bluuebunny/crossref_metadata_2025 huggingface dataset:
Zika Virus Infection: Review Of Neuroimage Studies And The Relationship Between Findings And Time Of Infection
Authors: Radaelli Graciane , Lahorgue Nunes Magda , Bernardi Soder Ricardo , Monteiro de Oliveira Júlia , Konat Bruzzo Fernanda Thays , Neto Felipe Kalil , Leal Conceição Eduardo , Portuguez Mirna Wetters , da Costa Jaderson Costa
Published: September 2019

AIM

To conduct a systematic literature review on neuroimage findings in children with microcephaly by Zika virus (ZIKV).

METHOD

We performed a literature search in PubMed, Cochrane Library and Web of Science for full-text articles reporting neuroimage exam of computed tomography scan or magnetic resonance imaging.

RESULTS

Were identified 2,214 publications. Of these 2,170 were excluded by the analysis of titles and abstracts, resulting in 7 articles included. The abnormalities presented in neuroimage showed the highest occurrence in the first trimester: decreased brain volume + increased extra-axial CSF space (100%), subcortical calcifications (89.1%), microcephaly (89.1%), ventriculomegaly (72.9%), malformation of cortical development (40.5%), basal ganglia calcifications (40.5%), megacisterna magna (39.1%). In relation to the second trimester of ZIKV infection, the most common were as follows: decreased brain volume + increased extra-axial CSF space (100%), subcortical calcifications (100%), microcephaly (85.7%), ventriculomegaly (71.4%), malformation of cortical development (71.4%), basal ganglia calcifications (19%), megacisterna magna (4.7%). In relation to the neuroimage abnormalities detected in the 3rd trimester 2 cases were found.

INTERPRETATION

This systematic review is the first that evaluates brain changes in newborns with different neuroimage techniques (CT and MRI exams) and related findings with the gestational period of ZIKV infection.
Nothing About Us Without Us: A Scoping Review and Priority-Setting Partnership in Type 1 Diabetes and Exercise
Authors: Klaprat Nika M.D. , Askin Nicole , MacIntosh Andrea , Brunton Nicole , Hay Jacqueline L. , Yardley Jane E. , Marks Seth D. , Sibley Kathryn M. , Duhamel Todd A. , McGavock Jonathan M.
Published: September 2019

Objectives

Examine the characteristics of patient engagement (PE) practices in exercise-based randomized trials in type 1 diabetes (T1D), and facilitate T1D stakeholders in determining the top ten list of priorities for exercise research.

Design

Two methodological approaches were employed: a scoping review and a modified James Lind Alliance priority-setting partnership.

Methods

Published (Medline, Embase, CINAHL, and Central databases) and grey literature (www.clinicaltrials.gov) were searched to identify randomized controlled trials of exercise interventions lasting minimum four weeks and available in English. We extracted information on PE and patient-reported outcomes (PROMs) to identify if patient perspectives had been implemented. Based on results, we set out to determine exercise research priorities as a first step towards a patient-engaged research agenda. An online survey was distributed across Canada to collect research questions from patients, caregivers and healthcare providers. We qualitatively analyzed submitted questions and compiled a long-list that a twelve-person stakeholder steering committee used to identify the top ten priority research questions.

Results

Of 9,962 identified sources, 19 published trials and 4 trial registrations fulfilled inclusion criteria. No evidence of PE existed in any included study. Most commonly measured PROMs were frequency of hypoglycemia (n=7) and quality of life (n=4). The priority-setting survey yielded 194 submitted research questions. Steering committee rankings identified 10 priorities focused on lifestyle factors and exercise modifications to maintain short-term glycemic control.

Conclusion

Recent exercise-based randomized trials in T1D have not included PE and PROMs. Patient priorities for exercise research have yet to be addressed with adequately designed clinical trials.
Machine learning based prediction of antibiotic sensitivity in patients with critical illness
Authors: Ghosh Debabrata , Sharma Shivam , Hasan Eeshan , Ashraf Shabina , Singh Vaibhav , Tewari Dinesh , Singh Seema , Kapoor Mudit , Sengupta Debarka
Published: September 2019

Rising antibiotic resistance inflicts a heavy burden on healthcare, both clinically and economically. Owing to the time required to obtain culture and sensitivity test results, quite often the clinicians rely on their experience and static clinical guidelines to prescribe antibiotics. Such empirical treatment often fails to account for patient-specific attributes and changes in the antibiotic resistance patterns with time and location. The aim of this study was to analyze the patient and hospital specific features regarding their prognostic relevance to treat bacterial infections of patients in the intensive care units (ICUs). We performed a single-center retrospective cohort analysis across 25526 positive cultures recorded in MIMIC-III critical care database. We retrieved a number of clinically relevant relationships from association analysis between patient factors and bacterial strains. For instance, higher elapsed time from patient admission to sample collection for culture showed strong association with blood stream infection caused by Enterococcus faecium, Pseudomonas aeruginosa, and Staphylococcus, indicating that these infections are possibly hospital acquired. To predict antibiotic sensitivity at the level of individual patients we developed an ensemble of machine learning algorithms. The model provided superior prediction accuracy (about 87%) and area under the ROC curve (around 0.91 on an average) for the four most common sample types as compared to a number of off-the-shelf techniques. We demonstrate the predictive power of commonly recorded patient attributes in personalised prediction of antibiotic efficacy.
BITACORA: A comprehensive tool for the identification and annotation of gene families in genome assemblies
Authors: Vizueta Joel , Sánchez-Gracia Alejandro , Rozas Julio
Published: September 2019

Gene annotation is a critical bottleneck in genomic research, especially for the comprehensive study of very large gene families in the genomes of non-model organisms. Despite the recent progress in automatic methods, the tools developed for this task often produce inaccurate annotations, such as fused, chimeric, partial or even completely absent gene models for many family copies, which require considerable extra efforts to be amended. Here we present BITACORA, a bioinformatics solution that integrates sequence similarity search tools and Perl scripts to facilitate both the curation of these inaccurate annotations and the identification of previously undetected gene family copies directly from DNA sequences. We tested the performance of the BITACORA pipeline in annotating the members of two chemosensory gene families of different sizes in seven available chelicerate genome drafts. Despite the relatively high fragmentation of some of these drafts, BITACORA was able to improve the annotation of many members of these families and detected thousands of new chemoreceptors encoded in genome sequences. The program generates an output file in the general feature format (GFF) files, with both curated and novel gene models, and a FASTA file with the predicted proteins. These outputs can be easily integrated in genomic annotation editors, greatly facilitating subsequent manual annotation and downstream evolutionary analyses.
The genome of Caenorhabditis bovis
Authors: Stevens Lewis , Rooke Stefan , Falzon Laura C , Machuka Eunice M , Momanyi Kelvin , Murungi Maurice K , Njoroge Samuel M , Odinga Christian O , Ogendo Allan , Ogola Joseph , Fèvre Eric M , Blaxter Mark
Published: September 2019

The free-living nematode Caenorhabditis elegans is a key laboratory model for metazoan biology. C. elegans is also used as a model for parasitic nematodes despite being only distantly related to most parasitic species. All ∼65 Caenorhabditis species currently in culture are free-living with most having been isolated from decaying plant or fungal matter. Caenorhabditis bovis is a particularly unusual species, having been isolated several times from the inflamed ears of Zebu cattle in Eastern Africa where it is believed to be the cause of bovine parasitic otitis. C. bovis is therefore of particular interest to researchers interested in the evolution of nematode parasitism and in Caenorhabditis diversity. However, as C. bovis is not in laboratory culture, it remains little studied and details of its prevalence, role in bovine parasitic otitis and relationships to other Caenorhabditis species are scarce. Here, by sampling livestock markets and slaughterhouses in Western Kenya, we successfully reisolate C. bovis from the ear of adult female Zebu. We sequence the genome of C. bovis using the Oxford Nanopore MinION platform in a nearby field laboratory and use the data to generate a chromosome-scale draft genome sequence. We exploit this draft genome to reconstruct the phylogenetic relationships of C. bovis to other Caenorhabditis species and reveal the changes in genome size and content that have occurred during its evolution. We also identify expansions in several gene families that have been implicated in parasitism in other nematode species, including those associated with resistance to antihelminthic drugs. The high-quality draft genome and our analyses thereof represent a significant advancement in our understanding of this unusual Caenorhabditis species.
Superior temporal sulcus hypoperfusion in children with autism spectrum disorder: an arterial spin-labeling magnetic resonance study
Authors: Saitovitch Ana , Rechtman Elza , Lemaitre Hervé , Tacchella Jean-Marc , Vinçon-Leite Alice , Douard Elise , Calmon Raphael , Grévent David , Philippe Anne , Chabane Nadia , Brunelle Francis , Boddaert Nathalie , Zilbovicius Monica
Published: September 2019

Advances in neuroimaging techniques have significantly improved our understanding of the neural basis of autism spectrum disorder (ASD). Several attempts have been made to label the main neuroimaging phenotype of ASD, mostly by anatomical and functional activation studies, but none of the frameworks have been without controversy. Over the past decade, a renewed interest for rest brain functioning has emerged in the scientific community, reflected on a large number of resting state fMRI (rs-fMRI) studies, but results remain heterogeneous. It is possible today to investigate rest brain functioning by measuring rest cerebral blood flow (CBF) with MRI using arterial spin labeling (ASL). Here, we investigated rest CBF abnormalities using non-invasive ASL-MRI in 18 children with ASD without cognitive delay (10.4 ± 2.8 y) and 30 typically developing children (10.6 ± 3.0 y). Following quality control, images from a final sample of 12 children with ASD (11.2 ± 2.9 y) and 28 typically developing children (10.1 ± 2.5 y) were analyzed. Whole brain voxel-by-voxel analysis showed significant rest CBF decrease in temporal regions, mainly in the superior temporal sulcus (STS), in children with ASD. This hypoperfusion was individually detected in 83% of children with ASD. Finally, negative correlation was observed between ASD severity scores and rest CBF in the right posterior STS. Strikingly, despite the small sample studied here, our results are extremely similar to previous PET and SPECT findings describing decreased rest CBF in the same superior temporal regions at group and individual levels, as well as correlation with symptoms severity. The congruence between these results, with different methods and in different ASD profiles, reinforce the strength of rest functional abnormalities within these superior temporal regions in ASD and strongly indicates it might be a core characteristic of the disorder. Identifying a core dysfunctional region in ASD bears direct implications to the development of novel therapeutic interventions, such as transcranial magnetic stimulation. In addition, if confirmed in a larger sample, rest temporal hypoperfusion could become a reliable brain imaging biomarker in ASD.
Light-Activated Nanoscale Gas Vesicles Selectively Kill Tumor Cells
Authors: Fernando Ann , Gariépy Jean
Published: September 2019

Protein-based nanobubbles such as halophilic archaeabacterial gas vesicles (GVs) represent a new class of stable, homogeneous nanoparticles with acoustic properties that allow them to be visualized by ultrasound (US) waves. To design GVs as theranostic agents, we modified them to respond to light, with a view to locally generate reactive oxygen species that can kill cancer cells. Specifically, up to 60,000 photoreactive chlorine6 (Ce6) molecules were chemically attached to lysine ε-amino groups present on the surface of each purifiedHalobacterium sp.NRC-1 GV. The resulting fluorescent NRC-1 Ce6-GVs have dimensions comparable to that of native GVs and were efficiently taken up by human breast [MCF-7] and human hypopharyngeal [FaDu-GFP] cancer cells as monitored by confocal microscopy and flow cytometry. When exposed to light, internalized Ce6-GVs were 200-fold more effective on a molar basis than free Ce6 at killing cells. These results demonstrate the potential of Ce6-GVs as novel and promising nanomaterials for image-guided photodynamic therapy.
State Space Methods for Phase Amplitude Coupling Analysis
Authors: Soulat Hugo , Stephen Emily P. , Beck Amanda M. , Purdon Patrick L.
Published: September 2019

Phase Amplitude Coupling (PAC) is thought to play a fundamental role in the dynamic coordination of brain circuits and systems. There are however growing concerns that existing methods for PAC analysis are prone to error and misinterpretation. Improper frequency band selection can render true PAC undetectable, while non-linearities or abrupt changes in the signal can produce spurious PAC. Current methods require substantial amounts of data and lack formal statistical inference tools. We describe here a novel approach for PAC analysis that substantially addresses these problems. We use a state space model to estimate the component oscillations, avoiding problems with frequency band selection, nonlinearities, and sharp signal transitions. We represent cross-frequency coupling in parametric and time-varying forms to further improve statistical efficiency and estimate the posterior distribution of the coupling parameters to derive their credible intervals. We demonstrate the method using simulated data, rat LFP data, and human EEG data.
Direct detection of molecular intermediates from first-passage times
Authors: Thorneywork Alice L. , Gladrow Jannes , Qing Yujia , Rico-Pasto Marc , Ritort Felix , Bayley Hagan , Kolomeisky Anatoly B. , Keyser Ulrich F.
Published: September 2019

All natural phenomena are governed by energy landscapes. However, the direct measurement of this fundamental quantity remains challenging, particularly in complex systems involving intermediate states. Here, we uncover key details of the energy landscapes that underpin a range of experimental systems through quantitative analysis of first-passage time distributions. By combined study of colloidal dynamics in confinement, transport through a biological pore and the folding kinetics of DNA hairpins, we demonstrate conclusively how a short-time, power-law regime of the first-passage time distribution universally reflects the number of intermediate states associated with each process, irrespective of the lengthscales, timescales or interactions in the system. We thereby establish a powerful method for investigating the underlying mechanisms of complex molecular processes.
Effect of osmoprotectants on the survival of bacterial endophytes in lyophilized beet roots
Authors: Szymanska Sonia , Sikora Marcin , Hrynkiewicz Katarzyna , Tyburski Jaroslaw , Tretyn Andrzej , Golebiewski Marcin
Published: September 2019

The increase of human population and associated increasing demand for agricultural products lead to soil over-exploitation. Biofertilizers based on lyophilized plant material containing living plant growth-promoting microorganisms (PGPM) could be an alternative to conventional fertilizers that fits into sustainable agricultural technologies ideas. We aimed to: (i) assess the diversity of endophytic bacteria in beet roots and (ii) determine the influence of osmoprotectants addition during lyophilization on bacterial density, viability, salt tolerance. Microbiome diversity was assessed based on 16S rRNA amplicons sequencing, bacterial density and salt tolerance was evaluated in cultures, while bacterial viability was calculated by using fluorescence microscopy and flow cytometry. Here we show that plant genotype shapes its endophytic microbiome diversity and determines physicochemical rhizosphere soil properties. Sea beet endophytic microbiome, consisting of genera characteristic for extreme environments, is more diverse and salt resistant than its crop relative. Supplementing osmoprotectants during root tissue lyophilization exerts a positive effect on bacterial community salt stress tolerance, viability and density. Trehalose improves these parameters more effectively than ectoine, moreover its use is economically advantageous.
Extended snake venomics by top-down in-source decay: Investigating the newly discovered Anatolian Meadow viper subspecies,Vipera anatolica senliki
Authors: Hempel Benjamin-Florian , Damm Maik , Mrinalini  , Göçmen Bayram , Karış Mert , Nalbantsoy Ayse , Kini R. Manjunatha , Süssmuth Roderich D.
Published: September 2019

Herein we report on the venom proteome ofVipera anatolica senliki,a recently discovered and hitherto unexplored subspecies of the critically endangered Anatolian Meadow viper endemic to the Antalya Province of Turkey. Integrative venomics, including venom gland transcriptomics as well as complementary bottom-up and top-down proteomic analyses, were applied to fully characterize the venom ofV. a. senliki. Furthermore, the classical top-down venomics approach was extended to elucidate the venom proteome by an alternative in-source decay (ISD) proteomics workflow using the reducing matrix 1,5-diaminonaphthalene (1,5-DAN). Top-down ISD proteomics allows for disulfide bond mapping as well as effectivede novoidentification of high molecular weight venom constituents, both of which are difficult to achieve by commonly established top-down approaches. Venom gland transcriptome analysis identified 42 venom transcript annotations from 13 venom toxin families. Relative quantitative snake venomics revealed snake venom metalloproteinases (svMP, 42.9%) as the most abundant protein family, followed by several less dominant toxin families. Online mass profiling and top-down venomics provide a detailed insight into the venom proteome ofV. a. senlikiand facilitates a comparative analysis of venom variability for the closely related subspecies,V. a. anatolica.

TOC Figure
Selective loss of the GABAAα1subunit from Purkinje cells is sufficient to induce a tremor phenotype
Authors: Nietz Angela , Krook-Magnuson Chris , Gutierrez Haruna , Klein Julia , Sauve Clarke , Krook-Magnuson Esther
Published: September 2019

Background

Increased circuit level insights into Essential tremor, the most prevalent movement disorder, are needed. Previously, an Essential Tremor-like phenotype was noted in animals with a global knockout of the GABAAα1subunit. However, global knockout of the GABAAα1subunit has limitations, including potential early mortality and limited circuit level insights into the tremor.

Methods

Given the hypothesized role of the cerebellum in tremor, including Essential Tremor, we used transgenic mice to selectively knock out the GABAAα1subunit from cerebellar Purkinje cells. As previous work suggested background strain may influence phenotype in this model, we used two different background strains (a Black6 and a Mixed background). We examined the resulting phenotype regarding impacts on inhibitory postsynaptic currents, survival rates, gross motor abilities, and expression of tremor.

Results

We found that GABAA-mediated synaptic currents are abolished in Purkinje cells from Purkinje cell specific knockout mice, while GABAA-mediated inhibition to cerebellar molecular layer interneurons remains intact. Selective loss of GABAAα1from Purkinje cells did not produce gross motor deficits, as measured by the accelerating rotarod, nor did it result in decreased survival rates. However, a tremor phenotype was apparent, regardless of sex or background strain. This tremor mimicked the tremor seen in animals with a global knockout of the GABAAα1subunit, and, like Essential Tremor in patients, was responsive to ethanol.

Conclusions

These findings indicate that reduced inhibition to Purkinje cells is sufficient to induce a tremor phenotype, highlighting the importance of the cerebellum, inhibition, and Purkinje cells, in tremor.
Aceclofenac Fast Dispersible Tablet Formulations: Effect of different concentration levels of Avicel PH102 on the compactional, mechanical and drug release characteristics
Authors: Yasmin Riffat , Shoaib Muhammad Harris , Ahmed Farrukh Rafiq , Qazi Faaiza , Ali Huma , Zafar Farya
Published: September 2019

Objective of this study was based on the formulation development of fast dispersible Aceclofenac tablets (100mg) and to evaluate the influence of pharmaceutical mixtures of directly compressible Avicel PH102 with Mannitol and Acdisol on the compressional, mechanical characteristics and drug release properties. Fifteen different aceclofenac formulations were developed by central composite rotatable design (CCRD). Among them best possible formulations (FA–FH) were selected on the basis of micromeritic properties, appropriate tablet weight and disintegration time for further study. Tablets were compressed by direct compression method using hand held hydraulic press with a compressional force ranging from 8 to 80 MN/m2 (MPa). Pre and post compression studies were performed and the compressed formulations (FA-FH) were assessed for different quality tests. The Heckel and Kawakita equations were applied for determination of compressional behavior of formulations. The quality attributes suggested that formulation (FB) containing avicel PH 102 (20%), mannitol (25%) and ac-di-sol (3%) as best optimized formulation showing better mechanical strength i.e. hardness 37.75 ± 0.14N, tensile strength 5.67MN/m2 and friability 0.34%. Furthermore, compressional analysis of FB showed lowest PY value 59.52 MN/m2 and Pk value 1.040 MN/m indicating plasticity of the material. Formulation FB disintegrated rapidly within 21 seconds and released 99.92 % drug after 45min in phosphate buffer pH 6.8. Results of drug release kinetics showed that formulations FA-FH followed Weibull and First-order models in three different dissolution media. Avicel based formulation mixture exhibit excellent compactional strength with rapid disintegration and drug release.
State-dependent differences in the frequency of TMS-evoked potentials
Authors: Stanfield Candice T. , Wiener Martin
Published: September 2019

Previous evidence suggests different cortical areas naturally oscillate at distinct frequencies, reflecting tuning properties of each region. The concurrent use of transcranial magnetic stimulation (TMS) and electroencephalography (EEG) has been used to perturb cortical regions, resulting in an observed post-stimulation response that is maximal at the natural frequency of that region. However, little is known about the spatial extent of TMS-induced activation differences in cortical regions when comparing resting state (passive) versus active task performance. Here, we employed TMS-EEG to directly perturb three cortical areas in the right hemisphere while measuring the resultant changes in maximal evoked frequency in healthy human subjects during a resting state (N=12) and during an active sensorimotor task (N=12). Our results revealed that the brain engages a higher dominant frequency mode when actively engaged in a task, such that the frequency evoked during a task is consistently higher across cortical regions, regardless of the region stimulated. These findings suggest that a distinct characteristic of active performance versus resting state is a higher state of natural cortical frequencies.
Trends of the Florida manatee (Trichechus manatus latirostris) rehabilitation admissions 1991-2017
Authors: Ball Ray L. , Malmi Markuu , Zgibor Janice
Published: September 2019

A retrospective study of admission data of 401 West Indian manatees (Trichechus manatus latirostris) presented to the David A. Straz Jr. Manatee Critical Care Center at ZooTampa at Lowry Park (ZooTampa) for rehabilitation from August 1991 through October 2017. Causes of admittance, location of rescue, gender, and age class were all recorded for each manatee admitted. Admittance categories as defined by the Florida Fish and Wildlife Conservation Commission (FWC) included watercraft collisions, natural causes, entanglement, entrapment, orphaned calves, captive born, mothers of rescued calves, calves of rescued mothers, human, and other. The admitted population was primarily from the southwest and northwest coasts and related waterways of Florida. The gender difference was relatively equivocal (54% female) while the adults comprised 79% of the admissions. The overall total admissions increased steadily over the study period as did the admissions for each individual categories of admission. Watercraft collisions and natural causes combined were 71% of all admissions for the entire study period and are the dominant causes of admission. Watercraft collisions are more likely to occur during May through October, whereas natural causes of admittance are more likely to occur between December and March. Rehabilitated manatees may reduce overall manatee mortality and can provide insight into population-based health concerns if evaluated appropriately. Future efforts can incorporate physical examination findings, hematology, biochemistry profiles, and ancillary diagnostic testing to continue to improve the individual welfare of this marine mammal in its natural range. Admissions data could also potentially serve the wider conservation and recovery efforts if it is proven that the data obtained is at least as informative as that obtained by the carcass salvage program. Limited conservation resources could then be re-directed as new challenges arise with the expanding population and potentially expanding range of this species.
Synergic action of Vitamin D3 and 17β-estradiol on behavioral impairments induced by unpredictable mild stress in the adult ovariectomized female rats
Authors: Baranenko Denis , Mironova Vera , Fedotova Julia , van den Tol Annemieke Johanna Maria
Published: September 2019

The aim of the present study was study changes in antidepressant-like responses to Vitamin D3 (VD3) supplementation in three different doses (1.0, 2.5, and 5.0 mg/kg, s.c.) in long-term ovariectomized (OVX) rats treated with low dose of 17β-E2 (0.5 μg/rat, s.c.) during chronic unpredictable mild stress (CUMS). Sucrose preference (SPT), forced swimming (FST), and open-field (OFT) tests were administered to measure depression-like behavior. Brain-derived neurotrophic factor (BDNF), and serotonine (5-HT) and 5-hydroxyindoleacetic acid (5-HIAA) levels in the hippocampus were measured by ELISA, western blotting analysis, and by using high performance liquid chromatography (HPLC), respectively.

The findings demonstrated that VD3 (5.0 mg/kg, s.c.) in a combination with low dose of 17β-E2 increased sucrose consumption in the SPT and decreased depression-like in the FST of the long-term OVX rats exposed to CUMS. VD3 (5.0 mg/kg) resulted in significant elevated levels of hippocampal BDNF protein expression, as well as to the normalization of 5-HT and 5-HIAA levels in long-term OVX rats plus 17β-E2 compared to the OVX rats plus solvent or 17β-E2 submitted to CUMS. There were no significant effects of VD3 (1.0 and 2.5 mg/kg) treatment on both BDNF protein levels and 5-HT turnover in the hippocampus of the long-term OVX rats treated with 17β-E2 exposed to CUMS compared to the long-term OVX with CUMS rats plus solvent.

In conclusion, VD3 (5.0 mg/kg, s.c.) in a combination with low dose of 17β-E2 had a synergic antianhedonic- and antidepressant-like effects in the adult female rats following long-term ovariectomy submitted to CUMS. This is the first study in long-term OVX female rats showing beneficial effects of VD3 on depression-like behavior that are depended on the presence/absence of stressful factors.
Unexpected predicted length variation for the coding sequence of the sleep related gene,BHLHE41in gorilla amidst strong purifying selection across mammals
Authors: Unadkat Krishna , Whittall Justen B.
Published: September 2019

There is a molecular basis for many sleep patterns and disorders involving circadian clock genes. In humans, “short-sleeper” behavior has been linked to specific amino acid substitutions inBHLHE41(DEC2), yet little is known about variation at these sites and across this gene in mammals. We compareBHLHE41coding sequences for 27 mammals. The coding sequence alignment length was 1794bp, of which 55.0% of base pairs were invariant among the sampled mammals. The mean pairwise nucleotide identity was 92.2%. Of the 598 residue amino acid alignment for mammals, 71.7% of amino acids were identical. The pairwise percent identity for amino acids was 94.8%. No other mammals had the same “short-sleeper” amino acid substitutions previously described from humans. Phylogenetic analyses based on the nucleotides of the coding sequence alignment are consistent with established mammalian relationships. Significant purifying selection was detected in 66.2% of variable codons. No codons exhibited significant signs of positive selection. Unexpectedly, the gorillaBHLHE41sequence has a 318 bp insertion at the 5’ end of the coding sequence and a deletion of 195 bp near the 3’ end of the coding sequence (including the two short sleeper variable sites). Given the strong signal of purifying selection across this gene, phylogenetic congruence with expected relationships and generally conserved function among mammals investigated thus far, we suggest the unexpected indels predicted in the gorillaBHLHE41may represent an annotation error and warrant experimental validation.
IL-1-conferred gene expression pattern in ERα+ BCa and AR+ PCa cells is intrinsic to ERα− BCa and AR− PCa cells and promotes cell survival
Authors: Nawas Afshan F. , Kanchwala Mohammed , Thomas-Jardin Shayna E. , Dahl Haley , Daescu Kelly , Bautista Monica , Anunobi Vanessa , Wong Ally , Meade Rachel , Mistry Ragini , Ghatwai Nisha , Bayerl Felix , Xing Chao , Delk Nikki A.
Published: September 2019

Background

Breast (BCa) and prostate (PCa) cancers are hormone receptor (HR)-driven cancers. Thus, BCa and PCa patients are given therapies that reduce hormone levels or directly blocks HR activity; but most patients eventually develop treatment resistance. We have previously reported that interleukin-1 (IL-1) inflammatory cytokine downregulates ERα and AR mRNA in HR-positive (HR+) BCa and PCa cell lines, yet the cells can remain viable. Additionally, we identified pro-survival proteins and processes upregulated by IL-1 in HR+ BCa and PCa cells, that are basally high in HR− BCa and PCa cells. Therefore, we hypothesize that IL-1 confers a conserved gene expression pattern in HR+ BCa and PCa cells that mimics conserved basal gene expression patterns in HR− BCa and PCa cells to promote HR-independent survival and tumorigenicity.

Methods

We performed RNA sequencing (RNA-seq) for HR+ BCa and PCa cell lines exposed to IL-1 and for untreated HR− BCa and PCa cell lines. We confirmed expression patterns of select genes by RT-qPCR and used siRNA and/or drug inhibition to silence select genes in HR− BCa cell lines. Finally, we performed Ingenuity Pathway Analysis (IPA) to identify signaling pathways encoded by our RNA-seq data set.

Results

We identified 350 genes in common between BCa and PCa cells that are induced or repressed by IL-1 in HR+ cells that are, respectively, basally high or low in HR− cells. Among these genes, we identified Sequestome-1 (SQSTM1/p62) and SRY (Sex-Determining Region Y)-Box 9 (SOX9) to be essential for survival of HR− BCa and PCa cell lines. Analysis of publicly available data indicates that p62 and SOX9 expression are elevated in HR-independent BCa and PCa sublines generated in vitro, suggesting that p62 and SOX9 have a role in acquired treatment resistance. We also assessed HR− cell line viability in response to the p62-targeting drug, verteporfin, and found that verteporfin is cytotoxic for HR− cell lines.

Conclusions

Our 350 gene set can be used to identify novel therapeutic targets and/or biomarkers conserved among acquired (e.g. due to inflammation) or intrinsic HR-independent BCa and PCa.
Correlative three-dimensional super-resolution and block face electron microscopy of whole vitreously frozen cells
Authors: Hoffman David P. , Shtengel Gleb , Xu C. Shan , Campbell Kirby R. , Freeman Melanie , Wang Lei , Milkie Daniel E. , Pasolli H. Amalia , Iyer Nirmala , Bogovic John A. , Stabley Daniel R. , Shirinifard Abbas , Pang Song , Peale David , Schaefer Kathy , Pomp Wim , Chang Chi-Lun , Lippincott-Schwartz Jennifer , Kirchhausen Tom , Solecki David J. , Betzig Eric , Hess Harald
Published: September 2019

Living cells function through the spatial compartmentalization of thousands of distinct proteins serving a multitude of diverse biochemical needs. Correlative super-resolution (SR) fluorescence and electron microscopy (EM) has emerged as a pathway to directly view nanoscale protein relationships to the underlying global ultrastructure, but has traditionally suffered from tradeoffs of structure preservation, fluorescence retention, resolution, and field of view. We developed a platform for three-dimensional correlative cryogenic SR and focused ion beam milled block-face EM across entire vitreously frozen cells that addresses these issues by preserving native ultrastructure and enabling independent SR and EM workflow optimization. Application to a variety of biological systems revealed a number of unexpected protein-ultrastructure relationships and underscored the value of a comprehensive multimodal view of ultrastructural variability across whole cells.
Free Energy Principle in Human Postural Control System: Skin Stretch Feedback Reduces the Entropy
Authors: Hur Pilwon , Pan Yi-Tsen , DeBuys Christian
Published: September 2019

Human upright standing involves an integration of multiple sensory inputs such as vision, vestibular and somatosensory systems. It has been known that sensory deficits worsen the standing balance. However, how the modulation of sensory information contributes to postural stabilization still remains an open question for researchers. The purpose of this work was to formulate the human standing postural control system in the framework of the free-energy principle, and to investigate the efficacy of the skin stretch feedback in enhancing the human standing balance. Previously, we have shown that sensory augmentation by skin stretch feedback at the fingertip could modulate the standing balance of the people with simulated sensory deficits. In this study, subjects underwent ten 30-second trials of quiet standing balance with and without skin stretch feedback. Visual and vestibular sensory deficits were simulated by having each subject close their eyes and tilt their head back. We found that sensory augmentation by velocity-based skin stretch feedback at the fingertip reduced the entropy of the standing postural sway of the people with simulated sensory deficits. This result aligns with the framework of the free energy principle which states that a self-organizing biological system at its equilibrium state tries to minimize its free energy either by updating the internal state or by correcting body movement with appropriate actions. The velocity-based skin stretch feedback at the fingertip may increase the signal-to-noise ratio of the sensory signals, which in turn enhances the accuracy of the internal states in the central nervous system. With more accurate internal states, the human postural control system can further adjust the standing posture to minimize the entropy, and thus the free energy.
Machine learning-assisted neurotoxicity prediction in human midbrain organoids
Authors: Monzel Anna S. , Hemmer Kathrin , Mukendi Tony Kaoma , Lucarelli Philippe , Rosety Isabel , Zagare Alise , Bolognin Silvia , Antony Paul , Nickels Sarah L. , Krueger Rejko , Azuaje Francisco , Schwamborn Jens C.
Published: September 2019

A major challenge in the field of neurodegenerative diseases is the poor translation of pre-clinical models to clinical applications. The human brain is an immensely complex structure, which makes it difficult to recapitulate its development, function and disorders. In the recent years, brain organoids derived from human induced pluripotent stem cells have risen as novel tools to study neurodegenerative diseases such as Parkinson’s disease (PD). PD is a multifactorial disorder, with aging, genetics and environmental factors as key etiological elements. The majority of the PD cases are idiopathic and proposed to result from a complex interaction between genetic predisposition and environmental exposure. Consequently, the identification of potentially disease causing environmental factors is of critical importance. Organoids, as complex multi-cellular tissue proxies, are an ideal tool to study cellular response to environmental changes. However, with increasing complexity of the system, usage of quantitative tools becomes challenging. This led us to develop an automated high-content image analysis pipeline for image-based cell profiling in the organoid system. Here, we introduce a midbrain organoid system that recapitulates features of neurotoxin-induced PD, representing a platform for machine-learning-assisted prediction of neurotoxicity in high-content imaging data. This model is a valuable tool for advanced in vitro PD modeling and for the screening of putative neurotoxic compounds.
Mast cells and γδ T cells are largely dispensable for adaptive immune responses after laser-mediated epicutaneous immunization
Authors: Joubert Isabella , Kovacs Daniel , Scheiblhofer Sandra , Winter Petra , Korotchenko Evgeniia , Strandt Helen , Weiss Richard
Published: September 2019

Background

The skin resembles an attractive target for vaccination due to its accessibility and abundance of resident immune cells. Cells like γδ T cells and mast cells (MCs) are part of the first line of defence against exogenous threats. Despite being important mediators for eliciting TH2 immune responses after epithelial stress, γδ T cell and MC function still remains to be completely understood. Here, we aimed to characterize their roles in shaping adaptive immune responses after laser-mediated epicutaneous immunization (EPI).

Methods

γδ T cell knock out, MC depleted, and wildtype control mice were immunized with mannan-conjugated grass pollen allergen Phl p 5 (P5-MN) by laser-mediated EPI. After 2-3 immunizations, cytokine expression, T helper polarization, and antigen-specific IgG1/IgE levels were analysed. The local cytokine/chemokine milieu after laser microporation was determined.

Results

While the majority of inflammatory chemokines and cytokines induced by laser treatment was not affected by the presence of γδ T cells or MCs, RANTES, was elevated in γδ T cell knock out mice, and GROα and TSLP, were significantly decreased after MC depletion. However, absence of γδ T cells or depletion of MC had no substantial effect on adaptive humoral or cellular immune responses after laser-mediated EPI, except for slightly reduced IgG1 and effector T cell levels in MC depleted mice.

Conclusions

γδ T cells did not play a pivotal role in shaping the humoral and cellular adaptive immune response after laser-mediated EPI, whereas MC depletion decreased numbers of effector T cells, indicating a potential role of MCs in the activation and maturation of T cells after EPI.

Highlights

Laser microporation induces an inflammatory chemokine milieu at the site of immunization

γδ T cells and mast cells contribute to the steady-state or damage-induced cytokine milieu in the skin

γδ T cells and mast cells are dispensable for adaptive immunity after laser-mediated immunization
Microbiome-Gut-Brain-Axis communication influences metabolic switch in the mosquitoAnopheles culicifacies
Authors: Das De Tanwee , Sharma Punita , Tevatiya Sanjay , Chauhan Charu , Kumari Seena , Singla Deepak , Srivastava Vartika , Rani Jyoti , Hasija Yasha , Pandey Kailash C , Kajla Mayur , Dixit Rajnikant
Published: September 2019

Periodic ingestion of a protein-rich blood meal by adult female mosquitoes causes a drastic metabolic change in their innate physiological status, which is referred to as ‘metabolic switch. Although the down-regulation of olfactory factors is key to restrain host-attraction, how the gut ‘metabolic switch’ modulates brain functions, and resilience physiological homeostasis remains unexplored. Here, we demonstrate that the protein-rich diet induces mitochondrial function and energy metabolism, possibly shifting the brain’s engagement to manage organismal homeostasis. A dynamic expression pattern of neuro-signaling and neuro-modulatory genes in both the brain and gut indicates an optimal brain-distant organ communication. Even after decapitation, significant modulation of the neuro-modulator receptor genes as well as quantitative estimation of neurotransmitters (NTs), together confer the gut’s ability to serve as a ‘second brain’. Finally, data on comparative metagenomic analysis and altered NTs dynamics of naïve and aseptic mosquitoes provide the initial evidence that gut-endosymbionts are key modulators for the synthesis of major neuroactive molecules. Conclusively, our data establish a new conceptual understanding of microbiome-gut-brain-axis communication in mosquitoes.

Abstract Figure

Graphical abstract

Highlights

Highly proteinaceous blood meal uptake causes gut ‘metabolic switch’ activity in mosquitoes.

Gut’s calling shifts the brain’s administrative function from external communication to inter-organ management.

‘Gut’, as a ‘Second brain’ plays a crucial role in the maintenance of physiological homeostasis.

Metabolic switch and proliferation of symbiotic bacteria establish microbiome-gut-brain axis communication in mosquitoes.
Expert Curation of the Human and Mouse Olfactory Receptor Gene Repertoires Identifies Conserved Coding Regions Split Across Two Exons
Authors: Barnes If H. A. , Ibarra-Soria Ximena , Fitzgerald Stephen , Gonzalez Jose M. , Davidson Claire , Hardy Matthew P. , Manthravadi Deepa , Van Gerven Laura , Jorissen Mark , Zeng Zhen , Khan Mona , Mombaerts Peter , Harrow Jennifer , Logan Darren W. , Frankish Adam
Published: September 2019

Olfactory receptor (OR) genes are the largest multi-gene family in the mammalian genome, with over 850 in human and nearly 1500 genes in mouse. The expansion of the OR gene repertoire has occurred through numerous duplication events followed by diversification, resulting in a large number of highly similar paralogous genes. These characteristics have made the annotation of the complete OR gene repertoire a complex task. Most OR genes have been predicted in silico and are typically annotated as intronless coding sequences. Here we have developed an expert curation pipeline to analyse and annotate every OR gene in the human and mouse reference genomes. By combining evidence from structural features, evolutionary conservation and experimental data, we have unified the annotation of these gene families, and have systematically determined the protein-coding potential of each locus. We have defined the non-coding regions of many OR genes, enabling us to generate full-length transcript models. We found that 13 human and 41 mouse OR loci have coding sequences that are split across two exons. These split OR genes are conserved across mammals, and are expressed at the same level as protein-coding OR genes with an intronless coding region. Our findings challenge the long-standing and widespread notion that the coding region of a vertebrate OR gene is contained within a single exon.
Inter- and intraspecific differences inDrosophilacold tolerance are linked to hindgut reabsorption capacity
Authors: Andersen Mads Kuhlmann , Overgaard Johannes
Published: September 2019

Maintaining extracellular osmotic and ionic homeostasis is crucial to maintain organismal function. In insects, hemolymph volume and ion content is regulated by the combined actions of the secretory Malpighian tubules and reabsorptive hindgut. When exposed to stressful cold, homeostasis is gradually disrupted, characterized by a debilitating increase in extracellular K+concentration (hyperkalemia). In accordance with this paradigm, studies have found a strong link between the cold tolerance of insect species and their ability to maintain ion and water homeostasis at low temperature. This is also the case for drosophilids where studies have already established how inter- and intra-specific differences in cold tolerance are linked to the secretory capacity of Malpighian tubules. However, presently there is little information on the effects of temperature on the reabsorptive capacity of the hindgut inDrosophila.To address this question we developed a novel method that allows for continued measurements of hindgut ion and fluid reabsorption inDrosophila.Firstly we demonstrate that this assay is temporally stable (> 3 hours) and that the preparation is responsive to humoral stimulation and pharmacological intervention of active and passive transport in accordance with the current insect hindgut reabsorption model. Using this method at benign (24°C) and low temperature (3°C) we investigated how cold acclimation or cold adaptation affected the thermal sensitivity of osmoregulatory function. We found that cold tolerantDrosophilaspecies and cold-acclimatedD. melanogasterare innately better at maintaining rates of fluid and Na+reabsorption at low temperature. Furthermore, cold adaptation and acclimation causes a relative reduction in K+reabsorption at low temperature. These characteristic responses of cold adapted/acclimatedDrosophilawill act to promote maintenance of ion and water homeostasis at low temperature and therefore provide further links between adaptations in osmoregulatory capacity of insects and their ability to tolerate cold exposure.