bluuebunny/crossref_metadata_2025 huggingface dataset:
Case Report: Retinal Toxicity Secondary to Ritonavir
Authors: Louie Alyssa K. , Jones Heather N.
Published: May 2019

SIGNIFICANCE

Because patients with HIV have increased life expectancies with the advent of new drug therapies, complications from iatrogenic syndromes such as drug toxicity can occur. Ritonavir-induced retinal toxicity is one such complication but has rarely been reported in the literature.

PURPOSE

This case report describes a patient with bilateral maculopathy and bone spicule–like pigmentary changes in the midperipheral retina due to ritonavir use. In addition, novel optical coherence tomography findings are described.

CASE REPORT

A 53-year-old man presented with gradual-onset blurry vision and difficulty seeing at night. He had been diagnosed as having HIV infection 19 years prior and had previously taken ritonavir for 7 years as part of highly active antiretroviral therapy. Best-corrected acuities were 20/30 in the right eye and 20/25 in the left eye. Clinical examination revealed a subtle annular pattern of retinal pigment epithelium mottling around the fovea and bone spicule–like pigment changes in the midperiphery of both retinas. Optical coherence tomography imaging revealed abnormal subfoveal hyperreflectivity of the ellipsoid zone with relative attenuation centrally, annular parafoveal ellipsoid zone loss, and punctate hyperreflectivity within the ellipsoid zone more eccentrically. Fundus autofluorescence in both eyes showed annular hyperautofluorescence in the parafoveal region, geographic hyperautofluorescence in the areas underlying the midperipheral pigmentary changes, and discrete patches of hyperautofluorescence along the far inferotemporal arcades in areas that appeared normal with biomicroscopy. A diagnosis of retinal toxicity secondary to ritonavir use was made based on the patient's history and clinical examination.

CONCLUSIONS

Ritonavir retinal toxicity seems to be an uncommon adverse event that can cause decreased visual function. This case report provides further evidence of the retinal toxicity and reviews the reported clinical and optical coherence tomography manifestations of the disease.
Case Report: Varicella-zoster Encephalitis with Acute Retinal Necrosis and Oculomotor Nerve Palsy
Authors: Quan Steven Charles , Skondra Dimitra
Published: May 2019

SIGNIFICANCE

Varicella-zoster virus is a common cause of morbidity and vision loss in patients worldwide. It can affect any structure of the eye, from keratitis to acute retinal necrosis. Rapid diagnosis and treatment significantly improve clinical outcomes and quality of life.

PURPOSE

The purpose of this study was to demonstrate a case where urgent referral to the emergency department was required to treat a patient with disseminated herpes zoster infection.

CASE REPORT

This is a rare case of varicella-zoster virus encephalitis in a 70-year-old immunocompetent white man who initially presented to the eye clinic for vertical diplopia and floaters. He also had prior thoracic dermatomal rash, followed by new-onset headaches and cerebellar ataxia. Examination revealed a partial oculomotor nerve palsy in the right eye with bilateral optic disc edema and areas of retinitis consistent with acute retinal necrosis in both eyes. Polymerase chain reaction analysis of his aqueous humor and cerebrospinal fluid confirmed an active zoster infection. He received combination systemic and intravitreal antiviral medication until his retinitis resolved but required adjustments for recalcitrant disease and drug-induced nephrotoxicity. While on maintenance dosing of oral valacyclovir, he experienced reactivation in the form of bilateral vasculitis, which was successfully managed once restarting therapeutic oral dosing.

CONCLUSIONS

This case describes a successful clinical course of acute retinal necrosis with strategies for its treatment in the setting of varicella-zoster encephalitis. Antiviral medication should be given as soon as possible, as prompt treatment has been shown to improve patient outcomes, although prognosis is typically poor in these cases. Multiple specialists are often needed to address different clinical challenges, including central nervous system involvement, viral strain resistance, disease reactivation, and drug toxicity.
Glaucoma Patient Preferences for Video Education on Eye Drop Technique
Authors: Davis Scott A. , Carpenter Delesha M. , Blalock Susan J. , Budenz Donald L. , Lee Charles , Muir Kelly W. , Robin Alan L. , Sleath Betsy
Published: May 2019

SIGNIFICANCE

Glaucoma patients express a strong need for practical instruction on instilling eye drops correctly. To maximize the benefit of a video intervention to improve eye drop technique, patients recommend that video education be provided both in the clinic setting and online.

PURPOSE

The purposes of this study were to (1) describe glaucoma patients' perspectives on how to improve an online eye drop technique video and how to disseminate it to other glaucoma patients and (2) examine how these perspectives differ across demographics.

METHODS

Glaucoma patients (N = 43) who viewed an online eye drop technique educational video as part of a randomized controlled trial were interviewed to assess their overall rating of the video on a 4-point scale, with whom they had watched the video, whether they would recommend the video to others, how the video helped them, how they would recommend improving the video, and how they would like the video to be disseminated to other glaucoma patients.

RESULTS

Patients' mean (SD) rating of the video was 3.4 (0.8), with a higher mean rating of 3.8 among African Americans (P = .02). All 43 patients said that they would recommend that others watch the video. Patients most commonly said that the video helped them learn to block the tear duct correctly, put the cap down on its side, mix the medication correctly, and close the eye after instillation. Patients preferred viewing the video in the doctor's office examination room and a website.

CONCLUSIONS

Eye drop technique videos should be disseminated in the doctor's office and online. Health systems that integrate educational videos into their everyday practice may be able to use technique videos to improve patient technique at low cost and little time burden to the provider.
Effect of Progestin Usage on the Interpretation of Cervical High-grade Squamous Intraepithelial Lesion
Authors: Wang Yiying , Chen Hao , Jiang Qingping , Luo Rongzhen , Zhou Ping , Wang Yan , Zhao Ruijiao , Fadare Oluwole , Zheng Wenxin
Published: May 2019

Progestin usage can alter the histologic and cytologic features of HSIL, which may potentially lead to the under-diagnosis of this precancerous lesion. The objective of the present study was to assess the relationship between the usage of progesterone-based contraceptives and the cytologic features of high-grade squamous intraepithelial lesion (HSIL) of the cervix. In this case-control study, we assembled 46 cases of cervical HSIL (CIN 3), including samples from 26 patients with known history of progestin usage (study group) and 20 samples from patients with no history of any exogenous hormone usage (control group). Cell image analysis was performed on all samples using a proprietary software. Immunohistochemical studies for Ki67, p16, estrogen receptor and progesterone receptor were performed on all cases, as was RNA in situ hybridization for HPV subtypes 16 and 18. Compared with the control group cases, the average nuclear size (21.5±1.80 μm) and the nuclear: cytoplasmic ratio (0.28±0.015) of HSILs in the study group cases were significantly smaller (P=0.026) and reduced (P=0.005), respectively. In addition, the study group cases showed reduced nuclear atypia and pleomorphism and significantly reduced mitotic figures (1.74±1.86/mm in study group versus 5.94±1.3/mm in control group, P<0.0001). The later was likely a consequence of the significantly reduced mitotic figures in the superficial and middle epithelial layers of the study group cases compared with their control group counterparts (0.73±0.88/mm vs. 7.3±2.6/mm, P<0.0001). Progestin usage has no discernible effects on p16 immunoreactivity, Ki67 proliferative index, hormone receptor expression, and HPV RNA levels of HSIL lesions. Being aware of progestin induced morphologic changes on those cervical precancerous lesions will be ultimately improve patient care quality in our daily practice.
Silicone Implant Illness: Science versus Myth?
Authors: Rohrich Rod J. , Kaplan Jordan , Dayan Erez
Published: May 2019

The purpose of this Special Topic article is to present the current state of scientific evidence related to the safety of silicone breast implants. There is presently overwhelming evidence to support the safety of silicone breast implants. Ultimately, the decision to obtain, keep, or remove breast implants is the choice of the patient. If a patient chooses to have her breast implants removed, it is important to find a board-certified plastic surgeon with expertise in breast surgery. Ongoing studies are strongly encouraged in all areas, from cancer detection to autoimmune disease, as we strive for improved patient safety, patient awareness, and patient education. To the best of our body of scientific knowledge to date, there have not been any concrete or evidence-based studies or peer-reviewed data concerning the formation of a new syndrome: “silicone implant illness.” Silicone breast implants are used in nearly 300,000 breast augmentation and 100,000 breast reconstruction operations annually in the United States.
1
Silicone gel–filled implants were first approved by the U.S. Food and Drug Administration in 1962. Since that time, few medical devices have been studied as closely for their safety and associated adverse outcomes. Despite multiple generations of implant shells and gel fillers, the basic components remain as originally designed.
2,3
Attitudes About Coping With Fatigue in Patients With Gastric Cancer
Authors: Yeun Eun Ja , Jeon Misoon
Published: May 2019

Cancer-related fatigue is the most common symptom in patients with cancer. Coping methods for cancer-related fatigue differ from those of patients without cancer, as the situations faced by patients with cancer are unique. This study aimed to identify subjectivity concerning coping with fatigue in Korean patients with gastric cancer. Q-methodology was used to examine subjective perceptions regarding coping with fatigue among Korean patients with gastric cancer. A convenience sample of 33 participants, who had been hospitalized in 2 university hospitals in South Korea, was recruited to participate in the study and 37 selected Q-samples were classified into a normal forced distribution using a 9-point bipolar grid. The obtained data were analyzed by using PC-QUANL for Windows. Three factors representing distinct attitudes about coping with fatigue emerged among Korean patients with gastric cancer: an optimistic mind, dependency on medicine, and exercise preference. The 3 factors explained 39.4% of the total variance (23.7%, 7.9%, and 7.8%, respectively). Based on the study findings, it is important to develop customized nursing interventions that consider the characteristics of each patient group with gastric cancer. Health professionals should assess the attitudes of patients with gastric cancer about coping with fatigue, explore their situation, and consider their lifestyle.
Novel engraftment and T cell differentiation of human hematopoietic cells inArt-/-IL2RG-/SCID pigs
Authors: Boettcher Adeline N , Li Yunsheng , Ahrens Amanda P. , Kiupel Matti , Byrne Kristen A. , Loving Crystal L. , Cino-Ozuna A. Giselle , Wiarda Jayne E. , Adur Malavika , Schultz Blythe , Swanson Jack J. , Snella Elizabeth M. , Ho Chak-Sum (Sam) , Charley Sara E. , Kiefer Zoe E. , Cunnick Joan E. , Powell Ellis J. , Dell’Anna Giuseppe , Jens Jackie , Sathe Swanand , Goldman Frederick , Westin Erik R. , Dekkers Jack C. M. , Ross Jason W. , Tuggle Christopher K.
Published: May 2019

Pigs with severe combined immunodeficiency (SCID) are an emerging biomedical animal model. Swine are anatomically and physiologically more similar to humans than mice, making them an invaluable tool for preclinical regenerative medicine and cancer research. One essential step in further developing this model is the immunological humanization of SCID pigs. In this work we have generated T-B-NK-SCID pigs through site directed CRISPR/Cas9 mutagenesis ofIL2RGwithin a naturally occurringDCLRE1C(Artemis)-/-genetic background. We confirmedArt-/-IL2RG-/Ypigs lacked T, B, and NK cells in both peripheral blood and lymphoid tissues. Additionally, we and successfully performed a bone marrow transplant on oneArt-/-IL2RG-/Ymale SCID pig with a bone marrow from a complete swine leukocyte antigen (SLA) matched donor without conditioning to reconstitute porcine T and NK cells. Next, we performedin uteroinjections of cultured human CD34+selected cord blood cells into the fetalArt-/-IL2RG-/YSCID pigs. At birth, human CD45+CD3ε+cells were detected in peripheral blood ofin uteroinjected SCID piglets. Human leukocytes were also detected within the bone marrow, spleen, liver, thymus, and mesenteric lymph nodes of these animals. Taken together, we describe critical steps forwards the development of an immunologically humanized SCID pig model.

One sentence summary

We have generated a T-B-NK-SCID pig model through site directed mutagenesis ofIL2RGin a naturally occurringArtemisnull background and show successful engraftment of human T and B cells in blood and lymphoid organs afterin uteroinjection of human hematopoietic stem cells.
Mapping interactions of microbial metabolites and human receptors
Authors: Colosimo Dominic A. , Kohn Jeffrey A. , Luo Peter M. , Han Sun M. , Pickard Amanda J. , Rao Arka , Cross Justin R. , Cohen Louis J. , Brady Sean F.
Published: May 2019

Despite evidence linking the human microbiome to health and disease, the mechanistic details of how the microbiota affects human physiology remain largely unknown. Metabolites encoded by bacteria are expected to play an integral role in the microbiota’s effect on its human host. Assigning function to these metabolites is therefore critical to determining the molecular underpinnings of the host-microbe relationship and ultimately developing microbiota inspired therapies. Here we use large-scale functional screening of small molecules produced by individual members of a simplified human microbiota to identify bacterial metabolites that agonize G-protein coupled receptors (GPCR). This analysis revealed a complex network of metabolite host receptor interactions and guided our identification of multiple microbiota derived agonists of GPCRs associated with diverse biological functions within the nervous and immune systems, among others. Collectively, the metabolite-receptor pairs we uncovered indicate that diverse aspects of human health are potentially modulated by structurally simple metabolites arising from primary bacterial metabolism.

Statement of Significance

Bacteria residing within the human body have been shown to influence human health. It is likely that physiological responses to the human microbiota are mediated by the collection of small molecules encoded within these bacteria. In this study we use direct functional screening of small molecules produced by individual members of a simplified human microbiota to identify new G protein coupled receptor-metabolite interactions that seek to explain the molecular underpinnings of the microbiota’s influence on its human host.
Dividing subpopulation of Escherichia coli in stationary phase
Authors: Jõers Arvi , Liske Eliis , Tenson Tanel
Published: May 2019

The bacterial growth cycle contains different phases: after the growth substrate is exhausted of the toxic waste products accumulate the growth stops. In this non-growing culture the number of colony forming bacteria remains constant or starts to decrease. It has been shown that during prolonged incubation there is constant growth and death of bacteria and certain mutant populations take over the culture. Here we show that the dynamic cell division and death balance can be obtained even before mutants take over the culture.
Novel Pure αVβ3 Integrin Antagonists That Do Not Induce Receptor Extension, Prime the Receptor, or Enhance Angiogenesis at Low Concentrations
Authors: Li Jihong , Fukase Yoshiyuki , Shang Yi , Zou Wei , Muñoz-Félix José M. , Buitrago Lorena , Buitrago Lorena , van Agthoven Johannes , Zhang Yixiao , Hara Ryoma , Tanaka Yuta , Okamoto Rei , Yasui Takeshi , Nakahata Takashi , Imaeda Toshihiro , Aso Kazuyoshi , Zhou Yuchen , Locuson Charles , Nesic Dragana , Duggan Mark , Takagi Junichi , Vaughan Roger D. , Walz Thomas , Hodivala-Dilke Kairbaan , Teitelbaum Steven L. , Amin Arnaout M. , Filizola Marta , Foley Michael A. , Coller Barry S.
Published: May 2019

The integrin αVβ3 receptor has been implicated in several important diseases, but no αVβ3 antagonists are approved for human therapy. One possible limitation of current small-molecule antagonists is their ability to induce a major conformational change in the receptor that induces it to adopt a high-affinity ligand-binding state. In response, we used structural inferences from a pure peptide antagonist to design the small-molecule pure antagonists TDI-4161 and TDI-3761. Both compounds inhibit αVβ3-mediated cell adhesion to αVβ3 ligands, but do not induce the conformational change as judged by antibody binding, electron microscopy, X-ray crystallography, and receptor priming studies. Both compounds demonstrated the favorable property of inhibiting bone resorptionin vitro, supporting potential value in treating osteoporosis. Neither, however, had the unfavorable property of the αVβ3 antagonist cilengitide of paradoxically enhancing aortic sprout angiogenesis at concentrations below its IC50, which correlates with cilengitide’s enhancement of tumor growthin vivo.

Significance Statement

αVβ3 is a potential therapeutic target for several important human diseases, but there are currently no αVβ3 antagonists approved for human therapy. Current candidates are primarily based on the Arg-Gly-Asp (RGD) motif and act as partial agonists in that they induce αVβ3 to undergo a conformational change that converts it into a high-affinity ligand-binding state. We have used structure-guided design to produce pure small-molecule αVβ3 antagonists that do not induce the conformational change as judged by protein crystallography, electron microscopy, and receptor priming. These compounds inhibit αVβ3-mediated bone resorptionin vitro, but unlike the partial agonist cilengitide, do not enhance angiogenesis at low doses, a property that correlates with low-dose cilengitide’s enhancement of tumor growthin vivo. These pure αVβ3 antagonists can help define αVβ3’s role in animal models. If they demonstrate benefits over partial agonists in these model systems, they may be appropriate to consider for human therapy.
A minimal model for microbial biodiversity can reproduce experimentally observed ecological patterns
Authors: Marsland Robert , Cui Wenping , Mehta Pankaj
Published: May 2019

Surveys of microbial biodiversity such as the Earth Microbiome Project (EMP) and the Human Microbiome Project (HMP) have revealed robust ecological patterns across different environments. A major goal in ecology is to leverage these patterns to identify the ecological processes shaping microbial ecosystems. One promising approach is to use minimal models that can relate mechanistic assumptions at the microbe scale to community-level patterns. Here, we demonstrate the utility of this approach by showing that the Microbial Consumer Resource Model (MiCRM) – a minimal model for microbial communities with resource competition, metabolic crossfeeding and stochastic colonization – can qualitatively reproduce patterns found in survey data including compositional gradients, dissimilarity/overlap correlations, richness/harshness correlations, and nestedness of community composition. By using the MiCRM to generate synthetic data with different environmental and taxonomical structure, we show that large scale patterns in the EMP can be reproduced by considering the energetic cost of surviving in harsh environments and HMP patterns may reflect the importance of environmental filtering in shaping competition. We also show that recently discovered dissimilarity-overlap correlations in the HMP likely arise from communities that share similar environments rather than reflecting universal dynamics. We identify ecologically meaningful changes in parameters that alter or destroy each one of these patterns, suggesting new mechanistic hypotheses for further investigation. These findings highlight the promise of minimal models for microbial ecology.
Trajectory-based differential expression analysis for single-cell sequencing data
Authors: Van den Berge Koen , de Bézieux Hector Roux , Street Kelly , Saelens Wouter , Cannoodt Robrecht , Saeys Yvan , Dudoit Sandrine , Clement Lieven
Published: May 2019

Trajectory inference has radically enhanced single-cell RNA-seq research by enabling the study of dynamic changes in gene expression levels during biological processes such as the cell cycle, cell type differentiation, and cellular activation. Downstream of trajectory inference, it is vital to discover genes that are associated with the lineages in the trajectory to illuminate the underlying biological processes. Furthermore, genes that are differentially expressed between developmental/activational lineages might be highly relevant to further unravel the system under study. Current data analysis procedures, however, typically cluster cells and assess differential expression between the clusters, which fails to exploit the continuous resolution provided by trajectory inference to its full potential. The few available non-cluster-based methods only assess broad differences in gene expression between lineages, hence failing to pinpoint the exact types of divergence. We introduce a powerful generalized additive model framework based on the negative binomial distribution that allows flexible inference of (i) within-lineage differential expression by detecting associations between gene expression and pseudotime over an entire lineage or by comparing gene expression between points/regions within the lineage and (ii) between-lineage differential expression by comparing gene expression between lineages over the entire lineages or at specific points/regions. By incorporating observation-level weights, the model additionally allows to account for zero inflation, commonly observed in single-cell RNA-seq data from full-length protocols. We evaluate the method on simulated and real datasets from droplet-based and full-length protocols, and show that the flexible inference framework is capable of yielding biological insights through a clear interpretation of the data.
Functional integration of “undead” neurons in the olfactory system
Authors: Prieto-Godino Lucia L. , Silbering Ana F. , Khallaf Mohammed A. , Cruchet Steeve , Bojkowska Karolina , Pradervand Sylvain , Hansson Bill S. , Knaden Markus , Benton Richard
Published: May 2019

Programmed cell death (PCD) is widespread during neurodevelopment, typically eliminating the surpluses of neuronal production. Employing theDrosophilaolfactory system, we examined the potential of cells fated to die to contribute to circuit evolution. Inhibition of PCD is sufficient to generate many new cells that express neural markers and exhibit odor-evoked activity. These “undead” neurons express a subset of olfactory receptors that, intriguingly, is enriched for recent receptor duplicates and include some normally found in other chemosensory organs and life-stages. Moreover, undead neuron axons integrate into the olfactory circuitry in the brain, forming novel receptor/glomerular couplings. Comparison of homologous olfactory lineages across drosophilids reveals natural examples of fate changes from death to a functional neuron. Finally, we provide evidence that PCD contributes to evolutionary differences in carbon dioxide-sensing circuit formation inDrosophilaand mosquitoes. These results reveal the remarkable potential of alterations in PCD patterning to evolve new neural pathways.
Evidence for purifying selection on conserved noncoding elements in the genome ofDrosophila melanogaster
Authors: Tristan Berr , Aurelie Peticca , Annabelle Haudry
Published: May 2019

Identification of regulatory regions within genomes is a key challenge for understanding the influence of functional traits on species evolution. Development of whole-genome sequencing programs in the early 2000s has been associated with the rise of comparative genomics as a powerful tool for predicting functional regions in genomes, using structural characteristics of DNA sequences. Conserved Noncoding Elements (CNEs,i.e. untranslated sequences highly similar across divergent species) were early identified as candidate regulatory regions in metazoans, plants, and fungi. CNEs have been repeatedly discriminated from mutational cold-spots, but only few studies have assessed their functional relevance at a genome-wide scale. In the present study, we used a whole-genome alignment of 27 insect species to build a coherent mapping of CNEs in the genome ofDrosophila melanogaster. We then exploited polymorphism data from 48 European populations ofD. melanogasterto estimate levels of nucleotide diversity and adaptive evolution in CNEs. We show here that about 35% ofD. melanogasterautosomes fall into conserved noncoding regions that exhibit reduced genetic diversity and undergo purifying selection. In addition, we report six insertions of Transposable Elements (TEs) in the genome ofD. melanogastershowing high levels of conservation across Drosophila species. Half of these insertions are located in untranslated transcribed regions (UTRs) of genes involved in developmental pathways and thus represent potential relics of ancient TE domestication events.
Biomarkers for aging identified in cross-sectional studies tend to be non-causative
Authors: Nelson Paul G. , Promislow Daniel E. L. , Masel Joanna
Published: May 2019

Biomarkers are important tools for diagnosis, prognosis, and identification of the causal factors of physiological conditions. Biomarkers are typically identified by correlating biological measurements with the status of a condition in a sample of subjects. Cross-sectional studies sample subjects at a single timepoint, while longitudinal studies follow a cohort through time. Identifying biomarkers of aging is subject to unique challenges. Individuals who age faster have intrinsically higher mortality rates and so are preferentially lost over time, in a phenomenon known as cohort selection. In this paper, we use simulations to show that cohort selection biases cross-sectional analysis away from identifying causal loci of aging, to the point where cross-sectional studies are less likely to identify loci that cause aging than if loci had been chosen at random. We go on to show this bias can be corrected by incorporating correlates of mortality identified from longitudinal studies, allowing cross sectional studies to effectively identify the causal factors of aging.
Pharmacodynamics of linezolid-plus-fosfomycin against vancomycin-susceptible and -resistant enterococci in vitro and in vivo of a Galleria mellonella larval infection model
Authors: Qi Caifen , Xu Shuangli , Wu Maomao , Zhu Shuo , Liu Yanyan , Huang Hong , Zhang Guijun , Li Jiabin , Huang Xiaohui
Published: May 2019

Objective

To explore the in vitro and in vivo antibacterial activity of linezolid/fosfomycin combination against vancomycin-susceptible and -resistant enterococci (VSE and VRE), providing theoretical basis for the treatment of VRE.

Methods

The checkerboard method and time-kill curve study were used to evaluate the synergistic effect of linezolid combined with fosfomycin against VSE and VRE. The transmission electron microscopy (TEM) was employed to observe the bacterial cell morphology followed by each drug alone and in combination, elucidating the possible result of antibiotic combination therapy. The Galleria mellonella infection model was constructed to demonstrate the in vivo efficacy of linezolid plus fosfomycin for VSE and VRE infection.

Results

The fractional inhibitory concentration index (FICI) values of all strains suggested that linezolid showed synergy or additivity in combination with fosfomycin against five of the six strains. Time-kill experiments demonstrated that the combination of linezolid-fosfomycin at 1×MIC or 2×MIC led to higher degree of bacterial killing without regrowth for all isolates tested than each monotherapy. TEM imaging showed that the combination treatment damaged the bacterial cell morphology more obviously than each drug alone. In the Galleria mellonella infection model, the enhanced survival rate of the combination treatment was revealed compared to linezolid monotherapy (P<0.05).

Conclusions

Our data manifest that the combination of linezolid and fosfomycin may be a possible therapeutic regimen for VRE infection. The combination displays excellent bacterial killing and inhibits amplification of fosfomycin-resistant subpopulations.
Intraspecific diversity of fission yeast mitochondrial genomes
Authors: Tao Yu-Tian , Suo Fang , Tusso Sergio , Wang Yan-Kai , Huang Song , Wolf Jochen B. W. , Du Li-Lin
Published: May 2019

The fission yeastSchizosaccharomyces pombeis an important model organism, but its natural diversity and evolutionary history remain under-studied. In particular, the population genomics of theS. pombemitochondrial genome (mitogenome) has not been thoroughly investigated. Here, we assembled the complete circular-mapping mitogenomes of 192S. pombeisolatesde novo, and found that these mitogenomes belong to 69 non-identical sequence types ranging from 17618 bp to 26910 bp in length. Using the assembled mitogenomes, we identified 20 errors in the reference mitogenome and discovered two previously unknown mitochondrial introns. Analysing sequence diversity of these 69 types of mitogenomes revealed two highly distinct clades, with only three mitogenomes exhibiting signs of inter-clade recombination. This diversity pattern suggests that currently availableS. pombeisolates descend from two long-separated ancestral lineages. This conclusion is corroborated by the diversity pattern of the recombination-repressedK-region located between donor mating-type locimat2andmat3in the nuclear genome. We estimated that the two ancestralS. pombelineages diverged about 31 million generations ago. These findings shed new light on the evolution ofS. pombeand the datasets generated in this study will facilitate future research on genome evolution.
Gene editing preserves visual function in a mouse model of retinal degeneration
Authors: Vagni Paola , Perlini Laura E. , Chenais Naïg A. L. , Marchetti Tommaso , Parrini Martina , Contestabile Andrea , Cancedda Laura , Ghezzi Diego
Published: May 2019

Inherited retinal dystrophies are a large and heterogeneous group of degenerative diseases caused by mutations in various genes. Given the favourable anatomical and immunological characteristics of the eye, gene therapy holds great potential for their treatment. We used a tailored CRISPR/Cas9-based gene editing system to prevent retinal photoreceptor death in the Rd10 mouse model of retinitis pigmentosa. We tested the gene editing toolin vitroand then usedin vivosubretinal electroporation to deliver it to one of the retinas of mouse pups at different stages of photoreceptor differentiation. Three months after gene editing, the treated eye exhibited a higher visual acuity compared to the untreated eye. Moreover, we observed preservation of light-evoked responses both in explanted retinas and in the visual cortex of treated animals. Our study validates a CRISPR/Cas9-based therapy as a valuable new approach for the treatment of retinitis pigmentosa caused by autosomal recessive loss-of-function point mutations.
Microbial metabolite fluxes in a model marine anoxic ecosystem
Authors: Louca Stilianos , Astor Yrene M. , Doebeli Michael , Taylor Gordon T. , Scranton Mary I.
Published: May 2019

Permanently anoxic regions in the ocean are widespread, and exhibit unique microbial metabolic activity exerting substantial influence on global elemental cycles and climate. Reconstructing microbial metabolic activity rates in these regions has been challenging, due to the technical difficulty of direct rate measurements. In Cariaco Basin, which is the largest permanently anoxic marine basin and an important model system for geobiology, long-term monitoring has yielded time series for the concentrations of biologically important compounds; however the underlying metabolite fluxes remain poorly quantified. Here we present a computational approach for reconstructing vertical fluxes and in situ net production/consumption rates from chemical concentration data, based on a 1-dimensional time-dependent diffusive transport model that includes adaptive penalization of overfitting. We use this approach to estimate spatiotemporally resolved fluxes of oxygen, nitrate, hydrogen sulfide, ammonium, methane and phosphate within the sub-euphotic Cariaco Basin water column (depths 150–900 m, years 2001–2014), and to identify hotspots of microbial chemolithotrophic activity. Predictions of the fitted models are in excellent agreement with the data, and substantially expand our knowledge of the geobiology in Cariaco Basin. In particular, we find that the diffusivity, and consequently fluxes of major reductants such as hydrogen sulfide and methane, are about two orders of magnitude greater than previously estimated, thus resolving a long standing apparent conundrum between electron donor fluxes and measured dark carbon assimilation rates.
Computational and experimental analysis of the glycophosphatidylinositol-anchored proteome of the human parasitic nematodeBrugia malayi
Authors: Mersha Fana B. , Cortes Leslie K. , Luck Ashley N. , McClung Colleen M. , Ruse Cristian I. , Taron Christopher H. , Foster Jeremy M.
Published: May 2019

Further characterization of essential systems in the parasitic filarial nematodeBrugia malayiis needed to better understand its biology, its interaction with its hosts, and to identify critical components that can be exploited to develop novel treatments. The production of glycophosphatidylinositol-anchored proteins (GPI-APs) is essential in humans, yeast, and the nematodeCaenorhabditis elegans. In addition, GPI-APs perform many important roles for cells. In this study, we characterized theB. malayiGPI-anchored proteome using both computational and experimental approaches. We used bioinformatic strategies to show the presence or absence ofB. malayiGPI-AP biosynthetic pathway genes and to compile a putativeB. malayiGPI-AP proteome using available prediction programs. We verified thesein silicoanalyses using proteomics to identify GPI-AP candidates prepared from the surface of intact worms and from membrane enriched extracts. Our study represents the first description of the GPI-anchored proteome inB. malayiand lays the groundwork for further exploration of this essential protein modification as a target for novel anthelmintic therapeutic strategies.
MHC genotyping from rhesus macaque exome sequences
Authors: Caskey John R. , Wiseman Roger W. , Karl Julie A. , Baker David A. , Lee Taylor , Raveendran Muthuswamy , Harris R. Alan , Hu Jianhong , Muzny Donna M. , Rogers Jeffrey , O’Connor David H.
Published: May 2019

Indian rhesus macaque major histocompatibility complex (MHC) variation can influence the outcomes of transplantation and infectious disease studies. Frequently, rhesus macaques are MHC genotyped to identify variants that could account for unexpected results. Since the MHC is only one region in the genome where variation could impact experimental outcomes, strategies for simultaneously profiling variation in the macaque MHC and the remainder of the protein coding genome would be useful. Here we introduce macaque exome sequence (MES) genotyping, in which MHC class I and class II genotypes are determined with high confidence using target-enrichment probes that are enriched for MHC sequences. For a cohort of 27 Indian rhesus macaques, we describe two methods for obtaining MHC genotypes from MES data and demonstrate that the MHC class I and class II genotyping results obtained with these methods are 98.1% and 98.7% concordant, respectively, with expected MHC genotypes. In contrast, conventional MHC genotyping results obtained by deep sequencing of short multiplex PCR amplicons were only 92.6% concordant with expectations for this cohort.
The transcriptional correlates of divergent electric organ discharges inParamormyropselectric fish
Authors: Losilla Mauricio , Gallant Jason R.
Published: May 2019

Background

Understanding the genomic basis of phenotypic diversity can be greatly facilitated by examining adaptive radiations with hypervariable traits. In this study, we focus on a rapidly diverged species group of mormyrid electric fish in the genusParamormyrops, which are characterized by extensive phenotypic variation in electric organ discharges (EODs). The main components of EOD diversity are waveform duration, complexity and polarity. Using an RNA-sequencing based approach, we sought to identify gene expression correlates for each of these EOD waveform features by comparing 11 specimens ofParamormyropsthat exhibit variation in these features.

Results

Patterns of gene expression amongParamormyropsare highly correlated, and 3,274 genes (16%) were differentially expressed. Using our most restrictive criteria, we detected 71-144 differentially expressed genes correlated with each EOD feature, with little overlap between them. The predicted functions of several of these genes are related to extracellular matrix, cation homeostasis, lipid metabolism, and cytoskeletal and sarcomeric proteins. These genes are of significant interest given the known morphological differences between electric organs that underlie differences in the EOD waveform features studied.

Conclusions

In this study, we identified plausible candidate genes that may contribute to phenotypic differences in EOD waveforms among a rapidly diverged group of mormyrid electric fish. These genes may be important targets of selection in the evolution of species-specific differences in mate-recognition signals.
Intercellular Conduction Optimizes Arterial Network Function and Conserves Blood Flow Homeostasis during Cerebrovascular Challenges
Authors: Zechariah Anil , T. Tran Cam Ha , Hald Bjorn O. , Sandow Shaun L. , Sancho Maria , Fabris Sergio , Tuor Ursula I. , Gordon Grant R.J. , Welsh Donald G.
Published: May 2019

Cerebral arterial networks match blood flow delivery with neural activity. Neurovascular response begins with a stimulus and a focal change in vessel diameter, which by themselves is inconsequential to blood flow magnitude, until they spread and alter the contractile status of neighboring arterial segments. We sought to define the mechanisms underlying integrated vascular behavior and considered the role of intercellular electrical signalling in this phenomenon. Electron microscopic and histochemical analysis revealed the structural coupling of cerebrovascular cells and the expression of gap junctional subunits at the cell interfaces, enabling intercellular signaling among vascular cells. Indeed, robust vasomotor conduction was detected in human and mice cerebral arteries after focal vessel stimulation; a response attributed to endothelial gap junctional communication, as its genetic alteration attenuated this behavior. Conducted responses was observed to ascend from the penetrating arterioles, influencing the contractile status of cortical surface vessels, in a simulated model of cerebral arterial network. Ascending responses recognisedin vivoafter whisker stimulation, were significantly attenuated in mice with altered endothelial gap junctional signalling confirming that gap junctional communication drives integrated vessel responses. The diminishment in vascular communication also impaired the critical ability of the cerebral vasculature to maintain blood flow homeostasis and hence tissue viability, after stroke. Our findings establish the integral role of intercellular electrical signalling in transcribing focal stimuli into coordinated changes in cerebrovascular contractile activity and expose, a hitherto unknown mechanism for flow regulation after stroke.

Significance

Neurovascular responses are viewed as a one step process whereby stimuli derived from neural cells focally diffuse to a neighboring vessel, altering its contractile state. While focal changes in tone can subtly tune flow distribution, they can’t substantively change “perfusion magnitude” as vascular resistance is broadly distributed along the cerebral arterial tree. We report that nature overcomes this biophysical constraint by conducting electrical signals among coupled vascular cells, along vessels, and across branch points. Our quantitative exploration of intercellular conduction illustrates how network coordination optimizes blood flow delivery in support of brain function. Diminishing the ability of vascular cells to electrically communicate, mitigates the brain’s ability to regulate perfusion during functional hyperemia and after stroke, the latter advancing tissue injury.
Novel application method for mesenchymal stem cell therapy utilizing its attractant–responsive accumulation property
Authors: Ueda Nobuyuki , Atsuta Ikiru , Ayukawa Yasunori , Yamaza Takayoshi , Furuhashi Akihiro , Narimatsu Ikue , Matsuura Yuri , Kondo Ryosuke , Watanabe Yu , Zhang Xiaoxu , Koyano Kiyoshi
Published: May 2019

Objectives

It remains difficult to control the delivery of appropriate amounts of mesenchymal stem cell (MSC)-based cell therapies. To examine the ability of MSCs to accumulate at sites of damage and potential therapeutic benefit of providing continuous migration of MSCs to these sites, we observed the effect of MSCs administered in a collagen gel scaffold on healing of a tooth extraction site.

Materials and Methods

MSCs isolated from the bone marrow of green fluorescent protein (GFP)-expressing donor mice were expanded for 3 weeks in three-dimensional (3-D) culture using a collagen gel scaffold, and evaluated to confirm the efficacy of the scaffold. Next, MSCs suspended in collagen gel were subcutaneously administered into the backs of mice. Two days later, extraction of the maxillary first molar was carried out. Numbers of MSCs in scaffolds, migration and accumulation around the extracted tooth cavity, extraction site healing, and presence of MSCs in vital organs were evaluated.

Results

MSCs cultured in the collagen gel scaffold maintained stemness for 2 weeks. After subcutaneous administration, numbers of MSCs in scaffolds slightly decreased over time, but cells survived for at least 2 weeks. After tooth extraction, GFP-expressing MSCs were confirmed in the surrounding mucosa of the extracted tooth cavity; in the scaffold group, numbers of MSCs increased over time and fewer were observed in lung tissue. Wound healing was enhanced by injection of MSCs via the tail vein or into the back compared with the untreated control group.

Conclusions

Delivery in a collagen gel could maintain the characteristics of MSCs, which migrated to the damaged area and promoted wound healing without side effects occurring with conventional administration methods.
Changes of TLQP-21 in Response to Glucose Load
Authors: Corda Giulia , Noli Barbara , Manconi Barbara , Brancia Carla , Pellegrini Manuela , Naro Fabio , Ferri Gian-Luca , Cocco Cristina
Published: May 2019

The TLQP-21 peptide peripherally potentiates glucose-stimulated insulin secretion. The aim of this study was to investigate a possible endocrine mechanism through which TLQP-21 increases the insulin secretion. Using an antibody specific for the common N-terminal portion of the TLQP peptides, we studied pancreas and plasma of mice subjected to intraperitoneal glucose load, by immunohistochemistry and immunosorbent assay (ELISA), alone or coupled to High Performance Liquid Chromatography (HLPC). Mice underwent a period of starvation hence have received a glucose load, or saline, and were sacrificed 30 or 120 minutes later. In normal endocrine pancreas, the TLQP-antiserum stained either peripheral or central cells. Interestingly, 30 min after a glucose load, TLQP immunostaining was disappeared in pancreas and, when analysed by ELISA, the TLQP-levels started to increase in plasma reaching peak concentration at 120 min. (controls vs. 30 and 120 min.: p<0.05 and p<0.001, respectively). The analysis of plasma and pancreas extracts using HLPC coupled to ELISA demonstrated the presence of the TLQP-21, with statistically significant increase of this peptide in plasma at 120 min (vs. controls p<0.05) in agreement to the changes seen by measuring the totality of the TLQP peptides. In pancreas sections we found the presence of the C3a-R1, involved in insulin secretion, and previously identified as a TLQP-21 receptor. Hence, after a glucose load, TLQP-21, may be released by the pancreas into the plasma, returning to the pancreas in order to modulate the insulin secretion through the C3a-R1.
Mating strategy is determinant of Adenovirus prevalence in European bats
Authors: Rossetto Federica , Iglesias-Caballero Maria , Liedtke H. Christoph , Gomez-Mestre Ivan , Berciano Jose M. , Pérez-Suárez Gonzalo , de Paz Oscar , Echevarría Juan E. , Casas Inmaculada , Juste Javier
Published: May 2019

Adenoviruses are double-strained DNA viruses found in a great number of vertebrates, including humans. In order to understand their transmission dynamics, it is crucial, even from a human health perspective, to investigate how host traits influence their prevalence. Bats are important reservoirs for Adenoviruses, and here we use the results of recent screenings in Western Europe to evaluate the association between characteristic traits of bat species and their probability of hosting Adenoviruses, taking into account their phylogenetic relationships. Across species, we found an important phylogenetic component in the presence of Adenoviruses and mating strategy as the most determinant factor conditioning the prevalence of Adenoviruses across bat species. Contrary to other more stable mating strategies (e.g. harems), swarming could hinder transmission of Adenoviruses since this strategy implies that contacts between individuals are too short. Alternatively, bat species with more promiscuous behavior may develop a stronger immune system. Outstandingly high prevalence of Adenoviruses was reported for the Iberian species Pipistrellus pygmaeus, P. kuhlii and Nyctalus lasiopterus and we found that in the latter, males were more likely to be infected by Adenoviruses than females, due to the immunosuppressing consequence of testosterone during the mating season. As a general trend across species, we found that the number of Adenoviruses positive individuals was different across localities and that the difference in prevalence between populations was correlated with their geographic distances (P. pygmaeus). These results increase our knowledge about the transmission mechanisms of Adenoviruses.

Author Summary

Adenoviruses are DNA viruses with a wide range of vertebrate hosts, including humans, causing ocular, respiratory and gastrointestinal diseases. Here, we focus on the prevalence of Adenoviruses in bats, which are known to be natural reservoir of many viruses, using the results of recent screenings for prevalence of these viruses in 33 European bat species. Our aim is to find association between Adenoviruses prevalence and biological and behavioral host traits, considering the heterogeneity both between and within species in order to have a deeper understanding of mechanisms of viral transmission.

Our results highlight the importance of mating strategy: bats species using swarming as mating strategy are less likely to be infected by Adenoviruses. Moreover, we found that locality of capture can explain a higher prevalence of Adenovirus within species. However, no general pattern has been found in the analysis at individual level, suggesting a strong species specificity and complex viral transmission dynamics.