bluuebunny/crossref_metadata_2025 huggingface dataset:
BRD9-containing non-canonical BAF complexes safeguard cell identity and prevent reprogramming
Authors: Sevinç Kenan , Sevinç Gülben Gürhan , Cavga Ayşe Derya , Philpott Martin , Kelekçi Simge , Can Hazal , Cribbs Adam P. , Ayar Enes Sefa , Arabacı Dilşad H. , Dunford James E. , Demir Ata B. , Sigua Logan H. , Qi Jun , Oppermann Udo , Onder Tamer T.
Published: May 2021

Epigenetic reprogramming requires extensive remodeling of chromatin landscapes to silence cell-type specific gene expression programs. ATP-dependent chromatin-remodeling complexes are important regulators of chromatin structure and gene expression; however, the role of Bromodomain-containing protein 9 (BRD9) and the associated ncBAF (non-canonical BRG1-associated factors) complex in reprogramming remains unknown. Here, we show that genetic suppression of BRD9 as well as ncBAF complex subunit GLTSCR1, but not the closely related BRD7, increase the efficiency by which induced pluripotent stem cells (iPSCs) can be generated from human somatic cells. Chemical inhibition and acute degradation of BRD9 phenocopied this effect. Interestingly, we find that BRD9 is dispensable for establishment and maintenance of human pluripotency but required for mesendodermal lineage commitment during differentiation. Mechanistically, BRD9 inhibition downregulates somatic cell type-specific genes and decreases chromatin accessibility at somatic enhancers. Collectively, these results establish BRD9 as an important safeguarding factor for somatic cell identity whose inhibition lowers chromatin-based barriers to reprogramming.
Systematic evaluation of NIPT aneuploidy detection software tools with clinically validated NIPT samples
Authors: Paluoja Priit , Teder Hindrek , Ardeshirdavani Amin , Bayindir Baran , Vermeesch Joris , Salumets Andres , Krjutškov Kaarel , Palta Priit
Published: May 2021

Motivation

Non-invasive prenatal testing (NIPT) is a powerful screening method for fetal aneuploidy detection, relying on laboratory and computational analysis of cell-free DNA. Although several published computational NIPT analysis tools are available, no comprehensive and direct accuracy comparison of these tools is published. Here, we evaluate and determine the precision of five commonly used computational NIPT aneuploidy analysis tools, considering diverse sequencing depth (coverage) and fetal DNA fraction (FF) on clinically validated NIPT samples.

Methods

We evaluated computational NIPT aneuploidy analysis tools WisecondorX, NIPTeR, NIPTmer, RAPIDR, and GIPseq, on the same set of clinically validated samples, subsampled to different sequencing coverages between 1.25–20M reads per sample (RPS). These clinically validated samples consisted of 423 samples, including 19 samples with fetal chromosome 21 trisomy (T21, Down syndrome), eight trisomy 18 (T18, Edwards syndrome) and three trisomy 13 (T13, Patau syndrome) samples. For each software and sequencing coverage, we determined the number of false-negative and false-positive trisomy/euploidy calls. For a uniform trisomy detection interpretation, we defined a framework based on the percent-point function for determining the cut-off threshold for calling aneuploidy based on the sample Z-score and the reference group Z-score distribution. We also determined the effect of the naturally occurring arbitrary read placement driven uncertainty on T21 detection at very low sequencing coverage and the effect of cell-free fetal DNA fraction (FF) on the accuracy of these computational tools in the case of various sequencing coverages.

Results

This is the first head-to-head comparison of NIPT aneuploidy detection tools for the low-coverage whole-genome sequencing approach. We determined that, with the currently available software tools, the minimum sequencing coverage with no false-negative trisomic cases was 5M RPS. Secondly, for these compared tools, the number of false-negative trisomic cases could be reduced if the trisomy call cut-off threshold considers the Z-score distribution of euploid reference samples. Thirdly, we observed that in the case of low FF, both aneuploidy Z-score and FF inference was considerably less accurate, especially in NIPT assays with 5M RPS or lower coverage.

Conclusions

We determined that all compared computational NIPT tools were affected by lower sequencing depth, resulting in systematically increasing the proportions of false-negative trisomy results as the sequencing depth decreased. Trisomy detection for lower coverage NIPT samples (e.g. 2.5M RPS) is technically possible but can increase the proportion of false-positive and false-negative trisomic cases, especially in the case of low FF.
Crystal structures of alphavirus nonstructural protein 4 (nsP4) reveal an intrinsically dynamic RNA-dependent RNA polymerase fold
Authors: Tan Yaw Bia , Lello Laura Sandra , Liu Xin , Law Yee-Song , Kang Congbao , Lescar Julien , Zheng Jie , Merits Andres , Luo Dahai
Published: May 2021

Alphaviruses such as Ross River virus (RRV), chikungunya virus, Sindbis virus (SINV), and Venezuelan equine encephalitis virus are mosquito-borne pathogens that can cause arthritis or encephalitis diseases. Nonstructural protein 4 (nsP4) of alphaviruses possesses RNA-dependent RNA polymerase (RdRp) activity essential for viral RNA replication. No 3D structure has been available for nsP4 of any alphaviruses despite its importance for understanding alphaviral RNA replication and for the design of antiviral drugs. Here, we report crystal structures of the RdRp domain of nsP4 from both RRV and SINV determined at resolutions of 2.6 and 1.9 Å. The structure of the alphavirus RdRp domain appears most closely related to RdRps from pestiviruses, noroviruses, and picornaviruses. Hydrogendeuterium exchange mass spectrometry (HDX-MS) and nuclear magnetic resonance (NMR) methods, showed that in solution, nsP4 is highly dynamic with an intrinsically disordered N-terminal domain. Both full-length nsP4 and the RdRp domain were capable to catalyze RNA polymerization. Structure-guided mutagenesis using atrans-replicase system identified nsP4 regions critical for viral RNA replication.

Key Points

Crystal structures of alphavirus nsP4 RNA polymerase domain from RRV and SINV.

nsP4 protein is highly dynamic with an intrinsically disordered N-terminal domain.

Optimized RNA elongation activity assay to facilitate antiviral discovery.
The legacy of maternal SARS-CoV-2 infection on the immunology of the neonate
Authors: Gee Sarah , Chandiramani Manju , Seow Jeffrey , Modestini Carlotta , Das Abhishek , Doores Katie J , Tribe Rachel M , Gibbons Deena L
Published: May 2021

Despite extensive and ongoing studies of SARS-CoV-2 and evidence that pregnant women are at increased risk of severe COVID-19, the effect of maternal infection on the developing infant remains unclear. To determine the potential impact of exposure to SARS-CoV-2in uteroon the neonate, we have assessed the immunological status of infants born to mothers with confirmed SARS-CoV-2 infection during gestation. No evidence of vertical transmission of SARS-CoV-2 was observed, but transfer of maternal SARS-CoV-2 specific IgG to infants was apparent, although to a lesser extent in cases of active or recent maternal infection. Infants born to mothers with recent/ongoing infection had elevated circulating pro-inflammatory cytokines and enhanced percentages of innate immune cells compared to that seen in infants born to uninfected mothers. In tandem, higher frequencies of FOXP3+regulatory T cells and circulating IL-10 demonstrated a further nuance to the neonatal effector response. Interestingly, cytokine functionality was enhanced in infants born to mothers exposed to SARS-CoV-2 at any time during pregnancy. This indicates that maternal SARS-CoV-2 infection influencesin uteropriming of the fetal immune system.
Cellular-resolution monitoring of ischemic stroke pathologies in the rat cortex
Authors: Chornyy Sergiy , Das Aniruddha , Borovicka Julie A. , Patel Davina , Chan Hugh H. , Hermann John K. , Jaramillo Thomas C. , Machado Andre G. , Baker Kenneth B. , Dana Hod
Published: May 2021

Stroke is a leading cause of disability in the Western world. Current post-stroke rehabilitation treatments are only effective in approximately half of the patients. Therefore, there is a pressing clinical need for developing new rehabilitation approaches for enhancing the recovery process, which requires the use of appropriate animal models. Here we study the activity patterns of multiple cortical regions in the rat brain using two-photon microscopy. We longitudinally recorded the fluorescence signal from thousands of neurons labeled with a genetically-encoded calcium indicator before and after an ischemic stroke injury, and found substantial functional changes across motor, somatosensory, and visual cortical regions during the post-stroke cortical reorganization period. We show that a stroke injury in the primary motor cortex has an effect on the activity patterns of neurons not only in the motor and somatosensory cortices, but also in the more distant visual cortex, and that these changes include modified firing rates and kinetics of neuronal activity patterns in response to a sensory stimulus. Changes in neuronal population activity provided animal-specific, circuit-level information on the poststroke cortical reorganization process, which may be essential for evaluating the efficacy of new approaches for enhancing the recovery process.
Distinct cellular immune signatures in acute Zika virus infection are associated with high or low persisting neutralizing antibody titers
Authors: McCarthy Elizabeth E. , Odorizzi Pamela M. , Lutz Emma , Smullin Carolyn P. , Tenvooren Iliana , Stone Mars , Simmons Graham , Hunt Peter W. , Feeney Margaret E. , Norris Philip J. , Busch Michael P. , Spitzer Matthew H. , Rutishauser Rachel L.
Published: May 2021

Although the formation of a durable neutralizing antibody response after an acute viral infection is a key component of protective immunity, little is known about why some individuals generate high versus low neutralizing antibody titers to infection or vaccination. Infection with Zika virus (ZIKV) during pregnancy can cause devastating fetal outcomes, and efforts to understand natural immunity to this infection are essential for optimizing vaccine design. In this study, we leveraged the high-dimensional single-cell profiling capacity of mass cytometry (CyTOF) to deeply characterize the cellular immune response to acute and convalescent ZIKV infection in a cohort of blood donors in Puerto Rico incidentally found to be viremic during the 2015-2016 epidemic in the Americas. During acute ZIKV infection, we identified widely coordinated responses across innate and adaptive immune cell lineages. High frequencies of multiple activated innate immune subsets, as well as activated follicular helper CD4+ T cells and proliferating CD27-IgD-B cells, during acute infection were associated with high titers of ZIKV neutralizing antibodies at 6 months post-infection. On the other hand, low titers of ZIKV neutralizing antibodies were associated with immune features that suggested a cytotoxic-skewed immune “set-point.” Our study offers insight into the cellular coordination of immune responses and identifies candidate cellular biomarkers that may offer predictive value in vaccine efficacy trials for ZIKV and other acute viral infections aimed at inducing high titers of neutralizing antibodies.

One Sentence Summary

Mass cytometry reveals acute ZIKV infection cellular immune signatures that predict high or low neutralizing antibody titers 6 months post-infection.
RNA folding using quantum computers
Authors: Fox Dillion M. , MacDermaid Christopher M. , Schreij Andrea M.A. , Zwierzyna Magdalena , Walker Ross C.
Published: May 2021

The 3-dimensional fold of an RNA molecule is largely determined by patterns of intramolecular hydrogen bonds between bases. Predicting the hydrogen bonding network from the sequence, also referred to as RNA secondary structure prediction or RNA folding, is a nondeterministic polynomial-time (NP)-complete computational problem. The structure of the molecule is strongly predictive of its functions and biochemical properties, and therefore the ability to accurately predict the structure is a crucial tool for biochemists. Many methods have been proposed to efficiently sample possible secondary structure patterns. Classic approaches employ dynamic programming, and recent studies have explored approaches inspired by evolutionary algorithms. This work demonstrates leveraging quantum computing hardware to predict the secondary structure of RNA. A Hamiltonian written in the form of a Binary Quadratic Model (BQM) is derived to drive the system toward maximizing the number of base pairs while simultaneously maximizing the average length of the stems. An Adiabatic Quantum Computer (AQC) is compared to a Replica Exchange Monte Carlo (REMC) algorithm programmed with the same objective function, with the AQC being shown to be highly competitive at rapidly identifying low energy solutions. The method proposed in this study was compared to three algorithms from literature and was found to have the highest success rate.
Subcutaneous infusion of neurosecretory protein GL promotes fat accumulation in mice
Authors: Narimatsu Yuki , Fukumura Keisuke , Iwakoshi-Ukena Eiko , Mimura Ayaka , Furumitsu Megumi , Ukena Kazuyoshi
Published: May 2021

We recently identified a novel small secretory protein, neurosecretory protein GL (NPGL), in the vertebrate hypothalamus. We revealed that NPGL is involved in energy homeostasis using intracerebroventricular infusion in rodents. However, the effect of NPGL through peripheral administration remains to be elucidated and may be important for therapeutic use. In this study, we performed subcutaneous infusion of NPGL in mice for 12 days and found that it accelerated fat accumulation in white adipose tissue (WAT) without increasing in body mass gain and food intake. The mass of the testis, liver, kidney, heart, and gastrocnemius muscle remained unchanged. Analysis of mRNA expression by quantitative reverse transcription-polymerase chain reaction showed that proopiomelanocortin was suppressed in the hypothalamus by the infusion of NPGL. We observed a decreasing tendency in serum triglyceride levels due to NPGL, while serum glucose, insulin, leptin, and free fatty acids levels were unchanged. These results suggest that the peripheral administration of NPGL induces fat accumulation in WAT via the hypothalamus.
Sex-specific transcriptome of spinal microglia in neuropathic pain due to peripheral nerve injury
Authors: Fiore Nathan T , Yin Zhuoran , Guneykaya Dilansu , Gauthier Christian D , Hayes Jessica , D’Hary Aaron , Butovsky Oleg , Moalem-Taylor Gila
Published: May 2021

Recent studies have suggested a sexually dimorphic role of microglia in the maintenance of neuropathic pain in rodents. Here, we utilized RNA sequencing analysis and in vitro primary cultures of microglia to characterize the sex differences in microglia in pain-related regions in nerve injury and chemotherapy-induced peripheral neuropathy mouse models. Whilst mechanical allodynia and behavioral changes were observed in all models, transcriptomic analysis revealed a substantial change in microglial gene expression only within the ipsilateral lumbar spinal cord 7-days after nerve injury. Both sexes upregulated genes associated with inflammation, phagosome, and lysosome activation, though males revealed a prominent global transcriptional shift not observed in female mice, reflecting acute activation. Further, in vitro studies revealed that only male microglia from nerve-injured mice developed a reactive phenotype with increased phagocytotic activity. This study indicates distinct sex differences in spinal microglia and suggests they contribute to the sex-specific pain processing following nerve injury.
Diverse Genetic Determinants of Nitrofurantoin Resistance in UK Escherichia coli
Authors: Wan Yu , Mills Ewurabena , Leung Rhoda C.Y. , Vieira Ana , Jauneikaite Elita , Zhi Xiangyun , Croucher Nicholas J. , Woodford Neil , Ellington Matthew J. , Sriskandan Shiranee
Published: May 2021

Antimicrobial resistance in enteric or urinary Escherichia coli is a risk factor for invasive E. coli infections. Due to widespread trimethoprim resistance amongst urinary E. coli and increased bacteraemia incidence, a national recommendation to prescribe nitrofurantoin for uncomplicated urinary tract infection was made in 2018. Nitrofurantoin resistance is reported in <6% urinary E. coli isolates in the UK. However, mechanisms underpinning nitrofurantoin resistance in these isolates remain unknown. This study aimed to identify genetic determinants of nitrofurantoin resistance in a local E. coli collection and assess their prevalence in a larger dataset of E. coli genomes. Deleterious point mutations and gene-inactivating insertion sequences in both chromosomal nitroreductase genes nfsA and nfsB were identified in genomes of nine nitrofurantoin-resistant urinary E. coli isolates collected from north west London. Eight types of genetic alterations were identified when comparing sequences of nfsA, nfsB, and the associated gene ribE in 12,412 E. coli genomes collected from across the UK. Evolutionary analysis revealed homoplasic mutations and explained the order of stepwise mutations. An algorithm was developed to predict nitrofurantoin susceptibility and predictions for 20 accessible isolates were experimentally validated. Only one genome carrying oqxAB, a mobile gene complex associated with reduced nitrofurantoin susceptibility, was identified. In conclusion, mutations and insertion sequences in nfsA and nfsB are leading causes of nitrofurantoin resistance in UK E. coli. As nitrofurantoin exposure increases in human populations, the prevalence of nitrofurantoin resistance in carriage E. coli isolates and those from urinary and bloodstream infections should be monitored.

Importance

This study expands knowledge about the genetic basis of nitrofurantoin resistance in E. coli isolates using whole-genome sequencing and genomic analysis. We report novel and previously known deleterious mutations of chromosomal genes nfsA, nfsB, and ribE as well as the interruption of nfsA and nfsB by insertion sequences, recapitulating the roles of oxygen-insensitive nitroreductases in the development of nitrofurantoin resistance in E. coli. We revealed and categorised the genotypic diversity in these three genes in a large collection of UK E. coli genomes. A scoring algorithm is provided to predict nitrofurantoin susceptibility from genotypes. Our predictions suggest that acquired nitrofurantoin resistance is not of immediate concern in the UK. However, experimental validation of predictions suggested the involvement of mechanisms other than alterations in nfsA, nfsB, or ribE in determining nitrofurantoin susceptibility, emphasising the need for monitoring nitrofurantoin resistance amongst E. coli.
Age- and gender-dependent differences in attitudes towards COVID-19 vaccination and underlying psychological processes
Authors: Tanaka Toshiko , Nihonsugi Tsuyoshi , Ohtake Fumio , Haruno Masahiko
Published: May 2021

The most promising way to prevent the explosive spread of COVID-19 infection is to achieve herd immunity through vaccination. It is therefore important to motivate those who are less willing to be vaccinated. To address this issue, we conducted an online survey of 6232 Japanese people to investigate age- and gender-dependent differences in attitudes towards COVID-19 vaccination and the underlying psychological processes. We asked participants to read one of nine different messages about COVID-19 vaccination and rate their willingness to be vaccinated. We also collected their 17 social personality trait scores and demographic information. We found that males 10-20 years old showed the minimum willingness to be vaccinated. We also found that prosocial traits are the driving force for young people, but the motivation in older people also depends on risk aversion and self-interest. Furthermore, an analysis of 9 different messages demonstrated that for young people (particularly males), the message emphasizing the majority’s intention to vaccinate and scientific evidence for the safety of the vaccination had the strongest positive effect on the willingness to be vaccinated, suggesting that the herding effect arising from the “majority + scientific evidence” message nudges young people to show their prosocial nature in action.
Novel approach to diagnosis of His bundle capture using individualized left ventricular lateral wall activation time as reference
Authors: Jastrzębski Marek , Moskal Paweł , Kukla Piotr , Bednarek Agnieszka , Kiełbasa Grzegorz , Rajzer Marek , Curila Karol , Vijayaraman Pugazhendhi
Published: May 2021

Aims

During non-selective His bundle (HB) pacing, it is clinically important to confirm His bundle capture vs. right ventricular septal (RVS) capture. The present study aimed to validate the hypothesis that during HB capture left ventricular lateral wall activation time, approximated by the V6R-wave peak time (V6RWPT), will not be longer than the corresponding activation time during native conduction.

Methods

Consecutive patients with permanent HB pacing were recruited; cases with abnormal His-ventricle interval or left bundle branch block were excluded. Two corresponding intervals were compared: stimulus-V6RWPT and native HBpotential-V6RWPT. Difference between these two intervals (delta V6RWPT), diagnostic of lack of HB capture, was identified using receiver operating characteristic (ROC) curve analysis.

Results

A total of 723 ECGs (219 with native rhythm, 172 with selective HB, 215 with non-selective HB, and 117 with RVS capture) were obtained from 219 patients. The native HB-V6RWPT, non-selective-, and selective-HB paced V6RWPT were nearly equal, while RVS V6RWPT was 32.0 (±9.5) ms longer. The ROC curve analysis indicated delta V6RWPT > 12 ms as diagnostic of lack of HB capture (specificity of 99.1% and sensitivity of 100%). A blinded observer correctly diagnosed 96.7% (321/332) of ECGs using this criterion.

Conclusion

We validated a novel criterion for HB capture that is based on the physiological left ventricular activation time as an individualized reference. HB capture can be diagnosed when paced V6RWPT does not exceed the value obtained during native conduction by more than 12 ms, while longer paced V6RWPT indicates RVS capture.
A New Functional F-Statistic for Gene-Based Inference Involving Multiple Phenotypes
Authors: Dugan Adam J. , Fardo David W. , Zaykin Dmitri V. , Vsevolozhskaya Olga A.
Published: May 2021

Genetic pleiotropy is the phenomenon where a single gene or genetic variant influences multiple traits. Numerous statistical methods exist for testing for genetic pleiotropy at the variant level, but fewer methods are available for testing genetic pleiotropy at the gene-level. In the current study, we derive an exact alternative to the Shen and Faraway functional F-statistic for functional-on-scalar regression models. Through extensive simulation studies, we show that this exact alternative performs similarly to the Shen and Faraway F-statistic in gene-based, multi-phenotype analyses and both F-statistics perform better than existing methods in small sample, modest effect size situations. We then apply all methods to real-world, neurodegenerative disease data and identify novel associations.
DNMT3A harboring leukemia-associated mutations directs sensitivity to DNA damage at replication forks
Authors: Venugopal Kartika , Nowialis Pawel , Feng Yang , Shabashvili Daniil E. , Berntsen Cassandra M. , Krajcik Kathryn I. , Taragjini Christina , Zaroogian Zachary , Román Heidi L. Casellas , Posada Luisa M. , Gunaratne Chamara , Li Jianping , Dupéré-Richer Daphné , Bennett Richard L. , Pondugula Santhi , Riva Alberto , Cogle Christopher R. , Opavsky Rene , Law Brian K. , Kubicek Stefan , Staber Philipp B. , Licht Jonathan D. , Bird Jonathan E. , Guryanova Olga A.
Published: May 2021

Mutations in the DNA methyltransferase 3A (DNMT3A) gene are recurrent inde novoacute myeloid leukemia (AML) and are associated with resistance to standard chemotherapy, disease relapse, and poor prognosis, especially in advanced-age patients. Previous gene expression studies in cells withDNMT3Amutations identified deregulation of cell cycle-related signatures implicated in DNA damage response and replication fork integrity, suggesting sensitivity to replication stress. Here we tested whether pharmacologically-induced replication fork stalling creates a therapeutic vulnerability in cells withDNMT3A(R882) mutations. We observed increased sensitivity to nucleoside analogs such as cytarabine in multiple cellular systems expressing mutantDNMT3A, ectopically or endogenously,in vitroandin vivo. Analysis of DNA damage signaling in response to cytarabine revealed persistent intra-S phase checkpoint activation, accompanied by accumulation of DNA damage in theDNMT3A(R882) overexpressing cells, which was only partially resolved after drug removal and carried through mitosis, resulting in micronucleation. Pulse-chase double-labeling experiments with EdU and BrdU after cytarabine wash-out demonstrated that cells withDNMT3A(mut)were able to restart replication but showed a higher rate of fork collapse. Gene expression profiling by RNA-seq identified deregulation of pathways associated with cell cycle progression and p53 activation, as well as metabolism and chromatin. Together, our studies show that cells withDNMT3Amutations have a defect in recovery from replication fork arrest and subsequent accumulation of unresolved DNA damage, which may have therapeutic tractability. These results demonstrate that, in addition to its role in epigenetic control, DNMT3A contributes to preserving genome integrity during DNA replication.
Mitochondrial cyclophilin D promotes disease tolerance by licensing NK cell development and IL-22 production against influenza virus
Authors: Downey Jeffrey , Randolph Haley E. , Pernet Erwan , Tran Kim A. , Khader Shabaana A. , King Irah L. , Barreiro Luis B. , Divangahi Maziar
Published: May 2021

Immunity to infectious disease involves a combination of host resistance, which eliminates the pathogen, and disease tolerance, which limits tissue damage. While the severity of most pulmonary viral infections, including influenza A virus (IAV), is linked to excessive inflammation, our mechanistic understanding of this observation remains largely unknown. Here we show that mitochondrial cyclophilin D (CypD) protects against IAV infection via disease tolerance. Mice deficient in CypD (CypD-/-mice) are significantly more susceptible to IAV infection despite comparable antiviral immunity. Instead, this susceptibility resulted from damage to the lung epithelial barrier caused by a significant reduction of IL-22 production by conventional NK cells in IAV-infectedCypD-/-mice. Transcriptomic and functional data revealed that the compromised IL-22 production by NK cells resulted from dysregulated lymphopoiesis, stemming from increased cell death in NK cell progenitors, as well as the generation of immature NK cells that exhibited altered mitochondrial metabolism. Importantly, following IAV infection, administration of recombinant IL-22 abrogated pulmonary damage and enhanced survival ofCypD-/-mice. Collectively, these results demonstrate a key role for CypD in NK cell-mediated disease tolerance.
Seasonal variations of 137Cs concentration in freshwater charr through uptake and metabolism in 1–2 years after the Fukushima accident
Authors: Okada Kengo , Sakai Masaru , Gomi Takashi , Iwamoto Aimu , Negishi Junjiro N. , Nunokawa Masanori
Published: May 2021

Understanding the factors influencing 137Cs concentrations in freshwater salmonids is crucial for reviving inland fisheries in polluted regions. We studied seasonal variations of 137Cs concentration in charr (Salvelinus leucomaenis) through uptake and metabolism in forested headwaters at Fukushima and Gunma sites. Charr consumed both terrestrial and aquatic animals, and terrestrial prey was predated more in summer at both sites. The 137Cs concentrations in litter, which is a dominant basal food resource of both forest and stream ecosystems, differed between forest and stream due to 137Cs leaching effect on litter submerged in streams. The concentration difference in both litter and prey was greater at Fukushima site than at Gunma site. The estimated prey 137Cs concentration at Fukushima site peaked in summer when terrestrial preys are most available, whereas it remained relatively constant at Gunma site because of the small difference of 137Cs concentrations in between terrestrial and aquatic preys. The specific metabolic rate of charr was commonly changed with stream water temperature, greatest in summer and lowest in winter at both sites. Because both prey 137Cs concentrations and specific metabolic rates peaked in summer, the combination of uptake and metabolism at Fukushima site largely negated seasonal 137Cs fluctuations in charr, whereas specific metabolic rate fluctuations could be the major determinant of charr 137Cs concentrations at Gunma site. Our results suggested that 137Cs concentrations in prey items, whose seasonality are varied due to initial 137Cs fallout volume, were expected to be an important determinant for 137Cs concentrations in charr.
Label-free imaging of membrane potentials by intramembrane field modulation, assessed by Second Harmonic Generation Microscopy
Authors: de Coene Yovan , Jooken Stijn , Deschaume Olivier , Van Steenbergen Valerie , Berghe Pieter Vanden , Van den Haute Chris , Baekelandt Veerle , Callewaert Geert , Van Cleuvenbergen Stijn , Verbiest Thierry , Bartic Carmen , Clays Koen
Published: May 2021

Optical interrogation of cellular electrical activity has proven itself essential for understanding cellular function and communication in complex networks. Voltage-sensitive dyes are important tools for assessing excitability but these highly lipophilic sensors may affect cellular function. Label-free techniques offer a major advantage as they eliminate the need for these external probes. In this work, we show that endogenous second harmonic generation (SHG) from live cells is highly sensitive to changes in membrane potential. Simultaneous electrophysiological control of a living (HEK293T) cell, through whole-cell voltage clamp reveals a linear relation between the SHG intensity and membrane voltage. Our results suggest that due to the high ionic strengths and fast optical response of biofluids, membrane hydration is not the main contributor to the observed field sensitivity. We further provide a conceptual framework that indicates that the SHG voltage sensitivity reflects the electric field within the biological asymmetric lipid bilayer owing to a nonzero tensor. Changing the membrane potential without surface modifications such as electrolyte screening offers high optical sensitivity to membrane voltage (~40% per 100 mV), indicating the power of SHG for label-free read-out. These results hold promise for the design of a non-invasive label-free read-out tool for electrogenic cells.
Spectral dependency of the human pupillary light reflex. Influences of pre-adaptation and chronotype
Authors: Zauner Johannes , Plischke Herbert , Strasburger Hans
Published: May 2021

Non-visual photoreceptors (ipRGCs) and rods both exert a strong influence on the human pupil, yet pupil models regularly use cone-derived sensitivity as their basis. This inconsistency is further exacerbated by the fact that circadian effects can modulate the wavelength sensitivity. We assessed the pupillary reaction to monochromatic light stimuli in the mesopic range. Pupil size for eighty-three healthy participants with normal color vision was measured in nine experimental protocols with varying series of continuous or discontinuous light stimuli under Ganzfeld conditions, presented after 90 seconds of dark adaptation. One hundred and fifty series of stimulation were conducted across three experiments, and were analyzed for wavelength-dependency on the pupillary constriction amplitude (PCA), conditional on experimental settings and individual traits. Traits were surveyed by questionnaire; color vision was tested by Ishihara plates or the Lanthony D15 test. Data were analyzed with generalized additive mixed models (GAMM). The pupillary constriction amplitude response is consistent with L+M-cone derived sensitivity when the series of light stimuli is continuous, i.e., is not interrupted by periods of darkness, but not otherwise. The results also show that a mesopic illuminance weighing led to an overall best prediction of pupillary constriction compared to other types of illuminance measures. IpRGC influence on PCA is not readily apparent from the results. When we explored the interaction of chronotype and time of day on the wavelength dependency, differences consistent with ipRGC influence became apparent. The models indicate that subjects of differing chronotype show a heightened or lowered sensitivity to short wavelengths, depending on their time of preference. IpRGC influence is also seen in the post-illumination pupil reflex if the prior light-stimulus duration is one second. However, shorter wavelengths than expected become more important if the light-stimulus duration is fifteen or thirty seconds. The influence of sex on PCA was present, but showed no interaction with wavelength. Our results help to define the conditions, under which the different wavelength sensitivities in literature hold up for monochromatic light settings. The chronotype effect might signify a mechanism for strengthening the individual’s chronotype, but demands replication in a controlled study.
Short- and long-term effects of amoxicillin/clavulanic acid or doxycycline on the gastrointestinal microbiome of growing cats
Authors: Stavroulaki Evangelia M. , Suchodolski Jan S. , Pilla Rachel , Fosgate Geoffrey T. , Sung Chi-Hsuan , Lidbury Jonathan A. , Steiner Jörg M. , Xenoulis Panagiotis G.
Published: May 2021

Antibiotic treatment in early life influences gastrointestinal (GI) microbial composition and function. In humans, the resultant intestinal dysbiosis is associated with an increased risk for certain diseases later in life. The objective of this study was to determine the temporal effects of antibiotic treatment on the GI microbiome of young cats. Fecal samples were collected from cats randomly allocated to receive either amoxicillin/clavulanic acid (20 mg/kg q12h) for 20 days (AMC group; 15 cats) or doxycycline (10 mg/kg q24h) for 28 days (DOX group;15 cats) as part of the standard treatment of upper respiratory tract infection. In addition, feces were collected from healthy control cats (CON group;15 cats). All cats were approximately two months of age at enrolment. Samples were collected on days 0 (baseline), 20 or 28 (AMC and DOX, respectively; last day of treatment), 60, 120, and 300. DNA was extracted and sequencing of the 16S rRNA gene and qPCR assays were performed. Fecal microbial composition was different on the last day of treatment for AMC cats, and 1 month after the end of antibiotic treatment for DOX cats, compared to CON cats. Species richness was significantly greater in DOX cats compared to CON cats on the last day of treatment. Abundance of Enterobacteriales was increased, and that of Erysipelotrichi was decreased in cats of the AMC group on the last day of treatment compared to CON cats. The abundance of the phylum Proteobacteria was increased in cats of the DOX group on days 60 and 120 compared to cats of the CON group. Only minor differences in abundances between the treatment groups and the control group were present on day 300. Both antibiotics appear to delay the developmental progression of the microbiome, and this effect is more profound during treatment with amoxicillin/clavulanic acid and one month after treatment with doxycycline. Future studies are required to determine if these changes influence microbiome function and whether they have possible effects on disease susceptibility in cats.
Zones of Cellular Damage Around Pulsed-Laser Wounds
Authors: O’Connor James , Akbar Fabiha Bushra , Hutson M. Shane , Page-McCaw Andrea
Published: May 2021

After a tissue is wounded, cells surrounding the wound adopt distinct wound-healing behaviors to repair the tissue. Considerable effort has been spent on understanding the signaling pathways that regulate immune and tissue-resident cells as they respond to wounds, but these signals must ultimately originate from the physical damage inflicted by the wound. Tissue wounds comprise several types of cellular damage, and recent work indicates that different types of cellular damage initiate different types of signaling. Hence to understand wound signaling, it is important to identify and localize the types of wound-induced cellular damage. Laser ablation is widely used by researchers to create reproducible, aseptic wounds in a tissue that can be live-imaged. Because laser wounding involves a combination of photochemical, photothermal and photomechanical mechanisms, each with distinct spatial dependencies, cells around a pulsed-laser wound will experience a gradient of damage. Here we exploit this gradient to create a map of wound-induced cellular damage. Using genetically-encoded fluorescent proteins, we monitor damaged cellular and sub-cellular components of epithelial cells in living Drosophila pupae in the seconds to minutes following wounding. We hypothesized that the regions of damage would be predictably arrayed around wounds of varying sizes, and subsequent analysis found that all damage radii are linearly related over a 3-fold range of wound size. Thus, around laser wounds, the distinct regions of damage can be estimated after measuring any one. This report identifies several different types of cellular damage within a wounded epithelial tissue in a living animal. By quantitatively mapping the size and placement of these different types of damage, we set the foundation for tracing wound-induced signaling back to the damage that initiates it.
Virus-host interactions and genetic diversity of Antarctic sea ice bacteriophages
Authors: Demina Tatiana A. , Luhtanen Anne-Mari , Roux Simon , Oksanen Hanna M.
Published: May 2021

Despite generally appreciated significant roles of microbes in sea ice and polar waters, detailed studies of virus-host systems from such environments have been so far limited by only a few isolates. Here, we investigated infectivity under various conditions, infection cycles, and genetic diversity of Antarctic sea ice bacteriophages: PANV1, PANV2, OANV1, and OANV2. The phages infect common sea ice bacteria belonging to the generaParaglaciecolaorOctadecabacter. Although the phages are marine and cold-active, replicating at 0-5 °C, they all survived temporal incubations at ≥30 °C and remained infectious without any salts or supplemented only with magnesium, suggesting a robust virion assembly maintaining integrity under a wide range of conditions. Host recognition in the cold proved to be effective, and the release of progeny viruses occurred as a result of cell lysis. The analysis of viral genome sequences showed that nearly half of the gene products of each virus are unique, highlighting that sea ice harbors unexplored virus diversity. Based on predicted genes typical for tailed double-stranded DNA phages, we suggest placing the four studied viruses in the classCaudoviricetes. Searching against viral sequences from metagenomic assemblies revealed that related viruses are not restricted to Antarctica, but also found in distant marine environments.

Importance

Very little is known about sea ice microbes despite the significant role of sea ice in the global oceans as well as microbial input into biogeochemical cycling. Studies on the sea ice viruses have been typically limited to -omics-based approaches and microscopic examinations of sea ice samples. Up to date, only four cultivable viruses have been isolated from Antarctic sea ice. Our study of these unique isolates advances the understanding of the genetic diversity of viruses in sea ice environments, their interactions with host microbes, and possible links to other biomes. Such information contributes to more accurate future sea ice biogeochemical models.
L-arginine ameliorates defective autophagy in GM2 gangliosidoses by mTOR modulation
Authors: Castejón-Vega Beatriz , Lendines-Cordero Débora , Rubio Alejandro , Pérez-Pulido Antonio J. , Bullón Pedro , Quiles José L. , Lane Jon D. , Domínguez Beatriz Fernández , Cachón-González María Begoña , Martín-Ruiz Carmen , Sanz Alberto , Cox Timothy M. , Alcocer-Gómez Elísabet , Cordero Mario D.
Published: May 2021

Tay-Sachs and Sandhoff diseases (GM2 gangliosidosis) are autosomal recessive disorders of lysosomal function that cause fatal and progressive neurodegeneration in infants and young children. Impaired hydrolysis catalysed by β-hexosaminidase A (HexA) leads to the accumulation of its specific substrate, GM2 ganglioside, in neuronal lysosomes. Despite the development of a florid storage phenotype, the role of autophagy and its regulation by the mammalian target of rapamycin (mTOR) has yet to be explored in the neuropathogenesis. Accordingly, we investigated the effects on autophagy and lysosomal integrity using skin fibroblasts obtained from patients with Tay-Sachs and Sandhoff diseases. Pathological autophagosomes, with enhanced expression of the p62/SQSTM1 protein, suggested impaired autophagic flux, an abnormality confirmed by electron microscopy and biochemical studies revealing the accelerated release of mature cathepsins and HexA into the cytosol, indicating increased lysosomal permeability. GM2 fibroblasts showed inappropriately diminished mTOR signalling with reduced basal mTOR activity. Accordingly, provision of a positive nutrient signal by L-arginine supplementation partially restored mTOR activity and ameliorated the cytopathological abnormalities - and immediately suggests an avenue for therapeutic exploration in this cruel disease. We also contend that the expression of autophagy/lysosome/mTOR-associated molecules may prove useful peripheral biomarkers for facile monitoring of systemic treatment of GM2 gangliosidosis and neurodegenerative disorders that affect the lysosomal function and disrupt autophagy
Detecting effective starting point of genomic selection by divergent trends from BLUP and ssGBLUP in pigs, beef cattle, and broilers
Authors: Abdollahi-Arpanahi Rostam , Lourenco Daniela , Misztal Ignacy
Published: May 2021

Genomic selection has been adopted nationally and internationally in different livestock and plant species. However, understanding whether genomic selection has been effective or not is an essential question for both industry and academia. Once genomic evaluation started being used, estimation of breeding values with pedigree BLUP became biased because this method does not consider selection using genomic information. Hence, the effective start point of genomic selection can be detected in two possible ways including the divergence of genetic trends and Realized Mendelian sampling (RMS) trends obtained with BLUP and Single-step genomic BLUP (ssGBLUP). This study aimed to find the start date of genomic selection for a set of economically important traits in three livestock species by comparing trends obtained using BLUP and ssGBLUP. For this purpose, three datasets comprised a pig dataset with 117k genotypes and 1.3M animals in pedigree, Angus cattle dataset consisted of ~842k genotypes and 11.5M animals in pedigree, and a purebred broiler chicken dataset included ~154k genotypes and 1.3M birds in pedigree were used. The genetic trends for pigs diverged for the genotyped animals born in 2014 for average daily gain and backfat. In beef cattle, the trends started diverging in 2009 for weaning weight and in 2016 for postweaning gain, with little diverging for birth weight. In broiler chickens, the genetic trends estimated by ssGBLUP and BLUP diverged at breeding cycle 6 for two out of three production traits. The RMS trends for the genotyped pigs diverged for animals born in 2014, more for average daily gain than for backfat. In beef cattle, the RMS trends started diverging in 2009 for weaning weight and in 2016 for postweaning gain, with a trivial trend for birth weight. In broiler chickens, the RMS trends from ssGBLUP and BLUP diverged strongly for two production traits at breeding cycle 6, with a slight divergence for another trait. Divergence of the genetic trends from ssGBLUP and BLUP indicates onset of the genomic selection. Presence of trends for RMS indicates selective genotyping, with or without the genomic selection. The onset of genomic selection and genotyping strategies agree with industry practices across the 3 species. In summary, the effective start of genomic selection can be detected by the divergence between genetic and RMS trends from BLUP and ssGBLUP.
Differences in social brain function in autism spectrum disorder are linked to the serotonin transporter
Authors: Wong Nichol M.L. , Dipasquale Ottavia , Turkheimer Federico , Findon James L. , Wichers Robert H. , Dimitrov Mihail , Murphy Clodagh M. , Stoencheva Vladimira , Robertson Dene M. , Murphy Declan G. , Daly Eileen , McAlonan Grainne M.
Published: May 2021

Alterations in the serotonergic control of brain pathways responsible for facial-emotion processing in people with autism spectrum disorder (ASD) may be a target for intervention. However, the molecular underpinnings of autistic-neurotypical serotonergic differences are challenging to access in vivo. Receptor-Enriched Analysis of functional Connectivity by Targets (REACT) has helped define molecular-enriched fMRI brain networks based on a priori information about the spatial distribution of neurochemical systems from available PET templates. Here, we used REACT to estimate the dominant fMRI signal related to the serotonin transporter (5-HTT) distribution during processing of aversive facial expressions of emotion processing in adults with and without ASD. We first predicted a group difference in baseline (placebo) functioning of this system. We next used a single 20 mg oral dose of citalopram, i.e. a serotonin reuptake inhibitor, to test the hypothesis that network activity in people with and without ASD would respond differently to inhibition of 5-HTT. To confirm the specificity of our findings, we also repeated the analysis with 5-HT1A, 5-HT1B, 5-HT2A, and 5-HT4 receptor maps.

We found a baseline group difference in the 5-HTT-enriched response to faces in the ventromedial prefrontal cortex. A single oral dose of citalopram ‘shifted’ the response in the ASD group towards the neurotypical baseline but did not alter response in the control group.

Our findings suggest that the 5HTT-enriched functional network is dynamically different in ASD during processing of socially relevant stimuli. Whether this acute neurobiological response to citalopram in ASD translates to a clinical target will be an important next step.