and reliable research for resuscitations in the pediatric emergency department, investigators from 3 pediatric centers, each with experience completing successful single-center, video-based studies, formed the Videography In Pediatric Emergency Research (VIPER) collaborative.

Methods

Our initial effort was the development of a multicenter, video-based registry and simulation-based testing of the feasibility and reliability of the VIPER registry. Feasibility of data collection was assessed by the frequency of an indeterminate response for all data elements in the registry. Reliability was assessed by the calculation of Cohen κ for dichotomous data elements and intraclass correlation coefficients for continuous data elements.

Results

Video-based data collection was completed for 8 simulated pediatric resuscitations, with at least 2 reviewers per case. Data were labeled as indeterminate by at least 1 reviewer for 18 (3%) of 524 relevant data fields. The Cohen κ for all dichotomous data fields together was 0.81 (95% confidence interval, 0.61–1.0). For all continuous (time–based) variables combined, the intraclass correlation coefficient was 0.88 (95% confidence interval, 0.70–0.96).

Conclusions

Initial simulation-based testing suggests video-based data collection using the VIPER registry is feasible and reliable. Our next step is to assess feasibility and reliability for actual pediatric resuscitations and to complete several prospective, hypothesis-based studies of specific aspects of resuscitative care, including of cardiopulmonary resuscitation, tracheal intubation, and teamwork and communication.
A National Patient Safety Curriculum in Pediatric Emergency Medicine
Authors: Stankovic Curt , Wolff Meg , Chang Todd P , Macias Charles
Published: August 2018

Background

Patient safety has become an important and required topic in medical education. A needs assessment showed that pediatric emergency medicine program directors were interested in a common pediatric emergency-specific safety curriculum.

Objective

The objective of this study was to describe the development and performance of a web-based patient safety curriculum in pediatric emergency medicine.

Methods

A web-based curriculum was created by the Committee on Quality Transformation of the Section of Emergency Medicine for the American Academy of Pediatrics. The curriculum consisted of emergency-specific safety topic didactic sessions with a pretest and posttest assessment. Vignette-based scenarios were also included and were discussed locally by the program directors.

Results

Fifty-two percent (37/71) of US Pediatric Emergency Medicine fellowship programs enrolled their fellows in the patient safety curriculum. Overall, 183 Pediatric Emergency Medicine fellows participated in the curriculum. Only 22% (40/183) of fellow participants completed the entire curriculum. The curriculum showed significant improved safety knowledge based upon the pretest and posttest results. Sixty-five percent of responders thought more about safety topics after the curriculum was completed, and 85% witnessed a safety event in the past month, whereas only 48% reported them.

Conclusions

An online centralized curriculum is an effective platform for teaching content in quality and safety to a national group of physicians. Local oversight by program directors may improve compliance with curriculum completion.
Acute Hemorrhagic Edema of Infancy With Associated Hemorrhagic Lacrimation
Authors: Sneller Hannah , Vega Carolina , Zemel Lawrence , Chicaiza Henry P.
Published: August 2018

Acute hemorrhagic edema of infancy is a rare leukocytoclastic vasculitis that affects infants and children aged 4 to 24 months. We report a case of a 5-month-old girl with purpuric lesions with associated hemorrhagic lacrimation and epistaxis.
Outcome and Complications following Vertical Rectus Abdominis Myocutaneous Flap Surgery to Reconstruct Sacrectomy Defects
Authors: Houdek Matthew T. , Bakri Karim , Tibbo Meagan E. , Wagner Eric R. , Rose Peter S. , Sim Franklin H. , Moran Steven L.
Published: August 2018

Background:

The vertical rectus abdominis myocutaneous flap has been used to reliably reconstruct posterior soft-tissue defects following resection of high sacral tumors, providing skin and soft-tissue bulk. Current literature examining the use of these flaps for high sacral reconstruction is limited. The purpose of this study was to report the authors’ institution's outcome on the use of the vertical rectus abdominis myocutaneous flap to reconstruct a high sacral defect following an oncologic resection.

Methods:

Eighty-seven patients (29 female and 58 male) underwent vertical rectus abdominis myocutaneous flap surgery to reconstruct a posterior wound following high sacral tumor resection from 1994 to 2016. The mean age and body mass index were 52 years and 27.8 kg/m2, respectively. The mean follow-up was 6 years.

Results:

Sixty-eight patients (79 percent) sustained a complication, most commonly a wound complication [n = 41 (47 percent)]. Twenty patients (23 percent) sustained a donor-site wound complication, most commonly a wound dehiscence (n = 10). Complications resulted in a reoperation in 44 patients (51 percent), with total flap failure occurring in one (1 percent). Preoperative radiotherapy and obesity were found to increase the risk of wound complications (p = 0.004 and p = 0.02, respectively) and deep infection (p = 0.03 and p = 0.02, respectively).

Conclusions:

Complications were common following vertical rectus abdominis myocutaneous flap surgery; however, total flap loss was not. Patients with obesity and preoperative radiotherapy should be cautioned on their increased risk of complications. Currently, the vertical rectus abdominis myocutaneous flap is the authors’ preferred means of soft-tissue reconstruction following high sacral tumor resection.

CLINICAL QUESTION/LEVEL OF EVIDENCE:

Therapeutic, IV.
Vulnerabilities at First Sex and Their Association With Lifetime Gender-Based Violence and HIV Prevalence Among Adolescent Girls and Young Women Engaged in Sex Work, Transactional Sex, and Casual Sex in Kenya
Authors: Becker Marissa L. , Bhattacharjee Parinita , Blanchard James F. , Cheuk Eve , Isac Shajy , Musyoki Helgar K. , Gichangi Peter , Aral Sevgi , Pickles Michael , Sandstrom Paul , Ma Huiting , Mishra Sharmistha ,   on behalf of the Transitions Study Team
Published: August 2018

Background:

Adolescent girls and young women (AGYW) experience high rates of HIV early in their sexual life course. We estimated the prevalence of HIV-associated vulnerabilities at first sex, and their association with lifetime gender-based violence (GBV) and HIV.

Methods:

We conducted a cross-sectional biobehavioral survey among AGYW (14–24 years) in Mombasa, Kenya in 2015. We compared the prevalence of first sex vulnerabilities across AGYW who self-identified as engaging in sex work (N = 408), transactional sex (N = 177), or casual sex (N = 714) and used logistic regression to identify age-adjusted associations between first sex vulnerabilities and outcomes (GBV after first sex; HIV).

Results:

The median age at first sex was 16 years (interquartile range 14–18). A total of 43.6% received gifts or money at first sex; 41.2% and 11.2% experienced a coerced and forced first sex, respectively. First sex vulnerabilities were generally more common among AGYW in sex work. GBV (prevalence 23.8%) and HIV (prevalence 5.6%) were associated with first sex before age 15 [GBV adjusted odds ratio (AOR) 1.4, 95% confidence interval (CI): 1.0 to 1.9; HIV AOR 1.9, 95% CI: 1.1 to 1.3]; before or within 1 year of menarche (GBV AOR 1.3, 95% CI: 1.0 to 1.7; HIV AOR 2.1, 95% CI: 1.3 to 3.6); and receipt of money (GBV AOR 1.9, 95% CI: 1.4 to 2.5; HIV AOR 2.0, 95% CI: 1.2 to 3.4).

Conclusions:

HIV-associated vulnerabilities begin at first sex and potentially mediate an AGYW's trajectory of risk. HIV prevention programs should include structural interventions that reach AGYW early, and screening for a history of first sex vulnerabilities could help identify AGYW at risk of ongoing GBV and HIV.
Addition of Anti-CD40 Monoclonal Antibody to Nonmyeloablative Conditioning With Belatacept Abrogated Allograft Tolerance Despite Induction of Mixed Chimerism
Authors: Oura Tetsu , Hotta Kiyohiko , Rosales Ivy , Dehnadi Abbas , Kawai Kent , Lee Hang , Benedict Cosimi A. , Kawai Tatsuo
Published: August 2018

Background

We recently reported anti-CD40 monoclonal antibody and rapamycin (aCD40/rapa) to be a reliable, nontoxic, immunosuppressive regimen for combined islet and kidney transplantation (CIKTx) in nonhuman primates. In the current study, we attempted to induce allograft tolerance through the mixed chimerism approach using a conditioning regimen with aCD40 and belatacept (Bela).

Methods

Five CIKTx or kidney transplant alone recipients were treated with aCD40/rapa for 4 months. All recipients then received a conditioning regimen including horse antithymocyte globulin and aCD40/Bela. The results were compared with previous reports of recipients treated with Bela-based regimens.

Results

All 3 CIKTx recipients developed mixed chimerism, which was significantly superior to that observed in the previous Bela-based studies. Nevertheless, all CIKTx recipients in this study lost their islet and renal allografts as a result of cellular and humoral rejection on days 140, 89, and 84. The 2 kidney transplant-alone recipients were treated with the same conditioning regimen and suffered rejection on days 127 and 116, despite the development of excellent chimerism. B lymphocyte reconstitution dominated by memory phenotypes was associated with early development of donor-specific antibodies in 4 of 5 recipients. In vitro assays showed no donor-specific regulatory T cell expansion, which has been consistently observed in tolerant recipients with our mixed chimerism approach.

Conclusions

Despite displaying excellent immunosuppressive efficacy, costimulatory blockade with anti-CD40 monoclonal antibody (2C10R4) may inhibit the induction of renal or islet allograft tolerance via a mixed chimerism approach.
Codon pair bias deoptimization of the major oncogene meq of a very virulent Marek’s disease virus
Authors: Khedkar Pratik Hemant , Osterrieder Nikolaus , Kunec Dusan
Published: August 2018

Codon pair bias deoptimization (CPBD) has been successfully used to attenuate several RNA viruses. CPBD involves recoding a viral protein-coding sequence to maximize the number of codon pairs that are statistically underrepresented in the host, which presumably slows protein translation and, hence, causes virus attenuation. However, since recoding preserves the amino acid composition and codon bias, attenuated and parental viruses are antigenically identical. To determine if Marek’s disease virus (MDV), a highly oncogenic herpesvirus of the chicken with a large double-stranded DNA genome, can be attenuated by CPBD of its major oncogene meq, we recoded the gene to minimize (meq-D), maximize (meq-O), or preserve (meq-R) the level of codon pairs that are overrepresented in the chicken protein-coding sequences. Unexpectedly, mutants carrying recoded genes produced comparable or increased levels of Meq in the context of viral infection in cultured cells. In addition, parental virus and mutant viruses carrying recoded meq genes replicated with comparable kinetics in vitro and in vivo, and were equally virulent in susceptible chickens. In summary, CPBD of meq failed to produce any quantifiable attenuation of MDV and confirms differences in the complexity of applying CPBD to large DNA viruses versus RNA viruses.
Unbiased Age-Appropriate Structural Brain Atlases for Chinese Pediatrics
Authors: Zhao Tengda , Liao Xuhong , Fonov Vladimir S. , Men Weiwei , Wang Yanpei , Qin Shaozheng , Tan Shuping , Gao Jia-Hong , Evans Alan , Tao Sha , Dong Qi , He Yong
Published: August 2018

In magnetic resonance imaging (MRI) studies of children brain development, structural brain atlases usually serve as important references of pediatric population in which individual images are spatially normalized into a common or standard stereotactic space. However, the existing popular children brain atlases (e.g., National Institutes of Health pediatric atlases, NIH-PD atlases) are made mostly based on MR images from Western populations, and are thus insufficient to characterize the brains of Chinese children due to the neuroanatomical differences that are relevant to genetic and environmental factors. By collecting high-quality T1- and T2- weighted MR images from 328 typically developing Chinese children aged from 6 to 12 years old, we created a set of age-appropriate Chinese pediatric (CHN-PD) atlases using an unbiased template construction algorithm. The CHN-PD atlases included the head/brain templates, the symmetric brain template, the gender-specific brain templates and the corresponding tissue probability atlases. Moreover, the atlases contained multiple age-specific templates with a one-year interval. A direct comparison of the CHN-PD and the NIH-PD atlases revealed remarkable anatomical differences bilaterally in the lateral frontal and parietal regions and somatosensory cortex. While applying the CHN-PD atlases to two independent Chinese pediatric datasets (N = 114 and N = 71, respectively), machine-learning regression approaches revealed higher prediction accuracy on brain ages than the usage of NIH-PD atlases. These results suggest that the CHN-PD brain atlases are necessary and important for future typical and atypical developmental studies in Chinese pediatric population. Currently, the CHN-PD atlases have been released on the NITRC website (https://www.nitrc.org/projects/chn-pd).
Atlas of Neuromuscular Organization in the Ctenophore, Pleurobrachia bachei (A. Agassiz, 1860)
Authors: Moroz Leonid L , Norekian Tigran P
Published: August 2018

Enigmatic ctenophores are descendants of one of the earliest branching metazoan lineage. Their nervous systems are equally elusive. The lack of convenient neurogenic molecules and neurotransmitters suggests an extensive parallel evolution and independent origins of neurons and synapses. However, the field is logged behind due to the lack of microanatomical data about the neuro-muscular systems in this group of animals. Here, using immunohistochemistry and scanning electron microscopy, we describe the organization of both muscular and nervous systems in the sea gooseberry, Pleurobrachia bachei, from North Pacific. The diffused neural system of Pleurobrachia consists of two subsystems: the subepithelial neural network and the mesogleal net with about 5000-7000 neurons combined. Our data revealed the unprecedented complexity of neuromuscular organization in this basal metazoan lineage. The anatomical diversity of cell types includes at least nine broad categories of neurons, five families of surface receptors and more than two dozen types of muscle cells as well as regional concentrations of neuronal elements to support ctenophore feeding, complex swimming, escape and prey capture behaviors. In summary, we recognize more than 80 total morphological cell types. Thus, in terms of cell type specification and diversity, ctenophores significantly exceed what we currently know about other prebilaterian groups (placozoan, sponges, and cnidarians), and some basal bilaterians.
Enlarged and highly repetitive plastome of Lagarostrobos and plastid phylogenomics of Podocarpaceae
Authors: Sudianto Edi , Wu Chung-Shien , Leonhard Lars , Martin William F. , Chaw Shu-Miaw
Published: August 2018

Podocarpaceae is the largest family in cupressophytes (conifers II), but their plastid genomes (plastomes) are poorly studied, with plastome data currently existing for only four of the 19 Podocarpaceous genera. In this study, we assembled the plastomes from representatives of eight additional genera, including Afrocarpus, Dacrydium, Lagarostrobos, Lepidothamnus, Microstrobos, Phyllocladus, Prumnopitys, and Saxegothaea. We found that Lagarostrobos, a monotypic genus native to Tasmania, has the largest plastome among any cupressophytes studied to date (151,496 bp). Plastome enlargement in Lagarostrobos coincides with increased intergenic spacers, repeats, and duplicated genes. Among Podocarpaceae, Lagarostrobos has the most rearranged plastome, but its substitution rates are modest. Plastid phylogenomic analyses clarify the positions of previously conflicting Podocarpaceous genera. Tree topologies firmly support the division of Podocarpaceae into two sister clades: (1) the Prumnopityoid clade and (2) the clade containing Podocarpoid, Dacrydioid, Microstrobos, and Saxegothaea. The Phyllocladus is nested within the Podocarpaceae, thus familial status of the monotypic Phyllocladaceae is not supported.
Generation of highly diverse peptide library by linear-double-stranded DNA based AND gate genetic circuit in mammalian cells
Authors: Li Shuai , Su Weijun , Zhang Chunze
Published: August 2018

DNA-encoded peptide libraries are ideal functional peptide discovery platforms for their extremely large capacity. However, it’s still difficult to build high content peptide library in intact mammalian cells, which offer advantages associated with appropriate protein modification, proper protein folding, and natural status of membrane protein. Our previous work established linear-double-stranded DNAs (ldsDNAs) as innovative biological parts to implement AND gate genetic circuits in mammalian cell line. In the current study, we employ ldsDNA with terminal NNK degenerate codons as AND gate input to build highly diverse peptide library in mammalian cells. This ldsDNA-based AND gate (LBAG) peptide strategy is easy to conduct, only PCR reaction and cell transfection experiments are needed. High-throughput sequencing (HTS) results reveal that our new LBAG strategy could generate peptide library with both amino acid sequence and peptide length diversities. Moreover, by a mammalian cell two-hybrid system, we pan an MDM2 protein interacting peptide through the LBAG peptide library. Our work establishes ldsDNA as biological parts for building highly diverse peptide library in mammalian cells.
To block or not to block: the adaptive manipulation of plague transmission
Authors: Gandon S. , Heitzmann L. , Sebbane F.
Published: August 2018

The ability of the agent of plague,Yersinia pestis, to form a biofilm blocking the gut of the flea has been considered to be a key evolutionary step in maintaining flea-borne transmission. However, blockage decreases dramatically the life expectancy of fleas, challenging the adaptive nature of blockage. Here we develop an epidemiological model of plague that accounts for its different transmission routes, as well as the within-host competition taking place between bacteria within the flea vector. We use this theoretical framework to identify the environmental conditions promoting the evolution of blockage. We also show that blockage is favored at the onset of an epidemic, and that the frequencies of bacterial strains exhibiting different strategies of blockage can fluctuate in seasonal environments. This analysis quantifies the contribution of different transmission routes in plague and makes testable predictions on the adaptive nature of blockage.

Significance statement

Plague transmission relies on the ability of infected fleas to inoculateY. pestisbacteria to vertebrate hosts. The production of a biofilm by the bacteria blocks the forgut of the flea and increases infectivity. But the adaptive nature of blockage remains controversial because it has a massive survival cost on the infected fleas and reduces dramatically the length of the infection: an extreme form of the classical virulence-transmission tradeoff. Here we develop a comprehensive model of the multiple routes of plague transmission, we determine when blockage can be viewed as an adaptive manipulation of its flea vector and we generate several testable predictions on the evolution of plague in both endemic and epidemic situations.
Demography and behaviour of polygyne nests of the supercolonial antCataglyphis niger: Does kinship matter?
Authors: Brodetzki Tali Reiner , Brodetzki Guy , Feinerman Ofer , Hefetz Abraham
Published: August 2018

The basic ant colony is presumed to have evolved through kin selection. However, ants show a remarkable diversity in their social organization, from a monogynous-monandrous queen to the more derived states of polygyny with polyandrous queens. The existence of polygyny is an evolutionary enigma, since kin selection theory predicts that while queens should strive for reproductive monopoly, workers are predicted to favor their own matriline in rearing gynes. Using a barcoding system that enables tracking of individual interactions, along with polymorphic DNA microsatellite markers that indicate the matriline and patriline of all individuals, we demonstrate the complex social interactions in polygyne nests ofCataglyphis niger.C. nigeris not only polygyne but also constitutes a supercolony at the study site. Our pioneering findings that both queens and workers are not necessarily related to each other support the supercolony structure of the population. Also in line with supercoloniality, we demonstrate that the workers contribute equally to the nest production and rearing of the queens. Unlike invasive supercolonial species,C. nigeris native to Israel, raising questions about the driving forces, apart from kin selection, that stabilize this society.
Bclaf1 critically regulates the type I interferon response and is degraded by alphaherpesvirus US3
Authors: Qin Chao , Zhang Rui , Lang Yue , Shao Anwen , Xu Aotian , Feng Wenhai , Han Jun , Wang Mengdong , He Wanwei , Yu Cuilian , Tang Jun
Published: August 2018

Type I interferon response plays a prominent role against viral infection, which is frequently disrupted by viruses. Here, we report Bcl-2 associated transcription factor 1 (Bclaf1) is degraded during the alphaherpesvirus Pseudorabies virus (PRV) and Herpes simplex virus type 1 (HSV-1) infections through the viral protein US3. We further reveal that Bclaf1 functions critically in type I interferon signaling. Knockdown or knockout of Bclaf1 in cells significantly impairs interferon-α (IFNα)-mediated gene transcription and viral inhibition against US3 deficient PRV and HSV-1. Mechanistically, Bclaf1 maintains a mechanism allowing STAT1 and STAT2 to be efficiently phosphorylated in response to IFNα, and more importantly, facilitates IFN-stimulated gene factor 3 (ISGF3) binding with IFN-stimulated response elements (ISRE) for efficient gene transcription by directly interacting with ISRE and STAT2. Our studies establish the importance of Bclaf1 in IFNα-induced antiviral immunity and in the control of viral infections.
Dissecting splicing decisions and cell-to-cell variability with designed sequence libraries
Authors: Mikl Martin , Hamburg Amit , Pilpel Yitzhak , Segal Eran
Published: August 2018

Most human genes are alternatively spliced, allowing for a large expansion of the proteome.The multitude of regulatory inputs to splicing limits the potential to infer general principles from investigating native sequences. Here, we created a rationally designed library of >32,000 splicing events to dissect the complexity of splicing regulation through systematicsequence alterations. Measuring RNA and protein splice isoforms allowed us to investigate bothcause and effect of splicing decisions, quantify diverse regulatory inputs and accurately predict (R2=0.75–0.85) isoform ratios from sequence and secondary structure. By profiling individual cells, we measure the cell-to-cell variability of splicing decisions and show that it can be encoded in the DNA and influenced by regulatory inputs, opening the door for a novel,single-cell perspective on splicing regulation.
Quantifying biosynthetic network robustness across the human oral microbiome
Authors: Bernstein David B. , Dewhirst Floyd E. , Segrè Daniel
Published: August 2018

Metabolic interactions, such as cross-feeding, play a prominent role in microbial communitystructure. For example, they may underlie the ubiquity of uncultivated microorganisms. We investigated this phenomenon in the human oral microbiome, by analyzing microbial metabolic networks derived from sequenced genomes. Specifically, we devised a probabilistic biosynthetic network robustness metric that describes the chance that an organism could produce a given metabolite, and used it to assemble a comprehensive atlas of biosynthetic capabilities for 88 metabolites across 456 human oral microbiome strains. A cluster of organisms characterized by reduced biosynthetic capabilities stood out within this atlas. This cluster included several uncultivated taxa and three recently co-culturedSaccharibacteria(TM7) phylum species. Comparison across strains also allowed us to systematically identify specific putative metabolic interdependences between organisms. Our method, which provides a new way of converting annotated genomes into metabolic predictions, is easily extendible to other microbial communities and metabolic products.
Global cooling & the rise of modern grasslands: Revealing cause & effect of environmental change on insect diversification dynamics
Authors: Davis Katie E. , Bakewell Adam T. , Hill Jon , Song Hojun , Mayhew Peter
Published: August 2018

Utilising geo-historical environmental data to disentangle cause and effect in complex natural systems is a major goal in our quest to better understand how climate change has shaped life on Earth. Global temperature is known to drive biotic change over macro-evolutionary time-scales but the mechanisms by which it acts are often unclear. Here, we model speciation rates for Orthoptera within a phylogenetic framework and use this to demonstrate that global cooling is strongly correlated with increased speciation rates. Transfer Entropy analyses reveal the presence of one or more additional processes that are required to explain the information transfer from global temperature to Orthoptera speciation. We identify the rise of C4grasslands as one such mechanism operating from the Miocene onwards. We therefore demonstrate the value of the geological record in increasing our understanding of climate change on macro-evolutionary and macro-ecological processes.
Molecular flexibility of DNA as a key determinant of RAD51 recruitment
Authors: Paoletti Federico , El-Sagheer Afaf , Allard Jun , Brown Tom , Dushek Omer , Esashi Fumiko
Published: August 2018

The timely activation of homologous recombination is essential for the maintenance of genome stability, in which the RAD51 recombinase plays a central role. Biochemically, human RAD51 polymerises faster on single-stranded DNA (ssDNA) compared to double-stranded DNA (dsDNA), raising a key conceptual question: how does it discriminate between them? In this study, we tackled this problem by systematically assessing RAD51 binding kinetics on ssDNA and dsDNA differing in length and flexibility using surface plasmon resonance. By fitting detailed polymerisation models informed by our experimental datasets, we show that RAD51 is a mechano-sensor that exhibits a larger polymerisation rate constant on flexible ssDNA compared to rigid ssDNA or dsDNA. This model presents a new general framework suggesting that the flexibility of DNA, which may increase locally as a result of DNA damage, plays an important role in rapidly recruiting repair factors that multimerise at sites of DNA damage.
Cell Diameter inBacillus subtilisis Determined by the Opposing Actions of Two Distinct Cell Wall Synthetic Systems
Authors: Dion Michael F. , Kapoor Mrinal , Sun Yingjie , Wilson Sean , Ryan Joel , Vigouroux Antoine , Teeffelen Sven van , Oldenbourg Rudolf , Garner Ethan C.
Published: August 2018

Rod shaped bacteria grow by adding material into their cell wall via the action of two spatially distinct enzymatic systems: The Rod system moves around the cell circumference, while the class A penicillin-binding proteins (aPBPs) are unorganized. To understand how the combined action of these two systems defines bacterial dimensions, we examined how each system affects the growth and width ofBacillus subtilis, as well as the mechanical anisotropy and orientation of material within their sacculi. We find that rod diameter is not determined by MreB, rather it depends on the balance between the systems: The Rod system reduces diameter, while aPBPs increase it. RodA/PBP2A can both thin or widen cells, depending on its levels relative to MreBCD. Increased Rod system activity correlates with an increased density of directional MreB filaments, and a greater fraction of directionally moving PBP2A molecules. This increased circumferential synthesis increases the amount of oriented material within the sacculi, increasing their mechanical anisotropy and reinforcing rod shape. Together, these experiments explain how the combined action of the two main cell wall synthetic systems build rods of different widths, a model that appears generalizable:Escherichia colicontaining Rod system mutants show the same relationship between the density of directionally moving MreB filaments and cell width.
Functional dissection of theARGONAUTE7promoter
Authors: Hoyer J. Steen , Pruneda-Paz Jose L. , Breton Ghislain , Hassert Mariah A. , Holcomb Emily E. , Fowler Halley , Bauer Kaylyn M. , Mreen Jacob , Kay Steve A. , Carrington James C.
Published: August 2018

ARGONAUTES are the central effector proteins of RNA silencing which bind target transcripts in a small RNA-guided manner.Arabidopsis thalianahas tenARGONAUTE(AGO) genes, with specialized roles in RNA-directed DNA methylation, post-transcriptional gene silencing, and antiviral defense. To better understand specialization amongAGOgenes at the level of transcriptional regulation we tested a library of 1497 transcription factors for binding to the promoters ofAGO1, AGO10, andAGO7using yeast 1-hybrid assays. A ranked list of candidate DNA-binding TFs revealed binding of theAGO7promoter by a number of proteins in two families: the miR156-regulated SPL family and the miR319-regulated TCP family, both of which have roles in developmental timing and leaf morphology. Possible functions for SPL and TCP binding are unclear: we showed that these binding sites are not required for the polar expression pattern ofAGO7, nor for the function ofAGO7in leaf shape. NormalAGO7transcription levels and function appear to depend instead on an adjacent 124-bp region. Progress in understanding the structure of this promoter may aid efforts to understand how the conserved AGO7-triggeredTAS3pathway functions in timing and polarity.
Global climate changes will lead to regionally divergent trajectories for ectomycorrhizal communities in North American Pinaceae forests
Authors: Steidinger Brian S. , Bhatnagar Jennifer M. , Vilgalys Rytas , Taylor John W. , Bruns Thomas D. , Peay Kabir G.
Published: August 2018

Ectomycorrhizal fungi (ECMF) are partners in a globally distributed tree symbiosis that enhanced ecosystem carbon (C)-sequestration and storage. However, resilience of ECMF to future climates is uncertain. We sampled ECMF across a broad climatic gradient in North America, modeled climatic drivers of diversity and community composition, and then forecast ECMF response to climate changes over the next 50 years. We predict ECMF richness will decline over nearly half of North American Pinaceae forests, with median species losses as high as 21%. Mitigation of greenhouse gas emissions can reduce these declines, but not prevent them. Warming of forests along the boreal-temperate ecotone results in projected ECMF species loss and declines in the relative abundance of C demanding, long-distance foraging ECMF species, but warming of eastern temperate forests has the opposite effect. Sites with more ECMF species had higher activities of nitrogen-mineralizing enzymes, suggesting that ECMF species-losses will compromise their associated ecosystem functions.
Decoding semantic predictions from EEG prior to word onset
Authors: Heikel Edvard , Sassenhagen Jona , Fiebach Christian J.
Published: August 2018

The outstanding speed of language comprehension necessitates a highly efficient implementation of cognitive-linguistic processes. The domain-general theory of Predictive Coding suggests that our brain solves this problem by continuously forming linguistic predictions about expected upcoming input. The neurophysiological implementation of these predictive linguistic processes, however, is not yet understood. Here, we use EEG (human participants, both sexes) to investigate the existence and nature of online-generated, category-level semantic representations during sentence processing. We conducted two experiments in which some nouns – embedded in a predictive spoken sentence context – were unexpectedly delayed by 1 second. Target nouns were either abstract/concrete (Experiment 1) or animate/inanimate (Experiment 2). We hypothesized that if neural prediction error signals following (temporary) omissions carry specific information about the stimulus, the semantic category of the upcoming target word is encoded in brain activity prior to its presentation. Using time-generalized multivariate pattern analysis, we demonstrate significant decoding of word category from silent periods directly preceding the target word, in both experiments. This provides direct evidence for predictive coding during sentence processing, i.e., that information about a word can be encoded in brain activity before it is perceived. While the same semantic contrast could also be decoded from EEG activity elicited by isolated words (Experiment 1), the identified neural patterns did not generalize to pre-stimulus delay period activity in sentences. Our results not only indicate that the brain processes language predictively, but also demonstrate the nature and sentence-specificity of category-level semantic predictions preactivated during sentence comprehension.

STATEMENT OF SIGNIFICANCE

The speed of language comprehension necessitates a highly efficient implementation of cognitive-linguistic processes. Predictive processing has been suggested as a solution to this problem, but the underlying neural mechanisms and linguistic content of such predictions are only poorly understood. Inspired by Predictive Coding theory, we investigate whether the meaning of expected, but not-yet heard words can be decoded from brain activity. Using EEG, we can predict if a word is, e.g., abstract (as opposed to concrete), or animate (vs. inanimate), from brain signals preceding the word itself. This strengthens predictive coding theory as a likely candidate for the principled neural mechanisms underlying online processing of language and indicates that predictive processing applies to highly abstract categories like semantics.
Gene silencing by double-stranded RNA fromC. elegansneurons reveals functional mosaicism of RNA interference
Authors: Ravikumar Snusha , Devanapally Sindhuja , Jose Antony M
Published: August 2018

Delivery of double-stranded RNA (dsRNA) into animals can silence genes of matching sequence in diverse cell types through mechanisms that have been collectively called RNA interference. In the nematodeC. elegans, dsRNA from multiple sources can trigger the amplification of silencing signals. Amplification occurs through the production of small RNAs by two RNA-dependent RNA polymerases (RdRPs) that are thought to be tissue-specific - EGO-1 in the germline and RRF-1 in somatic cells. Here we analyze instances of silencing in somatic cells that lack RRF-1. By varying dsRNA sources and target genes, we find that silencing in the absence of RRF-1 is most obvious when dsRNA from neurons is used to silence genes in intestinal cells. This silencing requires EGO-1, but the lineal identity of cells that can use EGO-1 varies. This variability could be because random sets of cells can either receive different amounts of dsRNA from the same source or use different RdRPs to perform the same function. As a result, all cells appear similarly functional despite underlying differences that vary from animal to animal. This functional mosaicism cautions against the use of a few molecules as proxies for predicting the behavior of a cell.

Graphical Abstract

Random sets of cells can either receive different amounts of double-stranded RNA from neurons or use different RdRPs – RRF-1 only versus RRF-1 or EGO-1 – to perform the same function.
The perils of intralocus recombination for inferences of molecular convergence
Authors: Mendes Fábio K. , Livera Andrew , Hahn Matthew W.
Published: August 2018

Accurate inferences of convergence require that the appropriate tree topology be used. If there is a mismatch between the tree a trait has evolved along and the tree used for analysis, then false inferences of convergence (“hemiplasy”) can occur. To avoid problems of hemiplasy when there are high levels of gene tree discordance with the species tree, researchers have begun to construct tree topologies from individual loci. However, due to intralocus recombination even locus-specific trees may contain multiple topologies within them. This implies that the use of individual tree topologies discordant with the species tree can still lead to incorrect inferences about molecular convergence. Here we examine the frequency with which single exons and single protein-coding genes contain multiple underlying tree topologies, in primates and Drosophila, and quantify the effects of hemiplasy when using trees inferred from individual loci. In both clades we find that there are most often multiple diagnosable topologies within single exons and whole genes, with 91% of Drosophila protein-coding genes containing multiple topologies. Because of this underlying topological heterogeneity, even using trees inferred from individual protein-coding genes results in 25% and 38% of substitutions falsely labeled as convergent in primates and Drosophila, respectively. While constructing local trees can reduce the problem of hemiplasy, our results suggest that it will be difficult to completely avoid false inferences of convergence. We conclude by suggesting several ways forward in the analysis of convergent evolution, for both molecular and morphological characters.
FastqCleaner: an interactive Bioconductor application for quality-control, filtering and trimming of FASTQ files
Authors: Roser Leandro Gabriel , Agüero Fernán , Sánchez Daniel Oscar
Published: August 2018

Background

Exploration and processing of FASTQ files are the first steps in state-of-the-art data analysis workflows of Next Generation Sequencing (NGS) platforms. The large amount of data generated by these technologies has put a challenge in terms of rapid analysis and visualization of sequencing information. Recent integration of the R data analysis platform with web visual frameworks has stimulated the development of user-friendly, powerful, and dynamic NGS data analysis applications.

Results

This paper presents FastqCleaner, a Bioconductor visual application for both quality-control (QC) and pre-processing of FASTQ files. The interface shows diagnostic information for the input and output data and allows to select a series of filtering and trimming operations in an interactive framework. FastqCleaner combines the technology of Bioconductor for NGS data analysis with the data visualization advantages of a web environment.

Conclusions

FastqCleaner is an user-friendly, offline-capable tool that enables access to advanced Bioconductor infrastructure. The novel concept of a Bioconductor interactive application that can be used without the need for programming skills, makes FastqCleaner a valuable resource for NGS data analysis.
Multimodal gradients across mouse cortex
Authors: Fulcher Ben D. , Murray John D. , Zerbi Valerio , Wang Xiao-Jing
Published: August 2018

The primate cerebral cortex displays a hierarchy that extends from primary sensorimotor to association areas, supporting increasingly integrated function underpinned by a gradient of heterogeneity in the brain's microcircuits. The extent to which these hierarchical gradients are unique to primate or may reflect a conserved mammalian principle of brain organization remains unknown. Here we report the topographic similarity of large-scale gradients in cytoarchitecture, gene expression, interneuron cell densities, and long-range axonal connectivity, which vary from primary sensory through to prefrontal areas of mouse cortex, highlighting an underappreciated spatial dimension of mouse cortical specialization. Using the T1w:T2w magnetic resonance imaging map as a common spatial reference for comparison across species, we report interspecies agreement in a range of large-scale cortical gradients, including a significant correspondence between gene transcriptional maps in mouse cortex with their human orthologs in human cortex, as well as notable interspecies differences. Our results support the view of systematic structural variation across cortical areas as a core organizational principle that may underlie hierarchical specialization in mammalian brains.
MyocardialNotch-Rbpjdeletion does not affect heart development or function
Authors: Salguero-Jiménez Alejandro , Grego-Bessa Joaquim , D’Amato Gaetano , Jiménez-Borreguero Luis J. , Pompa José Luis de la
Published: August 2018

During vertebrate cardiac development NOTCH signaling activity in the endocardium is essential for the crosstalk between endocardium and myocardium that initiates ventricular trabeculation and valve primordium formation. This crosstalk leads later to the maturation and compaction of the ventricular chambers and the morphogenesis of the cardiac valves, and its alteration may lead to disease. Although endocardial NOTCH signaling has been shown to be crucial for heart development, its physiological role in the myocardium has not been clearly established. Here we have used a genetic strategy to evaluate the role of NOTCH in myocardial development. We have inactivated the unique and ubiquitous NOTCH effector RBPJ in the early cardiomyocytes progenitors, and examined its consequences in cardiac development and function. Our results demonstrate that mice withcTnT-Cre-mediated myocardial-specific deletion ofRbpjdevelop to term, with homozygous mutant animals showing normal expression of cardiac development markers, and normal adult heart function. Similar observations have been obtained afterNotch1deletion withcTnT-Cre. We have also deletedRbpjin both myocardial and endocardial progenitor cells, using theNkx2.5-Credriver, resulting in ventricular septal defect (VSD), double outlet right ventricle (DORV), and bicuspid aortic valve (BAV), due to NOTCH signaling abrogation in the endocardium of cardiac valves territories. Our data demonstrate that NOTCH-RBPJ inactivation in the myocardium does not affect heart development or adult cardiac function.
Reducing tau ameliorates behavioural and transcriptional deficits in a novel model of Alzheimer’s disease
Authors: Pickett Eleanor K , Herrmann Abigail G , McQueen Jamie , Abt Kimberly , Dando Owen , Tulloch Jane , Jain Pooja , Dunnett Sophie , Sohrabi Sadaf , Fjeldstad Maria , Calkin Will , Murison Leo , Jackson Rosemary , Tzioras Makis , Stevenson Anna , D’Orange Marie , Hooley Monique , Davies Caitlin , Oren Iris , Rose Jamie , McKenzie Chris-Anne , Allison Elizabeth , Smith Colin , Hardt Oliver , Henstridge Christopher M , Hardingham Giles , Spires-Jones Tara L.
Published: August 2018

One of the key knowledge gaps blocking development of effective therapeutics for Alzheimer’s disease (AD) is the lack of understanding of how amyloid beta (Aβ) and tau cooperate in causing disease phenotypes. Within a mouse tau deficient background, we probed the molecular, cellular and behavioural disruption triggered by wild-type human tau’s influence on human Aβ-induced pathology. We find that Aβ and tau work cooperatively to cause a hyperactivity phenotype and to cause downregulation of gene transcription including many involved in synaptic function. In both our mouse model and in human post-mortem tissue, we observe accumulation of pathological tau in synapses, supporting the potential importance of synaptic tau. Importantly, tau depletion in the mice, initiated after behavioural deficits emerge, was found to correct behavioural deficits, reduce synaptic tau levels, and substantially reverse transcriptional perturbations, suggesting that lowering tau levels, particularly at the synapse, may be beneficial in AD.

Highlights

- Expression of human familial Alzheimer’s associated mutant amyloid precursor protein and presenillin 1 with wild-type human tau in the absence of endogenous tau in a novel MAPT-AD mouse model results in behavioural deficits and downregulation of genes involved in synaptic function.

- Tau is present in pre and postsynaptic terminals in MAPT-AD mice and human AD brain. In mice, lowering synaptic tau levels was associated with improved cognition and recovered gene expression.

- These data suggest that Aβ and tau act cooperatively in impairing synaptic function and that lowering tau at synapses could be a beneficial therapeutic approach in AD.
NGseqBasic - a single-command UNIX tool for ATAC-seq, DNaseI-seq, Cut-and-Run, and ChIP-seq data mapping, high-resolution visualisation, and quality control
Authors: Telenius Jelena ,   The WIGWAM Consortium, Hughes Jim R.
Published: August 2018

With decreasing cost of next-generation sequencing (NGS), we are observing a rapid rise in the volume of ‘big data’ in academic research, healthcare and drug discovery sectors. The present bottleneck for extracting value from these ‘big data’ sets is data processing and analysis. Considering this, there is still a lack of reliable, automated and easy to use tools that will allow experimentalists to assess the quality of the sequenced libraries and explore the data first hand, without the need of investing a lot of time of computational core analysts in the early stages of analysis.

NGseqBasic is an easy-to-use single-command analysis tool for chromatin accessibility (ATAC, DNaseI) and ChIP sequencing data, providing support to also new techniques such as low cell number sequencing and Cut-and-Run. It takes in fastq, fastq.gz or bam files, conducts all quality control, trimming and mapping steps, along with quality control and data processing statistics, and combines all this to a single-click loadable UCSC data hub, with integral statistics html page providing detailed reports from the analysis tools and quality control metrics. The tool is easy to set up, and no installation is needed. A wide variety of parameters are provided to fine-tune the analysis, with optional setting to generate DNase footprint or high resolution ChIP-seq tracks. A tester script is provided to help in the setup, along with a test data set and downloadable example user cases.

NGseqBasic has been used in the routine analysis of next generation sequencing (NGS) data in high-impact publications 1,2. The code is actively developed, and accompanied with Git version control and Github code repository. Here we demonstrate NGseqBasic analysis and features using DNaseI-seq data from GSM689849, and CTCF-ChIP-seq data from GSM2579421, as well as a Cut-and-Run CTCF data set GSM2433142, and provide the one-click loadable UCSC data hubs generated by the tool, allowing for the ready exploration of the run results and quality control files generated by the tool.

Availability

Download, setup and help instructions are available on the NGseqBasic web site http://userweb.molbiol.ox.ac.uk/public/telenius/NGseqBasicManual/external/

Bioconda users can load the tool as library “ngseqbasic”. The source code with Git version control is available in https://github.com/Hughes-Genome-Group/NGseqBasic/releases.

Contact

jelena.telenius@imm.ox.ac.uk