bluuebunny/crossref_metadata_2025 huggingface dataset:
Management of tooth extraction in a patient with ELANE gene mutation-induced cyclic neutropenia
Authors: Aota Keiko , Kani Koichi , Yamanoi Tomoko , Momota Yukihiro , Ninomiya Masami , Yumoto Hiromichi , Azuma Masayuki
Published: September 2019

Introduction:

Cyclic neutropenia (CyN) is a rare hematological disease, and patients with CyN often experience an early onset of severe periodontitis and are forced to undergo tooth extraction. Here, we report a case of a patient with CyN who showed different periodicity and oscillations of neutrophil count compared with her mother, despite sharing the same novel genetic mutation.

Patient concerns:

A 17-year-old Japanese girl who had been diagnosed with CyN shortly after birth presented to our hospital with a complaint of mobility of her teeth and gingivitis. Upon presentation, an intraoral examination was performed and revealed redness and swelling of the marginal and attached gingiva. Radiographs revealed extreme resorption of the alveolar bone and apical lesions in her mandibular lateral incisors. The patient's hematologic data demonstrated a lack of blood neutrophils (0/μL). The patient had no history of dental extraction, and her mother also had a history of CyN.

Diagnoses:

The patient was diagnosed with severe periodontitis that was associated with CyN. Gene testing showed a novel heterozygous mutation in exon 4 of theELANEgene (c.538delC, p.Leu180Ser fsX11).

Interventions:

Based on the clinical findings, we planned to extract the patient's mandibular lateral incisors. Although the tooth extraction was scheduled considering the cyclic variation in neutrophil count, the patient's neutrophil count was 0/μL on the day before the planned extraction. Therefore, granulocyte-colony stimulating factor (G-CSF) was administered to increase the patient's neutrophil count. On the day of the patient's admission for the tooth extraction, she presented with fever (body temperature, 38.5°C), tonsillitis, and stomatitis. The extraction was subsequently delayed, and the patient was administered antibiotics and G-CSF for 4 days. At this time, the neutrophil count increased to 750/μL, and the tooth extraction was carried out safely.

Outcomes:

The postoperative course was uneventful, and the healing process at the extraction site was excellent.

Conclusion:

There is a possibility that the periodicity and oscillations of neutrophil count may change with growth in patients with CyN. Therefore, it is important to frequently examine and treat patients with fluctuating neutrophil levels for the management of invasive dental treatment in patients with CyN.
Rare adverse effects of bisphosphonate therapy
Authors: Ilyas Zubair , Camacho Pauline M.
Published: September 2019

Purpose of review

To give an update on the latest developments regarding rare adverse effects of bisphosphonate therapy.

Recent findings

Recent studies covering osteonecrosis of the jaw (ONJ) and atypical femoral fractures (AFFs) provided several updates to the literature. Identification of ONJ in large population databases is a challenge but based on one systematic review, the ICD-10 diagnosis code K10.2 (inflammatory conditions of the jaw) seems to be the most commonly used code for this condition. Duration of bisphosphonate therapy was determined to be an important predictor of AFFs. Appropriate duration of therapy followed by a timely drug holiday was shown to be the best strategy for improving bone mineral density and reducing fracture risk, while minimizing risk of rare adverse effects of therapy. The utility of bone turnover markers as a monitoring tool during drug holidays needs to be further investigated.

ONJ and AFFs are two of the rare adverse effects associated with bisphosphonate therapy. Population-level trends of bisphosphonate use suggest a decline in prescriptions, pointing to broad fears of these side effects. Careful patient evaluation, duration of bisphosphonate therapy, and use of drug holidays can help limit any risk associated with therapy.
Identifying Differences Between a Straight Face and a Posed Smile Using the Homologous Modeling Technique and the Principal Component Analysis
Authors: Yasuda Kousuke , Nakano Hiroyuki , Yamada Tomohiro , Albougha Safieh , Inoue Kazuya , Nakashima Azusa , Kamata Yu , Sugiyama Goro , Tajiri Shiho , Sumida Tomoki , Mishima Katsuaki , Mori Yoshihide
Published: September 2019

Recently, a homologous modeling method was developed to simulate 3D human body forms, which can visualize principal component analysis (PCA) results and facilitate its detailed comparison with results of previous method. Herein, we aimed to construct a homologous model of the face to identify differences between a straight face and a posed smile. Thirty-eight volunteers (19 males and 19 females, 38 straight faces and 38 posed smiles) with no medical history associated with a posed smile were enrolled. Three-dimensional images were constructed using the Homologous Body Modeling software and the HBM-Rugle; 9 landmarks were identified on the 3D-model surfaces. The template model automatically fitted into an individually scanned point cloud of the face by minimizing external and internal energy functions. Faces were analyzed using PCA; differences between straight faces and posed smiles were analyzed using paired t tests. Contribution of the most important principal component was 23.8%; 8 principal components explained >75% of the total variance. A significant difference between a straight face and a posed smile was observed in the second and the fourth principal components. The second principal component images revealed differences between a straight face and a posed smile and changes around the chin area with regard to length, shape, and anteroposterior position. Such changes were inclusive of individual differences. However, the fourth principal component image only revealed differences between a straight face and a posed smile; observed differences included simultaneous shortening of upper and lower eyelid length, evaluation of the nasal ala ase, swelling of the cheek area, and elevation of the mouth angle. Although these results were clinically apparent, we believe that this article is the first to statistically verify the same.

Consequently, the homologous model technique and PCA are useful for evaluation of the facial soft-tissue changes.
Large Anterior Oronasal Fistula Repair Using Pedicled Buccal Fat Pad and Fibroepithelial Tissue
Authors: Olsson Bernardo , Sebastiani Aline Monise , Trento Guilherme dos Santos , Kluppel Leandro Eduardo , Costa Delson Joao da , Giovanini Allan Fernando , Rebellato Nelson Luis Barbosa , Scariot Rafaela
Published: September 2019

Oronasal fistula (ONF) is the most common complication after palatoplasty in patients with cleft lip and palate (CLP). When left untreated, it may negatively affect the quality of life, leading to development of other comorbidities. This study reports for the first time, the use of a portion of a hyperplasic tissue associated with pedicled buccal fat pad flap to repair a large anterior ONF in a 60-year-old man. The hyperplasic tissue may have developed due to the combination of a loose fitting upper denture and long-term use of dihydropyridine calcium channel blocker (amlodipine besylate). There is controversy in the literature about use of pedicled buccal fat pad flap in the anterior region. However, in this study, we report successful repair of a large anterior ONF using a portion of a fibroepithelial hyperplasic tissue associated with pedicled buccal fat pad flap.
Lower Face Reconstruction Using the Visor Flap
Authors: Kilinc Hidir , Dinç Orhan Gazi
Published: September 2019

We present an alternative method instead of classical methods for lower face reconstruction in this study involving clinical experiences. We aimed to achieve more esthetic and functional results using visor flap. This flap has been used for the reconstruction of lower lip and submental region in two patients. Satisfactory functional and cosmetic outcomes were obtained in patients. Flaps and donor sides healed with no complications. The hair follicles on the flap continued to grow in new locations. The visor flap is a useful alternative method for lower face reconstruction. This technique offers perfect color and texture matching and hair growth.
Cavernous Lymphangioma in the Maxillary Sinus
Authors: Lee Dong Hoon , Yoon Tae Mi , Lee Joon Kyoo , Lim Sang Chul
Published: September 2019

Lymphangioma in the maxillary sinus is rare. Herein, the authors report an unusual case of cavernous lymphangioma, in the maxillary sinus, with imaging examinations. Clinicians should be aware of the possibility of lymphangioma in the maxillary sinus, and be capable of distinguishing it, from other benign cystic lesions.
The Relationship Between Vitamin D and Postpartum Depression
Authors: Tiderencel Kelly A. , Zelig Rena , Parker Anna
Published: September 2019

There is increased interest in the relationship between vitamin D and postpartum depression. This review evaluates the 3 studies that have examined associations between prenatal vitamin D status and postpartum depressive symptoms. Based on the evidence, there is an association between low prenatal vitamin D levels and an increased risk of postpartum depressive symptoms. Vitamin D at a dose of 2000 IU/d may be a convenient choice to correct serum levels safely and reduce the incidence of depressive symptoms. Health care professionals should facilitate adequate vitamin D intake during pregnancy to mitigate depressive consequences of deficiency in the postpartum period.
Insights from the revised complete genome sequences of Acinetobacter baumannii strains AB307-0294 and ACICU belonging to global clones 1 and 2
Authors: Hamidian Mohammad , Wick Ryan R. , Hartstein Rebecca M. , Judd Louise M. , Holt Kathryn E. , Hall Ruth M.
Published: September 2019

The

Acinetobacter baumannii

global clone 1 isolate AB307-0294, recovered in the USA in 1994, and the global clone 2 (GC2) isolate ACICU, isolated in 2005 in Italy, were among the first

A. baumannii

isolates to be completely sequenced. AB307-0294 is susceptible to most antibiotics and has been used in many genetic studies, and ACICU belongs to a rare GC2 lineage. The complete genome sequences, originally determined using 454 pyrosequencing technology, which is known to generate sequencing errors, were re-determined using Illumina MiSeq and MinION (Oxford Nanopore Technologies) technologies and a hybrid assembly generated using Unicycler. Comparison of the resulting new high-quality genomes to the earlier 454-sequenced versions identified a large number of nucleotide differences affecting protein coding sequence (CDS) features, and allowed the sequences of the long and highly repetitive bap and blp1 genes to be properly resolved for the first time in ACICU. Comparisons of the annotations of the original and revised genomes revealed a large number of differences in the protein CDS features, underlining the impact of sequence errors on protein sequence predictions and core gene determination. On average, 400 predicted CDSs were longer or shorter in the revised genomes and about 200 CDS features were no longer present.
Cellular compartment analysis of temporal activity by fluorescent in situ hybridization (catFISH) in the transcardially perfused rat brain
Authors: Gheidi Ali , Kumar Vivek , Fitzpatrick Christopher J , Atkinson Rachel L , Morrow Jonathan D
Published: September 2019

Cellular compartment analysis of temporal activity by fluorescent in situ hybridization (catFISH) allows high spatiotemporal resolution mapping of immediate early genes in the brain in response to internal/external stimuli. One caveat of this technique and indeed other methods of in situ hybridization is the necessity of flash-freezing the brain prior to staining. Often however, the mammalian brain is transcardially perfused to use the brain tissue for immunohistochemistry, the most widely-used technique to study gene expression. The present study illustrates how the original catFISH protocol can be modified for use in adult rats that have been transcardially perfused with 4% paraformaldehyde. c-Fos activity induced by either an auditory tone or status epilepticus was visualized using the catFISH procedure. Analysis of the rat prefrontal cortex, hippocampus and amygdala shows that a clear distinction can be made between the compartmental distribution of c-Fos mRNA in the nuclei and cytoplasmic regions. Furthermore, the qualitative proportion of c-Fos compartmentalization is similar to previous reports of c-Fos expression pattern in rodents navigating novel environments. c-Fos catFISH on perfused rodent brains is an valuable addition to the traditional histological methods using fluorescently labeled riboprobes, and opens several avenues for future investigations.
Improving the coverage of credible sets in Bayesian genetic fine-mapping
Authors: Hutchinson Anna , Watson Hope , Wallace Chris
Published: September 2019

Genome Wide Association Studies (GWAS) have successfully identified thousands of loci associated with human diseases. Bayesian genetic fine-mapping studies aim to identify the specific causal variants within GWAS loci responsible for each association, reporting credible sets of plausible causal variants, which are interpreted as containing the causal variant with some “coverage probability”.

Here, we use simulations to demonstrate that the coverage probabilities are over-conservative in most fine-mapping situations. We show that this is because fine-mapping data sets are not randomly selected from amongst all causal variants, but from amongst causal variants with larger effect sizes. We present a method to re-estimate the coverage of credible sets using rapid simulations based on the observed, or estimated, SNP correlation structure, we call this the “corrected coverage estimate”. This is extended to find “corrected credible sets”, which are the smallest set of variants such that their corrected coverage estimate meets the target coverage.

We use our method to improve the resolution of a fine-mapping study of type 1 diabetes. We found that in 27 out of 39 associated genomic regions our method could reduce the number of potentially causal variants to consider for follow-up, and found that none of the 95% or 99% credible sets required the inclusion of more variants – a pattern matched in simulations of well powered GWAS.

Crucially, our correction method requires only GWAS summary statistics and remains accurate when SNP correlations are estimated from a large reference panel. Using our method to improve the resolution of fine-mapping studies will enable more efficient expenditure of resources in the follow-up process of annotating the variants in the credible set to determine the implicated genes and pathways in human diseases.

Author summary

Pinpointing specific genetic variants within the genome that are causal for human diseases is difficult due to complex correlation patterns existing between variants. Consequently, researchers typically prioritise a set of plausible causal variants for functional validation - these sets of putative causal variants are called “credible sets”. We find that the probabilistic interpretation that these credible sets do indeed contain the true causal variant is variable, in that the reported probabilities often underestimate the true coverage of the causal variant in the credible set. We have developed a method to provide researchers with a “corrected coverage estimate” that the true causal variant appears in the credible set, and this has been extended to find “corrected credible sets”, allowing for more efficient allocation of resources in the expensive follow-up laboratory experiments. We used our method to reduce the number of genetic variants to consider as causal candidates for follow-up in 27 genomic regions that are associated with type 1 diabetes.
The mitochondrial Ca2+uniporter MCU is required for normal glucose-stimulated insulin secretionin vitroandin vivo
Authors: Haythorne Elizabeth , Georgiadou Eleni , Dickerson Matthew T. , Lopez-Noriega Livia , Pullen Timothy J. , da Silva Xavier Gabriela , Davis Samuel P.X. , Martinez-Sanchez Aida , Semplici Francesca , Rizzuto Rosario , McGinty James A. , French Paul M. , Cane Matthew C. , Jacobson David A. , Leclerc Isabelle , Rutter Guy A.
Published: September 2019

Mitochondrial oxidative metabolism is central to glucose-stimulated insulin secretion (GSIS). Whether Ca2+uptake into pancreatic β-cell mitochondria potentiates or antagonises this process is still a matter of debate. Although the mitochondrial importer (MCU) complex is thought to represent the main route for Ca2+transport across the inner mitochondrial membrane, its role in β-cells has not previously been examinedin vivo. Here, we inactivated the pore-forming subunit MCUa (MCU) selectively in the β-cell in mice usingIns1Cre-mediated recombination. Glucose-stimulated mitochondrial Ca2+accumulation, ATP production and insulin secretion were strongly (p<0.05 and p<0.01) inhibited inMCUnull animals (βMCU-KO)in vitro. Interestingly, cytosolic Ca2+concentrations increased (p<0.001) whereas mitochondrial membrane depolarisation improved in βMCU-KO animals. Male βMCU-KO mice displayed impairedin vivoinsulin secretion at 5 (p<0.001) but not 15 min. post intraperitoneal (IP) injection of glucose while the opposite phenomenon was observed following an oral gavage at 5 min. Unexpectedly, glucose tolerance was improved (p<0.05) in young βMCU-KO (<12 weeks), but not older animals. We conclude that MCU is crucial for mitochondrial Ca2+uptake in pancreatic β-cells and is required for normal GSIS. The apparent compensatory mechanisms which maintain glucose tolerance in βMCU-KO mice remain to be established.
EAGLE: an algorithm that utilizes a small number of genomic features to predict tissue/cell type-specific enhancer-gene interactions
Authors: Gao Tianshun , Qian Jiang
Published: September 2019

Long-range regulation by distal enhancers is crucial for many biological processes. The existing methods for enhancer-target gene prediction often require many genomic features. This makes them difficult to be applied to many cell types, in which the relevant datasets are not always available. Here, we design a tool EAGLE, an enhancer and gene learning ensemble method for identification of Enhancer-Gene (EG) interactions. Unlike existing tools, EAGLE used only six features derived from the genomic features of enhancers and gene expression datasets. Cross-validation revealed that EAGLE outperformed other existing methods. Enrichment analyses on special transcriptional factors, epigenetic modifications, and eQTLs demonstrated that EAGLE could distinguish the interacting pairs from non- interacting ones. Finally, EAGLE was applied to mouse and human genomes and identified 7,680,203 and 7,437,255 EG interactions involving 31,375 and 43,724 genes, 138,547 and 177,062 enhancers across 89 and 110 tissue/cell types in mouse and human, respectively. The obtained interactions are accessible through an interactive database enhanceratlas.org. The EAGLE method is available at https://github.com/EvansGao/EAGLE and the predicted datasets are available in http://www.enhanceratlas.org/.

Author summary

Enhancers are DNA sequences that interact with promoters and activate target genes. Since enhancers often located far from the target genes and the nearest genes are not always the targets of the enhancers, the prediction of enhancer-target gene relationships is a big challenge. Although a few computational tools are designed for the prediction of enhancer-target genes, it’s difficult to apply them in most tissue/cell types due to a lack of enough genomic datasets. Here we proposed a new method, EAGLE, which utilizes a small number of genomic features to predict tissue/cell type-specific enhancer-gene interactions. Comparing with other existing tools, EAGLE displayed a better performance in the 10-fold cross-validation and cross-sample test. Moreover, the predictions by EAGLE were validated by other independent evidence such as the enrichment of relevant transcriptional factors, epigenetic modifications, and eQTLs.

Finally, we integrated the enhancer-target relationships obtained from human and mouse genomes into an interactive database EnhancerAtlas, http://www.enhanceratlas.org/.
The sensitivity of transcriptomics BMD modeling to the methods used for microarray data normalization
Authors: Mezencev Roman , Auerbach Scott
Published: September 2019

Whole-genome expression data generated by microarray studies have shown promise for quantitative human health risk assessment. While numerous approaches have been developed to determine benchmark doses (BMDs) from probeset-level dose responses, sensitivity of the results to methods used for normalization of the data has not yet been systematically investigated. Normalization of microarray data converts raw hybridization signals to expression estimates that are expected to be proportional to the amounts of transcripts in the profiled specimens. Different approaches to normalization have been shown to greatly influence the results of some downstream analyses, including biological interpretation. In this study we evaluate the influence of microarray normalization methods on the transcriptomic BMDs. We demonstrate using in vivo data that the use of alternative pipelines for normalization of Affymetrix microarray data can have a considerable impact on the number of detected differentially expressed genes and pathways (processes) determined to be treatment responsive, which may lead to alternative interpretations of the data. In addition, we found that normalization can have a considerable effect (as much as ∼30-fold in this study) on estimation of the minimum biological potency (transcriptomic point of departure). We argue for consideration of alternative normalization methods and their data-informed selection to most effectively interpret microarray data for use in human health risk assessment.
DNAJB1-PRKACA fusion induces liver inflammation in zebrafish model of Fibrolamellar Hepatocellular Carcinoma
Authors: de Oliveira Sofia , Houseright Ruth A. , Korte Benjamin G. , Huttenlocher Anna
Published: September 2019

Fibrolamellar Hepatocellular Carcinoma (FLC) is a rare liver cancer that primarily affects adolescents and young adults. Up to now there is only one identified molecular target responsible for driving the disease, the chimeric protein encoded by DNAJB1-PRKACA (J-PKAca). Immune cells have been identified as key players in liver cancer biology, however the effect of J-PKAca on inflammation in the liver microenvironment is not known. Here we report a new zebrafish model of FLC with non-invasive live imaging capabilities that allows the study of the interactions between immune cells and transformed hepatocytes. We found that overexpression of the dnajb1a-prkcaaa fusion gene specifically in hepatocytes induces early malignancy features in FLC transgenic larvae, such as increased liver and hepatocyte size. In addition, this aberrant form of PKA promotes a pro-inflammatory liver microenvironment by increasing the number of neutrophils and macrophages in the liver area and inducing macrophage polarization to a pro-inflammatory phenotype. Increased caspase-a activity was also found in the liver of FLC transgenic larvae. Importantly, pharmacological inhibition of TNFα secretion and caspase-a activity decreased liver size and inflammation. Overall, these findings suggest that inflammation may be an early feature of FLC involved in progression, and that targeting TNFαand caspase-1 may be beneficial in treating FLC.
Identification of a parasitic symbiosis between respiratory metabolisms in the biogeochemical chlorine cycle
Authors: Barnum Tyler P. , Cheng Yiwei , Hill Kaisle A. , Lucas Lauren N. , Carlson Hans K. , Coates John D.
Published: September 2019

A key step in the chlorine cycle is the reduction of perchlorate (ClO4-) and chlorate (ClO3-) to chloride by microbial respiratory pathways. Perchlorate-reducing bacteria and chlorate-reducing bacteria differ in that the latter cannot use perchlorate, the most oxidized chlorine compound. However, a recent study identified a bacterium with the chlorate reduction pathway dominating a community provided only perchlorate. Here we confirm a metabolic interaction between perchlorate- and chlorate-reducing bacteria and define its mechanism. Perchlorate-reducing bacteria supported the growth of chlorate-reducing bacteria to up to 90% of total cells in communities and co-cultures. Chlorate-reducing bacteria required the gene for chlorate reductase to grow in co-culture with perchlorate-reducing bacteria, demonstrating that chlorate is responsible for the interaction, not the subsequent intermediates chlorite and oxygen. Modeling of the interaction suggested that cells specialized for chlorate reduction have a competitive advantage for consuming chlorate produced from perchlorate, especially at high concentrations of perchlorate, because perchlorate and chlorate compete for a single enzyme in perchlorate-reducing cells. We conclude that perchlorate-reducing bacteria inadvertently support large populations of chlorate-reducing bacteria in a parasitic relationship through the release of the intermediate chlorate. An implication of these findings is that undetected chlorate-reducing bacteria have likely negatively impacted efforts to bioremediate perchlorate pollution for decades.
High-resolution MEMRI characterizes laminar specific ascending and descending spinal cord pathways in rats
Authors: Krishnan Vijai , Xu Jiadi , Mendoza German Alberto , Koretsky Alan , Anderson Stasia A , Pelled Galit
Published: September 2019

Manganese Enhanced MRI (MEMRI) utilizing different manganese chloride (MnCl2) delivery methods, has yielded valuable architectural, functional and connection information about the brain. MEMRI also has the potential in characterizing neural pathways in the spinal cord. The spinal cord grey matter is anatomically composed of nine distinct cellular laminae, where each of the laminae receives input from a specific type of neuronal population and process or serves as a relay region in a specific sensory or motor pathway. This type of laminar arrangement in the spinal cord is currently only visualized by histological methods. It is of significant interest to determine whether laminar specific enhancement by Mn2+ can be achieved in the spinal cord, as has been reported in the brain and olfactory pathway. Here we focus on using MEMRI to determine the specific laminae of the thoracic region of the spinal cord. We focus on MnCl2 changes in the ascending and descending tracts of the spinal cord. Major factors in applying this technique in the spinal cord are the ability to acquire high-resolution spinal cord images and to determine a noninvasive route of administration which will result in uptake by the central nervous system.

We have applied the MEMRI approach by intraperitoneal (i.p). delivery of MnCl2 and imaged lumbar and thoracic spinal cord levels in rats to determine whether T1 weighted MRI can detect spinal cord laminae 48 hours following MnCl2 administration. T1 weighted images of the lower lumbar level were obtained from MnCl2 injected and control rats. Here we demonstrate laminar specific signal enhancement in the spinal cord of rats administered with MnCl2 vs. controls in MRI of the cord with ultra-high, 69 μm in-plane resolution. We also report reduced T1 values over time in MnCl2 groups across laminae I-IX. The regions with the largest T1 enhancements were observed to correspond to laminae that contain either high cell density or large motor neurons, making MEMRI an excellent tool for studying spinal cord architecture, physiology and function in different animal models.
Components of the endocytic and recycling trafficking pathways interfere with the integrity of theLegionella-containing vacuole
Authors: Anand Ila S. , Choi Won Young , Isberg Ralph R.
Published: September 2019

Legionella pneumophilarequires the Dot/Icm translocation system to replicate in a vacuolar compartment within host cells. Strains lacking the translocated substrate SdhA form a permeable vacuole during residence in the host cell, exposing bacteria to the host cytoplasm. In primary macrophages, mutants are defective for intracellular growth, with a pyroptotic cell death response mounted due to bacterial exposure to the cytosol. To understand how SdhA maintains vacuole integrity during intracellular growth, we performed high-throughput RNAi screens against host membrane trafficking genes to identify factors that antagonize vacuole integrity in the absence of SdhA. Depletion of host proteins involved in endocytic uptake and recycling resulted in enhanced intracellular growth and lower levels of permeable vacuoles surrounding the ΔsdhAmutant. Of interest were three different Rab GTPases involved in these processes: Rab11b, Rab8b and Rab5 isoforms, that when depleted resulted in enhanced vacuole integrity surrounding thesdhAmutant. Proteins regulated by these Rabs are responsible for interfering with proper vacuole membrane maintenance, as depletion of the downstream effectors EEA1, Rab11FIP1, or VAMP3 rescued vacuole integrity and intracellular growth of thesdhAmutant. To test the model that specific vesicular components associated with these effectors could act to destabilize the replication vacuole, EEA1 and Rab11FIP1 showed enhanced colocalization with the vacuole surrounding thesdhAmutant compared with the WT vacuole. Depletion of Rab5 isoforms or Rab11b reduced this aberrant colocalization. These findings are consistent with SdhA interfering with both endocytic and recycling membrane trafficking events that act to destabilize vacuole integrity during infection.
A synthetic likelihood solution to the silent synapse estimation problem
Authors: Lynn Michael , Lee Kevin F.H. , Soares Cary , Naud Richard , Béïque Jean-Claude
Published: September 2019

Functional features of populations of synapses are typically inferred from random electrophysiological sampling of small subsets of synapses. Are these samples unbiased? Here, we developed a biophysically constrained statistical framework for addressing this question and applied it to assess the performance of a widely used method based on a failure-rate analysis to quantify the occurrence of silent (AMPAR-lacking) synapses in neural networks. We simulated this method in silico and found that it is characterized by strong and systematic biases, poor reliability and weak statistical power. Key conclusions were validated by whole-cell recordings from hippocampal neurons. To address these shortcomings, we developed a simulator of the experimental protocol and used it to compute a synthetic likelihood. By maximizing the likelihood, we inferred silent synapse fraction with no bias, low variance and superior statistical power over alternatives. Together, this generalizable approach highlights how a simulator of experimental methodologies can substantially improve the estimation of physiological properties.
White matter in infancy is prospectively associated with language outcome in kindergarten
Authors: Zuk Jennifer , Yu Xi , Sanfilippo Joseph , Figuccio Michael Joseph , Dunstan Jade , Carruthers Clarisa , Sideridis Georgios , Gagoski Borjan , Grant Patricia Ellen , Gaab Nadine
Published: September 2019

Language acquisition is of central importance to a child’s development. Although the trajectory of acquisition is shaped by input and experience postnatally, the neural basis for language emerges prenatally. Thus a fundamental question remains unexamined: to what extent may the structural foundations for language established in infancy predict long-term language abilities? In this longitudinal neuroimaging investigation of children from infancy to kindergarten, we find that white matter organization in infancy is prospectively associated with subsequent language abilities, specifically between: (i) the left arcuate fasciculus in infancy and subsequent phonological awareness and vocabulary knowledge, and (ii) the left corticospinal tract in infancy and phonological awareness and phonological memory in kindergarten. Results are independent of age and home literacy environment. These findings directly link white matter organization in infancy with language abilities after school entry, and suggest that structural organization in infancy sets an important foundation for subsequent language development.
Standing genetic variation and chromosomal rearrangements facilitate local adaptation in a marine fish
Authors: Cayuela Hugo , Rougemont Quentin , Laporte Martin , Mérot Claire , Normandeau Eric , Dorant Yann , Tørresen Ole K. , Hoff Siv Nam Khang , Jentoft Sissel , Sirois Pascal , Castonguay Martin , Jansen Teunis , Praebel Kim , Clément Marie , Bernatchez Louis
Published: September 2019

Population genetic theory states that adaptation most frequently occurs from standing genetic variation, which results from the interplay between different evolutionary processes including mutation, chromosomal rearrangements, drift, gene flow and selection. To date, empirical work focusing on the contribution of standing genetic variation to local adaptation in the presence of high gene flow has been limited to a restricted number of study systems. Marine organisms are excellent biological models to address this issue since many species have to cope with variable environmental conditions acting as selective agents despite high dispersal abilities. In this study, we examined how, demographic history, standing genetic variation linked to chromosomal rearrangements and shared polymorphism among glacial lineages contribute to local adaptation to environmental conditions in the marine fish, the capelin (Mallotus villosus). We used a comprehensive dataset of genome-wide single nucleotide polymorphisms (25,904 filtered SNPs) genotyped in 1,359 individuals collected from 31 spawning sites in the northwest Atlantic (North America and Greenland waters). First, we reconstructed the history of divergence among three glacial lineages and showed that they diverged from 3.8 to 1.8 MyA. Depending on the pair of lineages considered, historical demographic modelling provided evidence for divergence with gene flow and secondary contacts, shaped by barriers to gene flow and linked selection. We next identified candidate loci associated with reproductive isolation of these lineages. Given the absence of physical or geographic barriers, we thus propose that these lineages may represent three cryptic species of capelin. Within each of these, our analyses provided evidence for largeNeand high gene flow at both historical and contemporary time scales among spawning sites. Furthermore, we detected a polymorphic chromosomal rearrangement leading to the coexistence of three haplogroups within the Northwest Atlantic lineage, but absent in the other two clades. Genotype-environment associations revealed molecular signatures of local adaptation to environmental conditions prevailing at spawning sites. Altogether, our study shows that standing genetic variation associated with both chromosomal rearrangements and ancestral polymorphism contribute to local adaptation in the presence of high gene flow.
Resection and repair of a Cas9 double-strand break at CTG trinucleotide repeats induces local and extensive chromosomal rearrangements
Authors: Mosbach Valentine , Viterbo David , Descorps-Declère Stéphane , Poggi Lucie , Vaysse-Zinkhöfer Wilhelm , Richard Guy-Franck
Published: September 2019

Microsatellites are short tandem repeats, ubiquitous in all eukaryotes and represent ∼2% of the human genome. Among them, trinucleotide repeats are responsible for more than two dozen neurological and developmental disorders. Targeting microsatellites with dedicated DNA endonucleases could become a viable option for patients affected with dramatic neurodegenerative disorders. Here, we used theStreptococcus pyogenesCas9 to induce a double-strand break within the expanded CTG repeat involved in myotonic dystrophy type 1, integrated in a yeast chromosome. Repair of this double-strand break generated unexpected large chromosomal rearrangements around the repeat tract. These rearrangements depended onRAD52,DNL4andSAE2, and both non-homologous end-joining and single-strand annealing pathways were involved. Resection and repair of the double-strand break (DSB) were totally abolished in arad50Δ strain, whereas they were impaired in asae2Δ mutant, only on the DSB end containing most of the repeat tract. This proved that Sae2 plays significant different roles in resecting a DSB end containing a repeated and structured sequence as compared to a non-repeated DSB end.

In addition, we also discovered that gene conversion was less efficient when the DSB could be repaired using a homologous template, suggesting that the trinucleotide repeat may interfer with gene conversion too. Altogether, these data show thatSpCas9 is probably not a good choice when inducing a double-strand break at or near a microsatellite, especially in mammalian genomes that contain many more dispersed repeated elements than the yeast genome.
Quantifying normal and parkinsonian gait features from home movies: Practical application of a deep learning–based 2D pose estimator
Authors: Sato Kenichiro , Nagashima Yu , Mano Tatsuo , Iwata Atsushi , Toda Tatsushi
Published: September 2019

Objective

Gait movies recorded in daily clinical practice are usually not filmed with specific devices, which prevents neurologists benefitting from leveraging gait analysis technologies. Here we propose a novel unsupervised approach to quantifying gait features and to extract cadence from normal and parkinsonian gait movies recorded with a home video camera by applying OpenPose, a deep learning–based 2D-pose estimator that can obtain joint coordinates from pictures or videos recorded with a monocular camera.

Methods

Our proposed method consisted of two distinct phases: obtaining sequential gait features from movies by extracting body joint coordinates with OpenPose; and estimating cadence of periodic gait steps from the sequential gait features using the short-time pitch detection approach.

Results

The cadence estimation of gait in its coronal plane (frontally viewed gait) as is frequently filmed in the daily clinical setting was successfully conducted in normal gait movies using the short-time autocorrelation function (ST-ACF). In cases of parkinsonian gait with prominent freezing of gait and involuntary oscillations, using ACF-based statistical distance metrics, we quantified the periodicity of each gait sequence; this metric clearly corresponded with the subjects’ baseline disease statuses.

Conclusion

The proposed method allows us to analyze gait movies that have been underutilized to date in a completely data-driven manner, and might broaden the range of movies for which gait analyses can be conducted.
Commensalism in theMimiviridaegiant virus family
Authors: Jeudy Sandra , Bertaux Lionel , Alempic Jean-Marie , Lartigue Audrey , Legendre Matthieu , Belmudes Lucid , Santini Sébastien , Philippe Nadège , Beucher Laure , Biondi Emanuele G. , Juul Sissel , Turner Daniel J. , Couté Yohann , Claverie Jean-Michel , Abergel Chantal
Published: September 2019

Acanthamoeba-infecting Mimiviridae belong to three clades: Mimiviruses (A), Moumouviruses (B) and Megaviruses (C). The uniquely complex mobilome of these giant viruses includes virophages and linear 7 kb-DNA molecules called “transpovirons”. We recently isolated a virophage (Zamilon vitis) and two transpovirons (maBtv and mvCtv) respectively associated to B-clade and C-clade mimiviruses. We used the capacity of the Zamilon virophage to replicate both on B-clade and C-clade host viruses to investigate the three partite interaction network governing the propagation of transpovirons. We found that the virophage could transfer both types of transpovirons to B-clade and C-clade host viruses provided they were devoid of a resident transpoviron (permissive effect). If not, only the resident transpoviron was replicated and propagated within the virophage progeny (dominance effect). Although B- and C-clade viruses devoid of transpoviron could replicate both maBtv and mvCtv, they did it with a lower efficiency across clades, suggesting an ongoing process of adaptive co-evolution. We performed proteomic comparisons of host viruses and virophage particles carrying or cleared of transpovirons in search of proteins involved in this adaptation process. These experiments revealed that transpoviron-encoded proteins are synthetized during the combined mimiviruses/virophage/transpoviron replication process and some of them are specifically incorporated into the virophage and giant virus particles together with the cognate transpoviron DNA. This study also highlights a unique example of intricate commensalism in the viral world, where the transpoviron uses the virophage to propagate from one host virus to another and where the Zamilon virophage and the transpoviron depend on their host giant virus to replicate, this without affecting the giant virus infectious cycle, at least in laboratory conditions.

Author Summary

The Mimiviridae are giant viruses with dsDNA genome up to 1.5 Mb. They build huge viral factories in the host cytoplasm in which the nuclear-like virus-encoded functions (transcription and replication) take place. They are themselves the target of infections by 20 kb-dsDNA virophages, replicating in the giant virus factories. They can also be found associated with 7kb-DNA episomes, dubbed transpovirons. We investigated the relationship between these three players by combining competition experiments involving the newly isolated Zamilon vitis virophage as a vehicle for transpovirons of different origins with proteomics analyses of virophage and giant virus particles. Our results suggest that relationship of the virophage, the transpoviron, and their host giant virus, extend the concept of commensalism to the viral world.
Ligand Entry into Fatty Acid Binding Protein via Local Unfolding instead of Gap Widening
Authors: Xiao T , Lu Y , Fan J , Yang D
Published: September 2019

Fatty acid binding proteins (FABPs) play an important role in transportation of fatty acids. Despite intensive studies, how fatty acids enter the protein cavity for binding is still controversial. Here, a gap-closed variant of human intestinal FABP was generated by mutagenesis, in which the gap is locked by a disulfide bridge. According to its structure determined here by NMR, this variant has no obvious openings as the ligand entrance and the gap cannot be widened by internal dynamics. Nevertheless, it still uptakes fatty acids and other ligands. NMR relaxation dispersion, chemical exchange saturation transfer and hydrogen-deuterium exchange experiments show that the variant exists in a major native state, two minor native-like state, and two locally unfolded states in aqueous solution. Local unfolding of either βB–βD or helix 2 can generate an opening large enough for ligands to enter the protein cavity, but only the fast local unfolding of helix 2 is relevant to the ligand entry process.

Statement of Significance

Fatty acid binding proteins transport fatty acids to specific organelles in the cell. To enable the transport, fatty acids must enter and leave the protein cavity. In spite of many studies, how fatty acids enter the protein cavity remains controversial. Using mutagenesis and biophysical techniques, we have resolved the disagreement and further showed that local unfolding of the second helix can generate a transient opening to allow ligands to enter the protein cavity. Since lipid binding proteins are highly conserved in 3D structures and ligand binding, all of them may use the same local unfolding mechanism for ligand uptake and release.
Ease of product assembly through a time-based design methodology
Authors: Desai Anoop
Published: September 2019

Purpose

This paper aims to present a design methodology to enable product design for ease of assembly. It is corroborated by means of a case study. The methodology is based on standard time data. This enables quick computation of assembly time as well as comparing different design options for ease of assembly.

Design/methodology/approach

Component design that is easy to assemble is likely to take less time and vice versa. Assembly time is a function of product design attributes such as geometric shape, weight, center of gravity, type of material, number of fasteners and types of fasteners. The methodology uses standard data to achieve its objective. Numeric scores are developed for each design feature based on the aforementioned design attributes. This enables not only computation of assembly time for a brand new product but also comparison of two or more alternative design configurations from the point of view of ease of assembly.

Findings

The value of the system is corroborated by means of case studies of actual product designs. It is demonstrated that changing any of the underlying design attributes (such as type of fastener used, number of fasteners used, material of the component and component shape) is likely to result in changing the amount of time taken to assemble the product. The scoring system facilitates the quick computation of assembly time

Originality/value

The amount of time to assemble a product before the product is ever designed is facilitated by this system. Assembly time is a direct function of product design attributes. Process time is calculated using standard data, specifically, the Methods Time Measurement (MTM) system. This is accomplished by converting design features into time measurement units (TMUs). Assembly cost can then be easily computed by using assembly time as the basis. The computation of assembly time and cost is important inasmuch as its role in influencing productivity. This is of obvious value not only to the designer but the company as a whole.
Managers’ learning process during a health-promoting leadership intervention
Authors: Tjulin Åsa , Landstad Bodil , Vinberg Stig , Eriksson Andrea , Hagqvist Emma
Published: September 2019

Purpose

The increasingly demanding psychosocial working conditions in Swedish public sector workplaces call for implementation of workplace health promotion (WHP) interventions. There is a need to increase first-line public sector managers’ capacities for health-promoting leadership. The purpose of this paper is to investigate first-line managers’ experiences of participating in an intervention aimed at strengthening health-promoting leadership. More precisely, the aim is to study what obstacles and prerequisites the intervention have for their learning processes to become health-promoting managers.

Design/methodology/approach

A qualitative study in Northern Sweden at workplaces in the county council and municipalities was conducted. The data were gathered through individual interviews with 18 participating first-line managers. Inductive-content analysis was used to analyse the data.

Findings

The results identify time for reflection and collegial discussions about leadership as prerequisites for learning about health-promoting leadership. Managers experienced the intervention as a confirmation of the leadership behaviours already gained. However, the health-promoting leadership intervention was seen as a contradiction, since organisational prerequisites to implement WHP measures were perceived to be lacking. The managers were not involved in the planning of the intervention and questioned why the organisation did not involve them more when the educational activities were created.

Originality/value

When the organisation understands how and when its managers learn, what they need and want to learn about WHP, and what they already know, tailored participatory interventions can be facilitated that consider the unique prerequisites for the particular organisation.