bluuebunny/crossref_metadata_2025 huggingface dataset:
Congenital right diaphragmatic hernia in an adult
Authors: Al-Zayer Faisal , Aljaroof Abdulla H , Al-Marhoun Maram , Abualsaud Basem , Al-Zaher Mohammed , Meshikhes Abdul-Wahed
Published: November 2019

Diaphragmatic hernia in the absence of trauma in adults is very rare. It occurs as a result of unilateral diaphragmatic agenesis. The diagnosis of this rare condition is typically made in early infancy. However, in asymptomatic patients, the diagnosis is often delayed for months and even years. We present a case of a 27-year-old female, who was referred 48-hours after Caesarean section with suspected pulmonary embolism. Computed tomography scan revealed herniation of the liver as well as bowel loops into the right hemi-thorax. Exploration through a right thoracotomy revealed right diaphragmatic agenesis. The contents were reduced into the abdomen, and the defect was repaired using a mesh. The patient had an uneventful postoperative recovery and was discharged home 10 days later. This case highlights the acute late presentation of right diaphragmatic eventration with abdominal visceral herniation in adulthood. The condition may be triggered by the increasing size of gravid uterus.
‘As though Miles of Ocean did not Separate us’: Print and the Construction of a Transatlantic Free Love Community at the Fin de Siècle
Authors: Jones Sarah L
Published: November 2019

This article argues that British and American free lovers – radical sexual reformers committed to the cause of ‘sexual freedom’ – came together through print to build a transatlantic community at the fin de siècle. Challenging existing narratives that characterize free love as isolated or incoherent, it argues that through print free lovers from Britain and America were able to forge links with each other, and to construct an important, coherent collective identity that transcended national boundaries. In doing so it makes two major interventions. First, it provides unique new insights into the history of free love in both the British and American contexts, placing a new focus on often overlooked transnational connections and exchanges that helped to shape late nineteenth-century free love campaigns. Second, it encourages historians to rethink the ways we look for and make sense of cohesive international reform communities more broadly in this period. By exploring how a small, radical group like the free lovers were able to cohere through processes of contestation and negotiation played out entirely in print, this article will show that, where necessary, print was enough for transatlantic reformers to construct common identities and negotiate coherent reform ideas. As such, it argues that historians of fin-de-siècle social reform should look again at the print culture of other contemporary reformers otherwise labelled divided, isolated, or marginalized to look for threads of cohesion, cooperation, and compromise.
Negative Alcohol and Tobacco Consumption Behaviors in an Australian Army Combat Brigade
Authors: Selman Jason , Rogers Rona , Molloy Sara
Published: November 2019

Introduction

Western militaries have consumption rates of alcohol and tobacco which are higher than the associated civilian populations, and are concerned about the negative effects on health, wellbeing, and military performance that such high rates may have.

Materials and Methods

A survey questionnaire which collected nonidentifiable data was distributed to all accessible members of an Australian Army Combat Brigade over the annual induction training and prefield exercise period between January and March 2019. The survey was composed of personal and demographic questions, followed by questions concerning the personal consumption habits of alcohol and tobacco. 1,606 complete and valid surveys were returned, representing 55.3% of the Brigade’s posted strength. Ethical clearance for this project was provided by the Australian Defence Force Joint Health Command Low Risk Ethics Panel (18-012).

Results

Almost one quarter of the Combat Brigade exceeded the Australian daily risk guideline for alcohol consumption, and over three quarters exceeded the occasion risk guideline; with 6.1% of soldiers drinking alcohol daily. 24.3% identified as tobacco smokers, with 15.9% smoking daily. Smoking rates and volumes were higher when deployed on field training exercises and on international training and operational deployments; as was the consumption of roll-your-own cigarettes. Overall, the main determinants of the negative consumption behaviors were gender (male) and age (under 25).

Conclusions

This study confirmed that the members of an Australian Army Combat Brigade have higher negative health consumption behaviors concerning alcohol and tobacco than the general civilian population. The results also identified a cohort of Senior Non-Commissioned Officers and Warrant Officers (E5–E9) between the ages of 35 and 44 who had high negative consumption behaviors which could result in poor health outcomes. This could be a suitable cohort for a targeted campaign to reduce tobacco and alcohol consumption and to assist to make healthy life changes.
Neonatal follow-up programs in Canada: A national survey
Authors: Albaghli Fawaz , Church Paige , Ballantyne Marilyn , Girardi Alberta , Synnes Anne
Published: November 2019

Background

A 2006 Canadian survey showed a large variability in neonatal follow-up practices. In 2010, all 26 tertiary level Neonatal Follow-Up clinics joined the Canadian Neonatal Follow-Up Network (CNFUN) and agreed to implement a standardized assessment (including the Bayley Scales of Infant and Toddler Development-III (Bayley-III) at 18 months corrected age for children born < 29 weeks’ gestation. It is unknown whether the variability in follow-up practices lessened as a result.

Objectives

To describe the current status of neonatal follow-up services in Canada and changes over time.

Methods

A comprehensive online survey was sent to all tertiary level CNFUN Follow-up programs. Questions were based on previous survey results, current literature, and investigator expertise and consensus.

Results

Respondents included 23 of 26 (88%) CNFUN programs. All sites provide neurodevelopmental screening and referrals in a multidisciplinary setting with variations in staffing. CNFUN programs vary with most offering five to seven visits. Since 2006, assessments at 18 months CA increased from 84% to 91% of sites, Bayley-III use increased from 21% to 74% (P=0.001) and eligibility for follow-up was expanded for children with stroke, congenital diaphragmatic hernia and select anomalies detected in utero. Audit data is collected by > 80% of tertiary programs.

Conclusion

Care became more consistent after CNFUN; 18-month assessments and Bayley-III use increased significantly. However, marked variability in follow-up practices persists.
Translational Landscape of Protein-Coding and Non-Protein-Coding RNAs upon Light Exposure in Arabidopsis
Authors: Kurihara Yukio , Makita Yuko , Shimohira Haruka , Fujita Tomoya , Iwasaki Shintaro , Matsui Minami
Published: November 2019

Light is one of the most essential environmental clues for plant growth and morphogenesis. Exposure to blue monochromatic light from darkness is a turning point for plant biological activity, and as a result dramatic changes in gene expression occur. To understand the translational impacts of blue light, we have performed ribosome profiling analysis and called translated open reading frames (ORFs) de novo within not only mRNAs but also non-coding RNAs (ncRNAs). Translation efficiency of 3,823 protein-coding ORFs, such as nuclear chloroplast-related genes, was up-regulated by blue light exposure. Moreover, the translational activation of the microRNA biogenesis-related genes, DCL1 and HYL1, was induced by blue light. Considering the 3-nucleotide codon periodicity of ribosome footprints, a few hundred short ORFs lying on ncRNAs and upstream ORFs (uORFs) on mRNAs were found that had differential translation status between blue light and dark. uORFs are known to have a negative effect on the expression of the main ORFs (mORFs) on the same mRNAs. Our analysis suggests that the translation of uORFs is likely to be more stimulated than that of the corresponding mORFs, and uORF-mediated translational repression of the mORFs in five genes was alleviated by blue light exposure. With data-based annotation of the ORFs, our analysis provides insights into the translatome in response to environmental changes, such as those involving light.
Education Needs of Dutch Physical Therapists for the Treatment of Patients With Advanced Cancer: A Mixed Methods Study
Authors: Ten Tusscher Marieke R , Groen Wim G , Geleijn Edwin , Berkelaar Dagmar , Aaronson Neil K , Stuiver Martijn M
Published: November 2019

Background

The survival rates for patients with advanced cancer have increased over time. Many patients experience symptoms and functional limitations that impair activities of daily living and limit quality of life. A number of these health problems are amenable to physical therapist treatment. However, physical therapists caring for patients with advanced cancer require special training and skills.

Objective

The study aimed to assess the educational needs and clinical uncertainties of Dutch physical therapists in relation to treatment of patients with advanced cancer.

Design

This was a mixed methods study.

Methods

A survey and 2 focus groups were conducted among physical therapists working in primary care who had previously received at least basic oncology training.

Results

A total of 162 physical therapists completed the survey. The most frequently reported educational needs were related to effective interprofessional collaboration (61.7%), knowledge of medical treatment (49.4%), and current evidence on physical therapist interventions in this population (49.4%). In the focus groups, physical therapists (n = 17) voiced uncertainties about treating patients with bone metastases, setting realistic goals, when and how to end a treatment episode, interprofessional collaboration, finding and using evidence, and using clinimetrics.

Conclusion

These results support the need for specific education programs for physical therapists working with advanced cancer patients to increase the availability of high-quality oncology rehabilitation for this population.
The Practice-Based Implementation (PBI) Network: Technology (Tech) into Care pilot
Authors: Pratt Kimberly M , Branch LaToya Z , Houston Jorielle B
Published: November 2019

Technology can support the use of evidence-based behavioral health treatments, as well as serve as a link to care to improve patient engagement and adherence to treatment. While research suggests that mobile applications (apps) specifically have the potential to enhance the delivery of behavioral health treatment, little guidance exists on how clinicians can effectively and safely integrate mobile apps into their clinical practice. The purpose of this paper is to describe the Department of Defense Practice-Based Implementation (PBI) Network’s approach to implementation and present the results of the Technology (Tech) into Care pilot. The PBI Network conducted this pilot to address providers’ knowledge gaps regarding the integration of mobile apps into behavioral health care within the Military Health System (MHS) and examine the feasibility of widespread dissemination of the practice change in the MHS.

A mixed-method design guided by the Promoting Action on Research Implementation in Health Services framework was used to evaluate the approach and identify facilitators and barriers to practice change.

Positive preliminary support for the feasibility of the Tech into Care approach was demonstrated in improvements in providers’ knowledge, comfort, and perceived level of preparation to integrate mobile apps into care. Organizational challenges including time constraints and staff turnover negatively impacted implementation success. The PBI Network Tech into Care implementation approach is a feasible method to address knowledge gaps related to the integration of mobile apps into clinical practice within the MHS. Contextual factors, such as competing time demands, often impede providers’ ability to effectively integrate mobile apps into care.
Loss of BICD2 in muscle drives motor neuron loss in a developmental form of spinal muscular atrophy
Authors: Rossor AM , Sleigh JN , Groves M , Muntoni F , Reilly MM , Hoogenraad CC , Schiavo G
Published: November 2019

BICD2 is a key component of the dynein/dynactin motor complex. Autosomal dominant mutations in BICD2 cause Spinal Muscular Atrophy Lower Extremity Predominant 2 (SMALED2), a developmental disease of motor neurons. In this study we sought to examine the motor neuron phenotype of conditional Bicd2−/− mice. Bicd2−/− mice show a significant reduction in the number of motor axons of the L4 ventral root compared to wild type mice. Muscle-specific knockout of Bicd2, but not motor neuron-specific Bicd2 loss, results in a reduction in L4 ventral axons comparable to global Bicd2−/− mice. Rab6, a small GTPase required for the sorting of secretory vesicles from the TGN to the plasma membrane is a major binding partner of BICD2. We therefore examined the secretory pathway in SMALED2 patient fibroblasts and demonstrated impaired flow of constitutive secretory cargoes. Together, these data indicate that BICD2 loss from muscles is a major driver of non-cell autonomous pathology with important implications for future therapeutic approaches to SMALED2.

Missense mutations in the cargo adaptor protein BICD2 cause SMALED2, a developmental disease of motor neurons. In this study, the authors show that BICD2 mutations cause motor neuron loss by a non-cell autonomous mechanism determining a disabling impairment of muscle function.
An optimized 16S rRNA sequencing protocol for vaginal microbiome to avoid biased abundance estimation
Authors: Zhang Qiongqiong , Zhang Lei , Wang Ying , Zhao Meng , Chen Rui , Tao Zhi , Lyu Tao , Huang Zhenyu , Liao Qinping
Published: November 2019

We applied three 16S rRNA sequencing protocols on vaginal microbiome samples, to evaluate whether they produce unbiased estimation of vaginal microbiome composition. We modified the 27F primer (hereafter denoted as 27F’). Using vaginal samples from 28 healthy women and 10 women with bacterial vaginosis, we sequenced three 16S rRNA sequencing protocols, i.e., 27F-338R, 27F’-338R and 341F-806R protocols, naming after their PCR primer sets, to test whether the sequencing results are consistent with the clinical diagnostics, morphology and qPCR results. First, the 27F primer would not align withGardnerlla vaginalisvery well, leading to poor amplification of such species. By modifying the primer sequences, the modified 27F primer (27F’) was able to amplifyGardnerlla vaginalisvery well. Second, the DNA sequence of characteristic speciesLactobacillus crispatusis identical withLactobacillus garrinarum, leading to biased estimation of abundance ofLactobacillus crispatuswhen using V3-V4 as PCR target region; in contrast, such bias did not occur when using V1-V2 as a target region. Third, optimized 27F’-338R avoided above-mentioned biases and restored the well-established community state types (CSTs) clustering.

Importance

Vaginal microbiome has profound effects on the health of women and their newborns. Our study found that two well-established 16S rDNA sequencing protocols led to systementical biased estimation of characteristic species of vaginal microbiome. Subsequent analysis proved that the PCR primer fetching efficacy and target region identity were major contributor for such bias. With carefully selected target region and optimized PCR primer set, we were able to eliminate such biases and provide accurate estimation of vaginal microbiome, which showed high consistency with clinical diagnostics. We modified the 27F primer (27F’). Using the optimized PCR primer set of 27F’ and 338R to target the V1-V2 hyper-variable region, our 16S rRNA sequencing correctly evaluate the composition of vaginal microbiome.
An improved growth medium for enhanced inoculum production of the plant growth-promoting fungusSerendipita indica
Authors: Osman Mohamed , Stigloher Christian , Mueller Martin J. , Waller Frank
Published: November 2019

The plant endophytic fungusSerendipita indicacolonizes roots of a wide range of plant species and can enhance growth and stress resistance of these plants. Due to its ease of axenic cultivation and its broad host plant range including the model plant Arabidopsis thaliana and numerous crop plants, it is widely used as a model fungus to study beneficial fungus-root interactions. In addition, it was suggested to be utilized for commercial applications, e.g. to enhance yield in barley and other species. To produce inoculum,S. indicais mostly cultivated in a complex Hill-Käfer medium (CM medium), however, growth in this medium is slow, and yield of chlamydospores, which are often used for plant root inoculation, is relatively low. We tested and optimized a simple vegetable juice-based medium for an enhanced yield of fungal inoculum. The described vegetable juice (VJ) medium is based on commercially available vegetable juice and is easy to prepare. VJ medium was superior to the currently used CM medium with respect to biomass production in liquid medium and hyphal growth on agar plates. Using solid VJ medium supplemented with sucrose (VJS), a high amount of chlamydospores developed already after 8 days of cultivation, producing significantly more spores than on CM medium. Use of VJ medium is not restricted toS. indica, as it also supported growth of two pathogenic fungi often used in plant pathology experiments: the ascomyceteFusarium graminearum, the causal agent of Fusarium head blight disease on wheat and barley, andVerticillium longisporum, the causal agent of verticillium wilt. The described VJ medium is recommended for a streamlined and efficient production of inoculum for the plant endophytic fungusSerendipita indicaand might prove superior for the propagation of other fungi for research purposes.
Adventures in Multi-Omics I: Combining heterogeneous datasets via relationships matrices
Authors: Akdemir Deniz , Knox Ron , Isidro-Sánchez Julio
Published: November 2019

Private and public breeding programs, as well as companies and universities, have developed different genomics technologies which have resulted in the generation of unprecedented amounts of sequence data, which bring new challenges in terms of data management, query, and analysis. The magnitude and complexity of these datasets bring new challenges but also an opportunity to use the data available as a whole. Detailed phenotype data, combined with increasing amounts of genomic data, have an enormous potential to accelerate the identification of key traits to improve our understanding of quantitative genetics. Data harmonization enables cross-national and international comparative research, facilitating the extraction of new scientific knowledge. In this paper, we address the complex issue of combining high dimensional and unbalanced omics data. More specifically, we propose a covariance-based method for combining partial datasets in the genotype to phenotype spectrum. This method can be used to combine partially overlapping relationship/covariance matrices. Here, we show with applications that our approach might be advantageous to feature imputation based approaches; we demonstrate how this method can be used in genomic prediction using heterogenous marker data and also how to combine the data from multiple phenotypic experiments to make inferences about previously unobserved trait relationships. Our results demonstrate that it is possible to harmonize datasets to improve available information across gene-banks, data repositories or other data resources.

Key message

Several covariance matrices obtained from independent experiments can be combined as long as these matrices are partially overlapping. We demonstrate the usefulness of this methodology with applications in combining data from several partially linked genotypic and phenotypic experiments.

Author contribution statement

–DA: Conception or design of the work, statistics, R programs, simulations, drafting the article, and critical revision of the article.

–JIS: R programs, graphs, drafting the article, critical revision of the article.

–RK: Critical revision of the article.
Transgenic mice expressing human alpha-synuclein in noradrenergic neurons develop locus coeruleus pathology and non-motor features of Parkinson’s disease
Authors: Butkovich LM , Houser MC , Chalermpalanupap T , Porter-Stransky KA , Iannitelli AF , Boles JS , Lloyd GM , Coomes AS , Eidson LN , De Sousa Rodrigues ME , Oliver DL , Kelly SD , Chang J , Bengoa-Vergniory N , Wade-Martins R , Giasson BI , Joers V , Weinshenker D , Tansey MG
Published: November 2019

Degeneration of locus coeruleus (LC) neurons and dysregulation of noradrenergic signaling are ubiquitous features of Parkinson’s disease (PD). The LC is among the first brain regions affected by α-synuclein (asyn) pathology, yet how asyn affects these neurons remains unclear. LC-derived norepinephrine (NE) can stimulate neuroprotective mechanisms and modulate immune cells, while dysregulation of NE neurotransmission may exacerbate disease progression, particularly non-motor symptoms, and contribute to the chronic neuroinflammation associated with PD pathology. Although transgenic mice overexpressing asyn have previously been developed, transgene expression is usually driven by pan-neuronal promoters and thus has not been selectively targeted to LC neurons. Here we report a novel transgenic mouse expressing human wild-type asyn under control of the noradrenergic-specific dopamine β-hydroxylase promoter. These mice developed oligomeric and conformation-specific asyn in LC neurons, alterations in hippocampal and LC microglial abundance, upregulated GFAP expression, degeneration of LC fibers, decreased striatal dopamine (DA) metabolism, and age-dependent behaviors reminiscent of non-motor symptoms of PD that were rescued by adrenergic receptor antagonists. These mice provide novel insights into how asyn pathology affects LC neurons and how central noradrenergic dysfunction may contribute to early PD pathophysiology.

Significance statement

α-synuclein (asyn) pathology and loss of neurons in the locus coeruleus (LC) are two of the most ubiquitous neuropathologic features of Parkinson’s disease (PD). Dysregulated NE neurotransmission is associated with the non-motor symptoms of PD including sleep disturbances, emotional changes such as anxiety and depression, and cognitive decline. Importantly, loss of central NE may contribute to the chronic inflammation in, and progression of, PD. We have generated a novel transgenic mouse expressing human asyn in LC neurons to investigate how increased asyn expression affects the function of the central noradrenergic transmission and associated behaviors. We report cytotoxic effects of oligomeric and conformation-specific asyn, astrogliosis, LC fiber degeneration, disruptions in striatal dopamine metabolism, and age-dependent alterations in non-motor behaviors without inclusions.
Nanotopography enhances dynamic remodeling of tight junction proteins through cytosolic complexes
Authors: Huang Xiao , Shi Xiaoyu , Hansen Mollie Eva , Nemeth Cameron L. , Ceili Anna , Huang Bo , Mauro Theodora , Koval Michael , Desai Tejal A.
Published: November 2019

The epithelial tight junction regulates barrier function and is responsive to extracellular stimuli. Here we demonstrated that contact of synthetic surfaces with defined nanotopography at the apical surface of epithelial monolayers increased paracellular permeability of macromolecules. To monitor changes in tight junction morphology in live cells, we fluorescently tagged the scaffold protein zonula occludens-1 (ZO-1) through CRISPR/Cas9-based gene editing. Contact between cells and nanostructured surfaces destabilized junction-associated ZO-1 and promoted its arrangement into highly dynamic non-junctional cytosolic complexes that averaged ∼2 μm in diameter. Junction-associated ZO-1 rapidly remodeled, and we also observed the direct transformation of cytosolic complexes into junction-like structures. Claudin-family tight junction transmembrane proteins and F-actin also were associated with these ZO-1 containing cytosolic complexes. These data suggest that the cytosolic structures are novel intermediates formed in response to nanotopographic cues that facilitate rapid tight junction remodeling in order to regulate paracellular permeability.
Multiple roles for laccase2 in butterfly wing pigmentation, scale development, and cuticle tanning
Authors: Peng Ceili L. , Mazo-Vargas Anyi , Brack Benjamin J. , Reed Robert D.
Published: November 2019

Lepidopteran wing scales play important roles in a number of functions including color patterning and thermoregulation. Despite the importance of wing scales, however, we still have a limited understanding of the genetic mechanisms that underlie scale patterning, development, and coloration. Here we explore the function of the phenoloxidase-encoding gene laccase2 in wing and scale development in the nymphalid butterfly Vanessa cardui. Somatic deletion mosaics of laccase2 generated by CRISPR/Cas9 genome editing presented several distinct mutant phenotypes. Consistent with work in other non-lepidopteran insect groups, we observed reductions in melanin pigmentation and defects in cuticle formation. We were also surprised, however, to see distinct effects on scale development including complete loss of wing scales. This work highlights laccase2 as a gene that plays multiple roles in wing and scale development and provides new insight into the evolution of lepidopteran wing coloration.
TAT-Cx43266-283impairs metabolic plasticity in glioma stem cells in vitro and in vivo
Authors: Pelaz Sara G. , Jaraíz-Rodríguez Myriam , Talaverón Rocío , García-Vicente Laura , de Cedrón Marta Gómez , Tabernero María , de Molina Ana Ramírez , Lillo Concepción , Medina José M. , Tabernero Arantxa
Published: November 2019

Glioblastoma is the most aggressive primary brain cancer, with a median survival of 1 to 2 years1. These tumours contain glioma stem cells (GSCs), which are highly tumorigenic, resistant to conventional therapies2, 3, and exhibit metabolic plasticity to adapt to challenging environments4, 5. GSCs can be specifically targeted by a short cell-penetrating peptide based on connexin43 (Cx43) (TAT-Cx43266-283) that reduces tumour growth and increases survival in preclinical models6via c-Src inhibition7. Because several reports revealed poor clinical efficacy of various antitumoral drugs due to metabolic rewiring in cancer cells8–10, we investigated the effect of TAT-Cx43266-283on GSC metabolism and metabolic plasticity. Here we show that TAT-Cx43266-283decreases GSC glucose uptake and oxidative phosphorylation without a compensatory increase in glycolysis, with no effect on neuron or astrocyte metabolism. GSC changes were mediated by decreased hexokinase (HK) activity and aberrant mitochondrial localization, ultrastructure and function. Moreover, TAT-Cx43266-283reduced GSC growth and survival under different nutrient availability conditions by impairing the metabolic plasticity needed to exploit glucose as an energy source in the absence of other nutrients. Finally, GSCs intracranially implanted into mice together with TAT-Cx43266-283showed decreased levels of important targets for cancer therapy, such as HK-211, 12and glucose transporter 3 (GLUT-3)13, evidencing the reduced ability of treated GSCs to survive in challenging environments. Our results confirm the value of TAT-Cx43266-283for glioma therapy alone or in combination with therapies whose resistance relies on metabolic adaptation. More importantly, these results allow us to conclude that the advantageous metabolic plasticity of GSCs is a targetable vulnerability in malignant gliomas.
A male infertility mutation reverts NANOS1 activity from anti-apoptotic to pro-apoptotic by disrupting repression ofGADD45A,GADD45B,GADD45GandRHOBgenes
Authors: Janecki Damian M. , Ilaslan Erkut , Smialek Maciej J. , Sajek Marcin P. , Kotecki Maciej , Ginter-Matuszewska Barbara , Spik Anna , Krainski Patryk , Jaruzelska Jadwiga , Kusz-Zamelczyk Kamila
Published: November 2019

Background

While Nanos-mediated maintenance of germ cells inDrosophilaand mice has been related to regulation of apoptosis, the relevance of these findings to human physiology is uncertain. Previously we have described the p.[(Pro34Thr);(Ser83del)] doubleNANOS1mutation as associated with an absence of germ cells in the testes of infertile patients. The aim of this study was to identify the mechanism underlying infertility phenotype of patients bearing theNANOS1mutation.

Methods

Constructs encoding a wild-type or mutated NANOS1 protein were used for transfection of TCam-2 cell line, representing male germ cells in culture. Influence of this mutation on cell proliferation was performed using MTS assay while apoptosis and cell cycle were measured by flow cytometry. RNA-Seq analysis including quantitative RT-PCR was conducted for selecting pro-apoptotic genes, repressed by the wild-type NANOS1. Influence of the p.[(Pro34Thr);(Ser83del)] NANOS1 mutation on that repression was investigated by quantitative RT-PCR.

Results

We show here that the p.[(Pro34Thr);(Ser83del)] doubleNANOS1mutation causes NANOS1 to functionally switch from being anti-apoptotic to pro-apoptotic in the human male germ cell line TCam-2. This mutation disrupts repression of mRNAs encoding pro-apoptotic GADG45A, GADD45B, GADD45G and RHOB factors, which could contribute to an increase in apoptosis.

Conclusions

This report underscores the conservation of Nanos from flies to humans as a repressor of pro-apoptotic mRNAs in germ cells, and provides a basis for understanding NANOS1 functions in human reproductive health.
FLIP(L) determines p53 induced life or death
Authors: Lees Andrea , McIntyre Alexander J. , Falcone Fiammetta , Crawford Nyree T. , McCann Christopher , Quinn Gerard P. , Roberts Jamie Z. , Sessler Tamas , Gallagher Peter F. , Gregg Gemma M.A. , McAllister Katherine , McLaughlin Kirsty M. , Allen Wendy L. , Holohan Caitriona , Egan Laurence J. , Ryan Aideen E. , Labonte-Wilson Melissa , Dunne Phillip D. , Wappett Mark , Coyle Vicky M. , Johnston Patrick G. , Kerr Emma M. , Longley Daniel B. , McDade Simon S.
Published: November 2019

How p53 differentially activates cell cycle arrest versus cell death remains poorly understood. Here, we demonstrate that upregulation of canonical pro-apoptotic p53 target genes in colon cancer cells imposes a critical dependence on the long splice form of the caspase-8 regulator FLIP (FLIP(L)), which we identify as a direct p53 transcriptional target. Inhibiting FLIP(L) expression with siRNA or Class-I HDAC inhibitors promotes apoptosis in response to p53 activation by the MDM2 inhibitor Nutlin-3A, which otherwise predominantly induces cell-cycle arrest. When FLIP(L) upregulation is inhibited, apoptosis is induced in response to p53 activation via a novel ligand-independent TRAIL-R2/caspase-8 complex, which, by activating BID, induces mitochondrial-mediated apoptosis. Notably, FLIP(L) depletion inhibits p53-induced expression of the cell cycle regulator p21 and enhances p53-mediated upregulation of PUMA, with the latter activating mitochondrial-mediated apoptosis in FLIP(L)-depleted, Nutlin-3A-treated cells lacking TRAIL-R2/caspase-8. Thus, we report two previously undescribed, novel FLIP(L)-dependent mechanisms that determine cell fate following p53 activation.
GCNCDA: A New Method for Predicting CircRNA-Disease Associations Based on Graph Convolutional Network Algorithm
Authors: Wang Lei , You Zhu-Hong , Li Yang-Ming , Zheng Kai , Huang Yu-An
Published: November 2019

Numerous evidences indicate that Circular RNAs (circRNAs) are widely involved in the occurrence and development of diseases. Identifying the association between circRNAs and diseases plays a crucial role in exploring the pathogenesis of complex diseases and improving the diagnosis and treatment of diseases. However, due to the complex mechanisms between circRNAs and diseases, it is expensive and time-consuming to discover the new circRNA-disease associations by biological experiment. Therefore, there is increasingly urgent need for utilizing the computational methods to predict novel circRNA-disease associations. In this study, we propose a computational method called GCNCDA based on the deep learning Fast learning with Graph Convolutional Networks (FastGCN) algorithm to predict the potential disease-associated circRNAs. Specifically, the method first forms the unified descriptor by fusing disease semantic similarity information, disease and circRNA Gaussian Interaction Profile (GIP) kernel similarity information based on known circRNA-disease associations. The FastGCN algorithm is then used to objectively extract the high-level features contained in the fusion descriptor. Finally, the new circRNA-disease associations are accurately predicted by the Forest by Penalizing Attributes (Forest PA) classifier. The 5-fold cross-validation experiment of GCNCDA achieved 91.2% accuracy with 92.78% sensitivity at the AUC of 90.90% on circR2Disease benchmark dataset. In comparison with different classifier models, feature extraction models and other state-of-the-art methods, GCNCDA shows strong competitiveness. Furthermore, 10 of the top 15 circRNA-disease association candidates with the highest prediction scores were confirmed by recently published literature. These results suggest that GCNCDA can effectively predict potential circRNA-disease associations and provide highly credible candidates for biological experiments.

Author Summary

The recognition of circRNA-disease association is the key of disease diagnosis and treatment, and it is of great significance for exploring the pathogenesis of complex diseases. Computational methods can predicte the potential disease-related circRNAs quickly and accurately. Based on the hypothesis that circRNA with similar function tends to associate with similar disease, GCNCDA model is proposed to effectively predict the potential association between circRNAs and diseases by combining FastGCN algorithm. The performance of the model was verified by cross-validation experiments, different feature extraction algorithm and classifier models comparison experiments. Furthermore, 10 of the top 15 disease-associated circRNAs with the highest prediction scores were confirmed by recently published literature. It is anticipated that GCNCDA model can give priority to the most promising circRNA-disease associations on a large scale to provide reliable candidates for further biological experiment.
Large Ankyrin repeat proteins are formed with similar and energetically favorable units
Authors: Galpern Ezequiel A. , Freiberger María I. , Ferreiro Diego U.
Published: November 2019

Ankyrin containing proteins are one of the most abundant repeat protein families present in all extant organisms. They are made with tandem copies of similar amino acid stretches that fold into elongated architectures. Here, we build and curated a dataset of 200 thousand proteins that contain 1,2 million Ankyrin regions and characterize the abundance, structure and energetics of the repetitive regions in natural proteins. We found that there is a continuous roughly exponential variety of array lengths with an exceptional frequency at 24 repeats. We describe that individual repeats are seldom interrupted with long insertions and accept few deletions, consistently with the know tertiary structures. We found that longer arrays are made up of repeats that are more similar to each other than shorter arrays, and display more favourable folding energy, hinting at their evolutionary origin. The array distributions show that there is a physical upper limit to the size of an array of Ankyrin repeats of about 120 copies, consistent with the limit found in nature. Analysis of the identity patterns within the arrays suggest that they may have originated by sequential copies of more than one Ankyrin unit.

Author summary

Repeat proteins are coded in tandem copies of similar amino acid stretches. We built and curated a large dataset of Ankyrin containing proteins, one of the most abundant families of repeat proteins, and characterized the structure of the arrays formed by the repetitions. We found that large arrays are constructed with repetitions that are more similar to each other than shorter arrays. Also, the largest the array, the more energetically favourable its folding energy is. We speculate about the mechanistic origin of large arrays and hint into their evolutionary dynamics.
Temporal and spatial modulation of the immune response of the murine Gl261 glioma tumor microenvironment
Authors: McKelvey Kelly J , Hudson Amanda L , Kumar Ramyashree Prasanna , Wilmott James S , Attrill Grace H , Long Georgina V , Scolyer Richard A , Clarke Stephen J , Wheeler Helen R , Diakos Connie I , Howell Viive M
Published: November 2019

Glioblastoma, the most aggressive form of glioma, has a 5-year survival rate of <5%. While radiation and immunotherapies are routinely studied in the murine Gl261 glioma model, little is known about its inherent immune response. This study quantifies the temporal and spatial localization of immune cell populations and mediators during glioma development.

Eight-week old male C57Bl/6 mice were orthotopically inoculated with 1×106Gl261 cells and tumor morphology, local and systemic immune cell populations, and plasma cytokines/chemokines assessed at Day-0, 1, 3, 7, 14, and 21 post-inoculation by magnetic resonance imaging, chromogenic immunohistochemistry, multiplex immunofluorescent immunohistochemistry, flow cytometry and multiplex immunoassay respectively.

From Day-3 tumors were distinguishable with >30% Ki67 and increased tissue vascularization (p<0.05). Increasing tumor proliferation/malignancy and vascularization were associated with significant temporal changes in immune cell populations within the tumor (p<0.05) and systemic compartments (p=0.02 to p<0.0001). Of note, at Day-14 16/24 plasma cytokine/chemokines levels decreased coinciding with an increase in tumor cytotoxic T cells, natural killer and natural killer/T cells. Data derived provide baseline characterization of the local and systemic immune response during glioma development. They reveal that type II macrophages and myeloid-derived suppressor cells are more prevalent in tumors than regulatory T cells, highlighting these cell types for further therapeutic exploration.
Pathogenicity of urinary tract infectionEscherichia coliinCaenorhabditis elegans
Authors: Hashimoto Masayuki , Ma Yi-Fen , Wang Sin-Tian , Chen Chang-Shi , Teng Ching-Hao
Published: November 2019

UropathogenicEscherichia coli(UPEC) is a major bacterial pathogen that causes urinary tract infections (UTIs). Several virulence factors (VFs) in the bacteria have been associated with the pathogenicity. The mouse is an available UTI model for studying the pathogenicity; however,Caenorhabditis elegansrepresents as an alternative surrogate host for studying UPEC with the capacity for high-throughput analysis. Therefore, we established a simple assay for a UPEC infection model withC. elegansfor large-scale screening. AnE. coliculture to be tested and synchronizedC. eleganswere mixed in 96-well plates, and the pathogenicity was determined by comparison of the turbidity before and after incubation. A total of 133 clinically isolatedE. colistrains, which included UTI-associated and fecal isolates, were applied to demonstrate the liquid pathogenicity assay. TheE. coliisolates associated with UTIs showed higher pathogenicity inC. elegansthan the fecal isolates, suggesting that the simple assay withC. elegansis useful as a UPEC infectious model. From the screening, VFs involved with iron acquisition (chuA, fyuA, andirp2) were significantly associated with high pathogenicity.C. elegansis a heme auxotroph, and iron homeostasis also serves innate immunity inC. elegans. We then evaluated whether the VFs in UPEC were involved in the pathogenicity. Mutants ofE. coliUTI89 with defective iron acquisition systems were applied to a solid killing assay withC. elegans. As a result, the survival rate ofC. elegansfed with the mutants significantly increased compared to when fed with the parent strain. To our knowledge, this is the first report of the involvement of iron acquisition in the pathogenicity of UPEC in aC. elegansmodel.
Theoretical investigation of a genetic switch for metabolic adaptation
Authors: Laxhuber Kathrin S. , Morrison Muir J. , Phillips Rob
Published: November 2019

Membrane transporters carry key metabolites through the cell membrane and, from a resource standpoint, are hypothesized to be produced when necessary. The expression of membrane transporters in metabolic pathways is often upregulated by the transporter substrate. InE. coli, such systems include for example thelacY, araFGH, andxylFGHgenes, which encode for lactose, arabinose, and xylose transporters, respectively. As a case study of a minimal system, we build a generalizable physical model of thexapABRgenetic circuit, which features a regulatory feedback loop through membrane transport (positive feedback) and enzymatic degradation (negative feedback) of an inducer. Dynamical systems analysis and stochastic simulations show that the membrane transport makes the model system bistable in certain parameter regimes. Thus, it serves as a genetic “on-off” switch, enabling the cell to only produce a set of metabolic enzymes when the corresponding metabolite is present in large amounts. We find that the negative feedback from the degradation enzyme does not significantly disturb the positive feedback from the membrane transporter. We investigate hysteresis in the switching and discuss the role of cooperativity and multiple binding sites in the model circuit. Fundamentally, this work explores how a stable genetic switch for a set of enzymes is obtained from transcriptional auto-activation of a membrane transporter through its substrate.
Frequent extrachromosomal oncogene amplification drives aggressive tumors
Authors: Kim Hoon , Nguyen Nam , Turner Kristen , Wu Sihan , Liu Jihe , Deshpande Viraj , Namburi Sandeep , Chang Howard Y. , Beck Christine , Mischel Paul , Bafna Vineet , Verhaak Roel
Published: November 2019

Extrachromosomal DNA (ecDNA) amplification promotes high oncogene copy number, intratumoral genetic heterogeneity, and accelerated tumor evolution1–3, but its frequency and clinical impact are not well understood. Here we show, using computational analysis of whole-genome sequencing data from 1,979 cancer patients, that ecDNA amplification occurs in at least 26% of human cancers, of a wide variety of histological types, but not in whole blood or normal tissue. We demonstrate a highly significant enrichment for oncogenes on amplified ecDNA and that the most common recurrent oncogene amplifications arise on ecDNA. EcDNA amplifications resulted in higher levels of oncogene transcription compared to copy number matched linear DNA, coupled with enhanced chromatin accessibility. Patients whose tumors have ecDNA-based oncogene amplification showed increase of cell proliferation signature activity, greater likelihood of lymph node spread at initial diagnosis, and significantly shorter survival, even when controlled for tissue type, than do patients whose cancers are not driven by ecDNA-based oncogene amplification. The results presented here demonstrate that ecDNA-based oncogene amplification plays a central role in driving the poor outcome for patients with some of the most aggressive forms of cancers.
Cell-based simulations of Notch-dependent cell differentiation on growing domains
Authors: Stopka Anna , Boareto Marcelo , Iber Dagmar
Published: November 2019

Notch signalling controls cell differentiation and proliferation in many tissues. The Notch signal is generated by the interaction between the Notch receptor of one cell with the Notch ligand (Delta or Jagged) of a neighbouring cell. Therefore, the pathway requires cell-cell contact in order to be active. During organ development, cell differentiation occurs concurrently with tissue growth and changes in cell morphology. How growth impacts on Notch signalling and cell differentiation remains poorly understood. Here, we developed a modelling environment to simulate Notch signalling in a growing tissue. We use our model to simulate the differentiation process of pancreatic progenitor cells. Our results suggest that Notch-mediated differentiation in the developing pancreas is first mediated by geometric effects that result in loss of Notch signalling on the tissue boundary, leading to the differentiation of tip versus trunk cells. A second wave of differentiation further happens in the trunk cells due to a reduction in the expression of the ligandJagged, which has been shown to be controlled by signalling factors secreted from the surrounding mesenchyme. Our results bring new insights into how cells coordinate tissue growth with cell fate specification during organ development.
Synthesis, crystal structure and characterizations of di-μ-cyanido-1:2κ2N:C;2:3κ2C:N-bis(4,7,13,16,21,24-hexaoxa-1,10-diazabicyclo[8.8.8]hexacosane)-1κ8N1,N10,O4,O7,O13,O16,O21,O24;3κ8N1,N10,O4,O7,O13,O16,O21,O24-[5,10,15,20-tetrakis(4-chlorophenyl)porphyrinato-2κ4N]-2-iron(II)-1,3-dipotassium(I) tetrahydrofuran disolvate with an unknown solvent
Authors: Huang Tingting , Wang Haimang , Zhao Jianping
Published: November 2019

The title compound, [Fe(C44H24N8Cl4)(CN)2][K2(C18H36N2O6)2]·2C4H8O was synthesized and characterized by single-crystal X-ray diffraction as well as FTIR and UV–vis spectroscopy. The central FeIIion is coordinated by four pyrrole N atoms of the porphyrin core and two C atoms of the cyano groups in a slightly distorted octahedral coordination environment. The complex molecule crystallizes with two tetrahydrofuran solvent molecules, one of which was refined as disordered over two sets of sites with refined occupancies of 0.619 (5) and 0.381 (5). It has a distorted porphyrin core with mean absolute core-atom displacements Ca, Cb, Cmand Cavof 0.32 (3), 0.22 (3), 0.56 (2) and 0.37 (14) Å, respectively. The axial Fe—Ccyanobond lengths are 1.991 (2) and 1.988 (2) Å. The average Fe—Np(Npis a porphyrin N atom) bond length is 1.964 (10) Å. One of the O atoms and several C atoms of the 222 moiety [222 = 4,7,13,16,21,24-hexaoxa-1,10-diazabicyclo[8.8.8]hexacosane] were refined as disordered over two sets of sites with occupancy ratios of 0.739 (6):0.261 (6) and 0.832 (4):0.168 (4). Additional solvent molecules were found to be highly disordered and their contribution to the scattering was removed using the SQUEEZE procedure inPLATON[Spek (2015).Acta Cryst. C71, 9–18], which indicated a solvent cavity of volume 372 Å3containing approximately 83 electrons. These solvent molecules are not considered in the given chemical formula and other crystal data.
Crystal structure, Hirshfeld surface analysis and contact enrichment ratios of 1-(2,7-dimethylimidazo[1,2-a]pyridin-3-yl)-2-(1,3-dithiolan-2-ylidene)ethanone monohydrate
Authors: Bibila Mayaya Bisseyou Yvon , Ouattara Mahama , Soro Pénétjiligué Adama , Yao-Kakou R. C. A. , Tenon Abodou Jules
Published: November 2019

In the title hydrated hybrid compound C14H14N2OS2·H2O, the planar imidazo[1,2-a]pyridine ring system is linked to the 1,3-dithiolane moiety by an enone bridge. The atoms of the C—C bond in the 1,3-dithiolane ring are disordered over two positions with occupancies of 0.579 (14) and 0.421 (14) and both disordered rings adopt a half-chair conformation. The oxygen atom of the enone bridge is involved in a weak intramolecular C—H...O hydrogen bond, which generates an S(6) graph-set motif. In the crystal, the hybrid molecules are associated in R
2
2(14) dimeric units by weak C—H...O interactions. O—H...O hydrogen bonds link the water molecules, forming infinite self-assembled chains along the b-axis direction to which the dimers are connected via O—H...N hydrogen bonding. Analysis of intermolecular contacts using Hirshfeld surface analysis and contact enrichment ratio descriptors indicate that hydrogen bonds induced by water molecules are the main driving force in the crystal packing formation.