bluuebunny/crossref_metadata_2025 huggingface dataset:
Invasion of the body snatchers: the role of parasite introduction in host distribution and response to salinity in invaded estuaries
Authors: Blakeslee April M. H. , Pochtar Darby L. , Fowler Amy E. , Moore Chris S. , Lee Timothy S. , Barnard Rebecca B. , Swanson Kyle M. , Lukas Laura C. , Ruocchio Matthew , Torchin Mark E. , Miller A. Whitman , Ruiz Gregory M. , Tepolt Carolyn K.
Published: June 2021

In dynamic systems, organisms are faced with variable selective forces that may impose trade-offs. In estuaries, salinity is a strong driver of organismal diversity, while parasites shape species distributions and demography. We tested for trade-offs between low-salinity stress and parasitism in an invasive castrating parasite and its mud crab host along salinity gradients of two North Carolina rivers. We performed field surveys every six to eight weeks over 3 years to determine factors influencing parasite prevalence, host abundance, and associated taxa diversity. We also looked for signatures of low-salinity stress in the host by examining its response (time-to-right and gene expression) to salinity. We found salinity and temperature significantly affected parasite prevalence, with low-salinity sites (less than 10 practical salinity units (PSU)) lacking infection, and populations in moderate salinities at warmer temperatures reaching prevalence as high as 60%. Host abundance was negatively associated with parasite prevalence. Host gene expression was plastic to acclimation salinity, but several osmoregulatory and immune-related genes demonstrated source-dependent salinity response. We identified a genetic marker that was strongly associated with salinity against a backdrop of no neutral genetic structure, suggesting possible selection on standing variation. Our study illuminates how selective trade-offs in naturally dynamic systems may shape host evolutionary ecology.
Divergent regional evolutionary histories of a devastating global amphibian pathogen
Authors: Rothstein Andrew P. , Byrne Allison Q. , Knapp Roland A. , Briggs Cheryl J. , Voyles Jamie , Richards-Zawacki Corinne L. , Rosenblum Erica Bree
Published: June 2021

Emerging infectious diseases are a pressing threat to global biological diversity. Increased incidence and severity of novel pathogens underscores the need for methodological advances to understand pathogen emergence and spread. Here, we use genetic epidemiology to test, and challenge, key hypotheses about a devastating zoonotic disease impacting amphibians globally. Using an amplicon-based sequencing method and non-invasive samples we retrospectively explore the history of the fungal pathogen
Batrachochytrium dendrobatidis
(
Bd
) in two emblematic amphibian systems: the Sierra Nevada of California and Central Panama. The hypothesis in both regions is the hypervirulent Global Panzootic Lineage of
Bd
(
Bd
GPL) was recently introduced and spread rapidly in a wave-like pattern. Our data challenge this hypothesis by demonstrating similar epizootic signatures can have radically different underlying evolutionary histories. In Central Panama, our genetic data confirm a recent and rapid pathogen spread. However,
Bd
GPL in the Sierra Nevada has remarkable spatial structuring, high genetic diversity and a relatively older history inferred from time-dated phylogenies. Thus, this deadly pathogen lineage may have a longer history in some regions than assumed, providing insights into its origin and spread. Overall, our results highlight the importance of integrating observed wildlife die-offs with genetic data to more accurately reconstruct pathogen outbreaks.
Ecosystem function after the K/Pg extinction: decoupling of marine carbon pump and diversity
Authors: Birch Heather , Schmidt Daniela N. , Coxall Helen K. , Kroon Dick , Ridgwell Andy
Published: June 2021

The ocean biological pump is the mechanism by which carbon and nutrients are transported to depth. As such, the biological pump is critical in the partitioning of carbon dioxide between the ocean and atmosphere, and the rate at which that carbon can be sequestered through burial in marine sediments. How the structure and function of planktic ecosystems in the ocean govern the strength and efficiency of the biological pump and its resilience to disruption are poorly understood. The aftermath of the impact at the Cretaceous/Palaeogene (K/Pg) boundary provides an ideal opportunity to address these questions as both the biological pump and marine plankton size and diversity were fundamentally disrupted. The excellent fossil record of planktic foraminifera as indicators of pelagic-biotic recovery combined with carbon isotope records tracing biological pump behaviour, show that the recovery of ecological traits (diversity, size and photosymbiosis) occurred much later (approx. 4.3 Ma) than biological pump recovery (approx. 1.8 Ma). We interpret this decoupling of diversity and the biological pump as an indication that ecosystem function had sufficiently recovered to drive an effective biological pump, at least regionally in the South Atlantic.
Diel oxygen fluctuation drives the thermal response and metabolic performance of coastal marine ectotherms
Authors: Booth J. M. , Fusi M. , Giomi F. , Chapman E. C. N. , Diele K. , McQuaid C. D.
Published: June 2021

Coastal marine systems are characterized by high levels of primary production that result in diel oxygen fluctuations from undersaturation to supersaturation. Constant normoxia, or 100% oxygen saturation, is therefore rare. Since the thermal sensitivity of invertebrates is directly linked to oxygen availability, we hypothesized that (i) the metabolic response of coastal marine invertebrates would be more sensitive to thermal stress when exposed to oxygen supersaturation rather than 100% oxygen saturation and (ii) natural diel fluctuation in oxygen availability rather than constant 100% oxygen saturation is a main driver of the thermal response. We tested the effects of oxygen regime on the metabolic rate, and haemocyanin and lactate levels, of velvet crabs (
Necora puber
) and blue mussels (
Mytilus edulis
), under rising temperatures (up to 24°C) in the laboratory. Oxygen supersaturation and photosynthetically induced diel oxygen fluctuation amplified animal metabolic thermal response significantly in both species, demonstrating that the natural variability of oxygen in coastal environments can provide considerable physiological benefits under ocean warming. Our study highlights the significance of integrating ecologically relevant oxygen variability into experimental assessments of animal physiology and thermal response, and predictions of metabolic performance under climate warming. Given the escalating intensity and frequency of climate anomalies, oxygen variation caused by coastal vegetation will likely become increasingly important in mitigating the effects of higher temperatures on coastal fauna.
Sulfitobacter aestuariivivens sp. nov., isolated from a tidal flat
Authors: Park Sooyeon , Yoon Jung-Hoon
Published: June 2021

A Gram-stain-negative, aerobic, non-flagellated, coccoid, ovoid or rod-shaped bacterial strain, TSTF-M16T, was isolated from a tidal flat on the Yellow Sea, Republic of Korea. The neighbour-joining phylogenetic tree of 16S rRNA gene sequences showed that strain TSTF-M16T fell within a clade comprising the type strains of

Sulfitobacter

species. Strain TSTF-M16T exhibited 16S rRNA gene sequence similarities of 98.5 and 98.1 % to the type strains of

Sulfitobacter mediterraneus

and

Sulfitobacter sabulilitoris

, respectively, and 96.2–97.8 % to the type strains of the other

Sulfitobacter

species. The average nucleotide identity and digital DNA–DNA hybridization values between the genomic sequences of strain TSTF-M16T and the type strains of 16

Sulfitobacter

species were 70.6–74.2 and 17.9–19.0 %, respectively. The DNA G+C content of strain TSTF-M16T from genomic sequence data was 59.26 mol%. Strain TSTF-M16T contained Q-10 as the predominant ubiquinone and C18 : 1
 ω7c as the major fatty acid. The major polar lipids of strain TSTF-M16T were phosphatidylcholine, phosphatidylglycerol, one unidentified aminolipid and one unidentified lipid. Distinguished phenotypic properties, together with the phylogenetic and genetic distinctiveness, revealed that strain TSTF-M16T is separated from recognized

Sulfitobacter

species. On the basis of the data presented here, strain TSTF-M16T is considered to represent a novel species of the genus

Sulfitobacter

, for which the name Sulfitobacter aestuariivivens sp. nov. is proposed. The type strain is TSTF-M16T (=KACC 21645T=NBRC 114501T).
Hybrid-Quantum approach for the optimal lockdown to stop the SARS-CoV-2 community spread subject to maximizing nation economy globally
Authors: Zaman Sahil , Khan Alex , Sadhu Arindam , Das Kunal , Khan Faisal Shah
Published: June 2021

Owing to the SARS-CoV-2 epidemic (severe acute respiratory coronavirus 2 syndromes), the global situation has changed drastically. Several countries, including India, Europe, U.S.A., introduced a full state/nation lockdown to minimize the disease transmission through human interaction after the virus entered the population and to minimize the loss of human life. Millions of people have gone unemployed due to lockdown implementation, resulting in business and industry closure and leading to a national economic slowdown. Therefore, preventing the spread of the COVID-19 virus in the world while also preserving the global economy is an essential problem requiring an effective and immediate solution. Using the compartmental epidemiology S, E, I, R or D (Susceptible, Exposed, Infectious, Recovery or Death) model extended to multiple population regions we predict the evolution of the SARS-CoV-2 disease and construct an optimally scheduled lockdown calendar to execute lockdown over phases, using the well-known Knapsack problem. A comparative analysis of both classical and quantum models shows that our model decreases SARS-CoV-2 active cases while retaining the average global economic factor, GDP, in contrast to the scenario with no lockdown.
The Refractive Error and Vision Impairment Estimation With Spectacle data (REVIEWS) study
Authors: Moore Michael , Loughman James , Butler John S. , Ohlendorf Arne , Wahl Siegfried , Flitcroft Daniel I.
Published: June 2021

Objective

To investigate whether spectacle lens sales data can be used to estimate the population distribution of refractive error amongst ametropes and hence estimate the current and future risk of vision impairment.

Design

Cross Sectional Study

Subjects

A total 141,547,436 spectacle lens sales records from an international European lens manufacturer between the years 1998 and 2016.

Methods

Anonymized patient spectacle lens sales data including refractive error information was provided by a major European spectacle lens manufacturer. Data from the Gutenberg Health Survey was digitized to allow comparison of a representative, population-based sample to the spectacle lens sales data. A bootstrap analysis was completed to assess the comparability of both datasets. The expected level of vision impairment due to myopia at age 75 was calculated for both datasets using a previously published risk estimation equation combined with a saturation function.

Main Outcome Measures

Comparability of spectacle lens sales data on refractive error to typical population surveys of refractive error and its potential utility to predict vision impairment due to refractive error.

Results

Equivalent estimates of the population distribution of spherical equivalent refraction can be provided from spectacle lens data within limits. For myopia, the population distribution was equivalent to the Gutenberg Health Survey (≤ 5% deviation) for levels ≤-2.0 dioptres, while for hyperopia the distribution was equivalent (≤ 5% deviation) for levels ≥ +3.0 diopters. The estimated rates of vision impairment due to myopia were not statistically significantly different (χ2 = 182, DoF = 169, p = 0.234) between the spectacle lens data and Gutenberg Health Survey data.

Conclusions

The distribution of refractive error and hence the risk of vision impairment due to refractive error within a population can be determined using spectacle lens sales data. Pooling this type of data from multiple industry sources could provide a cost effective, timely and globally representative mechanism for monitoring the evolving epidemiology of refractive error and associated vision impairment.
Clinical profiles at the time of diagnosis of COVID-19 in Costa Rica during the pre-vaccination period using a machine learning approach
Authors: Molina-Mora Jose Arturo , González Alejandra , Jiménez-Morgan Sergio , Cordero-Laurent Estela , Brenes Hebleen , Soto-Garita Claudio , Sequeira-Soto Jorge , Duarte-Martínez Francisco
Published: June 2021

Background

The clinical manifestations of COVID-19 disease, caused by the SARS-CoV-2 virus, define a large spectrum of symptoms that are mainly dependent on the human host conditions. In Costa Rica, almost 319 000 cases have been reported during the first third of 2021, contrasting to the 590 000 fully vaccinated people. In the pre-vaccination period (the year 2020), this country accumulated 169 321 cases and 2185 deaths.

Methods

To describe the clinical presentations at the time of diagnosis of COVID-19 in Costa Rica during the pre-vaccination period, we implemented a symptom-based clustering using machine learning to identify clusters or clinical profiles among 18 974 records of positive cases. Profiles were compared based on symptoms, risk factors, viral load, and genomic features of the SARS-CoV-2 sequence.

Results

A total of seven COVID-19 clinical profiles were identified, which were characterized by a specific composition of symptoms. In the comparison between clusters, a lower viral load was found for the asymptomatic group, while the risk factors and the SARS-CoV-2 genomic features were distributed among all the clusters. No other distribution patterns were found for age, sex, vital status, and hospitalization.

Conclusion

During the pre-vaccination time in Costa Rica, the clinical manifestations at the time of diagnosis of COVID-19 were described in seven profiles. The host co-morbidities and the SARS-CoV-2 genotypes are not specific of a particular profile, rather they are present in all the groups, including asymptomatic cases. In further analyses, these results will be compared against the profiles of cases during the vaccination period.

Abstract Figure
Mapping lignification dynamics with a combination of chemistry, data segmentation and ratiometric analysis
Authors: Morel Oriane , Lion Cedric , Neutelings Godfrey , Stefanov Jonathan , Baldacci-Cresp Fabien , Simon Clemence , Gierlinger Notburga , Biot Christophe , Hawkins Simon , Spriet Corentin
Published: June 2021

This article describes a new methodology for detailed mapping of the lignification capacity of plant cell walls that we have called “REPRISAL” for REPorter Ratiometrics Integrating Segmentation for Analyzing Lignification. REPRISAL consists of the combination of three separate approaches. In the first approach, H*, G* and S* monolignol chemical reporters, corresponding to p-coumaryl alcohol, coniferyl alcohol and sinapyl alcohol, are used to label the growing lignin polymer in a fluorescent triple labelling strategy based on the sequential use of 3 main bioorthogonal chemical reactions. In the second step, an automatic parametric and/or artificial intelligence (AI) segmentation algorithm is developed that assigns fluorescent image pixels to 3 distinct cell wall zones corresponding to cell corners (CC), compound middle lamella (CML) and secondary cell walls (SCW). The last step corresponds to the exploitation of a ratiometric approach enabling statistical analyses of differences in monolignol reporter distribution (ratiometric method 1) and proportions (ratiometric method 2) within the different cell wall zones. In order to demonstrate the potential of REPRISAL for investigating lignin formation we firstly describe its use to map developmentally-related changes in the lignification capacity of WT Arabidopsis interfascicular fiber cells. We then show how it can be used to reveal subtle phenotypical differences in lignification by analyzing the Arabidopsis prx64 peroxidase mutant and provide further evidence for the implication of the AtPRX64 protein in floral stem lignification. Finally, we demonstrate the general applicability of REPRISAL by using it to map lignification capacity in poplar, flax and maize.
A tRNA processing enzyme is a central regulator of the mitochondrial unfolded protein response
Authors: Held James P. , Saunders Benjamin R. , Pereira Claudia V. , Patel Maulik R.
Published: June 2021

The mitochondrial unfolded protein response (UPRmt) has emerged as a predominant mechanism that preserves mitochondrial function. Consequently, multiple pathways likely exist to modulate UPRmt. We unexpectedly discovered that the tRNA processing enzyme, homolog of ELAC2 (HOE-1), is central to UPRmt regulation in Caenorhabditis elegans. We find that nuclear HOE-1 is necessary and sufficient to robustly activate UPRmt. We show that HOE-1 acts via transcription factors ATFS-1 and DVE-1 that are crucial for UPRmt. Mechanistically, we show that HOE-1 likely mediates its effects via tRNAs, as blocking tRNA export prevents HOE-1-induced UPRmt. Interestingly, we find that HOE-1 does not act via the integrated stress response, which can be activated by uncharged tRNAs, pointing towards its reliance on a new mechanism. Finally, we show that the subcellular localization of HOE-1 is responsive to mitochondrial stress and is subject to negative regulation via ATFS-1. Together, we have discovered a novel RNA-based cellular pathway that modulates UPRmt.
DNA Mutations via Chern-Simons Currents
Authors: Bajardi Francesco , Altucci Lucia , Benedetti Rosaria , Capozziello Salvatore , Del Sorbo Maria Rosaria , Franci Gianluigi , Altucci Carlo
Published: June 2021

We test the validity of a possible schematization of DNA structure and dynamics based on the Chern-Simons theory, that is a topological field theory mostly considered in the context of effective gravity theories. By means of the expectation value of the Wilson Loop, derived from this analogue gravity approach, we find the point-like curvature of genomic strings in KRAS human gene and COVID-19 sequences, correlating this curvature with the genetic mutations. The point-like curvature profile, obtained by means of the Chern-Simons currents, can be used to infer the position of the given mutations within the genetic string. Generally, mutations take place in the highest Chern-Simons current gradient locations and subsequent mutated sequences appear to have a smoother curvature than the initial ones, in agreement with a free energy minimization argument.
Assembled Cell-Decorated Collagen (AC-DC) bioprinted implants mimic musculoskeletal tissue properties and promote functional recovery
Authors: Christensen Kyle W. , Turner Jonathan , Coughenour Kelly , Maghdouri-White Yas , Bulysheva Anna A. , Sergeant Olivia , Rariden Michael , Randazzo Alessia , Sheean Andrew J. , Christ George J. , Francis Michael P.
Published: June 2021

Musculoskeletal tissue injuries, including the damage and rupture of ligaments and tendons, and volumetric muscle loss (VML), are exceptionally commonplace and often lead to permanent disability and deformation. We developed an advanced biomanufacturing platform producing cellularized collagen microfiber implants to facilitate functional repair and regeneration of musculoskeletal soft tissues. This Assembled Cell-Decorated Collagen (AC-DC) bioprinting process rapidly and reproducibly forms 3D implants using clinically relevant cells and strong, microfluidic extruded collagen fibers. Quantitative analysis showed that the directionality and distribution of cells throughout AC-DC implants mimic the cellular properties of native musculoskeletal tissue. AC-DC bioprinted implants further approximate or exceed the strength and stiffness of human tendons and ligaments and exceeded the properties of commonplace collagen hydrogels by orders of magnitude. The regenerative potential of AC-DC implants was also assessed in vivo in a rodent VML model. A critically sized muscle injury in the hindlimb was created and repaired, and limb torque generation potential was measured over 12 weeks. Both acellular and cellular implants were found to promote functional recovery compared to the unrepaired group, with AC-DC implants containing therapeutic muscle progenitor cells promoting the highest degree of recovery. Histological analysis and automated image processing of explanted muscle cross-sections revealed increased total muscle fiber count, median muscle fiber size, and increased cellularization for injuries repaired with cellularized implants. These studies introduce the tremendous potential of an advanced bioprinting method for generating tissue analogs with near-native biological and biomechanical properties with the potential to repair numerous challenging musculoskeletal injuries.

One Sentence Summary

Bioprinted collagen microfiber-based implants mimic musculoskeletal tissue properties in vitro and promote functional recovery in vivo.
A-type lamins are critical for the recruitment of RPA and RAD51 to stalled replication forks to maintain fork stability
Authors: Graziano Simona , Coll-Bonfill Nuria , Teodoro-Castro Barbara , Kuppa Sahiti , Jackson Jessica , Shashkova Elena , Mahajan Urvashi , Vindigni Alessandro , Antony Edwin , Gonzalo Susana
Published: June 2021

Lamins provide a nuclear scaffold for compartmentalization of genome function that is important for genome integrity. The mechanisms whereby lamins regulate genome stability remain poorly understood. Here, we demonstrate a crucial role for A-type lamins preserving the integrity of the replication fork (RF) during replication stress (RS). We find that lamins bind to nascent DNA strands, especially during RS, and ensure the recruitment of fork protective factors RPA and RAD51. These ssDNA-binding proteins, considered the first and second responders to RS respectively, play crucial roles in the stabilization, remodeling and repair of the stalled fork to ensure proper restart and genome stability. Reduced recruitment of RPA and RAD51 upon lamins depletion elicits replication fork instability (RFI) depicted by MRE11 nuclease-mediated degradation of nascent DNA, RS-induced accumulation of DNA damage, and increased sensitivity to replication inhibitors. Importantly, in contrast to cells deficient in various homology recombination repair proteins, the RFI phenotype of lamins-depleted cells is not linked to RF reversal. This suggests that the point of entry of nucleases is not the reversed fork, but regions of ssDNA generated during RS that are not protected by RPA and RAD51. Consistently, RFI in lamins-depleted cells is rescued by forced elevation of the heterotrimeric RPA complex or RAD51. These data unveil a clear involvement of structural nuclear proteins in the protection of ssDNA from the action of nucleases during RS by warranting proper recruitment of ssDNA binding proteins RPA and RAD51 to stalled RFs. In support of this model, we show physical interaction between RPA and lamins. Our study also suggests that RS is a major source of genomic instability in laminopathies and in lamins-depleted tumors.
Cis-Regulatory Hubs: a new 3D Model of Complex Disease Genetics with an Application to Schizophrenia
Authors: Mangnier Loïc , Joly-Beauparlant Charles , Droit Arnaud , Bilodeau Steve , Bureau Alexandre
Published: June 2021

The 3-dimensional (3D) conformation of the chromatin creates complex networks of noncoding regulatory regions (distal elements) and promoters impacting gene regulation. Despite the importance of the role of noncoding regions in complex diseases, little is known about their interplay within regulatory hubs and implication in multigenic diseases like schizophrenia. Here we show that cis-regulatory hubs (CRHs) in neurons highlight functional interactions between distal elements and promoters, providing a model to explain epigenetic mechanisms involved in complex diseases. CRHs represent a new 3D model, where distal elements interact to create a complex network of active genes. In a disease context, CRHs highlighted strong enrichments in schizophrenia-associated genes, schizophrenia-associated SNPs and schizophrenia heritability compared to equivalent structures. Finally, CRHs exhibit larger proportions of genes differentially expressed in schizophrenia compared to promoter-distal element pairs or TADs. CRHs thus capture causal regulatory processes improving the understanding of complex disease etiology such as schizophrenia. These multiple lines of genetic and statistical evidence support CRHs as 3D models to study dysregulation of gene expression in complex diseases more generally.

Summary Blurb

Genes and their regulatory elements are organized within 3D networks in neurons which model functional structures and explain schizophrenia genetic etiology.
Gut Microbiota predicts Healthy Late-life Aging in Male Mice
Authors: Ke Shanlin , Mitchell Sarah J. , MacArthur Michael R. , Kane Alice E. , Sinclair David A. , Venable Emily M. , Chadaideh Katia S. , Carmody Rachel N. , Grodstein Francine , Mitchell James R. , Liu Yang-Yu
Published: June 2021

Calorie restriction (CR) extends lifespan and retards age-related chronic diseases in most species. There is growing evidence that the gut microbiota has a pivotal role in host health and age-related pathological conditions. Yet, it is still unclear how CR and the gut microbiota are related to healthy aging. Here we report findings from a small longitudinal study of male C57BL/6 mice maintained on either ad libitum or mild (15%) CR diets from 21 months of age and tracked until natural death. We demonstrate that CR results in a significant reduction in frailty index (FI), a well-established indicator of aging. We observed significant alterations in bacterial load, diversity, and compositional patterns of the mouse gut microbiota during the aging process. Interrogating the FI-related microbial features using machine learning techniques, we show that gut microbial signatures from 21-month-old mice can predict the healthy aging of 30-month-old mice with reasonable accuracy. This study deepens our understanding of the links between CR, gut microbiota, and frailty in the aging process of mice.
Vigilance and behavioral state-dependent modulation of cortical neuronal activity throughout the sleep/wake cycle
Authors: Brécier Aurélie , Borel Mélodie , Urbain Nadia , Gentet Luc J.
Published: June 2021

GABAergic inhibitory neurons, through their molecular, anatomic and physiological diversity, provide a substrate for the modulation of ongoing cortical circuit activity throughout the sleep-wake cycle. Here, we investigated neuronal activity dynamics of parvalbumin (PV), vasoactive intestinal polypeptide (VIP) and somatostatin (SST) neurons in naturally-sleeping head-restrained mice at the level of layer 2/3 of the primary somatosensory barrel cortex of mice. Through calcium-imaging and targeted single-unit loose-patch or whole-cell recordings, we found that PV action potential (AP) firing activity was largest during both NREM (non-rapid eye movement) and REM sleep stages, that VIP neurons were activated during REM sleep and that the overall activity of SST neurons remained stable throughout the sleep/wake cycle. Analysis of neuronal activity dynamics uncovered rapid decreases in PV cell firing at wake onset followed by a progressive recovery during wake. Simultaneous local field potential (LFP) recordings further revealed that, except for SST neurons, a large proportion of neurons were modulated by ongoing delta and theta waves. During NREM sleep spindles, PV and SST activity increased and decreased, respectively. Finally, we uncovered the presence of whisking behavior in mice during REM sleep and show that the activity of VIP and SST is differentially modulated during awake and sleeping whisking bouts, which may provide a neuronal substrate for internal brain representations occurring during sleep.
Tissue-specific modification of cellular bioelectrical activities using the chemogenetic tool, DREADD, in zebrafish
Authors: Silic Martin R. , Zhang GuangJun
Published: June 2021

Cellular electronic activity plays an essential role in neuronal communication. Manipulation and visualization of cellular membrane potential remain essential tasks in order to study electrical signaling in living organisms. Light-controlled optogenetic and designed chemical-controlled chemogenetic tools were developed to manipulate cellular electric activities for neuroscience research. One of the most common chemogenetic tools is DREADD (designer receptors exclusively activated by designer drugs). It has been extensively utilized due to its convenience and long-lasting effects in murine and primate models, but not in zebrafish, a leading model organism in various research fields. Here, we first establish multiple tissue-specific transgenic zebrafish lines that express two different DREADDs with a genetically encoded voltage indicator, ASAP2s. We observed voltage changes in zebrafish melanophores, epidermis, and neurons by hM4DGi or rM3DGs receptors measured by ASAP2s fluorescence intensity. Alteration to melanophore bioelectricity by DREADD generated dynamic electric signals and resulted in morphological alterations to pigment cells. We also tested a few agonists and found that the latest generation performs better than clozapine N-oxide (CNO). Collectively, our experiments demonstrate that DREADD can be utilized to manipulate cell-specific membrane potential in the zebrafish model. The availability of this tool in zebrafish will offer a new resource for a variety of bioelectricity research fields such as neuroscience, cardiology, and developmental biology.
Mechanistic target of rapamycin complex 1 (mTORC1) activity occurs predominantly in the periphery of human skeletal muscle fibers, in close proximity to focal adhesion complexes, following anabolic stimuli
Authors: Hodson Nathan , Mazzulla Michael , Kumbhare Dinesh , Moore Daniel R.
Published: June 2021

Following anabolic stimuli (e.g. mechanical loading and/or amino acid provision) the mechanistic target of rapamycin complex 1 (mTORC1), a master regulator of protein synthesis, translocates toward the cell periphery. However, it is unknown if mTORC1 activity occurs prior to or following this translocation. We therefore aimed to determine the cellular location of mTORC1 activity in human skeletal muscle following anabolic stimuli. Fourteen young, healthy males either ingested a protein-carbohydrate beverage (0.25g/kg protein, 0.75g/kg carbohydrate) alone (n=7, 23±5yrs, 76.8±3.6kg, 13.6±3.8%BF, FED) or following a whole-body resistance exercise bout (n=7, 22±2yrs, 78.1±3.6kg, 12.2±4.9%BF, EXFED). Vastus lateralis muscle biopsies were obtained at rest (PRE) and 120 and 300min following anabolic stimuli. The spatial regulation of mTORC1 activity was assessed through immunofluorescent staining of p-RPS6Ser240/244, an mTORC1-specific phosphorylation event. p-RPS6Ser240/244 measured by immunofluorescent staining or immunoblot was positively correlated (r=0.76, p<0.001). Peripheral staining intensity of p-RPS6Ser240/244 increased above PRE in both FED and EXFED at 120min (~54% and ~138% respectively, p<0.05) but was greater in EXFED at both post-stimuli time points (p<0.05). The peripheral-central ratio of p-RPS6240/244 staining was displayed a similar pattern, suggesting mTORC1 activity occurs predominantly in the periphery of fibers. Moreover, p-RPS6Ser240/244 intensity within paxillin-positive regions, a marker of focal adhesion complexes, was elevated at 120min irrespective of stimulus (p=0.006) before returning to PRE at 300min. These data confirm that mTORC1 activity occurs in the region of human muscle fibers to which mTORC1 translocates following anabolic stimuli and identifies focal adhesion complexes as a potential site of mTORC1 activation in vivo.
Atypical integrative element with strand-biased circularization activity assists interspecies antimicrobial resistance gene transfer from Vibrio alfacsensis
Authors: Nonaka Lisa , Masuda Michiaki , Yano Hirokazu
Published: June 2021

The exchange of antimicrobial resistance (AMR) genes between aquaculture and terrestrial microbial populations has emerged as a serious public health concern. However, the nature of the mobile genetic elements in marine bacteria is poorly documented. To gain insight into the genetic mechanisms underlying AMR gene transfer from marine bacteria, we mated a multidrug-resistant Vibrio alfacsensis strain with an Escherichia coli strain, and then determined the complete genome sequences of the donor and the transconjugant strains. Sequence analysis revealed a conjugative multidrug resistance plasmid in the donor strain, which was integrated into the chromosome of the recipient. The plasmid backbone in the transconjugant chromosome was flanked by two copies of a 7.1 kb unclassifiable integrative element harboring a β-lactamase gene. The 7.1 kb element and the previously reported element Tn6283 share four coding sequences, two of which encode the catalytic R-H-R-Y motif of tyrosine recombinases. Polymerase chain reaction and sequencing experiments revealed that these elements generate a circular copy of one specific strand without leaving an empty site on the donor molecule, in contrast to the movement of integron gene cassettes or ICE/IMEs discovered to date. These elements are termed SEs (strand-biased circularizing integrative elements): SE-6945 (the 7.1 kb element) and SE-6283 (Tn6283). The copy number and location of SE-6945 in the chromosome affected the antibiotic resistance levels of the transconjugants. SEs were identified in the genomes of other Vibrio species. Overall, these results suggest that SEs are involved in the spread of AMR genes among marine bacteria.
Genome-Scale Metabolic Model Accurately Predicts Fermentation of Glucose by Chromochloris zofingiensis
Authors: Meagher Michelle , Metcalf Alex , Ramsey S. Alex , Prentice Walter , Boyle Nanette R.
Published: June 2021

Algae have the potential to be sources of renewable fuels and chemicals. One particular strain, Chromochloris zofingiensis, is of interest due to the co-production of triacylglycerols (TAGs) and astaxanthin, a valuable nutraceutical. To aid in future engineering efforts, we have developed the first genome-scale metabolic model on C. zofingiensis, iChr1915. This model includes 1915 genes, 3413 metabolic reactions and 2652 metabolites. We performed detailed biomass composition analysis for three growth conditions: autotrophic, mixotrophic and heterotrophic and used this data to develop biomass formation equations for each growth condition. The completed model was then used to predict flux distributions for each growth condition; interestingly, for heterotrophic growth, the model predicts the excretion of fermentation products due to overflow metabolism. We confirmed this experimentally via metabolomics of spent medium and fermentation product assays. An in silico gene essentiality analysis was performed on this model, as well as a flux variability analysis to test the production capabilities of this organism. In this work, we present the first genome scale metabolic model of C. zofingiensis and demonstrate its use predicting metabolic activity in different growth conditions, setting up a foundation for future metabolic engineering studies in this organism.
Horizontal transposon transfer and its implications for the ancestral ecology of hydrophiine snakes
Authors: Galbraith James D. , Ludington Alastair J. , Sanders Kate L. , Amos Timothy G. , Thomson Vicki A. , Tuipulotu Daniel Enosi , Dunstan Nathan , Edwards Richard J. , Suh Alexander , Adelson David L.
Published: June 2021

Transposable elements (TEs), also known as jumping genes, are sequences able to move or copy themselves within a genome. As TEs move throughout genomes they often act as a source of genetic novelty, hence understanding TE evolution within lineages may help in understanding environmental adaptation. Studies into the TE content of lineages of mammals such as bats have uncovered horizontal transposon transfer (HTT) into these lineages, with squamates often also containing the same TEs. Despite the repeated finding of HTT into squamates, little comparative research has examined the evolution of TEs within squamates. Here we examine a diverse family of Australo-Melanesian snakes (Hydrophiinae) to examine if the previously identified, order-wide pattern of variable TE content and activity holds true on a smaller scale. Hydrophiinae diverged from Asian elapids ∼30 Mya and have since rapidly diversified into six amphibious, ∼60 marine and ∼100 terrestrial species which fill a broad range of ecological niches. We find TE diversity and expansion differs between hydrophiines and their Asian relatives and identify multiple HTTs into Hydrophiinae, including three likely transferred into the ancestral hydrophiine from fish. These HTT events provide the first tangible evidence that Hydrophiinae reached Australia from Asia via a marine route.
Whole blood metabolomics of dementia patients reveal classes of disease-linked metabolites
Authors: Teruya Takayuki , Chen Yung-Ju , Kondoh Hiroshi , Fukuji Yasuhide , Yanagida Mitsuhiro
Published: June 2021

Dementia is caused by factors that damage neurons. We quantified small molecular markers in whole blood of dementia patients, using non-targeted liquid chromatography-mass spectroscopy (LC-MS). Thirty-three metabolites, classified into 5 groups (A-E), differed significantly in dementia patients, compared with healthy elderly subjects. Seven Group A metabolites present in plasma, including quinolinic acid, kynurenine, and indoxyl-sulfate, increased. Possibly they act as neurotoxins in the central nervous system (CNS). The remaining 26 compounds (Groups B-E) decreased, possibly causing a loss of support or protection of the brain in dementia. Six Group B metabolites, normally enriched in red blood cells (RBCs) of healthy subjects, all contain trimethylated ammonium moieties. These metabolites include ergothioneine and structurally related compounds have scarcely been investigated as dementia markers, validating the examination of RBC metabolites. Ergothioneine, a potent anti-oxidant, is significantly decreased in various cognition-related disorders, such as mild cognitive impairment and frailty. Group C compounds, also include some oxidoreductants and are normally abundant in RBCs (NADP+, glutathione, ATP, pantothenate, S-adenosyl-methionine, and gluconate). Their decreased levels in dementia patients may also contribute to depressed brain function. Groups D (12) contains plasma compounds, such as amino acids, glycerophosphocholine, dodecanoyl-carnitine, 2-hydroxybutyrate, which normally protect the brain, but their diminution in dementia may reduce that protection. Seven Group D compounds have been identified previously as dementia markers. Group B-E compounds may be critical to maintain the CNS by acting directly or indirectly. How RBC metabolites act in the CNS and why they diminish so significantly in dementia remain to be determined.

Significance Statement

Dementia is a slowly progressing, chronic, and usually irreversible decline in cognitive function. Mechanistic causes and definitive treatments remain elusive. Using comprehensive metabolomics, we identified 5 groups of metabolites (A-E), 21 of which are novel, possibly useful for diagnosis and therapy of forms of dementia, such as Alzheimer’s disease. Seven Group A compounds may act as neurotoxins, whereas Group B-E compounds may protect the CNS against oxidative stress, maintain energy reserves, supply nutrients and neuroprotective factors. Five metabolites, ergothioneine,S-methyl-ergothioneine, trimethyl-histidine, methionine, and tryptophan identified in this study overlap with those reported for frailty. Interventions for cognitive diseases involving these dementia metabolomic markers may be accomplished either by inhibiting Group A compounds or by supplementing Group B-E compounds in patients.
Neuro-molecular characterization of fish cleaning interactions
Authors: Ramirez-Calero Sandra , Paula Jose Ricardo , Otjacques Eve , Rosa Rui , Ravasi Timothy , Schunter Celia
Published: June 2021

Coral reef fish exhibit a large variety of behaviours crucial for fitness and survival. The cleaner wrasse Labroides dimidiatus displays cognitive abilities during interspecific interactions by providing services of ectoparasite cleaning, thus serving as a good example to understand the processes of complex social behaviour. However, little is known about the molecular underpinnings of cooperative behaviour between L. dimidiatus and a potential client fish (Acanthurus leucosternon). Therefore, we investigated the molecular mechanisms in three regions of the brain (fore-, mid-, and hindbrain) during the interaction of these fishes. Here we show, using transcriptomics, that most of the transcriptional response in both species was regulated in the hindbrain and forebrain regions and that the interacting behaviour responses of L. dimidiatus involved immediate early gene alteration, dopaminergic and glutamatergic pathways, the expression of neurohormones (such as isotocin) and steroids (e.g. progesterone and estrogen). In contrast, in the client, fewer molecular alterations were found, mostly involving pituitary hormone responses. The particular pathways found suggested learning and memory processes in the cleaner wrasse, while the client indicated stress relief.
Escherichia coli recombinant expression of SARS-CoV-2 protein fragments
Authors: McGuire Bailey E. , Mela Julia E. , Thompson Vanessa C. , Cucksey Logan R , Stevens Claire E. , McWhinnie Ralph L. , Winkler Dirk F. H. , Pelech Steven , Nano Francis E.
Published: June 2021

We have developed a method for the inexpensive, high-level expression of antigenic protein fragments of SARS-CoV-2 proteins in Escherichia coli. Our approach used the thermophilic family 9 carbohydrate-binding module (CBM9) as an N-terminal carrier protein and affinity tag. The CBM9 module was joined to SARS-CoV-2 protein fragments via a flexible proline-threonine linker, which proved to be resistant to E. coli proteases. Two CBM9-spike protein fragment fusion proteins and one CBM9-nucleocapsid fragment fusion protein largely resisted protease degradation, while most of the CBM9 fusion proteins were degraded at some site in the SARS-CoV-2 protein fragment. All fusion proteins were expressed in E. coli at about 0.1 g/L, and could be purified with a single affinity binding step using inexpensive cellulose powder. Three purified CBM9-SARS-CoV-2 fusion proteins were tested and found to bind antibody directed to the appropriate SARS-CoV-2 antigenic region. The largest intact CBM9 fusion protein incorporates spike protein amino acids 540-588, which is a conserved region immediately C-terminal to the receptor binding domain that is widely recognized by human convalescent sera and contains a putative protective epitope.
Impact of dose, duration and host immune status on ultrashort telacebec treatment in a mouse model of Buruli ulcer
Authors: Almeida Deepak V. , Converse Paul J. , Komm Oliver , Nuermberger Eric L.
Published: June 2021

Telacebec (Q203) is a new anti-tuberculosis drug in clinical development with extremely potent activity against Mycobacterium ulcerans, the causative agent of Buruli ulcer (BU). The potency of Q203 has prompted investigation of its potential role in ultra-short, even single-dose, treatment regimens for BU in mouse models. However, the relationships of Q203 dose and duration and host immune status to treatment outcomes remain unclear, as does the risk of emergence of drug resistance with Q203 monotherapy. In the present study, immunocompetent BALB/c and immunocompromised SCID-beige mice were infected in both hind footpads and treated eight weeks later. In both mouse strains, controls received rifampin-clarithromycin; others received Q203 at 0.5 or 2 mg/kg/d for 5 or 10 days. Additionally, BALB/c mice received a single dose of 2.5 or 10 mg/kg or 3.3 mg/kg/d for 3 days. Treatment response was based on changes in footpad swelling and CFU counts at the end of treatment as well as 4 and 13 weeks after stopping treatment. Efficacy depended on total dose more than duration. Total doses of 5-20 mg/kg rendered nearly all BALB/c mice culture-negative 13 weeks post-treatment without selection of Q203-resistant bacteria. Although less potent in SCID-beige mice, Q203 still rendered the majority of footpads culture-negative at total doses of 10-20 mg/kg. However, Q203 resistance was identified in relapse isolates from some SCID-beige mice. Overall, these results support the potential of Q203 monotherapy for single-dose or other ultra-short therapy for BU, although highly immunocompromised hosts may require higher doses or durations and/or combination therapy.
Fusobacterium nucleatum metabolically integrates commensals and pathogens in oral biofilms
Authors: Sakanaka Akito , Kuboniwa Masae , Shimma Shuichi , Alghamdi Samar A. , Mayumi Shota , Lamont Richard J. , Fukusaki Eiichiro , Amano Atsuo
Published: June 2021

Fusobacterium nucleatum is a common constituent of the oral microbiota in both periodontal health and disease. Previously, we discovered ornithine cross-feeding between F. nucleatum and Streptococcus gordonii, where S. gordonii secretes ornithine via an arginine-ornithine antiporter (ArcD), which in turn supports the growth and biofilm development of F. nucleatum; however, broader metabolic aspects of F. nucleatum within polymicrobial communities and their impact on periodontal pathogenesis have not been addressed. Here, we show that when co-cultured with S. gordonii, F. nucleatum increased amino acid availability to enhance the production of butyrate and putrescine, a polyamine produced by ornithine decarboxylation. Co-culture with Veillonella parvula, another common inhabitant of the oral microbiota, also increased lysine availability, promoting cadaverine production by F. nucleatum. We confirmed that ArcD-dependent ornithine excretion by S. gordonii results in synergistic putrescine production, and mass spectrometry imaging revealed this metabolic capability creates a putrescine-rich microenvironment inside F. nucleatum biofilms. We further demonstrated that polyamines caused significant changes in the biofilm phenotype of a periodontal pathogen, Porphyromonas gingivalis, with putrescine being a potent stimulator of biofilm development and dispersal, and confirmed that F. nucleatum-mediated conversion of ornithine to putrescine enhances biofilm formation by P. gingivalis. Lastly, analysis of plaque samples revealed cooccurrence of P. gingivalis with genetic modules for putrescine production by S. gordonii and F. nucleatum. Overall, our results highlight the ability of F. nucleatum to induce synergistic polyamine production within multi-species consortia, and provide insight into how the trophic web in oral biofilm ecosystems can eventually shape disease-associated communities.

Significance Statement

Periodontitis is caused by the pathogenic transition of subgingival microbiota ecosystems, which is accompanied by alterations to microbiome functions including metabolic systems and the establishment of metabolic cross-feeding. While Fusobacterium nucleatum is a major constituent of the periodontal microbiota, its metabolic integration within polymicrobial communities and the impact on periodontal pathogenesis are poorly understood. Here, we report that amino acids supplied by other commensal bacteria induce polyamine production by F. nucleatum, creating polyamine-rich microenvironments. We further show that this trophic web results in enhancement of biofilm formation and dispersal of a periodontal pathogen, Porphyromonas gingivalis. This work provides mechanistic insight into how cooperative metabolism within oral biofilms can tip the balance toward periodontitis.