bluuebunny/crossref_metadata_2025 huggingface dataset:
High Yield of Active Tuberculosis Case Finding Among HIV-Infected Patients Using Xpert MTB/RIF Testing
Authors: Kempker Russell R , Chkhartishvili Nikoloz , Kinkladze Inga , Schechter Marcos C , Harrington Kristin , Rukhadze Nino , Dzigua Lela , Tserstvadze Tengiz , del Rio Carlos , Blumberg Henry M , Tukvadze Nestani
Published: May 2019

Objective

Conduct an active case finding study in Tbilisi, Georgia, for pulmonary tuberculosis (TB) among people living with HIV (PLWH).

Methods

Newly diagnosed HIV patients were assessed for symptoms and asked to submit sputum samples for smear microscopy, culture, and molecular diagnostic testing (Xpert MTB/RIF).

Results

Among 276 PLWH, 131 agreed to participate and 103 submitted sputum samples. Most participants were male (70%) and mean age of 43 years. There were high rates of a positive hepatitis C virus (HCV) antibody test (46%) and the median CD4 count was 122 cells/mm3. A total of 15 (11.5%) persons were diagnosed with pulmonary TB, including 1 each with multidrug-resistant and isoniazid-resistant disease. Twelve had a positive culture for Mycobacterium tuberculosis and Xpert TB/RIF assay, and 4 had positive smear microscopy. Patients with pulmonary TB were more likely to use injection drugs (67% vs 36%, P = .02) and have a positive HCV antibody (73% vs 42%, P = .02). The presence and absence of any TB symptom had a sensitivity and negative predictive value for TB of 93% and 98%, respectively.

Conclusion

Our findings highlight the high prevalence of TB among newly diagnosed HIV-infected patients in an area with high rates of drug-resistant TB and the utility of an active case finding strategy for TB diagnosis.
Olatunbosun v State: Safeguarding Children Against Kidnapping in Worship Places
Authors: Akinloye Idowu A , Akinloye Aduragbemi
Published: May 2019

This discussion uses the Nigerian case of Olatunbosun v State to explore the need for Christian churches to take practical and proactive measures to reduce the risk of child kidnapping in their premises used for worship. It observes the increase in the recurrence of child kidnapping in Nigerian churches over the years is of concern because it poses a serious challenge to the victim, the victim's family and the religious organization. It recommends some measures that religious organizations may adapt to reduce the menace and its attendant risks.
PhePEBP family genes regulated by plant hormones and drought are associated with the activation of lateral buds and seedling growth in Phyllostachys edulis
Authors: Zhao Jianwen , Gao Peijun , Li Chunlong , Lin Xinchun , Guo Xiaoqin , Liu Shenkui
Published: May 2019

Development of lateral buds on the underground rhizome in moso bamboo is essentially the early stage of the development of aboveground branching, which is regulated by Phosphatidyl-Ethanolamine Binding Protein (PEBP) family genes, but it is unknown whether the PEBP family genes are involved in the activation and development of lateral buds underground. By scanning the whole-genome sequence of moso bamboo, we identified 25 PhePEBP family genes and amplified their full-length open reading frames (ORFs). A sequence analysis revealed that they are composed of four exons and three introns, except for PheFT10, which contains six exons and five introns. PheFT10 underwent alternative splicing, resulting in at least four transcripts (PheFT10α, PheFT10β, PheFT10γ and PheFT10δ). Although PhePEBP genes are generally expressed at low levels and show dramatically organ-specific expressions, the transcription levels of most PhePEBP genes, including the transcripts of PheFT10, change with plant age. Together with the observation that the expression of PhePEBP family genes can be regulated by plant hormones and drought, our data suggest that PhePEBP family genes might be involved in the activation of lateral buds and seedling growth. Particularly, PheFT9, PheTFL2 and PheTFL8 may play vital roles during the activation of dormant buds based on the analysis of amino acid substitution and expression profile. These findings provide insights for in-depth exploration of the biological functions of the PhePEBP family genes in regulating the activation of dormant bud and the development of seedling in moso bamboo.
Assessment of chemotherapy-induced organ damage with 68Ga-labeled duramycin
Authors: Rix Anne , Drude Natascha Ingrid , Mrugalla Anna , Baskaya Ferhan , Pak Koon Yan , Gray Brian , Kaiser Hans-Jürgen , Tolba René Hany , Fiegle Eva , Lederle Wiltrud , Mottaghy Felix Manuel , Kiessling Fabian
Published: May 2019

Compared to standard toxicological techniques in preclinical toxicity studies, non-invasive imaging of organ toxicity enables fast and longitudinal investigation of the whole animal. Therefore, we set out to evaluate [68Ga]Ga-NODAGA-duramycin as a positron emission tomography (PET)-tracer of cell death for detecting chemotherapy-induced organ toxicity.

Methods

NODAGA-duramycin was radiolabeled with 68Ga, and quality control was done by thin layer chromatography and high performance liquid chromatography. Tracer specificity was determined in vitro by performing competitive binding experiments on ethanol treated cells. To optimize the timing of the PET/CT-based tracer evaluation, kinetic studies were performed in untreated and cisplatin-treated (20 mg/kg BW, intraperitoneal (i.p.)) BALB/cAnNRj mice. Organ uptake was analyzed in doxorubicin (4 mg/kg BW, i.p.)-, busulfan (18.8 mg/kg KG, i.p.)-, and cisplatin-treated (20 mg/kg BW, i.p.) mice, and in untreated control mice 2 hours after intravenous injection of 5–10 MBq [68Ga]Ga-NODAGA-duramycin. For immunofluorescence validation, tissue sections were stained with anti-active caspase-3 antibody. Blood and serum samples were collected to determine platelet count, aspartate transaminase, alanine transaminase, urea, creatinine, and creatine kinase values.

Results

In vitro experiments confirmed specific binding of [68Ga]Ga-NODAGA-duramycin to dying cells. The biodistribution analysis revealed a blood half-life of 10–17 minutes and a predominantly urinary excretion of the radiotracer. Doxorubicin-, busulfan-, and cisplatin-induced organ toxicities were detected successfully using [68Ga]Ga-NODAGA-duramycin PET/CT and confirmed by immunohistochemistry as well as blood parameter analysis. Busulfan-related spleno-, cardio-, and pneumotoxicity as well as cisplatin-induced cardio- and pneumotoxicity were detected even earlier by [68Ga]Ga-NODAGA-duramycin PET/CT than by blood parameters and histological stainings. In livers and kidneys, differences between treated and untreated animals tended to occur in PET/CT at later time points than in histology due to the relatively high background in these organs. However, trends over time were comparable.

Conclusion

[68Ga]Ga-NODAGA-duramycin PET/CT was successfully applied to non-invasively detect chemotherapy-induced organ toxicity with high sensitivity in preclinical studies. It even depicted some toxic effects prior to immunohistochemistry and blood parameter analysis and represents a promising alternative or complementary method to standard toxicological analyses. Furthermore, the tracer has a high translational potential and may provide a valuable link between preclinical and clinical research.
The Emerging Gait Dysfunction Phenotype in Idiopathic Parkinson’s Disease
Authors: Skidmore Frank M. , Monroe William S , Hurt Christopher , Nicholas Anthony P , Gerstenecker Adam , Anthony Thomas , Jololian Leon , Cutter Gary , Bashir Adil , Denny Thomas , Standaert David , Disbrow Elizabeth A
Published: May 2019

Objective

Severity of motor symptoms in Parkinson’s disease (PD), and rate of change of these symptoms, suggests the existence of disease subgroups. One important PD subgroup is defined by postural instability and gait dysfunction (PIGD), which is associated with disability, lower quality of life, and cognitive deterioration. In this study, we evaluate what clinical factors at baseline are associated with early development of postural instability in PD.

Methods

Data was downloaded from the Parkinson’s Progressive Markers Initiative (PPMI). Several clinical features predict development of postural instability. We provisionally term the associated phenotype the emerging gait disorder (eGD) phenotype. We evaluate validity of the phenotype in two held-out populations.

Results

Individuals with the proposed eGD phenotype have a significantly higher risk of developing postural instability in both validation sets (p < 0.00001 in both sets). The proposed eGD phenotype occurred before development of postural instability (HY stage ≥ 3) in 289 of 301 paired comparisons (Fischer Exact Test, p < 0.000001), with a median progression time from development of eGD phenotype to postural instability of 972 days. Individuals with the proposed eGD phenotype at baseline had more rapid cognitive decline as measured by the Montreal Cognitive Assessment (p = 0.002) and Hopkins Verbal Learning Test (Total Recall, p = 0.008).

Interpretation

We describe a clinical phenotype, detectable at baseline in a subset of individuals with PD, that is associated with accelerated development of postural instability. Within the sample, development of the eGD phenotype reliably precedes development of disability, and is a harbinger of more rapid cognitive progression.
Multiple independent origins of apicomplexan-like parasites
Authors: Mathur Varsha , Kolisko Martin , Hehenberger Elisabeth , Irwin Nicholas AT , Leander Brian S. , Kristmundsson Árni , Freeman Mark A , Keeling Patrick J
Published: May 2019

Apicomplexans are a diverse group of globally important parasites, that include pathogens like Plasmodium, the causative agent of malaria. Despite their current obligate parasitic nature, apicomplexans evolved from photosynthetic algae and retain a remnant plastid (chloroplast). Such a complex evolutionary transition was unexpected, but here we show that it occurred at least three times independently. Using single-cell genomics and transcriptomics from diverse uncultivated parasites, we find that two genera previously classified within the Apicomplexa, Piridium and Platyproteum, form separately branching lineages in phylogenomic analyses. Both retain cryptic plastids with genomic and metabolic features convergent with apicomplexans. These findings suggest a predilection in this lineage for both the loss of photosynthesis and the transition to a morphologically similar parasitic lifestyle, resulting in multiple lineages of highly convergent animal parasites.
Survival status and predictors of mortality among Breast Cancer patients in Adult Oncology Unit at Black Lion Specialized Hospital, Addis Ababa, Ethiopia, 2018
Authors: Areri Habtamu Abera , Shibabaw Wondimeneh , Mulugeta Tefera , Asmare Yared , Yirga Tadesse
Published: May 2019

Introduction

Breast cancer is a foremost cause of death worldwide, ranks fifth among causes of death from all types of cancers; this is the most common cause of cancer death in women among both developing and developed countries. Breast cancer ranks first among most frequent cancers in women of Ethiopia. In spite of the high incidence, mortality rate, and survival status among breast cancer patients was not determined in Ethiopia.

Objective

The main aim of the study is to assess the survival status and predictor the mortality among Breast Cancer patients in Adult Oncology Unit at Black Lion Specialized Hospital in 2018.

Methods

An institution based retrospective follow up study was conducted in Adult Oncology Unit at Black Lion Specialized Hospital. All cases of breast cancer registered from 1stJanuary 2012 to 31thDecember,2014 were followed for the six-year survival (until 31thDecember, 2017). Kaplan-Meier survival curve together with log rank test was deployed to test for variations in the survival among predictor variables. Cox regression was used at 5% level of significance to determine the net effect of each independent variable on time to death of breast cancer clients.

Results

The results indicate that the incidence rate of mortality was 9.8 per 100 person/ years (95% CI: 8.49-11.47).The overall median survival time was 56.5(95% CI (53.46 - 60.83)) months. The overall estimated survival rate was recorded 27% (95% CI, 17.09 to 36.67 %) at 72 months of follow up, whereas at odd years (1, 3, and 5 years) were, 97.2%, 80.8%, and 46.2% respectively. Predictors of mortality were assessed at clinical stage (III&IV),(AHR =1.86), poorly differentiated histology (AHR: 3.1) & positive lymph node status (AHR:3.13),Whereas adjuvant hormone therapy (AHR: 0.67) and chemotherapy (AHR:0.72) were protective.

Conclusion

The overall probability of survival in Ethiopia was inferior when compared with other high and middle-income countries. Predictors of mortality were at advanced clinical stage, poorly differentiated histology grade, surgical margin involvement and positive lymph node status. In contrary, adjuvant hormone therapy, modified radical mastectomy and chemotherapy were protective factors. Hence, special emphasis could be given to early screening, stage diagnosis and initiation of treatment.
Acid and inflammatory sensitisation of naked mole-rat colonic afferent nerves
Authors: Hockley James R.F. , Barker Katie H. , Taylor Toni S. , Callejo Gerard , Husson Zoe M. , Bulmer David C. , Smith Ewan St. J.
Published: May 2019

Acid sensing in the gastrointestinal tract is required for gut homeostasis and the detection of tissue acidosis caused by ischaemia, inflammation and infection. In the colorectum, activation of colonic afferents by low pH contributes to visceral hypersensitivity and abdominal pain in human disease including during inflammatory bowel disease. The naked mole-rat (Heterocephalus glaber; NMR) shows no pain-related behaviour to subcutaneous acid injection and cutaneous afferents are insensitive to acid, an adaptation thought to be a consequence of the subterranean, likely hypercapnic, environment in which it lives. As such we sought to investigate NMR interoception within the gastrointestinal tract and how this differed from the mouse (Mus Musculus). Here we show the presence of calcitonin gene regulated peptide (CGRP) expressing extrinsic nerve fibres innervating both mesenteric blood vessels and the myenteric plexi of the smooth muscle layers of the NMR colorectum. Usingex vivocolonic-nerve electrophysiological recordings we show differential sensitivity of NMR, compared to mouse, colonic afferents to acid and the prototypic inflammatory mediator bradykinin, but not direct mechanical stimuli. In NMR, but not mouse, we observed mechanical hypersensitivity to acid, whilst both species sensitised to bradykinin. Collectively, these findings suggest that NMR colonic afferents are capable of detecting acidic stimuli, however, their intracellular coupling to downstream molecular effectors of neuronal excitability and mechanotransduction likely differs between species.
Three-gene PCR and high-resolution melting analysis for differentiating vertebrate species mitochondrial DNA for forensic and biodiversity research pipelines
Authors: Ouso Daniel O. , Otiende Moses Y. , Jeneby Maamun , Oundo Joseph W. , Bargul Joel L. , Miller Scott , Wambua Lillian , Villinger Jandouwe
Published: May 2019

Reliable molecular identification of vertebrate species from morphologically unidentifiable tissue is critical for the prosecution of illegally-traded wildlife products, conservation-based biodiversity research, and identification of blood-meal hosts of hematophagous invertebrates. However, forensic identification of vertebrate tissue relies on the sequencing of mitochondrial cytochrome oxidase I (COI) ‘barcode’ genes, which remains costly for purposes of screening large numbers of unknown samples during routine surveillance. Here, we adopted a rapid, low-cost approach to differentiate 10 domestic and 24 wildlife species that are common in the East African illegal wildlife products trade based on their unique high-resolution melting profiles from COI, cytochrome b, and 16S ribosomal RNA gene PCR products. Using the approach, we identified (i) giraffe among covertly sampled meat from Kenyan butcheries, and (ii) forest elephant mitochondrial sequences among savannah elephant reference samples. This approach is being adopted for high-throughput pre-screening of potential bushmeat samples in East African forensic science pipelines.
The nucleosome acidic patch directly interacts with subunits of the Paf1 and FACT complexes and controls chromatin architecture in vivo
Authors: Cucinotta Christine E. , Hildreth A. Elizabeth , McShane Brendan M. , Shirra Margaret K. , Arndt Karen M.
Published: May 2019

The nucleosome core regulates DNA-templated processes through the highly conserved nucleosome acidic patch. While structural and biochemical studies have shown that the acidic patch controls chromatin factor binding and activity, few studies have elucidated its functions in vivo. We employed site-specific crosslinking to identify proteins that directly bind the acidic patch in Saccharomyces cerevisiae and demonstrated crosslinking of histone H2A to Paf1 complex subunit Rtf1 and FACT subunit Spt16. Rtf1 bound to nucleosomes through its histone modification domain, supporting its role as a cofactor in H2B K123 ubiquitylation. An acidic patch mutant showed defects in nucleosome positioning and occupancy genome-wide. Our results provide new information on the chromatin engagement of two central players in transcription elongation and emphasize the importance of the nucleosome core as a hub for proteins that regulate chromatin during transcription.
Multiplexed imaging of immune cells in staged multiple sclerosis lesions by mass cytometry
Authors: Ramaglia Valeria , Sheikh-Mohamed Salma , Legg Karen , Rojas Olga L , Zandee Stephanie , Fu Fred , Ornatsky Olga , Swanson Eric C , Prat Alexandre , McKee Trevor D , Gommerman Jennifer L
Published: May 2019

Multiple Sclerosis (MS) is characterized by demyelinated and inflammatory lesions in the brain and spinal cord. Lesions contain immune cells with variable phenotypes and functions. Here we use imaging mass cytometry (IMC) to enable the simultaneous imaging of 15+ proteins within 11 staged MS lesions. Using this approach, we demonstrated that the majority of demyelinating macrophage-like cells in active lesions were derived from the resident microglial pool. Although CD8+ T cells predominantly infiltrated the lesions, CD4+ T cells were also abundant but localized closer to blood vessels. B cells with a predominant switched memory phenotype were enriched across all lesion stages and were found to preferentially infiltrate the tissue as compared to unswitched B cells which localized to the vasculature. We propose that IMC will enable a comprehensive analysis of single-cell phenotypes, their functional states and cell-cell interactions in relation to lesion morphometry and demyelinating activity in the MS brain.
Simultaneous 3D super-resolution fluorescence microscopy and atomic force microscopy: combined SIM and AFM platform for cell imaging
Authors: Gómez-Varela Ana I. , Stamov Dimitar R. , Miranda Adelaide , Alves Rosana , Barata-Antunes Cláudia , Dambournet Daphné , Drubin David G. , Paiva Sandra , De Beule Pieter A. A.
Published: May 2019

Correlating data from different microscopy techniques holds the potential to discover new facets of signaling events in cellular biology. Here we report for the first time a hardware set-up capable of achieving simultaneous imaging of spatially correlated super-resolution fluorescence microscopy and atomic force microscopy, a feat only obtained until now by fluorescence microscopy set-ups with spatial resolution restricted to the Abbe resolution limit. We hereby remove the need to perform independent measurement and subsequent data averaging required to eliminate cell-to-cell variation in observed signals. We detail system integration, demonstrate system performance and report imaging of sub-resolution fluorescent beads and genome-engineered human bone osteosarcoma epithelial cells.
Anophelesbionomic, insecticide resistance and malaria transmission in southwest Burkina Faso: a pre-intervention study
Authors: Soma Dieudonné Diloma , Zogo Barnabas Muhugnon , Somé Anthony , Tchiekoi Bertin N’Cho , de Sales Hien Domonbabele François , Pooda Hermann Sié , Coulibaly Sanata , Gnambani Jacques Edounou , Ouari Ali , Mouline Karine , Dahounto Amal , Ouédraogo Georges Anicet , Fournet Florence , Koffi Alphonsine Amanan , Pennetier Cédric , Moiroux Nicolas , Dabiré Roch Kounbobr
Published: May 2019

Background

The present study presents results of entomological surveys conducted to address the malaria vectors bionomic, insecticide resistance and transmission prior to the implementation of new strategies complement long-lasting insecticidal nets (LLINs) in the framework of a randomized control trial in southwest Burkina Faso.

Methods

We conducted entomological surveys in 27 villages during the dry cold season (January 2017), dry hot season (March 2017) and rainy season (June 2017). We carried out hourly catches (from 17:00 to 09:00) inside and outside 4 houses in each village using the Human Landing Catch technique. Mosquitoes were identified using morphological taxonomic keys. Specimens belonging to theAnopheles gambiaecomplex andFunestusGroup were identified using molecular techniques as well as detection ofPlasmodium falciparuminfection and insecticide resistance target-site mutations.

Results

EightAnophelesspecies were detected in the area.Anopheles funestus s.swas the main vector during the dry cold season. It was replaced byAnopheles coluzziiduring the dry hot season whereasAn. coluzziiandAn. gambiae s.s.were the dominant species during the rainy season. Species composition of theAnophelespopulation varied significantly among surveys. All researched target site mutation of insecticide resistance (kdr-w, kdr-eandace-1) were detected in all members of theAn. gambiaecomplex of the area but at different frequencies. We observed early and late biting phenotypes in the main malaria vector species. Entomological inoculation rates were 0.087, 0.089 and 0.375 infected bites per human per night during dry cold season, dry hot season and rainy season, respectively.

Conclusion

The intensity of malaria transmission was high despite the universal coverage with LLINs. We detected early and late biting phenotypes in the main malaria vector species as well as physiological insecticide resistance mechanisms. These vectors might mediate residual transmission. These data highlight the need to develop complementary tools in addition to LLINs in order to better control resistant malaria vectors and to monitor insecticide resistance.
RNA promotes phase separation of glycolysis enzymes into yeast G bodies in hypoxia
Authors: Fuller Gregory G. , Han Ting , Freeberg Mallory A. , Moresco James J. , Yates John R , Kim John K.
Published: May 2019

In hypoxic stress conditions, glycolysis enzymes assemble into singular cytoplasmic granules called glycolytic (G) bodies. Formation of G bodies in yeast is correlated with increased glucose consumption and cell survival. However, the physical properties and organizing principles that define G body formation are unclear. We demonstrate that glycolysis enzymes are non-canonical RNA binding proteins, sharing many common mRNA substrates that are also integral constituents of G bodies. Tethering a G body component, the beta subunit of the yeast phosphofructokinase, Pfk2, to nonspecific endoribonucleases reveals that RNA nucleates G body formation and subsequent maintenance of G body structural integrity. Consistent with a phase separation mechanism of G body formation, recruitment of glycolysis enzymes to G bodies relies on multivalent homotypic and heterotypic interactions. Furthermore, G bodies can fuse in live cells and are largely insensitive to 1,6-hexanediol treatment, consistent with a hydrogel-like state in its composition. Taken together, our results elucidate the biophysical nature of G bodies and demonstrate that RNA nucleates phase separation of the glycolysis machinery in response to hypoxic stress.
Nimodipine prevents the development of spasticity after spinal cord injury
Authors: Marcantoni Maite , Fuchs Andrea , Löw Peter , Kiehn Ole , Bellardita Carmelo
Published: May 2019

Spasticity, one of the most frequent comorbidities of spinal cord injury (SCI), disrupts motor recovery and quality of life. Despite major progress in neurorehabilitative and pharmacological approaches, no curative treatment for spasticity exists. Here, we show in a mouse model of chronic SCI that treatment with nimodipine — an FDA-approved L-type calcium channel blocker — starting in the acute phase of SCI completely prevents the development of spasticity measured as increased muscle tone and spontaneous spasms. The aberrant muscle activities are permanently blocked even after termination of the treatment. Constitutive and conditional silencing in neuronal subtypes of CaV 1.3 channels shows that preventive effect of nimodipine on spasticity after SCI is mediated by the neuronal CaV 1.3 channels. This study identifies a potentially curative treatment protocol with a specific target for the prevention of spasticity after SCI.
Hierarchical Discovery of Large-scale and Focal Copy Number Alterations in Low-coverage Cancer Genomes
Authors: Samir Khalil Ahmed Ibrahim , Khyriem Costerwell , Chattopadhyay Anupam , Sanyal Amartya
Published: May 2019

Motivation

Detection of copy number alterations (CNA) is critical to understand genetic diversity, genome evolution and pathological conditions such as cancer. Cancer genomes are plagued with widespread multi-level structural aberrations of chromosomes that pose challenges to discover CNAs of different length scales with distinct biological origin and function. Although several tools are available to identify CNAs using read depth (RD) of coverage, they fail to distinguish between large-scale and focal alterations due to inaccurate modeling of the RD signal of cancer genomes. These tools are also affected by RD signal variations, pronounced in low-coverage data, which significantly inflate false detection of change points and inaccurate CNA calling.

Results

We have developed CNAtra to hierarchically discover and classify ‘large-scale’ and ‘focal’ copy number gain/loss from whole-genome sequencing (WGS) data. CNAtra provides an analytical and visualization framework for CNV profiling using single sequencing sample. CNAtra first utilizes multimodal distribution to estimate the copy number (CN) reference from the complex RD profile of the cancer genome. We utilized Savitzy-Golay filter and Modified Varri segmentation to capture the change points. We then developed a CN state-driven merging algorithm to identify the large segments with distinct copy number. Next, focal alterations were identified in each large segment using coverage-based thresholding to mitigate the adverse effects of signal variations. We tested CNAtra calls using experimentally verified segmental aneuploidies and focal alterations which confirmed CNAtra’s ability to detect and distinguish the two alteration phenomena. We used realistic simulated data for benchmarking the performance of CNAtra against other detection tools where we artificially spiked-in CNAs in the original cancer profiles. We found that CNAtra is superior in terms of precision, recall, andf-measure. CNAtra shows the highest sensitivity of 93% and 97% for detecting focal and large-scale alterations respectively. Visual inspection of CNAs showed that CNAtra is the most robust detection tool for low-coverage cancer data.

Availability and implementation

CNAtra is an open source software implemented in MATLAB, and is available athttps://github.com/AISKhalil/CNAtra
High-throughput microcircuit analysis of individual human brains through next-generation multineuron patch-clamp
Authors: Peng Yangfan , Mittermaier Franz X. , Planert Henrike , Schneider Ulf C. , Alle Henrik , Geiger Jörg R.P.
Published: May 2019

Comparing neuronal microcircuits across different brain regions, species and individuals can reveal common and divergent principles of network computation. Simultaneous patch-clamp recordings from multiple neurons offer the highest temporal and subthreshold resolution to analyse local synaptic connectivity. However, its establishment is technically complex and the experimental performance is limited by high failure rates, long experimental times and small sample sizes. We introduce an in-vitro multipatch setup with an automated pipette pressure and cleaning system facilitating recordings of up to 10 neurons simultaneously and sequential patching of additional neurons. We present hardware and software solutions that increase the usability, speed and data throughput of multipatch experiments which allowed probing of 150 synaptic connections between 17 neurons in one human cortical slice and screening of over 600 connections in tissue from a single patient. This method will facilitate the systematic analysis of microcircuits and allow unprecedented comparisons at the level of individuals.
Analysis tools to quantify dissemination of pathology in zebrafish larvae
Authors: Stirling David R. , Suleyman Oniz , Gil Eliza , Elks Philip M. , Torraca Vincenzo , Noursadeghi Mahdad , Tomlinson Gillian S.
Published: May 2019

We used the zebrafish larval Mycobacterium marinum infection model of tuberculosis to develop image analysis software called QuantiFish, to enable rapid, objective quantitation of bacterial load and dissemination. Our analysis tools provide novel outcome measures of infection; the proportional distribution of bacteria between sites and their spatial distribution throughout the host. We anticipate the broader application of these parameters to other zebrafish models of infection and metastatic cancer.
Public health in genetic spaces: a statistical framework to optimize cluster-based outbreak detection
Authors: Chato Connor , Kalish Marcia L. , Poon Art F. Y.
Published: May 2019

Genetic clustering is a popular method for characterizing variation in transmission rates for rapidly-evolving viruses, and could potentially be used to detect outbreaks in ‘near real time’. However, the statistical properties of clustering are poorly understood in this context, and there are no objective guidelines for setting clustering criteria. Here we develop a new statistical framework to optimize a genetic clustering method based on the ability to forecast new cases. We analyzed the pairwise Tamura-Nei (TN93) genetic distances for anonymized HIV-1 subtype B pol sequences from Seattle (n = 1, 653) and Middle Tennessee, USA (n = 2, 779), and northern Alberta, Canada (n = 809). Under varying TN93 thresholds, we fit two models to the distributions of new cases relative to clusters of known cases: (1) a null model that assumes cluster growth is strictly proportional to cluster size, i.e., no variation in transmission rates among individuals; and (2) a weighted model that incorporates individual-level covariates, such as recency of diagnosis. The optimal threshold maximizes the difference in information loss between models, where covariates are used most effectively. Optimal TN93 thresholds varied substantially between data sets, e.g., 0.0104 in Alberta and 0.016 in Seattle and Tennessee, such that the optimum for one population will potentially mis-direct prevention efforts in another. The range of thresholds where the weighted model conferred greater predictive accuracy tended to be narrow (±0.005 units), but the optimal threshold for a given population also tended to be stable over time. We also extended our method to demonstrate that variation in recency of HIV diagnosis among clusters was significantly more predictive of new cases than sample collection dates (ΔAIC> 50). These results demonstrate that one cannot rely on historical precedence or convention to configure genetic clustering methods for public health applications. Our framework not only provides an objective procedure to optimize a clustering method, but can also be used for variable selection in forecasting new cases.
Risk Factors Associated to Types of Gallstone Diagnosed at Ibn-Sina Specialized Teaching Hospital, Khartoum, Sudan
Authors: Shaddad Mahasin Ibrahim , Fadl Azza Abdulrahman , Jervase Ayat , Garelnabi Nur Ibrahim Ali , Hakem Suzan Al , Hussein Tariq Mohamed , Ahmed Mohamed H , Almobark Ahmed Omer
Published: May 2019

Introduction

Gallstone disease (Cholelithiasis) affects 10 to 15% of the population of developed countries. Our study aimed to determine the risk factors associated to different types of gallstone in patients diagnosed in Khartoum State Ibnsina Gastroenterology Center.

Methods

A facility-based prospective cross-sectional study was implemented on a convenient sample of 47 participants diagnosed with gallstone through ultrasonography in Ibnsina Gastroenterology center and who underwent surgical interventions for gallstone removal. A standardized interviewer-administrated research tool comprising three parts was used to collect data related to the characteristics of the participants, their medical presentation and examination as well as information on types of gallstone, surgical interventions and outcomes. The data were computerized through Epi-info7and analyzed through SPSS 23. Descriptive statistics were firstly performed and association was tested through Chi square tests and ANOVA. A multinomial regression analysis established the relationship between types of gallstone and their associated risk factors. All statistical tests were considered as significant whenp< 0.05.

Results

The risk factors statistically associated to gallstone types were family history (p= 0.011) and duration of living in the residence area (p= 0.043) in pigment-cholesterol gallstone model vs mixed-cholesterol gallstone model. Other four risk factors contributing to the pathogenesis of gallstone were parity (OR = 1.623 [95% CI: 0.795-3.315]) vs (OR = 1.426, [95% CI: 0.729- 2.790]), waist circumference (OR= 1.014 [95% CI: 0.948-1.085]) vs (OR = 1.001 [95% CI: 0.942- 1.065]), chronic disease (OR = 0.698, [95% CI: 0.028 - 17.445]) vs (OR = 0.354, [95% CI: 0.021- 6.087]) and serum triglyceride (OR = 0.985, [95% CI: 0.950- 1.022]) vs (OR= 0.980, [95% CI: 0.949- 1.012]).

Conclusion

Our finding indicated six risk factors related to types of gallstone. Further multicenter research in Sudan on risk factors is needed to calibrate and validate our model.
Varied effects of algal symbionts on transcription factor NF-κB in a sea anemone and a coral: possible roles in symbiosis and thermotolerance
Authors: Mansfield Katelyn M. , Cleves Phillip A. , Van Vlack Emily , Kriefall Nicola G. , Benson Brooke E. , Camacho Dimitrios J. , Hemond Olivia , Pedroza Monique , Siggers Trevor , Pringle John R. , Davies Sarah W. , Gilmore Thomas D.
Published: May 2019

Many cnidarians, including the reef-building corals, undergo symbiotic mutualisms with photosynthetic dinoflagellate algae of the family Symbiodiniaceae. These partnerships are sensitive to temperature extremes, which cause symbiont loss and increased coral mortality. Previous studies have implicated host immunity and specifically immunity transcription factor NF-κB as having a role in the maintenance of the cnidarian-algal symbiosis. Here we have further investigated a possible role for NF-κB in establishment and loss of symbiosis in various strains of the anemone Exaiptasia (Aiptasia) and in the coral Pocillopora damicornis. Our results show that NF-κB expression is reduced in Aiptasia larvae and adults that host certain algae strains. Treatment of Aiptasia larvae with a known symbiosis-promoting cytokine, transforming growth factor β, also led to decreased NF-κB expression. We also show that aposymbiotic Aiptasia (with high NF-κB expression) have increased survival following infection with the pathogenic bacterium Serratia marcescens as compared to symbiotic Aiptasia (low NF-κB expression). Furthermore, a P. damicornis coral colony hosting Durusdinium spp. (formerly clade D) symbionts had higher basal NF-κB expression and decreased heat-induced bleaching as compared to two individuals hosting Cladocopium spp. (formerly clade C) symbionts. Lastly, genome-wide gene expression profiling and genomic promoter analysis identified putative NF-κB target genes that may be involved in thermal bleaching, symbiont maintenance, and/or immune protection in P. damicornis. Our results provide further support for the hypothesis that modulation of NF-κB and immunity plays a role in some, but perhaps not all, cnidarian-Symbiodiniaceae partnerships as well as in resistance to pathogens and bleaching.
COSS: A fast and user-friendly tool for spectral library searching
Authors: Shiferaw Genet Abay , Vandermarliere Elien , Hulstaert Niels , Gabriels Ralf , Martens Lennart , Volders Pieter-Jan
Published: May 2019

Spectral similarity searching to identify peptide-derived MS/MS spectra is a promising technique, and different spectrum similarity search tools have therefore been developed. Each of these tools, however, comes with some limitations, mainly due to low processing speed and issues with handling large databases. Furthermore, the number of spectral data formats supported is typically limited, which also creates a threshold to adoption. We have therefore developed COSS (CompOmics Spectral Searching), a new and user-friendly spectral library search tool supporting two scoring functions. COSS also includes decoy spectra generation for result validation. We have benchmarked COSS on three different spectral libraries and compared the results with established spectral search and sequence database search tool. Our comparison showed that COSS more reliably identifies spectra and is faster than other spectral library searching tools. COSS binaries and source code can be freely downloaded from https://github.com/compomics/COSS.
Distributed Biomanufacturing of Liquefied Petroleum Gas
Authors: Hoeven Robin , Hughes John M. X. , Amer Mohamed , Wojcik Emilia Z. , Tait Shirley , Faulkner Matthew , Yunus Ian Sofian , Hardman Samantha J. O. , Johannissen Linus O. , Chen Guo-Qiang , Smith Michael H. , Jones Patrik R. , Toogood Helen S. , Scrutton Nigel S.
Published: May 2019

Liquefied Petroleum Gas (LPG) is a major domestic and transport fuel. Its combustion lessens NOx, greenhouse gas and particulates emissions compared to other fuels. Propane – the major constituent of LPG – is a clean, high value ‘drop-in’ fuel that can help governments develop integrated fuels and energy policies with low carbon burden, providing solutions to the multi-faceted challenges of future energy supply. We show that bio-LPG (bio-propane and bio-butane) can be produced by microbial conversion of waste volatile fatty acids that can be derived from anaerobic digestion, industrial waste, or CO2via photosynthesis. Bio-LPG production was achieved photo-catalytically, using biomass propagated from bioengineered bacteria includingE. coli, Halomonas(in non-sterile seawater), andSynechocystis(photosynthetic). These fuel generation routes could be implemented rapidly in advanced and developing nations of the world to meet energy needs, global carbon reduction targets and clean air directives.
De novo phased assembly of the Vitis riparia grape genome
Authors: Girollet Nabil , Rubio Bernadette , Bert Pierre-François
Published: May 2019

Grapevine is one of the most important fruit species in the world. In order to better understand genetic basis of traits variation and facilitate the breeding of new genotypes, we sequenced, assembled, and annotated the genome of the American native Vitis riparia, one of the main species used worldwide for rootstock and scion breeding. A total of 164 Gb raw DNA reads were obtained from Vitis riparia resulting in a 225X depth of coverage. We generated a genome assembly of the V. riparia grape de novo using the PacBio long-reads that was phased with the 10x Genomics Chromium linked-reads. At the chromosome level, a 500 Mb genome was generated with a scaffold N50 size of 1 Mb. More than 34% of the whole genome were identified as repeat sequences, and 37,207 protein-coding genes were predicted. This genome assembly sets the stage for comparative genomic analysis of the diversification and adaptation of grapevine and will provide a solid resource for further genetic analysis and breeding of this economically important species.
TDP-43 α-helical structure tunes liquid-liquid phase separation and function
Authors: Conicella Alexander E. , Dignon Gregory L. , Zerze Gül H. , Schmidt Hermann Broder , D’Ordine Alexandra M. , Kim Young C. , Rohatgi Rajat , Ayala Yuna M. , Mittal Jeetain , Fawzi Nicolas L.
Published: May 2019

Liquid-liquid phase separation (LLPS) is involved in the formation of membraneless organelles (MLOs) associated with RNA processing. Present in several MLOs, TDP-43 undergoes LLPS and is linked to the pathogenesis of amyotrophic lateral sclerosis (ALS). While some disease variants of TDP-43 disrupt self-interaction and function, here we show that designed single mutations can enhance TDP-43 assembly and function via modulating helical structure. Using molecular simulation and NMR spectroscopy, we observe large structural changes in a dimeric TDP-43. Two conserved glycine residues (G335 and G338) are potent inhibitors of helical extension and helix-helix interaction, which are removed in part by variants including the ALS-associated G335D. Substitution to helix-enhancing alanine at either of these positions dramatically enhances phase separation in vitro and decreases fluidity of phase separated TDP-43 reporter compartments in cells. Furthermore, G335A increases TDP-43 splicing function in a mini-gene assay. Therefore, TDP-43 helical region serves as a short but uniquely tunable module that shows promise as for controlling assembly and function in cellular and synthetic biology applications of LLPS.
Interdependence of intra- and inter-domain motions in the PSD-95 PDZ12 tandem
Authors: Kovács Bertalan , Zajácz-Epresi Nóra , Gáspári Zoltán
Published: May 2019

PSD-95 is the most abundant scaffold protein in the postsynaptic density of neurons. Its two N-terminal PDZ domains form an autonomous structural unit and their interdomain orientation and dynamics was shown to be dependent on binding to various partner proteins. To understand the mechanistic details of the effect of ligand binding on interdomain structure and dynamics, we generated conformational ensembles using experimentally determined NOE interatomic distances and S2order parameters, available from the literature. In our approach no explicit restraints between the two domains were used and their fast dynamics was also treated independently. We found that intradomain structural changes induced by ligand binding have a profound effect on the interfaces where interdomain contacts can be formed, modulating the probability of the occurrence of specific domain-domain orientations. Our results suggest that the β2-β3 loop in the PDZ domains is a key regulatory region that, through interacting with the upstream residues of the C-terminal peptide ligand, influences both intradomain motions and supramodular rearrangement.
Visual pathways in the brain of the jumping spiderMarpissa muscosa
Authors: Steinhoff Philip O.M. , Uhl Gabriele , Harzsch Steffen , Sombke Andy
Published: May 2019

Some animals have evolved task differentiation among their eyes. A particular example is spiders, where most species have eight eyes, of which two (the principal eyes) are used for object discrimination, whereas the other three pairs (secondary eyes) detect movement. In the spider speciesCupiennius saleithese two eye types correspond to two visual pathways in the brain. Each eye is associated with its own first and second order visual neuropil. The second order neuropils of the principal eyes are connected to the arcuate body, whereas the second order neuropils of the secondary eyes are linked to the mushroom body. However, eye size and visual fields are considerably different in jumping spiders. We explored the principal- and secondary eye visual pathways of the jumping spiderMarpissa muscosa. We found that the connectivity of the principal eye pathway is the same as inC. salei, while there are differences in the secondary eye pathways. InM. muscosa,all secondary eyes are connected to their own first order visual neuropils. The first order visual neuropils of the anterior lateral and posterior lateral eyes are further connected with two second order visual neuropils, whereas the posterior median eyes lack second order visual neuropils and their axons project only to the arcuate body. This suggests that the posterior median eyes probably do not serve movement detection inM. muscosa.Furthermore, the second order visual neuropil (L2) inMarpissa muscosapotentially integrates information from the secondary eyes and might thus enable faster movement decisions.
Low-cost, open-access refractive index mapping of algal cells using the transport of intensity equation
Authors: Grant Stephen , Richford Kyle , Burdett Heidi , McKee David , Patton Brian R.
Published: May 2019

Phase contrast microscopy allows stain free imaging of transparent biological samples. One technique, using the transport of intensity equation (TIE), can be performed without dedicated hardware by simply processing pairs of images taken at known spacings within the sample. The resulting TIE images are quantitative phase maps of unstained biological samples. Therefore, spatially resolved refractive index information can also be determined.

Using low-cost, open-source hardware, we applied the TIE to living algal cells to measure their refractive index. We obtained refractive index values that were repeatable within species and differed by distinct amounts depending on the species being measured. We suggest TIE imaging as a method of discrimination between different algal species and, potentially, non-biological materials, based on refractive index. Potential applications in biogeochemical modelling and climate sciences are suggested.
Genetic and physiological mechanisms of freezing tolerance in locally adapted populations of a winter annual
Authors: Sanderson Brian J. , Park Sunchung , Jameel M. Inam , Kraft Joshua C. , Thomashow Michael F. , Schemske Douglas W. , Oakley Christopher G.
Published: May 2019

Premise of the study

Despite myriad examples of local adaptation, the phenotypes and genetic variants underlying such adaptive differentiation are seldom known. Recent work on freezing tolerance and local adaptation in ecotypes of Arabidopsis thaliana from Sweden and Italy provides the essential foundation for uncovering the genotype-phenotype-fitness map for an adaptive response to a key environmental stress.

Methods

Here we examine the consequences of a naturally occurring loss of function (LOF) mutation in an Italian allele of the gene that encodes the transcription factor CBF2, which underlies a major freezing tolerance locus. We used four lines with a Swedish genetic background, each containing a LOF CBF2 allele. Two lines had introgression segments containing of the Italian CBF2 allele, and two were created using CRISPR-Cas9. We used a growth chamber experiment to quantify freezing tolerance and gene expression both before and after cold acclimation.

Key results

Freezing tolerance was greater in the Swedish (72%) compared to the Italian (11%) ecotype, and all four experimental CBF2 LOF lines had reduced freezing tolerance compared to the Swedish ecotype. Differential expression analyses identified ten genes for which all CBF2 LOF lines and the IT ecotype showed similar patterns of reduced cold responsive expression compared to the SW ecotype.

Conclusions

We identified ten genes that are at least partially regulated by CBF2 that may contribute to the differences in cold acclimated freezing tolerance between the Italian and Swedish ecotypes. These results provide novel insight into the molecular and physiological mechanisms connecting a naturally occurring sequence polymorphism to an adaptive response to freezing conditions.