bluuebunny/crossref_metadata_2025 huggingface dataset:
Spatiotemporal components of sustained functional hyperemia are differentially modulated by locomotion and silenced with vascular chemogenetics
Authors: Peringod Govind , Yu Linhui , Murari Kartikeya , Gordon Grant R
Published: September 2021

Neural activity underlying sensation, movement or cognition drives regional blood flow enhancement – termed functional hyperemia – to increase the oxygen supply to respiring cells for as long as needed to meet energy demands. However, functional hyperemia is often studied under anesthesia which typically yields response profiles that appear temporally and spatially homogenous. We have insufficient understanding of the underlying kinetics of oxygen delivery in awake animals, especially during specific behaviours that may influence neurally-driven enhancements in cerebral blood flow. Using widefield intrinsic optical signal imaging in awake, head-fixed but active mice, we demonstrated distinct early and late components to changes in intravascular oxygenation in response to sustained (30s) whisker stimulation. We found that the late component (20-30s), but not the early component (1-5s), was strongly influenced by level of whisking/locomotion in the region of highest response and in surrounding regions. Optical flow analyses revealed complex yet stereotyped spatial properties of the early and late components that were related to location within the optical window and the initial state of the cerebral vasculature. In attempt to control these complex response characteristics, we drove a canonical microvasculature constriction pathway using mural cell Gq-chemogenetic mice. A low-dose of systemic C21 strongly limited both the magnitude and spatial extent of the sensory-evoked hemodynamic response, showing that functional hyperemia can be severely limited by direct mural cell activation. These data provide new insights into the cerebral microcirculation in the awake state and may have implications for interpreting functional imaging data.
Immunogenicity of a third dose viral-vectored COVID-19 vaccine after receiving two-dose inactivated vaccines in healthy adults
Authors: Yorsaeng Ritthideach , Suntronwong Nungruthai , Phowatthanasathian Harit , Assawakosri Suvichada , Kanokudom Sitthichai , Thongmee Thanunrat , Vichaiwattana Preeyaporn , Auphimai Chompoonut , Wongsrisang Lakkhana , Srimuan Donchida , Thatsanatorn Thaksaporn , Klinfueng Sirapa , Sudhinaraset Natthinee , Wanlapakorn Nasamon , Poovorawan Yong
Published: September 2021

In June 2021, Thailand was hit by the delta variant of SARS-CoV-2 resulting in the biggest wave of COVID-19. Due to the widespread delta variant, more than 600 healthcare workers had COVID-19 despite completion of two-dose CoronaVac. The Ministry of Public Health recommended that healthcare workers received a third dose of AZD1222 to increase level of protection against SARS-CoV-2. However, immune response after the third vaccination with AZD1222 are limited. In this study, sera from those who received a booster of AZD1222 in June-July 2021 were tested for SARS-CoV-2 spike receptor-binding-domain (RBD) IgG, anti-RBD total immunoglobulins and anti-spike protein 1 (S1) IgA. The neutralizing activities in a subset of serum samples were tested against the wild type and variants of concern (B.1.1.7, B.1.617.2, and B.1.351) using an enzyme-linked immunosorbent assay-based surrogate virus neutralization test. Participants who received the booster of AZD1222 possessed higher levels of spike RBD-specific IgG, total immunoglobulins, and anti-S1 IgA than that two-dose vaccines (p < 0.001). They also elicited higher neutralizing activity against the wild type and all variants of concern than those in the recipients of the two-dose vaccines. This study demonstrated a high immunogenicity of the AZD1222 booster who completed the two-dose inactivated vaccines.
SARS-CoV-2 epidemic in the South American Southern cone: can combined immunity from vaccination and infection prevent the spread of Gamma and Lambda variants while easing restrictions?
Authors: Fiori Marcelo , Bello Gonzalo , Wschebor Nicolás , Lecumberry Federico , Ferragut Andrés , Mordecki Ernesto
Published: September 2021

All South American countries from the Southern cone (Argentina, Brazil, Chile, Paraguay and Uruguay) experienced severe COVID-19 epidemic waves during early 2021 driven by the expansion of variants Gamma and Lambda, however, there was an improvement in different epidemic indicators since June 2021. To investigate the impact of national vaccination programs and natural infection on viral transmission in those South American countries, we analyzed the coupling between population mobility and the viral effective reproduction numberRt. Our analyses reveal that population mobility was highly correlated with viralRtfrom January to May 2021 in all countries analyzed; but a clear decoupling occurred since May-June 2021, when the rate of viral spread started to be lower than expected from the levels of social interactions. These findings support that populations from the South American Southern cone probably achieved the conditional herd immunity threshold to contain the spread of regional SARS-CoV-2 variants.
Global trade-offs in tree functional traits
Authors: Maynard Daniel S. , Bialic-Murphy Lalasia , Zohner Constantin M. , Averill Colin , van den Hoogen Johan , Ma Haozhi , Mo Lidong , Smith Gabriel Reuben , Aubin Isabelle , Berenguer Erika , Boonman Coline C.F. , Catford Jane , Cerabolini Bruno E. L. , Dias Arildo S. , González-Melo Andrés , Hietz Peter , Lusk Christopher H. , Mori Akira S. , Niinemets Ülo , Pillar Valério D. , Rosell Julieta A. , Schurr Frank M. , Sheremetev Serge N. , da Silva Ana Carolina , Sosinski Ênio , van Bodegom Peter M. , Weiher Evan , Bönisch Gerhard , Kattge Jens , Crowther Thomas W.
Published: September 2021

Abstract

Due to massive energetic investments in woody support structures, trees are subject to unique physiological, mechanical, and ecological pressures not experienced by herbaceous plants. When considering trait relationships across the entire plant kingdom, plant trait frameworks typically must omit traits unique to large woody species, thereby limiting our understanding of how these distinct ecological pressures shape trait relationships in trees. Here, by considering 18 functional traits—reflecting leaf economics, wood structure, tree size, reproduction, and below-ground allocation—we quantify the major axes of variation governing trait expression of trees worldwide. We show that trait variation within and across angiosperms and gymnosperms is captured by two independent processes: one reflecting tree size and competition for light, the other reflecting leaf photosynthetic capacity and nutrient economies. By exploring multidimensional relationships across clusters of traits, we further identify a representative set of seven traits which captures the majority of variation in form and function in trees: maximum tree height, stem conduit diameter, specific leaf area, seed mass, bark thickness, root depth, and wood density. Collectively, this work informs future trait-based research into the functional biogeography of trees, and contributes to our fundamental understanding of the ecological and evolutionary controls on forest biodiversity and productivity worldwide.
Seasonal variation of genotypes and reproductive plasticity in a facultative clonal freshwater invertebrate animal (Hydra oligactis) living in a temperate lake
Authors: Miklós Máté , Laczkó Levente , Sramkó Gábor , Barta Zoltán , Tökölyi Jácint
Published: September 2021

Facultative sexual organisms combine sexual and asexual reproduction within a single life cycle, often switching between reproductive modes depending on environmental conditions. These organisms frequently inhabit variable seasonal environments, where favourable periods alternate with unfavourable periods, generating temporally varying selection pressures that strongly influence life history decisions and hence population dynamics. Due to the rapidly accelerating changes in our global environment today, understanding the dynamics of and genetic changes in facultative sexual populations inhabiting seasonal environments is critical to assess and prepare for additional challenges that will affect such ecosystems. In this study we aimed at obtaining insights of the seasonal population dynamics of the facultative sexual freshwater cnidarianHydra oligactisthrough a combination of Restriction-site Associated Sequencing (RAD-Seq) genotyping and the collection of phenotypic data on the reproductive strategy of field-collected hydra strains. We found no significant genetic change during the two years in the study population. Clone lines were detected between seasons and even years, suggesting that clonal lineages can persist for a long time in a natural population. We also found that distinct genotypes differ in sexual reproduction frequency, but these differences did not affect whether genotypes reappeared across samplings. Our study describes changes in population genetic structure across the seasons in a hydra population for the first time, providing key insights into the biology of the species, while also contributing to understanding the population biology of facultative sexual species inhabiting freshwater ecosystems.
ppGpp Is Present in and Functions to Regulate Sleep in Drosophila
Authors: Young Way , Zhang Xiaohui , Daixi Huimin , Zhou Enxing , Liu Ying , Wang Tao , Zhang Wenxia , Zhang Xinxiang , Rao Yi
Published: September 2021

Discovery of molecules in living systems and demonstration of their functional roles are pivotal in furthering our understanding of the molecular basis of biology. ppGpp (guanosine-5’-diphosphate, 3’-diphosphate) has been detected in prokaryotes for more than five decades. Here we report that a genetic screen followed by chemical analysis revealed the presence of ppGpp in Drosophila. It can be detected in germ-free Drosophila and its level is controlled by an enzyme encoded by themesh1gene in Drosophila. Loss of function mutations inmesh1, which encoded the ppGpp degrading enzyme led to longer sleep latency and less total sleep. These phenotypes could be rescued by wild typemesh1, but not by the enzymatically defective mutant Mesh1E66A, functionally implicating ppGpp. Ectopic expression of RelA, theE. colisynthetase for ppGpp, phenocopiedmesh1knockout mutants, whereas overexpression ofmesh1resulted in the opposite phenotypes, supporting that ppGpp is both necessary and sufficient in sleep regulation.mesh1is expressed in a specific population of neurons, and a chemoconnectomic screen followed by genetic intersection experiments implicate the pars intercerebralis (PI) as the site of ppGpp function. Our results have thus revealed that ppGpp is present in animals after long lag since its discovery in bacteria. Furthermore, we have demonstrated that ppGpp in a specific subset of neurons plays a physiological role in regulating sleep. We speculate that ppGpp may play function in mammals.
The effect of mating complexity on gene drive dynamics
Authors: Verma Prateek , Reeves R. Guy , Simon Samson , Otto Mathias , Gokhale Chaitanya S.
Published: September 2021

Gene drive technology promises to deliver on some of the global challenges humanity faces to-day in healthcare, agriculture and conservation. However, there is a limited understanding of the consequences of releasing self-perpetuating transgenic organisms into the wild populations under complex ecological conditions. In this study, we analyze the impact of three such complexities, mate-choice, mating systems and spatial mating network, on the population dynamics for two distinct classes of modification gene drive systems. All three factors had a high impact on the modelling outcome. First, we demonstrate that distortion based gene drives appear to be more robust against the mate-choice than viability-based gene drives. Second, we find that gene drive spread is much faster for higher degrees of polygamy. Including a fitness cost, the drive is fastest for intermediate levels of polygamy. Finally, the spread of gene drive is faster and more effective when the individuals have fewer connections in a spatial mating network. Our results highlight the need to include mating complexities while modelling the properties of gene drives such as release thresholds, timescales and population-level consequences. This inclusion will enable a more confident prediction of the dynamics of engineered gene drives and possibly even inform on the origin and evolution of natural gene drives.
Cellular heterogeneity of human fallopian tubes in normal and hydrosalpinx disease states identified by scRNA-seq
Authors: Ulrich Nicole D , Shen Yu-chi , Ma Qianyi , Yang Kun , Hannum D Ford , Jones Andrea , Machlin Jordan , Randolph John F , Smith Yolanda R , Schon Samantha B , Shikanov Ariella , Marsh Erica E. , Li Jun Z , Hammoud Sue
Published: September 2021

Fallopian tube (FT) homeostasis requires dynamic regulation of heterogeneous cell populations and is disrupted in infertility and ovarian cancer. Here we applied single-cell RNAseq to profile 53,376 FT cells from 3 healthy pre-menopausal subjects. The resulting cell atlas contains 12 major cell types representing epithelial, stromal and immune compartments. Re-clustering of epithelial cells identified 4 ciliated and 6 non-ciliated secretory epithelial subtypes, two of which represent potential progenitor pools: one leading to mature secretory cells, while the other contributing to either ciliated cells or one of the stromal cell types. To understand how FT cell numbers and states change in a disease state, we analyzed ~15,000 cells from a hydrosalpinx sample and observed shifts in epithelial and stromal populations, and cell type-specific changes in extracellular matrix and TGF-β signaling, underscoring fibrosis pathophysiology. This resource is expected to facilitate future studies to understand fallopian tube homeostasis in normal development and disease.
A Novel Model of Estrogen Receptor-Positive Breast Cancer Bone Metastasis with Antiestrogen Responsiveness
Authors: Langsten Kendall L. , Shi Lihong , Wilson Adam S. , Westwood Brian , Xie Maria T. , Surratt Victoria E. , Turner JoLyn , Singh Ravi , Cook Katherine L. , Kerr Bethany A.
Published: September 2021

Most women diagnosed with breast cancer (BC) have estrogen receptor alpha positive (ER+) disease. ER+ BC preferentially metastasizes to bone; at which time it is considered incurable. Treatments for bone metastasis have not advanced in decades, in part due to a lack of appropriate ER+ BC bone metastasis models. We developed an immunocompetent ER+ BC murine model with spontaneous bone metastasis and antiestrogen responsiveness. To do this, we transduced triple-negative (TN) bone-tropic murine BC cell lines 4T1.2 and E0771/Bone to express ERα. These cells were then injected into the mammary fat pads of Balb/c (n=21) or C57Bl/6 (n=27), respectively. Once tumors established, mice were treated with either the selective estrogen receptor modulator (SERM) tamoxifen (TAM), the selective estrogen receptor degrader (SERD) ICI 182,780 (ICI, Faslodex, fulvestrant), or vehicle control for 21 days. Tumor volumes and weights significantly decreased in the ER+ groups treated with TAM and ICI compared with ER+ vehicle-treated groups. Staining for immune profiles and total RNA sequencing demonstrated modified immune cell infiltration between TN and ER-derived tumors. Approximately 25% of the mice with ER+ 4T1.2 tumors developed metastases to long bones while none of the mice with TN tumors developed metastases. This immunocompetent ER+ 4T1.2 BC model may allow for further exploration of ER+ BC bone metastasis mechanisms and for the development of new therapeutics for women diagnosed with bone metastasis from ER+ BC.

Simple Summary

Estrogen receptor alpha positive (ER+) breast cancer is the most common subtype of breast cancer. When it metastasizes to bone, it becomes incurable. Little advancement has occurred in the treatment of bone metastasis from ER+ breast cancer, partly due to the lack of animal models. To establish an animal model of ER+ BC, we genetically modified two triple-negative breast cancer cell lines to express ERα and injected the cell lines into murine mammary glands. Mice were treated with standard antiestrogen therapies, the selective estrogen receptor modulator tamoxifen or the selective estrogen receptor degrader ICI 182,780. We found that compared to mice with triple-negative breast cancer, mice with ER+ breast cancer developed bone metastases and were responsive to antiestrogen therapy. This model allows for further exploration of bone metastasis mechanisms and for the development of new therapeutics, translating into improved clinical outcomes for women with bone metastasis from ER+ breast cancer.
Hotter chili peppers by hybridisation: heterosis and reciprocal effects
Authors: Naves Emmanuel Rezende , Scossa Federico , Araújo Wagner L. , Nunes-Nesi Adriano , Fernie Alisdair R. , Zsögön Agustin
Published: September 2021

The selection of pure lines followed by crosses to create superior hybrids is one of the oldest strategies in crop breeding. However, in domesticated species of theCapsicumgenus hybrid breeding has lagged, in part due to a lack of detailed information about the phenotypic and metabolic consequences of hybridization. Here, we performed reciprocal crosses between four inbred varieties of two species of cultivatedC. chinense(cv. Habanero and Biquinho) andC. annuumvar.annuum(cv. Jalapeño and cv. Cascadura Ikeda). These varieties were specifically selected for their highly divergent traits, including plant growth habit, fruit size, shape and pungency: Habanero and Jalapeño peppers are highly pungent forms, particularly popular in Mexico. The Biquinho cultivar ofC. chinenseand the Cascadura Ikeda bell pepper are traditional sweet cultivars from Brazil. From the parental genotypes and from the progeny of the reciprocal crosses, we measured 28 phenotypic traits, including plant growth, and yield, 32 fruit shape parameters, and 50 fruit pericarp and placenta metabolites, including capsaicinoids. We found large differences for agronomic and metabolic traits between the genotypes, including heterosis for pungency and reciprocal effects for agronomic traits. We also show that the strong association between fruit shape and pungency can be broken in intraspecific hybrids, paving the way for the precision breeding of novel varieties.

Once sentence summary

Hybrids of Capsicum peppers display heterosis and reciprocal effects for agronomic traits and fruit pungency
Quantifying the propagation of parametric uncertainty on flux balance analysis
Authors: Dinh Hoang V. , Sarkar Debolina , Maranas Costas D.
Published: September 2021

Flux balance analysis (FBA) and associated techniques operating on stoichiometric genome-scale metabolic models play a central role in quantifying metabolic flows and constraining feasible phenotypes. At the heart of these methods lie two important assumptions: (i) the biomass precursors and energy requirements neither change in response to growth conditions nor environmental/genetic perturbations, and (ii) metabolite production and consumption rates are equal at all times (i.e., steady-state). Despite the stringency of these two assumptions, FBA has been shown to be surprisingly robust at predicting cellular phenotypes. In this paper, we formally assess the impact of these two assumptions on FBA results by quantifying how uncertainty in biomass reaction coefficients, and departures from steady-state due to temporal fluctuations could propagate to FBA results. In the first case, conditional sampling of parameter space is required to re-weigh the biomass reaction so as the molecular weight remains equal to 1 g/mmol, and in the second case, metabolite (and elemental) pool conservation must be imposed under temporally varying conditions. Results confirm the importance of enforcing the aforementioned constraints and explain the robustness of FBA biomass yield predictions.
No impact of biocontrol agent’s predation cues on development time or size of surviving Aedes albopictus under optimal nutritional availability
Authors: Russell Marie C. , Cator Lauren J.
Published: September 2021

Cyclopoid copepods have been applied successfully to limit populations of highly invasive Aedes albopictus mosquitoes that can transmit diseases of public health importance. However, there is concern that changes in certain mosquito traits, induced by exposure to copepod predation, might increase the risk of disease transmission. In this study, third instar Ae. albopictus larvae, hereafter referred to as “focal individuals”, were exposed to Megacyclops viridis predator cues associated with both consumption of newly-hatched mosquito larvae and attacks on focal individuals. The number of newly-hatched larvae surrounding each focal larva was held constant to control for density effects on size, and the focal individual’s day of pupation and wing length were recorded for each replicate.

Exposing late instar Ae. albopictus to predation decreased their chances of surviving to adulthood, and three focal larvae that died in the predator treatment showed signs of melanization, indicative of wounding. Among surviving focal Ae. albopictus, no significant difference in either pupation day or wing length was observed due to copepod predation. The absence of a significant sublethal impact from M. viridis copepod predation on surviving later-stage larvae in this analysis supports the use of M. viridis as a biocontrol agent against Ae. albopictus.

Graphical abstract
Assessment of Environmental and Occupational Risk Factors for the Mitigation and Containment of a COVID-19 Outbreak in a Meat Processing Plant
Authors: Walshe Nicola , Fennelly Mehael , Hellebust Stig , Wenger John , Sodeau John , Prentice Michael , Grice Charlene , Jordan Vincent , Comerford John , Downey Vicky , Perrotta Carla , Mulcahy Grace , Sammin Donal
Published: September 2021

Throughout the COVID-19 pandemic, meat processing plants have been vulnerable to outbreaks of SARS-CoV-2 infection. Transmission of the virus is difficult to control in these settings because of a combination of factors including environmental conditions and the specific nature of the work. This paper describes a retrospective outbreak investigation in a meat processing plant, a description of the measures taken to prevent or contain further outbreaks, and insights on how those with specific knowledge of the working environment of these plants can collaborate with public health authorities to ensure optimal outbreak control. The plant experienced 111 confirmed positive asymptomatic cases in total with an estimated attack rate of 38% during a five-week period. Four weeks after the first case, mass screening of all workers was conducted by the public health authorities. Thirty-two workers tested positive, of which 16 (50%) worked in one particular area of the plant, the boning hall (n=60). The research team prepared and carried out semi-structured interviews with the plant personnel who were charged with COVID control within the plant. They carried out assessments of operational risk factors and also undertook air quality monitoring in the boning hall and abattoir. The air quality measurements in the boning hall showed a gradual build-up of carbon dioxide and aerosol particles over the course of a work shift, confirming that this poorly ventilated area of the plant had an environment that was highly favourable for aerosol transmission of SARS-CoV-2. Assessment of operational conditions incorporated visual surveys of the plant during the working day. Prior to and during the first two weeks of the outbreak, multiple measures were introduced into the plant by management, including physical distancing, provision of educational material to workers, visitor restrictions, and environmental monitoring. After the implementation of these measures and their progressive refinement by plant management, the factory had no further linked cases (clusters) or outbreaks for the following 198 days. The tailored approach to risk mitigation adopted in this meat processing plant shows that generic risk mitigation measures, as recommended by public health authorities, can be successfully adapted and optimized by designated plant emergency response teams.
Single-Dose SARS-CoV-2 Vaccination With BNT162b2 and AZD1222 Induce Disparate Th1 Responses and IgA Production
Authors: Müller Michael , Volzke Johann , Subin Behnam , Müller Silke , Sombetzki Martina , Reisinger Emil C. , Müller-Hilke Brigitte
Published: September 2021

While vaccination programs against SARS-CoV-2 are globally ongoing, disparate strategies for the deployment of spike antigen show varying effectiveness. In order to explore this phenomenon, we sought to compare the early immune responses against AZD1222 and BNT162b2. SARS-CoV-2 seronegative participants received a single dose of either vaccine and were analyzed for immune cell, effector T cell and antibody dynamics. AZD1222 induced transient leukopenia and major changes among innate and adaptive subpopulations. Both vaccines induced spike protein specific effector T cells which were dominated by Th1 responses following AZD1222 vaccination. A significant reduction of anti-inflammatory T cells upon re-stimulation was also restricted to AZD1222 vaccinees. While IgM and IgG were the dominant isotypes elicited by AZD1222, BNT162b2 led to a significant production of IgG and IgA. Our results suggest that the strategy for spike antigen delivery impacts on how and to what extent immune priming against the main SARS-CoV-2 antigen proceeds.
Examining Health Service Rates Among Residents of Retirement Homes and Other Older Adult Populations in Ontario, Canada: A Population-Based Cohort Study
Authors: Manis Derek R. , Poss Jeffrey W. , Jones Aaron , Rochon Paula A. , Bronskill Susan E. , Campitelli Michael A. , Perez Richard , Stall Nathan M. , Rahim Ahmad , Babe Glenda , Tarride Jean-Éric , Abelson Julia , Costa Andrew P.
Published: September 2021

Background

There are no standardized reporting systems or assessments specific to residents of retirement homes in North America. As such, little is known about these older adults as a distinct population. We created a new population-level cohort of residents of retirement homes and examined their health service rates relative to other older adult populations.

Methods

We conducted a population-based retrospective cohort study in Ontario, Canada in 2018. The postal codes of all licensed retirement homes (n= 757) were classified and linked to individual-level health system administrative data to derive a cohort of residents of retirement homes. A generalized linear model with a gamma distribution and log link function was used to model rates of emergency department visits, hospitalizations, alternate levels of care (ALC) days, primary care visits, and specialist physician visits.

Results

Residents of retirement homes comprised two percent of the older adult population in Ontario (n= 54,773; 2.3%). After adjustment for relevant characteristics, residents of retirement homes had 10 times the rate of emergency department visits (Relative Rate [RR] 10.02, 95% Confidence Interval [CI] 9.83 to 10.21), 20 times the rate of hospitalizations (RR 20.43, 95% CI 20.08 to 20.78), and 44 times the rate ALC days (RR 43.91, 95% CI 43.28 to 44.54) compared to community-dwelling older adults.

Interpretation

Residents of retirement homes are a distinct older adult population with high rates of hospital-based care. Our findings contribute to policy debates about the provision of health care in privately operated congregate care settings for older adults.
A BioID-derived proximity interactome for SARS-CoV-2 proteins
Authors: May Danielle G. , Martin-Sancho Laura , Anschau Valesca , Liu Sophie , Chrisopulos Rachel J. , Scott Kelsey L. , Halfmann Charles T. , Peña Ramon Díaz , Pratt Dexter , Campos Alexandre R. , Roux Kyle J.
Published: September 2021

The novel coronavirus SARS-CoV-2 is responsible for the ongoing COVID-19 pandemic and has caused a major health and economic burden worldwide. Understanding how SARS-CoV-2 viral proteins behave in host cells can reveal underlying mechanisms of pathogenesis and assist in development of antiviral therapies. Here we use BioID to map the SARS-CoV-2 virus-host interactome using human lung cancer derived A549 cells expressing individual SARS-CoV-2 viral proteins. Functional enrichment analyses revealed previously reported and unreported cellular pathways that are in association with SARS-CoV-2 proteins. We have also established a website to host the proteomic data to allow for public access and continued analysis of host-viral protein associations and whole-cell proteomes of cells expressing the viral-BioID fusion proteins. Collectively, these studies provide a valuable resource to potentially uncover novel SARS-CoV-2 biology and inform development of antivirals.
Basal Gp78-dependent mitophagy promotes mitochondrial health and limits mitochondrial ROS
Authors: Alan Parsa , Vandevoorde Kurt R. , Joshi Bharat , Cardoen Ben , Gao Guang , Mohammadzadeh Yahya , Hamarneh Ghassan , Nabi Ivan R.
Published: September 2021

Mitochondria are major sources of cytotoxic reactive oxygen species (ROS) that contribute to cancer progression. Mitophagy, the selective elimination of mitochondria by autophagy, monitors and maintains mitochondrial health and integrity, eliminating ROS-producing mitochondria. However, mechanisms underlying mitophagic control of mitochondrial homeostasis under basal conditions remain poorly understood. Gp78 E3 ubiquitin ligase is an endoplasmic reticulum membrane protein that induces mitochondrial fission and mitophagy of depolarized mitochondria. Here, we report that CRISPR/Cas9 knockout of Gp78 in HT-1080 fibrosarcoma cells increased mitochondrial volume and rendered cells resistant to carbonyl cyanide m-chlorophenyl hydrazone (CCCP)-induced mitophagy. These effects were phenocopied by knockdown of the essential autophagy protein ATG5 in wild-type HT-1080 cells. Use of the mito-Keima mitophagy probe confirmed that Gp78 promoted both basal and damage-induced mitophagy. Application of a spot detection algorithm (SPECHT) to GFP-mRFP tandem fluorescent-tagged LC3 (tfLC3)-positive autophagosomes reported elevated autophagosomal maturation in wild-type HT-1080 cells relative to Gp78 knockout cells, predominantly in proximity to mitochondria. Mitophagy inhibition by either Gp78 knockout or ATG5 knockdown reduced mitochondrial potential and increased mitochondrial ROS. Live cell analysis of tfLC3 in HT-1080 cells showed the preferential association of autophagosomes with mitochondria of reduced potential. Basal Gp78-dependent mitophagic flux is therefore selectively associated with reduced potential mitochondria promoting maintenance of a healthy mitochondrial population and limiting ROS production.
Development of novel potent ligands for GPR85, an orphan G protein-coupled receptor expressed in the brain
Authors: Sakai Aya , Yasui Takeshi , Watanave Masashi , Tatsumi Rine , Yamamoto Yoshihiko , Takano Wataru , Tani Yuki , Okamura Izumi , Hirai Hirokazu , Takeda Shigeki
Published: September 2021

GPR85 is a member of the G protein-coupled receptor and is a super-conserved receptor expressed in the brain sub-family (SREB) with GPR27 and GPR173. These three receptors are “orphan receptors”; however, their endogenous ligands have not been identified. SREB has garnered the interest of many scientists because it is expressed in the central nervous system and is evolutionarily conserved. In particular, brain mass is reported to be increased and learning and memory are improved in GPR85 knockout mice (Matsumoto et al., 2008). In this study, we characterized newly synthesized compounds using a GPR85-Gsα fusion protein and the [35S]GTPγS binding assay and identified novel GPR85 inverse-agonists with IC50 values of approximately 1 µM. To analyze the neurochemical character of the compounds and investigate the physiological significance of GPR85, we used cerebellar Purkinje cells expressing GPR85 and an electrophysiological technique. Based on the results, the inverse-agonist compound for GPR85 modulated potassium channel opening. Together with the results of previous gene analysis of GPR85, we expect that the development of the GPR85 ligand will provide new insights into a few types of neurological disorders.
Copeptin response to acute physical stress during hypohydration: An exploratory secondary analysis
Authors: Carroll Harriet A. , Melander Olle
Published: September 2021

Purpose

Plasma copeptin (a surrogate marker of arginine vasopressin) is increasingly being used as a marker of stress in several research and clinical contexts. However, the response to an acute physical stressor in healthy adults has not yet been tested meaning it is unclear whether copeptin reflects dynamic changes in stress or whether this is moderated by different basal copeptin concentrations and how this relates to other stress hormones.

Methods

Secondary data analysis in a subsample of participants (n = 7; n = 1 woman) who opted-in for muscle biopsies in a randomised crossover study investigating the effects of acute hypohydration (HYPO) versus rehydration (RE) on metabolism.

Results

Plasma copeptin responded to the muscle biopsy stress stimulus, with a similar magnitude of difference according to basal concentrations during HYPO and RE; however, the peak was higher and concentrations typically took longer to return to baseline during HYPO. Despite large differences in copeptin concentrations, adrenocorticotropin hormone (ACTH) and cortisol showed a similar trends in response to the biopsies, regardless of hydration status.

Conclusion

Copeptin responded dynamically to an acute physical stressor (muscle biopsy). HYPO induced higher basal copeptin concentrations compared to RE, and resulted in a higher and prolonged copeptin response. Further research should investigate the mechanisms underlying the lack of differences in ACTH and cortisol according to hydration status.
On the origin and evolution of Drosophila new genes during spermatogenesis
Authors: Su Qianwei , He Huangyi , Zhou Qi
Published: September 2021

Origin of functional new genes is a basic biological process that has significant contribution to organismal diversity. Previous studies in both Drosophila and mammals showed that new genes tend to be expressed in testis, and avoid the X chromosome presumably because meiotic sex chromosome inactivation (MSCI). Here we analyze the published single-cell transcriptome data of Drosophila adult testis and find an enrichment of male germline mitotic genes, but an underrepresentation of meiotic genes on the X chromosome. This can be attributed to an excess of autosomal meiotic genes that were derived from their X-linked mitotic progenitors, which provides direct cell-level evidence for MSCI in Drosophila. We reveal that new genes, particularly those produced by retrotransposition, tend to exhibit an expression shift toward late spermatogenesis compared to their parental copies, probably due to the more intensive sperm competition or sexual conflict. Our results dissect the complex factors including the age, the origination mechanisms and the chromosomal locations that influence the new gene origination and evolution in testis, and identify new gene cases that show divergent cell-level expression pattern from their progenitors for future functional studies.
Influenza A (N1-N9) and Influenza B (B/Vic and B/Yam) Neuraminidase Pseudotypes as Tools for Pandemic Preparedness and Improved Influenza Vaccine design
Authors: da Costa Kelly A.S. , Del Rosario Joanne Marie M. , Ferrari Matteo , Vishwanath Sneha , Asbach Benedikt , Kinsley Rebecca , Wagner Ralf , Heeney Jonathan L. , Carnell George W. , Temperton Nigel J.
Published: September 2021

To better understand how inhibition of the influenza neuraminidase (NA) protein contributes to protection against influenza, and to investigate its breadth and cross-neutralizing activity, we have produced lentiviral vectors pseudotyped with an avian H11 hemagglutinin (HA) and the NA (N1-N9) of all influenza A and (B/Victoria and B/Yamagata) influenza B subtypes. These NA viral pseudotypes (PV) possess stable NA activity and can be utilized as target antigens in in vitro assays to assess vaccine immunogenicity. Employing these NA PV, we have developed an enzyme-linked lectin assay (pELLA) for routine serology to measure neuraminidase inhibition (NI) titers of reference antisera, monoclonal antibodies, and post-vaccination sera with various influenza antigens. We have also shown that pELLA is more sensitive than the commercially available NA-Fluor™ in detecting NA inhibition in these samples. Our studies may lead to establishing the protective NA titer that contributes to NA-based immunity. This will aid in the design of superior, longer lasting, and more broadly protective vaccines that can be employed together with HA-targeted vaccines in a pre-pandemic approach.
Single-Round Remodeling of the Active Site of an Artificial Metalloenzyme using an Ultrahigh-Throughput Double Emulsion Screening Assay
Authors: Vallapurackal Jaicy , Stucki Ariane , Liang Alexandria Deliz , Klehr Juliane , Dittrich Petra S. , Ward Thomas R.
Published: September 2021

The potential of high-throughput compartmentalization renders droplet microfluidics an attractive tool for directed evolution of enzymes as it permits maintenance of the phenotype-genotype linkage throughout the entire optimization procedure. In particular, water-in-oil-in-water double emulsions droplets (DEs) produced by microfluidics enable the analysis of reaction compartments at ultra-high-throughput using commercially available fluorescence-activated cell sorting (FACS) devices. Here we report a streamlined method applicable for the ultrahigh-throughput screening of an artificial metalloenzyme (ArM), an artificial deallylase (ADAse), in double emulsions. The DE-protocol was validated by screening a four hundred member, double-mutant streptavidin library for the CpRu-catalyzed uncaging of aminocoumarin. The most active variants, identified by next generation sequencing of the sorted DE droplets with highest fluorescent intensity, are in good agreement with 96-well plate screening hits. These findings, thus, pave the way towards the systematic implementation of commercially available FACS for the directed evolution of metalloenzymes making ultrahigh-throughput screening more broadly accessible. The use of microfluidics for the formation of uniform compartments with precise control over reagents and cell encapsulation further facilitates the establishment of highly reliable quantitative assays.
Large-scale two-photon calcium imaging in freely moving mice
Authors: Zong Weijian , Obenhaus Horst A. , Skytøen Emilie R. , Eneqvist Hanna , de Jong Nienke L. , Jorge Marina R. , Moser May-Britt , Moser Edvard I.
Published: September 2021

We developed a miniaturized two-photon microscope (MINI2P) for fast, high-resolution, multiplane calcium imaging of over 1,000 neurons at a time in freely moving mice. With a microscope weight below 3g and a highly flexible connection cable, MINI2P allowed imaging to proceed with no impediment of behavior in half-hour free-foraging trials compared to untethered, unimplanted animals. The improved cell yield was achieved through a new optical system design featuring an enlarged field of view (FOV) and a new micro-tunable lens with increased z-scanning range and speed that allowed for fast and stable imaging of multiple, interleaved planes as well as 3D functional imaging. A novel technique for successive imaging across multiple, adjacent FOVs enabled recordings from more than 10,000 neurons in the same animal. Large-scale proof-of-principle data were obtained from cell populations in visual cortex, medial entorhinal cortex, and hippocampus, revealing spatial tuning of cells in all areas, including visual cortex.

Highlights

We developed a lightweight 2-photon miniscope for imaging in freely-foraging mice

Activity can be monitored in volumes of over 1,000 visual or entorhinal-cortex cells

A new z-scanning module allows fast imaging across multiple interleaved planes

Successive imaging from adjacent regions enables imaging from more than 10,000 cells
Progenitor-intrinsic Metabolic Sensing Promotes Hematopoietic Homeostasis
Authors: Pizzato Hannah A. , Wang Yahui , Wolfgang Michael J. , Finck Brian N. , Patti Gary J. , Bhattacharya Deepta
Published: September 2021

Hematopoietic homeostasis is maintained by stem and progenitor cells in part by extrinsic feedback cues triggered by mature cell loss. We demonstrate a different mechanism by which hematopoietic progenitors intrinsically anticipate and prevent the loss of mature progeny through metabolic switches. We examined hematopoiesis in mice conditionally deficient in long-chain fatty acid oxidation (carnitine palmitoyltransferase 2,Cpt2), glutaminolysis (glutaminase,Gls), or mitochondrial pyruvate import (mitochondrial pyruvate carrier 2,Mpc2). While genetic ablation ofCpt2orGlsminimally impacted most blood lineages, deletion ofMpc2led to a sharp decline in mature myeloid cells. However, MPC2-deficient myeloid cells rapidly recovered due to a transient increase in myeloid progenitor proliferation. Competitive bone marrow chimera and stable isotope tracing experiments demonstrated that this proliferative burst was intrinsic to MPC2-deficient progenitors and accompanied by a metabolic switch to glutaminolysis. Thus, hematopoietic progenitors intrinsically adjust to metabolic perturbations independently of feedback from downstream mature cells to maintain homeostasis.
Methodological considerations in analyzing synchronization of resting-state brain networks with the intrinsic electrical rhythm of the stomach: Advantages of weighted phase-locking
Authors: Choe Ann S. , Tang Bohao , Smith Kimberly R. , Honari Hamed , Lindquist Martin A. , Caffo Brian S. , Pekar James J.
Published: September 2021

Purpose

To evaluate the amplitude-weighted phase-locking value (awPLV) as a measure of synchronization of brain resting-state networks (RSNs) with the gastric basal electrical rhythm (BER).

Methods

A recent study combined rsfMRI with concurrent cutaneous electrogastrography (EGG), in a highly-sampled individual who underwent 22 scanning sessions (two 15-minute runs per session) at 3.0 Tesla. After excluding three sessions due to weak EGG signals, 9.5 hours of data remained, from which 18 RSNs were estimated using spatial independent component analysis. Previously, using the phase-locking value (PLV), three of the 18 RSNs were determined to be synchronized with the BER. However, RSN power fluctuations in the gastric frequency band could reduce sensitivity of PLV. Accordingly, the current reanalysis used awPLV to unweight contributions from low power epochs. Mismatched EGG and rsfMRI data (from different days) served as surrogate data; for each RSN, empirical awPLV was compared with chance-level awPLV using a Wilcoxon rank test. P-values were adjusted using with a false discovery rate of 0.05. Additionally, simulations were performed to compare PLV and awPLV error rates under settings with a known ground truth.

Results

Simulations show high false-negative rates when using PLV, but not awPLV. Reanalysis of the highly-sampled individual data using awPLV indicates that 11 of the 18 RSNs were synchronized with the BER.

Conclusion

Simulations indicate that awPLV is a more sensitive measure of stomach/brain synchronization than PLV. Reanalysis results imply communication between the enteric nervous system and brain circuits not typically considered responsive to gastric state or function.
Semi-automated analysis of an optical ATP indicator in neurons
Authors: Dehkharghanian Taher , Hashemiaghdam Arsalan , Ashrafi Ghazaleh
Published: September 2021

Significance

The firefly enzyme luciferase has been used in a wide range of biological assays, including bioluminescence imaging of ATP. The biosensor Syn-ATP utilizes subcellular targeting of luciferase to nerve terminals for optical measurement of ATP in this compartment. Manual analysis of Syn-ATP signals is challenging due to signal heterogeneity and cellular motion in long imaging sessions. Here, we have leveraged machine learning tools to develop a method for analysis of bioluminescence images.

Aim

Our goal was to create a semi-automated pipeline for analysis of bioluminescence imaging to improve measurements of ATP content in nerve terminals.

Approach

We developed an image analysis pipeline that applies machine learning toolkits to distinguish neurons from background signals, and excludes neural cell bodies, while also incorporating user input.

Results

Side-by-side comparison of manual and semi-automated image analysis demonstrated that the latter improves precision and accuracy of ATP measurements.

Conclusions

Our method streamlines data analysis and reduces user-introduced bias, thus enhancing the reproducibility and reliability of quantitative ATP imaging in nerve terminals.
Crystal structure and magnetic properties of the layered hybrid organic–inorganic compounds M
2(OH)2(C14H8O4) (M = Mn, Fe)
Authors: Sibille Romain , Mazet Thomas , Diop Leopold V. B. , François Michel
Published: September 2021

The structure of M
2(OH)2(bpdc) (bpdc = biphenyl dicarboxylate, C14H8O4) is distinct from that of the isoreticular compounds M
2(OH)2(bdc) (bdc = benzene dicarboxylate, C8H4O4) (M = Mn, Fe), in the sense that no disorder of the bpdc molecules from one layer to the other needs to be considered. The global symmetry is lower in the bpdc compounds (P
1) than in the bdc compounds (C2/m). Both Mn2(OH)2(bpdc) and Fe2(OH)2(bpdc) order magnetically at 36.8 and 46.5 K, respectively, and can be considered as uncompensated antiferromagnets, whereas Mn2(OH)2(bdc) (Néel temperature T
N = 38.5 K) and Fe2(OH)2(bdc) (T
N = 66 K) are compensated antiferromagnets.
Crystal and magnetic structures of R
2Ni1.78In compounds (R = Tb, Ho, Er and Tm)
Authors: Baran Stanisław , Deptuch Aleksandra , Hoser Andreas , Penc Bogusław , Tyvanchuk Yuriy , Szytuła Andrzej
Published: September 2021

The crystal and magnetic structures in R
2Ni1.78In (R = Ho, Er and Tm) have been studied by neutron diffraction. The compounds crystallize in a tetragonal crystal structure of the Mo2FeB2 type (space group P4/mbm). At low temperatures, the magnetic moments, localized solely on the rare earth atoms, form antiferromagnetic structures described by the propagation vector k = [kx
, kx
, ½], with kx
equal to ¼ for R = Er and Tm or 0.3074 (4) for R = Ho. The magnetic moments are parallel to the c axis for R = Ho or lie within the (001) plane for R = Er and Tm. The obtained magnetic structures are discussed on the basis of symmetry analysis. The rare earth magnetic moments, determined from neutron diffraction data collected at 1.6 K, are 6.5 (1) μB (Er) and 6.09 (4) μB (Tm), while in the incommensurate modulated magnetic structure in Ho2Ni1.78In the amplitude of modulation of the Ho magnetic moment is 7.93 (8) μB. All these values are smaller than those expected for the respective free R
3+ ions. A symmetry analysis of the magnetic structure in Tb2Ni1.78In is also included, as such information is missing from the original paper [Szytuła, Baran, Hoser, Kalychak, Penc & Tyvanchuk (2013). Acta Phys. Pol. A, 124, 994–997]. In addition, the results of magnetometric measurements are reported for Tm2Ni1.78In. The compound shows antiferromagnetic ordering below the Néel temperature of 4.5 K. Its magnetic properties are found to originate from magnetic moments localized solely on the thulium atoms (the nickel atoms remain non-magnetic in Tm2Ni1.78In). The reduction of rare earth magnetic moments in the ordered state in R
2Ni1.78In (R = Tb, Ho, Er and Tm) and the change in direction of the moments indicate the influence of the crystalline electric field (CEF) on the stability of the magnetic order in the investigated compounds.