bluuebunny/crossref_metadata_2025 huggingface dataset:
High effectiveness of multimodal infection control interventions in preventing SARS-CoV-2 infections in healthcare professionals: a prospective longitudinal seroconversion study
Authors: Brehm Thomas Theo , Schwinge Dorothee , Lampalzer Sibylle , Schlicker Veronika , Küchen Julia , Thompson Michelle , Ullrich Felix , Huber Samuel , Schmiedel Stefan , Addo Marylyn M , Lütgehetmann Marc , Knobloch Johannes K , zur Wiesch Julian Schulze , Lohse Ansgar W
Published: August 2020

Objective

To assess the effectiveness of multimodal infection control interventions in the prevention of SARS-CoV-2 infections in healthcare professionals

Design

Sequential follow-up study

Setting

Largest tertiary care centre in northern Germany

Participants

1253 employees of the University Medical Center Hamburg-Eppendorf were sequentially assessed for the presence of SARS-CoV-2 IgG antibodies at the beginning of the covid-19 epidemic (20 March – 9 April), one month (20 April – 8 May), and another two months later (22 June – 24 July). Of those, 1026 were healthcare workers (HCWs) of whom 292 were directly involved in the care of covid-19 patients. During the study period, infection control interventions were deployed, those included i) strict barrier nursing of all known covid-19 patients including FFP2 (N95) masks, goggles, gloves, hoods and protective gowns, ii) visitor restrictions with access control at all hospital entries, iii) mandatory wearing of disposable face masks in all clinical settings, and iv) universal RT-PCR admission screening of patients.

Main Outcome Measures

SARS-CoV-2 IgG seroconversion rate

Results

At the initial screening, ten participants displayed significant IgG antibody ratios. Another ten individuals showed seroconversion at the second time point one month later, only two further participants seroconverted during the subsequent two months. The overall SARS-CoV-2 seroprevalence in the study cohort at the last follow-up was 1.8%, the seroconversion rate dropped from 0.81% to 0.08% per month despite a longer observation period. Amongst HCWs seropositivity was increased in those directly involved in the care of patients with SARS-CoV-2 infections (3.8%, n=11) compared to other HCWs (1.4%, n=10, P=0.025). However, after the adoption of all multimodal infection control interventions seroconversions were observed in only two more HCWs, neither of whom were involved in inpatient care.

Conclusion

Multimodal infection control and prevention interventions are highly effective in mitigating SARS-CoV-2 infections of healthcare professionals.
Smaug membraneless organelles regulate mitochondrial function
Authors: Fernández-Alvarez Ana J. , Thomas María Gabriela , Pascual Malena L. , Habif Martín , Pimentel Jerónimo , Corbat Agustín A. , Pessoa João P. , La Spina Pablo E. , Boscaglia Lara , Plessis Anne , Carmo-Fonseca Maria , Grecco Hernán E. , Casado Marta , Boccaccio Graciela L.
Published: August 2020

Smaug is a conserved translational repressor that recognizes specific RNA motifs in a large number of mRNAs, including nuclear transcripts that encode mitochondrial enzymes. Smaug orthologs have been shown to form membraneless organelles (MLOs) in several organisms and cell types. Using single-molecule FISH we show here that SDHB and UQCRC1 mRNAs associate with Smaug1 MLOs in the human cell line U2OS. Simultaneous loss of function of Smaug1 and Smaug2 affects both mitochondrial respiration and mitochondrial network morphology. Deletion of specific Smaug1 protein regions resulted in impaired MLO formation that correlates with mitochondrial defects. In addition, rotenone but not the respiratory chain uncoupling agent CCCP rapidly induces Smaug1 MLO dissolution. Finally, metformin elicits a similar effect on Smaug1 MLOs and provokes the release of bounded mRNAs. We propose that mitochondrial activity affects Smaug1 MLO dynamics, thus allowing for regulation of nuclear mRNAs that encode key mitochondrial proteins.
Disordered peptides impair neutrophil bacterial clearance and enhance tissue damage in septic patients
Authors: Timár Csaba I. , Kolonics Ferenc , Berzsenyi Viktor , Tamáska Eszter , Párkányi Anna , Merchant Michael L. , Wilkey Daniel W. , Iványi Zsolt , McLeish Kenneth R. , Ligeti Erzsébet
Published: August 2020

Neutrophilic granulocytes are required for antimicrobial defense, but they can also be harmful to the host organism. The current study demonstrates that disordered peptides in the 3-12 kDa size range in the plasma of septic patients alter effector functions of neutrophils from healthy donors. Those peptides stimulated exocytosis, increased extracellular release of reactive oxygen species (ROS), decreased ROS production in phagosomes, and impaired elimination of ROS-sensitive bacteria. Both the concentration of peptides in patients’ plasma and their effects on healthy cells were proportional to the clinical status of the patients. Proteomic analysis and in silico modeling indicate that multiple proteases generate the toxic peptides, with the greatest number of peptides cleaved by neutrophil elastase. We propose that neutrophils participate in an amplification loop in which proteolytic peptides stimulate extracellular release of proteases, resulting in production of more peptides. The enhanced extracellular ROS release contributes to tissue damage, while reduced intracellular ROS generation impairs elimination of certain bacteria. Breaking of this vicious cycle may offer a potential target for intervention.
Isolation, identification and functional characterization of cultivable bacteria from Arabian Sea and Bay of Bengal water samples reveals high diversity
Authors: Rajpathak Shriram N. , Patil Yugandhara M. , Banerjee Roumik , Khedkar Asmita M. , Mishra Pawan G. , Paingankar Mandar , Deobagkar Deepti D.
Published: August 2020

The oxygen minimum zone of the Arabian Sea (AS) and Bay of Bengal (BOB) is rich in organic matter and is an unusual niche. Bacteria present in the oceanic water play an important role in ecology since they are responsible for decomposing, mineralizing of organic matter and in elemental cycling like nitrogen, sulfur, phosphate. This study focuses on culturing bacteria from oxygen minimum zones (OMZ) and non-OMZ regions and their phylogenetic as well as the functional characterization. Genotypic characterization of the isolates using amplified rDNA based 16SrRNA sequencing grouped them into various phylogenetic groups such as alpha-proteobacteria, gamma-proteobacteria and unaffiliated bacteria. The cultivable bacterial assemblages encountered belonged to the genusHalomonas,Marinobacter,Idiomarina,PshyctobacterandPseudoalteromonas.Among the enzymatic activities, carbohydrate utilization activity was most predominant (100%) and microorganisms possessed amylase, cellulase, xylanase and chitinase. A large proportion of these bacteria (60%) were observed to be hydrocarbon consuming and many were resistant to ampicillin, chloramphenicol, kanamycin and streptomycin. The high diversity and high percentage of extracellular hydrolytic enzyme activities along with hydrocarbon degradation activity of the culturable bacteria reflects their important ecological role in oceanic biogeochemical cycling. Further assessment confirmed the presence of nitrogen reduction capability in these cultivable bacteria which highlights their importance in oceanic geochemical cycling.
Elucidating the mechanism of cyclodextrins in the treatment of Niemann-Pick Disease Type C using crosslinked 2-hydroxypropyl-β-cyclodextrin
Authors: Carradori Dario , Chen Hsintsung , Werner Beat , Shah Aagam , Leonardi Chiara , Usuelli Mattia , Mezzenga Raffaele , Platt Frances , Leroux Jean-Christophe
Published: August 2020

Niemann-Pick Disease Type C (NPC) is a severe neurovisceral disorder that is pathophysiologically characterized by intracellular transport abnormalities leading to cytoplasmic accumulation of lipids such as cholesterol and multiple sphingolipids, including sphingosine. The compound 2-hydroxypropyl-β-cyclodextrin (HPβCD) is a compound with high cholesterol complexation capacity and is currently under clinical investigation for the treatment of NPC. However, due to its short blood half-life, high doses are required to produce a therapeutic effect. It has been reported in mice that HPβCD’s circulation time and efficacy can be improved by increasing its sizeviapolymerization, but the biodegradable nature of these systems did not allow the contribution of the macromolecule to the activity to be determined. In this work, stable forms of polymerized HPβCD were generated (viaepichlorohydrin crosslinking) to investigate theirin vitromechanisms of action andin vivoeffects. Crosslinked CDs (8-312 kDa) displayed a 10-fold greater complexation capacity towards cholesterol than monomeric HPβCD but were taken up by cells to a lower extent (in a size-dependent fashion), resulting in an overall comparablein vitroeffect on intracellular cholesterol accumulation that was dependent on cholesterol complexation. When testedin vivo, the crosslinked 19.3 kDa HPβCD exhibited a longer terminal half-life than the monomeric HPβCD. However, it did not increase the life span ofNpc1mice, possibly due to reduced organ penetration and brain diffusion consequence of its large molecular weight. This could be circumvented by the application of magnetic resonance imaging-guided low intensity-pulsed focused ultrasound (MRIg-FUS), which increased the brain penetration of the CD. In conclusion, stable forms of polymerized HPβCD constitute valuable tools to elucidate CDs’ mechanism of action. Moreover, the use of MRIg-FUS to maximize CDs tissue penetration warrants further investigation, as it may be key to harnessing CDs full therapeutic potential in the treatment of NPC.

Graphical abstract

The 2-hydroxypropyl-β-cyclodextrin (HPβCD) is a well-established pharmaceutical excipient that can complex cholesterol and is currently under clinical investigation to treat Niemann-Pick Disease Type C (NPC). However, high doses of the drug are needed to achieve a therapeutic effect. Using stable and long circulating crosslinked HPβCDs, this study attempts to further understand the mechanisms behind CDs’ activity.
SARS-CoV-2 suppresses mRNA expression of selenoproteins associated with ferroptosis, endoplasmic reticulum stress and DNA synthesis
Authors: Wang Yijun , Huang Jinbao , Sun Yong , He Jun , Li Weiwei , Liu Zhirong , Taylor Ethan Will , Rayman Margaret P , Wan Xiaochun , Zhang Jinsong
Published: August 2020

A significant, positive association between selenium status and prognosis of SARS-CoV-2 infection has been identified among COVID-19 patients in China. Moreover, a German study revealed a pronounced deficit of serum selenium and SELENOP concentrations in COVID-19 patients, and selenium deficiency was associated with mortality risk from COVID-19. The present study investigated the influence of SARS-CoV-2 on gene expression of host selenoproteins which mediate many beneficial actions of selenium. We found that SARS-CoV-2 suppressed mRNA expression of selenoproteins associated with ferroptosis (GPX4), endoplasmic reticulum stress (SELENOF, SELENOK, SELENOMandSELENOS) and DNA synthesis (TXNRD3), while SARS-CoV-2 increased gene expression of IL-6 (an inflammatory cytokine positively correlated with severity of COVID-19), in Vero cells. These results provide a deeper insight into the connection between selenium and SARS-CoV-2 pathogenesis.
Intermitochondrial signaling regulates the uniform distribution of stationary mitochondria in axons
Authors: Matsumoto Nozomu , Hori Ikuma , Murase Tomoya , Tsuji Takahiro , Miyake Seiji , Inatani Masaru , Konishi Yoshiyuki
Published: August 2020

In the central nervous system, many neurons develop axonal arbors that are crucial for information processing. Previous studies have demonstrated that premature axons contain motile and stationary mitochondria, and their balance is important for axonal arborization. However, the mechanisms by which neurons determine the positions of stationary mitochondria as well as their turnover remain to be elucidated. In this study, we investigated the regulation of spatiotemporal group dynamics of stationary mitochondria. We observed that the distribution of stationary mitochondrial spots along the unmyelinated and nonsynaptic axons is not random but rather relatively uniform both in vitro and in vivo. Intriguingly, whereas the positions of each mitochondrial spot changed over time, the overall distribution remained uniform. In addition, local inactivation of mitochondria inhibited the translocation of mitochondrial spots in adjacent axonal regions, suggesting that functional mitochondria enhance the motility of neighboring mitochondria. Furthermore, we showed that the ATP concentration was relatively high around mitochondria, and treating axons with phosphocreatine, which supplies ATP, reduced the immobile mitochondria induced by local mitochondrial inhibition. These observations indicate that intermitochondrial interactions, mediated by ATP signaling, control the uniform distribution of axonal mitochondria. The present study reveals a novel cellular system that collectively regulates stationary mitochondria in axons.
Behavior-specific occupancy patterns of Pinyon Jays (Gymnorhinus cyanocephalus) in three Great Basin study areas and significance for pinyon-juniper woodland management
Authors: Boone John D. , Witt Chris , Ammon Elisabeth M.
Published: August 2020

Abstract

The Pinyon Jay is a highly-social, year-round inhabitant of pinyon-juniper woodlands in the western United States. Range-wide, Pinyon Jays have declined ~ 3 – 4% per year for at least the last half-century. At the same time, large acreages of pinyon-juniper woodland have been removed or thinned to improve habitat for Greater Sage-Grouse or other game species across much of the Great Basin, which is home to nearly half of the global population of Pinyon Jays. Occupancy patterns and habitat use of Pinyon Jays have not been well characterized across much of the species’ range, and obtaining this information is necessary for better understanding the causes of ongoing declines and determining useful conservation strategies. Our goal of this study was to identify the characteristics of areas used by Pinyon Jays for several critical life history components and to thereby facilitate the inclusion of Pinyon Jay conservation measures in the design of vegetation management projects. To accomplish this, we studied Pinyon Jays in three widely separated study areas using radio telemetry and direct observation, and measured key attributes of their locations and a separate set of randomly-selected control sites using the U. S. Forest Service’s Forest Inventory Analysis protocol. Data visualizations, non-metric dimension scaling ordinations, and logistic regressions of the resulting data indicated that Pinyon Jay occupancy was concentrated in a distinct subset of available pinyon-juniper woodland habitat, and further that Pinyon Jays used different habitats, arrayed along elevational and tree-cover gradients, for seed caching, foraging, and nesting. Caching was concentrated in low-elevation, relatively flat areas with low tree cover; foraging occurred at slightly higher elevations with moderate tree cover, and nesting was concentrated in somewhat higher areas with greater tree cover and higher stand density. All three of these Pinyon Jay behavior types were highly concentrated within the lower-elevation band of pinyon-juniper woodland close to the woodland-shrubland ecotone. Because woodland removal projects in the Great Basin are often concentrated in these same areas, it is critical to incorporate conservation measures informed by Pinyon Jay occupancy patterns into existing woodland management paradigms, protocols, and practices.
Temperature alters gene expression in mosquitoes during arbovirus infection
Authors: Wimalasiri-Yapa BMC Randika , Barrero Roberto A. , Stassen Liesel , Hafner Louise M. , McGraw Elizabeth A. , Pyke Alyssa T. , Jansen Cassie C. , Suhrbier Andreas , Yakob Laith , Hu Wenbiao , Devine Gregor J. , Frentiu Francesca D.
Published: August 2020

Arthropod-borne viruses (arboviruses) such as dengue, Zika and chikungunya constitute a significant proportion of the global disease burden. The principal vector of these pathogens is the mosquitoAedes(Ae.)aegypti, and its ability to transmit virus to a human host is influenced by environmental factors such as temperature. However, exactly how ambient temperature influences virus replication within mosquitoes remains poorly elucidated, particularly at the molecular level. Here, we use chikungunya virus (CHIKV) as a model to understand how the host mosquito transcriptome responds to arbovirus infection under different ambient temperatures. We exposed CHIKV-infected mosquitoes to 18 °C, 28 °C and 32 °C, and found higher temperature correlated with higher virus replication levels, particularly at early time points post-infection. Lower ambient temperatures resulted in reduced virus replication levels. Using RNAseq, we found that temperature significantly altered gene expression levels in mosquitoes, particularly components of the immune response. The highest number of significantly differentially expressed genes in response to CHIKV was observed at 28 °C, with a markedly more muted effect observed at either lower (18 °C) or higher (32 °C) temperatures. At the higher temperature, the expression of many classical immune genes, includingDicer-2in the RNAi pathway, was not substantially altered in response to CHIKV. Upregulation of Toll, IMD and JAK-STAT pathways was only observed at 28 °C. Time post infection also led to substantially different gene expression profiles, and this effect varied depending upon the which temperature mosquitoes were exposed to. Taken together, our data indicate temperature significantly modulates mosquito gene expression in response to infection, potentially leading to impairment of immune defences at higher ambient temperatures.
Fluorescent Nanosensors Reveal Dynamic pH Gradients During Biofilm Formation
Authors: Blunk Birte , Perkins Mark , Chauhan Veeren M. , Aylott Jonathan W. , Hardie Kim R.
Published: August 2020

Understanding the dynamic environmental microniches of biofilms will permit us to detect, manage and exploit these communities. The components and architecture of biofilms have been interrogated in depth, however, little is known about the environmental microniches present. This is primarily because of the absence of tools with the required measurement sensitivity and resolution to detect these changes. We describe the application of ratiometric fluorescent pH-sensitive nanosensors, as a novel tool, to observe physiological pH changes in biofilms in real-time. Nanosensors comprised two pH-sensitive fluorophores covalently encapsulated with a reference pH-insensitive fluorophore in an inert polyacrylamide nanoparticle matrix. The nanosensors were used to analyse the real-time three-dimensional pH variation for two model biofilm formers: (i) opportunistic pathogenPseudomonas aeruginosa, and (ii) oral pathogenStreptococcus mutans. The detection of sugar metabolism in real time by nanosensors provides a potential application to identify novel therapeutic solutions to improve oral health.
Pharmacological inhibition of an epigenetic regulator during the formation of extinction memory reveals sensory cortical and subcortical codes for the specificity of salient cues
Authors: Rotondo Elena K. , Bieszczad Kasia M.
Published: August 2020

Using a sound-reward extinction paradigm in male rats, we reveal both cortical and subcortical sensory codes for the cue-specificity of memory. In the auditory cortex, re-tuning narrowed frequency receptive field bandwidth, yielding more precise extinction behavior cued by acoustic frequency. Subcortical signals revealed in the auditory brainstem response (ABR) showed decreases in amplitude of select components of the ABR wave. Interestingly, treatment with an inhibitor of histone deacetylase 3 (HDAC3-i) facilitated both auditory cortical tuning bandwidth changes and ABR changes that were frequency-specific to the extinguished signal sound. Moreover, both changes were correlated to each other and with highly precise extinction memory at the level of behavior. Thus, we show for the first time that HDAC3 regulates the specificity of sensory features consolidated in extinction memory. Overall, the dynamics of auditory system plasticity associated with sound-specific extinction are complex. Changes in ABR amplitude induced by sound-reward learning disappeared after extinction, while changes in ABR slope that were initially induced by sound-reward learning were maintained through extinction. Moreover, plasticity of cortical re-tuning emerged only after extinction learning. HDAC3-i applied after extinction training sessions enabled sensory system plasticity to encode the extinguished sound with higher acoustic specificity (compared to vehicle controls). Both cortical and subcortical response changes to sound became unusually “tuned-in” to the acoustic frequency that had been presented under extinction conditions. Thus, HDAC3 regulates how specifically sensory features of experience are encoded into long-term memory and may exert its behavioral effects via multiple coding strategies along sensory system pathways.

SIGNIFICANCE STATEMENT

Epigenetic mechanisms have recently been implicated in memory and information processing. Here, we use a pharmacological inhibitor of histone deacetylase 3 (HDAC3) in a sensory model of learning to reveal, for the first time, its ability to enable unusually precise extinction memory. In so doing, we uncover neural coding strategies for memory’s “specificity” for sensory cues. Extinction induced multiple forms of change at different levels of sensory processing, which highlights the complexity of extinction memory encoding. HDAC3 appears to coordinate effects across sensory levels that determine specific cue saliency for behavior. Thus, epigenetic players may gate how sensory information is stored in long-term memory and their manipulation can be leveraged to reveal neural coding mechanisms for sensory detail in memory.
Repopulating Kupffer Cells Originate Directly from Hematopoietic Stem Cells
Authors: Fan Xu , Lu Pei , Cui Xianghua , Wu Peng , Lin Weiran , Zhang Dong , Yuan Shongzong , Liu Bing , Chen Fangyan , You Hong , Wei Handong , He Fuchu , Jia Jidong , Jiang Ying
Published: August 2020

Kupffer cells (KCs) originate from yolk sac progenitors before birth. Throughout adulthood, they self-maintain independently from the input of circulating monocytes (MOs) at stead state, and are replenished within 2 weeks after having been depleted, but the origin of repopulating KCs in adult remains unclear. The current paradigm dictates that repopulating KCs originate from preexisting KCs or monocytes, but there remains a lack of fate-mapping evidence. In current study, we firstly traced the fate of preexisting KCs and that of monocytic cells with tissue-resident macrophage-specific and monocytic cell-specific fate mapping mouse models, respectively, and found no evidences that repopulating KCs originate from preexisting KCs or MOs. Secondly, we performed genetic lineage tracing to determine the type of progenitor cells involved in response to KC depletion in mice, and found that in response to KC depletion, hematopoietic stem cells (HSCs) proliferated in the bone marrow, mobilized into the blood, adoptively transferred into the liver and differentiated into KCs. Finally, we traced the fate of HSCs in a HSC-specific fate-mapping mouse model, in context of chronic liver inflammation induced by repeated carbon tetrachloride treatment, and confirmed that repopulating KCs originated directly from HSCs. Taken together, these findings provided strong in vivo fate-mapping evidences that repopulating KCs originate directly from Hematopoietic stem cells not from preexisting KCs or from MOs.

Significance

There is a standing controversy in the field regarding the cellular origin of repopulating macrophages. This paper provides strong in vivo fate-mapping evidences that repopulating KCs originate directly from hematopoietic stem cells not from preexisting KCs or from MOs, which presenting a completely novel understanding of the cellular origin of repopulating Kupffer Cells and shedding light on the divergent roles of KCs in liver homeostasis and diseases.
A novel isoform ofACE2is expressed in human nasal and bronchial respiratory epithelia and is upregulated in response to RNA respiratory virus infection
Authors: Blume Cornelia , Jackson Claire L , Spalluto Cosma Mirella , Legebeke Jelmer , Nazlamova Liliya , Conforti Franco , Perotin-Collard Jeanne-Marie , Frank Martin , Crispin Max , Coles Janice , Thompson James , Ridley Robert A , Dean Lareb S N , Loxham Matthew , Azim Adnan , Tariq Kamran , Johnston David , Skipp Paul J , Djukanovic Ratko , Baralle Diana , McCormick Chris , Davies Donna E , Lucas Jane S , Wheway Gabrielle , Mennella Vito
Published: August 2020

Angiotensin-converting enzyme 2 (ACE2) is the main entry point in the airways for SARS-CoV-2. ACE2 binding to SARS-CoV-2 protein Spike triggers viral fusion with the cell membrane, resulting in viral RNA genome delivery into the host. Despite ACE2’s critical role in SARS-CoV-2 infection, an understanding of ACE2 expression, including in response to viral infection, remains unclear.

Until nowACE2was thought to encode five transcripts and one 805 amino acid protein. Here we identify a novel short isoform of ACE2. ShortACE2is expressed in the airway epithelium, the main site of SARS-CoV-2 infection; it is substantially upregulated in response to interferon stimulation and RV infection, but not in response to SARS-CoV-2 infection, and it shows differential regulation in asthma patients. This short isoform lacks SARS-CoV-2 spike glycoprotein high-affinity binding sites and altogether, our data are consistent with a model where shortACE2may influence host susceptibility to SARS-CoV-2 infection.
Exacerbation of mitochondrial fission in human CD34+cells halts erythropoiesis and hemoglobin biosynthesis
Authors: Gonzalez-Ibanez Alvaro M. , Ruiz Lina M. , Jensen Erik , Echeverria Cesar A. , Romero Valentina , Stiles Linsey , Shirihai Orian , Elorza Alvaro A.
Published: August 2020

Erythropoiesis is the most powerful cellular differentiation and proliferation system, with a production of 1011cells per day. In this fine-tuned process, the hematopoietic stem cells (HSCs) generate erythroid progenitors, which proliferate and mature into erythrocytes. During erythropoiesis, mitochondria are reprogrammed to drive the differentiation process before finally being eliminated by mitophagy. In erythropoiesis, mitochondrial dynamics (MtDy) is expected to be a regulatory key point that has not been described previously. We described that a specific MtDy pattern is occurring in human erythropoiesis from EPO-induced human CD34+cells, characterized by a predominant mitochondrial fusion at early stages followed by predominant fission at late stages. The fusion protein MFN1 and the fission protein FIS1 are shown to play a key role in the accurate progression of erythropoiesis. Fragmentation of the mitochondrial web by the overexpression of FIS1 (gain of fission) resulted in both the inhibition of hemoglobin biosynthesis and the arrest of erythroid differentiation, keeping cells in immature differentiation stages. These cells showed specific mitochondrial features as compared with control cells, such as an increase in round and large mitochondria morphology, low mitochondrial membrane potential and a drop in the expression of the respiratory complexes II and IV. Interestingly, treatment with the mitochondrial permeability transition pore (mPTP) inhibitor cyclosporin A, rescued mitochondrial morphology, hemoglobin biosynthesis and erythropoiesis. Studies presented in this work revealed MtDy as a hot spot in the regulation of erythroid differentiation which might be signaling downstream for metabolic reprogramming through the aperture/close of the mPTP.

Key Points

-. Excessive fission disrupts erythroid progression, heme biosynthesis and mitochondrial function, keeping cells mostly in progenitors and proerythroblast stage.

-. Mitochondrial Dynamics signaling for erythroid differentiation involves FIS1 and the mPTP
Transcript assembly improves expression quantification of transposable elements in single cell RNA-seq data
Authors: Shao Wanqing , Wang Ting
Published: August 2020

Transposable elements (TEs) are an integral part of the host transcriptome. TE-containing noncoding RNAs (ncRNAs) exhibit considerable tissue specificity and play crucial roles during development, including stem cell maintenance and cell differentiation. Recent advances in single cell RNA-seq (scRNA-seq) revolutionized cell-type specific gene expression analysis. However, scRNA-seq quantification tools tailored for TEs are lacking, limiting our ability to dissect TE expression dynamics at single cell resolution. To address this issue, we established a TE expression quantification pipeline that is compatible with scRNA-seq data generated across multiple technology platforms. We constructed TE containing ncRNA references using bulk RNA-seq data and demonstrated that quantifying TE expression at the transcript level effectively reduces noise. As proof of principle, we applied this strategy to mouse embryonic stem cells and successfully captured the expression profile of endogenous retroviruses in single cells. We further expanded our analysis to scRNA-seq data from early stages of mouse embryogenesis. Our results illustrated the dynamic TE expression at pre-implantation stages and revealed 137 TE-containing ncRNA transcripts with substantial tissue specificity during gastrulation and early organogenesis.
Limited predictability of amino acid substitutions in seasonal influenza viruses
Authors: Barrat-Charlaix Pierre , Huddleston John , Bedford Trevor , Neher Richard A.
Published: August 2020

Seasonal influenza viruses repeatedly infect humans in part because they rapidly change their antigenic properties and evade host immune responses, necessitating frequent updates of the vaccine composition. Accurate predictions of strains circulating in the future could therefore improve the vaccine match. Here, we studied the predictability of frequency dynamics and fixation of amino acid substitutions. Current frequency was the strongest predictor of eventual fixation, as expected in neutral evolution. Other properties, such as occurrence in previously characterized epitopes or highLocal Branching Index(LBI) had little predictive power. Parallel evolution was found to be moderately predictive of fixation. While the LBI had little power to predict frequency dynamics, it was still successful at picking strains representative of future populations. The latter is due to a tendency of the LBI to be high for consensus-like sequences that are closer to the future than the average sequence. Simulations of models of adapting populations, in contrast, show clear signals of predictability. This indicates that the evolution of influenza HA and NA, while driven by strong selection pressure to change, is poorly described by common models of directional selection such as travelling fitness waves.
SILAC proteomics implicates the ubiquitin conjugating enzyme UBE2D in SOCS1-mediated downmodulation of the MET receptor in hepatocytes
Authors: Santharam Madanraj Appiya , Shukla Akhil , Ihsan Awais Ullan , Cloutier Maryse , Levesque Dominique , Ramanathan Sheela , Boisvert François-Michel , Ilangumaran Subburaj
Published: August 2020

Suppressor of Cytokine Signaling 1 (SOCS1) functions as a tumor suppressor in hepatocellular carcinoma (HCC) and many other types of cancers. SOCS1 mediates its functions by inhibiting tyrosine kinases, promoting ubiquitination and proteasomal degradation of signal transducing proteins, and by modulating transcription factors. Here, we studied the impact of SOCS1 on the hepatocyte proteome using Stable Isotopic Labelling of Amino acids in Cell culture (SILAC)-based mass spectrometry on the Hepa1-6 murine HCC cell line stably expressing wildtype SOCS1 or a mutant SOCS1 with impaired SH2 domain. As SOCS1 regulates the hepatocyte growth factor (HGF) receptor MET, the SILAC-labelled cells were stimulated or not with HGF. Following mass spectrometry analysis, differentially modulated proteins were identified, quantified and analyzed for pathway enrichment. Of the 3440 proteins identified in Hepa-SOCS1 cells at steady state, 181 proteins were significantly modulated compared to control cells. The SH2 domain mutation and HGF increased the number of differentially modulated proteins. Protein interaction network analysis revealed enrichment of SOCS1-modulated proteins within multiprotein complexes such as ubiquitin conjugating enzymes, proteasome, mRNA spliceosome, mRNA exosome and mitochondrial ribosome. These findings suggest that SOCS1, induced by cytokines, growth factors and diverse other stimuli, may dynamically modulate of large macromolecular regulatory complexes to help maintain cellular homeostasis. Notably, the expression of UBE2D ubiquitin conjugating enzyme, which is implicated in the control of growth factor receptor tyrosine kinase signaling, was found to be regulated by SOCS1.
Gut microbiota alterations due to fecal transplant
Authors: Olekhnovich Evgenii I. , Ivanov Artem B. , Ulyantsev Vladimir I. , Ilina Elena N.
Published: August 2020

Background

Fecal microbiota transplantation (FMT) is currently used to treat recurrent clostridial colitis and other diseases. However, neither the therapeutic mechanism of the FMT nor the mechanism that allows the donor bacteria to colonize the intestine of the recipient has yet been described. Moreover, FMT is a great model for studying the ecology of host-associated microbial communities. This creates the need for experimentation with approaches to metagenomic data analysis which may be useful to the interpretation of observed biological phenomena.

Methods

Here the RECAST (Recipient intestinE Colonisation AnalysiS Tool) computational approach is presented, which is based on the shotgun reads sorting process in accordance with their origin in recipient metagenome. Using the RECAST algorithm, taxonomic/functional annotation, and machine learning, the shotgun metagenomic data from three FMT studies including healthy volunteers, patients with clostridial colitis and metabolic syndrome were analyzed.

Results

According to the analysis results, the colonizing and remaining microbial diversity in the post-FMT recipient metagenomic samples is clearly separated from the non-colonizers and lost. It is well explained by higher relative abundance in donor/pre-FMT recipient, Human Microbiome project metagenomes, and taxonomy. Moreover, the colonizing and remaining microbes are associated with lantibiotic and tetracyclines resistance genes.

Conclusion

Based on obtained results, the previously proposed “core” human gut microbiome concept may be elaborated. The top microbes of gut microbiota form “cores”, which, moreover, are mutually integrable between humans. Also, we assume that redistribution of microbial diversity in post-FMT recipients’ metagenomes is due to competition of donor/recipient microbes and to host immunity. The associations of top gut microbes with lantibiotic/antibiotic resistance can be related to gut microbiota colonization resistance phenomena or anthropogenic impact.
Retracing Schwann cell developmental transitions in embryonic dissociated DRG/Schwann cell cocultures in mice
Authors: Sundaram Venkat Krishnan , Jalkh Tatiana El , Barakat Rasha , Fernandez Camille Julie Isabelle , Massaad Charbel , Grenier Julien
Published: August 2020

Embryonic Dissociated Dorsal Root Ganglia cultures are often used to investigate the role of novel molecular pathways or drugs in Schwann cell development and myelination. These cultures largely recapitulate the order of cellular and molecular events that occur in Schwann cells of embryonic nerves. However, the timing of Schwann cell developmental transitions, notably the transition from Schwann Cell Precursors to immature Schwann cells and then to myelinating Schwann cells, has not been estimated so far in this culture system. In this study, we determined the expression profiles of Schwann cell developmental genes during the first week of culture and then compared our data to the expression profiles of these genes in developing spinal nerves. This helped in identifying that Schwann Cell Precursors transition into immature Schwann Cells between the 5thand 7thdayin vitro. Furthermore, we also investigated the transition of immature cells into pro-myelinating and myelinating Schwann cells upon the induction of myelinationin vitro. Our results suggest that Schwann cell differentiation beyond the immature stage can be observed as early as 4 days post the induction of myelination in cocultures. Finally, we compared the myelinating potential of coculture-derived Schwann cell monocultures to cultures established from neonatal sciatic nerves and found that both these cultures system exhibit similar myelinating phenotypes. In effect, our results allow for a better understanding and interpretation of coculture experiments especially in studies that aim to elucidate the role of a novel actor in Schwann Cell development and myelination.
Delta-band Cortical Tracking of Acoustic and Linguistic Features in Natural Spoken Narratives
Authors: Luo Cheng , Ding Nai
Published: August 2020

Speech contains rich acoustic and linguistic information. During speech comprehension, cortical activity tracks the acoustic envelope of speech. Recent studies also observe cortical tracking of higher-level linguistic units, such as words and phrases, using synthesized speech deprived of delta-band acoustic envelope. It remains unclear, however, how cortical activity jointly encodes the acoustic and linguistic information in natural speech. Here, we investigate the neural encoding of words and demonstrate that delta-band cortical activity tracks the rhythm of multi-syllabic words when naturally listening to narratives. Furthermore, by dissociating the word rhythm from acoustic envelope, we find cortical activity primarily tracks the word rhythm during speech comprehension. When listeners’ attention is diverted, however, neural tracking of words diminishes, and delta-band activity becomes phase locked to the acoustic envelope. These results suggest that large-scale cortical dynamics in the delta band are primarily coupled to the rhythm of linguistic units during natural speech comprehension.
The Exon Junction Complex and intron removal prevents resplicing of mRNA
Authors: Joseph Brian , Lai Eric C.
Published: August 2020

Accurate splice site selection is critical for fruitful gene expression. Here, we demonstrate theDrosophilaEJC suppresses hundreds of functional cryptic splice sites (SS), even though majority of these bear weak splicing motifs and appear incompetent. Mechanistically, the EJC directly conceals splicing elements through position-specific recruitment, preventing SS definition. We note that intron removal using strong, canonical SS yields AG|GU signatures at exon-exon junctions. Unexpectedly, we discover that scores of these minimal exon junction sequences are in fact EJC-suppressed 5’ and 3’ recursive SS, and that loss of EJC regulation from such transcripts triggers faulty mRNA resplicing. An important corollary is that intronless cDNA expression constructs from aforementioned targets yield high levels of unanticipated, truncated transcripts generated by resplicing. Consequently, we conclude the EJC has ancestral roles to defend transcriptome fidelity by (1) repressing illegitimate splice sites on pre-mRNAs, and (2) preventing inadvertent activation of such sites on spliced segments.
Long-read assembly of a Great Dane genome highlights the contribution of GC-rich sequence and mobile elements to canine genomes
Authors: Halo Julia V. , Pendleton Amanda L. , Shen Feichen , Doucet Aurélien J. , Derrien Thomas , Hitte Christophe , Kirby Laura E. , Myers Bridget , Sliwerska Elzbieta , Emery Sarah , Moran John V. , Boyko Adam R. , Kidd Jeffrey M.
Published: August 2020

Technological advances have allowed improvements in genome reference sequence assemblies. Here, we combined long- and short-read sequence resources to assemble the genome of a female Great Dane dog. This assembly has improved continuity compared to the existing Boxer-derived (CanFam3.1) reference genome. Annotation of the Great Dane assembly identified 22,182 protein-coding gene models and 7,049 long non-coding RNAs, including 49 protein-coding genes not present in the CanFam3.1 reference. The Great Dane assembly spans the majority of sequence gaps in the CanFam3.1 reference and illustrates that 2,151 gaps overlap the transcription start site of a predicted protein-coding gene. Moreover, a subset of the resolved gaps, which have an 80.95% median GC content, localize to transcription start sites and recombination hotspots more often than expected by chance, suggesting the stable canine recombinational landscape has shaped genome architecture. Alignment of the Great Dane and CanFam3.1 assemblies identified 16,834 deletions and 15,621 insertions, as well as 2,665 deletions and 3,493 insertions located on secondary contigs. These structural variants are dominated by retrotransposon insertion/deletion polymorphisms and include 16,221 dimorphic canine short interspersed elements (SINECs) and 1,121 dimorphic long interspersed element-1 sequences (LINE-1_Cfs). Analysis of sequences flanking the 3’ end of LINE-1_Cfs (i.e., LINE-1_Cf 3’-transductions) suggests multiple retrotransposition-competent LINE-1_Cfs segregate among dog populations. Consistent with this conclusion, we demonstrate that a canine LINE-1_Cf element with intact open reading frames can retrotranspose its own RNA and that of a SINEC_Cf consensus sequence in cultured human cells, implicating ongoing retrotransposon activity as a driver of canine genetic variation.

Significance

Advancements in long-read DNA sequencing technologies provide more comprehensive views of genomes. We used long-read sequences to assemble a Great Dane dog genome that provides several improvements over the existing reference derived from a Boxer dog. Assembly comparisons revealed that gaps in the Boxer assembly often occur at the beginning of protein-coding genes and have a high-GC content, which likely reflects limitations of previous technologies in resolving GC-rich sequences. Dimorphic LINE-1 and SINEC retrotransposon sequences represent the predominant differences between the Great Dane and Boxer assemblies. Proof-of-principle experiments demonstrated that expression of a canine LINE-1 could promote the retrotransposition of itself and a SINEC_Cf consensus sequence in cultured human cells. Thus, ongoing retrotransposon activity may contribute to canine genetic diversity.
The cell-autonomous clock of VIP receptor VPAC2 cells drives circadian behaviour
Authors: Hamnett Ryan , Chesham Johanna E. , Maywood Elizabeth S. , Hastings Michael H.
Published: August 2020

Circadian (∼daily) rhythms pervade mammalian behaviour. They are generated by cell-autonomous, transcriptional/translational feedback loops (TTFL), active in all tissues. This distributed clock network is co-ordinated by the principal circadian pacemaker, the hypothalamic suprachiasmatic nucleus (SCN). Its robust and accurate time-keeping arises from circuit-level interactions that bind its individual cellular clocks into a coherent time-keeper. Cells that express the neuropeptide vasoactive intestinal peptide (VIP) mediate retinal entrainment of the SCN, and in the absence of VIP, or its cognate receptor VPAC2, circadian behaviour is compromised because SCN cells cannot synchronise. The contributions to SCN pacemaking and circadian behaviour of other cell types, not least the VPAC2-expressing target cells of VIP, are, however, not understood. We therefore employed intersectional genetics to manipulate the cell-autonomous TTFL of VPAC2-expressing cells, creating temporally chimaeric mice. We could then determine whether and how VPAC2-expressing cells (a minority ∼35% of SCN cells) contribute to SCN time-keeping. Lengthening of the intrinsic TTFL period of VPAC2 cells by deletion of theCK1εTauallele concomitantly lengthened the period of circadian behavioural rhythms. It also increased the variability of the circadian period of bioluminescent TTFL rhythms in SCN slices recordedex vivo. Abrogation of circadian competence in VPAC2 cells by deletion ofBmal1severely disrupted circadian behavioural rhythms and compromised TTFL time-keeping in the corresponding SCN slices. Thus, VPAC2-expressing cells are a distinct, functionally powerful subset of the SCN circuit, contributing to computation of ensemble period and maintenance of circadian robustness. These findings extend our understanding of SCN circuit topology.
Vesicular release probability sets the strength of individual Schaffer collateral synapses
Authors: Dürst Céline D. , Wiegert J. Simon , Schulze Christian , Helassa Nordine , Török Katalin , Oertner Thomas G.
Published: August 2020

Information processing in the brain is controlled by quantal release of neurotransmitters, a tightly regulated process. From ultrastructural analysis, it is known that presynaptic boutons along single axons differ in the number of vesicles docked at the active zone. It is not clear whether the probability of these vesicles to get released (pves) is homogenous or also varies between individual boutons. Here, we optically measure evoked transmitter release at individual Schaffer collateral synapses at different calcium concentrations, using the genetically encoded glutamate sensor iGluSnFR. Fitting a binomial model to measured response amplitude distributions allowed us to extract the quantal parametersN, pves, andq. We find that Schaffer collateral boutons typically release single vesicles under lowpvesconditions and switch to multivesicular release in high calcium saline. Analyzing the variability of quantal parameters, we conclude that the vesicular release probability rather than the number of readily releasable vesicles or their transmitter content determines the potency of individual boutons.
Efficient population modification gene-drive rescue system in the malaria mosquitoAnopheles stephensi
Authors: Adolfi Adriana , Gantz Valentino M. , Jasinskiene Nijole , Lee Hsu-Feng , Hwang Kristy , Bulger Emily A. , Ramaiah Arunachalam , Bennett Jared B. , Terradas Gerard , Emerson J.J. , Marshall John M. , Bier Ethan , James Anthony A.
Published: August 2020

The development of Cas9/gRNA-mediated gene-drive systems has bolstered the advancement of genetic technologies for controlling vector-borne pathogen transmission. These include population suppression approaches, genetic analogs of insecticidal techniques that reduce the number of vector insects, and population modification (replacement/alteration) approaches, which interfere with competence to transmit pathogens. We developed a recoded gene-drive rescue system for population modification in the malaria vector,Anopheles stephensi, that relieves the load in females caused by integration of the drive into thekynurenine hydroxylasegene by rescuing its function. Non-functional resistant alleles are eliminated via a dominantly-acting maternal effect combined with slower-acting standard negative selection, and a functional resistant allele does not prevent drive invasion. Small cage trials show that single releases of gene-drive males robustly result in efficient population modification with ≥95% of mosquitoes carrying the drive within 5-11 generations over a range of initial release ratios.