bluuebunny/crossref_metadata_2025_split huggingface dataset:
Ex vivo infection of human skin with herpes simplex virus 1 reveals mechanical wounds as insufficient entry portals via the skin surface
Authors: De La Cruz Nydia , Möckel Maureen , Wirtz Lisa , Sunaoglu Katharina , Malter Wolfram , Zinser Max , Knebel-Mörsdorf Dagmar 
Published: June 2021

AbstractHerpes simplex virus 1 (HSV-1) enters its human host via the skin or mucosa. The open question is how the virus invades this highly protective tissue in vivo to approach its receptors in the epidermis and initiate infection. Here, we performed ex vivo infection studies in human skin to investigate how susceptible the epidermis and dermis are to HSV-1 and whether wounding facilitates viral invasion. Upon ex vivo infection of complete skin, only sample edges demonstrated infected cells. After removal of the dermis, HSV-1 efficiently invaded the basal layer, and from there, gained access to suprabasal layers supporting a high susceptibility of the epidermis. In contrast, only single infected cells were detected in the papillary layer of the separated dermis. Interestingly, after wounding, nearly no infection of the epidermis was observed via the skin surface. However, if the wounding of the skin samples led to breaks through the dermis, HSV-1 infected mainly keratinocytes via the wounded dermis. The application of latex beads revealed only occasional entry via the wounded dermis, however, facilitated penetration via the wounded skin surface. Thus, we suggest that the wounded human skin surface allows particle penetration but still provides barriers that prevent HSV-1 invasion.
A female-specific role for Calcitonin Gene-Related Peptide (CGRP) in rodent pain models
Authors: Paige Candler , Plasencia-Fernandez Isabel , Kume Moeno , Papalampropoulou-Tsiridou Melina , Lorenzo Louis-Etienne , Mejia Galo L. , Driskill Christopher , Ferrini Francesco , Feldhaus Andrew L. , Garcia-Martinez Leon F. , Akopian Armen N. , De Koninck Yves , Dussor Gregory , Price Theodore J. 
Published: June 2021

AbstractWe aimed to investigate a potentially sexually dimorphic role of Calcitonin Gene-Related Peptide (CGRP) in mouse and rat models of pain. Based on findings in migraine where CGRP has a preferential pain-promoting effect in female rodents, we hypothesized that CGRP antagonists and antibodies would attenuate pain sensitization more efficaciously in female than male mice and rats. In hyperalgesic priming induced by activation of interleukin 6 (IL-6) signaling, CGRP receptor antagonists, olcegepant and CGRP8-37, both given intrathecally, blocked and reversed hyperalgesic priming only in females. A monoclonal antibody against CGRP, given systemically, blocked priming specifically in female rodents but failed to reverse it. In the spared nerve injury (SNI) model, there was a transient effect of both CGRP antagonists, given intrathecally, on mechanical hypersensitivity in female mice only. Consistent with these findings, intrathecally applied CGRP caused a long-lasting, dose-dependent mechanical hypersensitivity in female mice but more transient effects in males. This CGRP-induced mechanical hypersensitivity was reversed by the KCC2 activator, CLP257 suggesting a role for anionic plasticity in the dorsal horn in the pain-promoting effects of CGRP in females. In spinal dorsal horn slices, CGRP shifted GABAA reversal potentials to significantly more positive values but, again, only in female mice. Therefore, CGRP may regulate KCC2 expression and/or activity specifically in females. However, KCC2 hypofunction promotes mechanical pain hypersensitivity in both sexes because CLP257 alleviated hyperalgesic priming in male and female mice. We conclude that CGRP promotes pain plasticity in female mice, but has a limited impact in male mice.Significance StatementThe majority of patients impacted by chronic pain are women. Mechanistic studies in rodents are creating a clear picture that molecular events promoting chronic pain are different in male and female animals. Far more is known about chronic pain mechanisms in male animals. We sought to build on recent evidence showing that CGRP is a more potent and efficacious promoter of headache pain in female than in male rodents. To test this, we used hyperalgesic priming and the spared nerve injury (SNI) neuropathic pain models in mice. Our findings show a clear sex dimorphism wherein CGRP promotes pain in female but not male mice. Our work suggests that CGRP antagonists could be tested for efficacy in women for a broader variety of pain conditions.
Why Blood Pressure and Body Mass Should be Controlled for in Resting-State Functional Magnetic Resonance Imaging Studies
Authors: Sjuls Guro Stensby , Specht Karsten 
Published: June 2021

AbstractReplicability has become an increasing focus within the scientific communities with the ongoing “replication crisis”. One area that appears to struggle with unreliable results is resting-state functional magnetic resonance imaging (rs-fMRI). Therefore, the current study aimed to improve the knowledge of endogenous factors that contribute to inter-individual variability. Arterial blood pressure, body mass, hematocrit, and glycated hemoglobin were investigated as potential sources of between-subject variability in rs-fMRI, in healthy individuals. Whether changes in resting state-networks (rs-networks) could be attributed to variability in the BOLD-signal, changes in neuronal activity, or both, was of special interest. Within-subject parameters were estimated utilizing Dynamic Causal Modelling (DCM) as it allows to make inferences on the estimated hemodynamic (BOLD-signal dynamics) and neuronal parameters (effective connectivity) separately. The results of the analyses imply that blood pressure and body mass can cause between-subject and between-group variability in the BOLD-signal and that all the included factors can affect the underlying connectivity. Given the results of the current and previous studies, rs-fMRI results appear to be susceptible to a range of factors, which is likely to contribute to the low degree of replicability of these studies. Interestingly, the highest degree of variability seems to appear within the much-studied Default Mode Network and its connections to other networks.
PyPlr: A versatile, integrated system of hardware and software for researching the human pupillary light reflex
Authors: Martin Joel T. , Pinto Joana , Bulte Daniel , Spitschan Manuel 
Published: June 2021

AbstractWe introduce PyPlr—a versatile, integrated system of hardware and software to support a broad spectrum of research applications concerning the human pupillary light reflex (PLR). PyPlr is a custom Python library for integrating a research-grade video-based eye-tracker system with a light source and streamlining stimulus design, optimisation and delivery, device synchronisation, and extraction, cleaning, and analysis of pupil data. We additionally describe how full-field, homogenous stimulation of the retina can be realised with a low-cost integrating sphere that serves as an alternative to a more complex Maxwellian view setup. Users can integrate their own light source, but we provide full native software support for a high-end, commercial research-grade 10-primary light engine that offers advanced control over the temporal and spectral properties of light stimuli as well as spectral calibration utilities. Here, we describe the hardware and software in detail and demonstrate its capabilities with two example applications: 1) pupillometer-style measurement and parametrisation of the PLR to flashes of white light, and 2) comparing the post-illumination pupil response (PIPR) to flashes of long and short-wavelength light. The system holds promise for researchers who would favour a flexible approach to studying the PLR and the ability to employ a wide range of temporally and spectrally varying stimuli, including simple narrowband stimuli.
EFR3 and phosphatidylinositol 4-kinase IIIα regulate insulin-stimulated glucose transport and GLUT4 dispersal in 3T3-L1 adipocytes
Authors: Koester Anna M. , Laidlaw Kamilla M. , Morris Silke , Cutiongco Marie F.A. , Stirrat Laura , Gadegaard Nikolaj , Boles Eckhard , Black Hannah L. , Bryant Nia J. , Gould Gwyn W. 
Published: June 2021

AbstractInsulin stimulates glucose transport in muscle and adipocytes. This is achieved by regulated delivery of intracellular glucose transporter (GLUT4)-containing vesicles to the plasma membrane where they dock and fuse, resulting in increased cell surface GLUT4 levels. Recent work identified a potential further regulatory step, in which insulin increases the dispersal of GLUT4 in the plasma membrane away from the sites of vesicle fusion. EFR3 is a scaffold protein that facilitates localisation of phosphatidylinositol 4-kinase type IIIα to the cell surface. Here we show that knockdown of EFR3 or phosphatidylinositol 4-kinase type IIIα impairs insulin-stimulated glucose transport in adipocytes. Using direct stochastic reconstruction microscopy, we also show that EFR3 knockdown impairs insulin stimulated GLUT4 dispersal in the plasma membrane. We propose that EFR3 plays a previously unidentified role in controlling insulin-stimulated glucose transport by facilitating dispersal of GLUT4 within the plasma membrane.
Automated ChIPmentation procedure on limited biological material of the human blood fluke Schistosoma mansoni
Authors: Lasica Chrystelle , de Carvalho Augusto Ronaldo , Mone Helene , Mouahid Gabriel , Chaparro Cristian , Veillard Anne-Clemence , Zelisko-Schmidt Agnieszka , Grunau Christoph 
Published: June 2021

AbstractAutomated ChIPmentation procedure is a convenient alternative to native chromatin immunoprecipitation (N-ChIP). It is now routinely used for ChIP-Seq. Using the human parasite Schistosoma mansoni, whose production requires scarifying animals and should therefore kept to a minimum, we show here that the automated ChIPmentation is suitable for limited biological material. We define as operational limit ≥20,000 cells. We also present a streamlined protocol for the preparation of ChIP input libraries.
Deep-rooted plant species recruit distinct bacterial communities in 3 m deep subsoil
Authors: Bak Frederik , Lyhne-Kjærbye Annemette , Tardif Stacie , Dresbøll Dorte Bodin , Nicolaisen Mette H. 
Published: June 2021

AbstractDeep-rooted plants can obtain water and nutrients from the subsurface, making them more resilient to climatic changes such as drought. In addition, the deeper root network also allow the plants to recruit bacteria from a larger reservoir in the soil. These bacteria might contribute to nutrient acquisition and provide other plant beneficial traits to the plant. However, the deep rhizosphere communities’ compositions and their assembly dynamics are unknown. Here, we show, using three perennial crops, Kernza, lucerne and rosinweed, grown in 4 m RootTowers, that deep rhizosphere bacterial communities are plant specific, but clearly distinct from the shallow communities. We found that the diversity decreased with depth in the rhizosphere, whereas abundance of 16S rRNA gene copies did not change with depth in lucerne and rosinweed. Furthermore, we identified a subgroup (4-8%) of ASVs in the rhizosphere communities that could not be retrieved in the corresponding bulk soil communities. The abundances of genes determined by qPCR involved in N-cycling: amoA, nifH, nirK, nirS and nosZ differed significantly between plant species, suggesting differences in N content in the root exudates of the plant species. Our results suggest that colonization of the rhizosphere by bulk soil bacteria is not limited by carbon supply, but rather by dispersal. Furthermore, the abundance of N cycling genes indicate that deep rhizosphere bacteria have the potential to provide N through nitrogen fixation.
Phytochemical Investigation of the Crude and Fractionated Extracts of two Nigerian Herbs, Mitragyna Inermis (Wild) and Lawsonia Inermis (Linn)
Authors: Onuh O.A. , Odugbo M. , Oladipo O.O. , Olobayotan I.W. 
Published: June 2021

ABSTRACTInvestigation was done to determine the phytochemicals present in the crude extracts and fractions of Mitragyna inermis (Wild) of the family, Rubiceae and Lawsonia inermis (Linn) of the family, Lythraceae- Loose - Strife using standard protocols to ascertain their bioactive molecules of pharmaceutical potentials. Successive extraction of the plant parts was carried out using hexane, ethyl acetate, methanol and water (aqueous). Eleven fractions were eluted from both plants using column and thin-layer chromatography. The study revealed the presence of alkaloids, flavonoids, saponins, phenols, tannins, steroids and carbohydrates in both plants while anthraquinone was present in only L. inermis. Quantitative study of some of the phytochemicals revealed various percentages ranging from 0.56% (flavonoids) to 21.58% (saponins). Alkaloids and phenols were present in more fractions (M6 – M11) of M. inermis extracts while tannins and anthraquinones were present in more fractions (L6 – L11) of L. inermis extracts than in other fractions. The phytochemicals present in these two plants could be responsible for their various therapeutic uses that have been reported. It is recommended that further research is done to isolate these bioactive molecules in their pure forms and evaluate the dosage required and toxicity levels.
Functional Human Genes Typically Exhibit Epigenetic Conservation
Authors: Rud Daniel , Marjoram Paul , Siegmund Kimberly , Shibata Darryl 
Published: June 2021

AbstractRecent DepMap CRISPR-Cas9 single gene disruptions have identified genes more essential to proliferation in tissue culture. It would be valuable to translate these finding with measurements more practical for human tissues. Here we show that DepMap essential genes and other literature curated functional genes exhibit cell-specific preferential epigenetic conservation when DNA methylation measurements are compared between replicate cell lines and between intestinal crypts from the same individual. Culture experiments indicate that epigenetic drift accumulates through time with smaller differences in more functional genes. In NCI-60 cell lines, greater targeted gene conservation correlated with greater drug sensitivity. These studies indicate that two measurements separated in time allow normal or neoplastic cells to signal through conservation which human genes are more essential to their survival in vitro or in vivo.
Prediction of pancreatic adenocarcinoma patient risk status using alternative splicing events
Authors: Kumar Rajesh , Lathwal Anjali , Raghava Gajendra P.S. 
Published: June 2021

AbstractIn literature, several mRNA, miRNA, lncRNA based biomarkers are identified by genomic analysis to stratify the patients into high and low risk groups of pancreatic adenocarcinoma (PAAD). The identified biomarkers are of limited use in terms of sensitivity and prediction ability. Thus, we aimed to identify the prognostic alternative splicing events and their related mutations in the PAAD. PAAD splicing data of 174 samples (17874 AS events in 6209 genes) and corresponding clinical information was obtained from the SpliceSeq and The Cancer Genome Atlas (TCGA), respectively. Prognostic-index based modeling was used to obtain the best predictive models for the seven AS types. However, model based on multiple spliced events genes (APP; LATS1; MRPL4; LAS1L; STARD10; PHF21A; NMRAL1) outperformed the single event models with a remarkable HR of 9.13 (p-value = 6.42e-10) as well as other existing models. Results from g:Profiler suggest that transcription factors ZF5, ER81, E2F-1/2/3, ER81, Erg, and PEA3 are most related to the prognostic spliced genes. We also identified 565 mutations across 160 spliced genes that have a strong association with the prognostic AS events. The analysis revealed that around 560 of these mutations were not reported before in context to splice event/region. Overall, we conclude that altered AS events may serve as strong indicators for overall survival in pancreatic cancer patients, and novel linkage of the known mutations to the survival-related AS events may provide a new dimension to the advancement of diagnostic and therapeutic interventions in these patients.
Disinfection performance of a drinking water bottle system with a UVC LED cap against waterborne pathogens and heterotrophic contaminants
Authors: Mariita Richard M. , Blumenstein Sébastien A. , Beckert Christian M. , Gombas Thomas , Randive Rajul V. 
Published: June 2021

AbstractBackground:The purgaty One systems (cap+bottle) are portable stainless-steel water bottles with ultraviolet subtype C (UVC) disinfection capability. This study examines the bottle design, verifies disinfection performance against Escherichia coli, Pseudomonas aeruginosa, Vibrio cholerae and heterotrophic contaminants and addresses the public health relevance of heterotrophic bacteria.Methods:Bottles were inoculated with bacterial strains and disinfection efficacy examined using colony forming unit (CFU) assay. The heterotrophic plate count (HPC) method was used to determine the disinfection performance against environmental contaminants at day 0 and after 3 days of water stagnation. All UVC irradiation experiments were performed under stagnant conditions to confirm that the preset application cycle of 55 seconds offers the desired disinfection performance under worst case condition. To determine effectiveness of purgaty One systems (cap+bottle) in disinfection, inactivation efficacy or log reduction value (LRV) was determined using bacteria concentration between UVC ON condition and controls (UVC OFF). The study utilized the 16S rRNA gene for isolate characterization by identifying HPC bacteria to confirm if they belong to groups that are of public health concern.Results:Purgaty One systems fitted with Klaran UVC LEDs achieved 99.99% inactivation (LRV4) efficacy against E. coli and 99.9% inactivation (LRV3) against P. aeruginosa, V. cholerae and heterotrophic contaminants. Based on the 16S rRNA gene analyses, the study determined that the identified HPC isolates enriched by UVC irradiation are of rare public health concern.Conclusion:The bottles satisfactorily inactivated the target pathogenic bacteria and HPC contaminants even after 3 days of water stagnation.
A Fully Implantable Wireless Bidirectional Neuromodulation System for Mice
Authors: Wright Jason , Wong Jason , Mathew Jose , Mughrabi Ibrahim , Jayaprakash Naveen , Zanos Theodoros P. , Abed Yousef Al , Zanos Stavros , Datta-Chaudhuri Timir 
Published: June 2021

AbstractNovel research in the field of bioelectronic medicine requires systems that pair high-performance neurostimulation and bio-signal acquisition hardware with advanced software signal processing and control algorithms. Although mice are the most commonly used animal in medical research, the size, weight, and power requirements of such systems either preclude their use or impose significant constraints on experimental design. Here, we describe a fully-implantable neuromodulation system suitable for use in mice, measuring 2.2 cm3 and weighing 2.8 g. A bidirectional wireless interface allows simultaneous readout of multiple physiological signals and complete control over stimulation parameters, and a wirelessly rechargeable battery provides a lifetime of up to 5 days on a single charge. The device was successfully implanted (N=12) and a functional neural interface (capable of inducing acute bradycardia) is demonstrated with functional lifetimes exceeding to three weeks. The design utilizes only commercially-available components and 3D-printed packaging, with the goal of accelerating discovery and translation of future bioelectronic therapeutics.
Klf5 establishes bi-potential cell fate by dual regulation of ICM and TE specification genes
Authors: Kinisu Martin , Choi Yong Jin , Cattoglio Claudia , Liu Ke , de Bezieux Hector Roux , Valbuena Raeline , Pum Nicole , Dudoit Sandrine , Huang Haiyan , Xuan Zhenyu , Kim Sang Yong , He Lin 
Published: June 2021

SummaryEarly blastomeres of mouse preimplantation embryos exhibit bi-potential cell fate, capable of generating both embryonic and extra-embryonic lineages in blastocysts. Here, we identified three major 2 cell (2C) specific endogenous retroviruses (ERVs) as the molecular hallmark of the bi-potential plasticity. Using the LTRs of all three 2C-ERVs, we identified Klf5 as their major upstream regulator. Klf5 is essential for bi-potential cell fate: a single Klf5-overexpressing ESC generated terminally differentiated embryonic and extra-embryonic lineages in chimeric embryos, and Klf5 directly induces both ICM and TE specification genes. Intriguingly, Klf5 and Klf4 act redundantly during ICM specification, whereas Klf5 deficiency alone impairs TE specification. Klf5 is regulated by multiple 2C-specific transcription factors, particularly Dux, and the Dux/Klf5 axis is evolutionarily conserved. Altogether, the 2C-specific transcription program converges on Klf5 to establish bi-potential cell fate, enabling a cell state with dual activation of ICM and TE genes.
Dive Performance and Aquatic Thermoregulation of the World’s Smallest Mammalian Diver, the American Water Shrew (Sorex palustris)
Authors: Gusztak Roman W. , MacArthur Robert A. , Campbell Kevin L. 
Published: June 2021

ABSTRACTAllometry predicts that the 12–17 g American water shrew (Sorex palustris)—the world’s smallest mammalian diver—will have the highest diving metabolic rate coupled with the lowest total body oxygen storage capacity, skeletal muscle buffering capacity, and glycolytic potential of any endothermic diver. Consistent with expectations, and potentially owing to their low thermal inertia, water shrews had a significantly higher diving metabolic rate in 10°C (8.77 mL O2 g−1 hr−1) compared to 30°C water (6.57 mL O2 g−1 hr−1). Unlike larger-bodied divers, muscle myoglobin contributed minimally (7.7–12.4%) to total onboard O2 stores of juvenile and adult water shrews, respectively, but was offset by high blood O2 carrying capacities (26.4–26.9 vol. %). Diving was predominantly aerobic, as only 1.2–2.3% of dives in 10 and 30°C water, respectively, exceeded the calculated aerobic dive limits at these temperatures (10.8–14.4 sec). The mean voluntary dive time of water shrews during 20-min trials in 3–30°C water was 5.0±0.1 sec (N=25, n=1628), with a mean maximum dive time of 10.1±0.4 sec. However, the average dive duration (6.9±0.2 sec, n=257) of radio-telemetered shrews exclusively foraging in a simulated riparian environment (3°C water) for 12- to 28-hr suggest that mean (but not maximum) dive times of water shrews in the wild may be longer. Mean dive duration, duration of the longest dive, and total time in water all decreased significantly as water temperature declined, suggesting that shrews employed behavioral thermoregulation to defend against immersion hypothermia. Additionally, free-diving shrews in the 24-hr trials consistently elevated core body temperature by ∼1°C immediately prior to initiating aquatic foraging bouts, and ended these bouts when body temperature was still at or above normal resting levels (∼37.8°C). We suggest this observed pre-dive hyperthermia aids to heighten the impressive somatosensory physiology, and hence foraging efficiency, of this diminutive predator while submerged.