bluuebunny/crossref_metadata_2025 huggingface dataset:
SPATIAL HETEROGENEITY OF NEIGHBORHOOD-LEVEL WATER AND SANITATION ACCESS IN INFORMAL URBAN SETTLEMENTS: A CROSS-SECTIONAL CASE STUDY IN BEIRA, MOZAMBIQUE
Authors: Victor Courtney , Ocasio Denisse Vega , Cumbe Zaida A. , Garn Joshua V. , Hubbard Sydney , Mangamela Magalhaes , McGunegill Sandy , Nalá Rassul , Snyder Jedidiah S. , Levy Karen , Freeman Matthew C
Published: January 2022

Rapid urbanization, resulting in population growth within informal settlements, has worsened exclusion and inequality in access to water and sanitation (WASH) services in the poorest and most marginalized communities. In this study, we describe the heterogeneity in water service satisfaction and WASH access in low-income, peri-urban neighborhoods of Beira, Mozambique, and examine whether this heterogeneity can be explained by distance to water distribution mains. Using spatial statistics and regression analyses, we identified statistical spatial heterogeneity in household WASH access, as well as consumer-reported satisfaction with water services (services, pressure, quality, and sufficient quantity). We found that as distance from the water main increased, both access to an improved water source at the household and satisfaction with water pressure decreased, controlling for household density and socioeconomic status. The odds of a household having access to a water source at the household or on the compound decreased with every 100-meter increase in distance from a water main pipe (odds ratio [OR] 0.87, 95% confidence interval [CI]: 0.82, 0.92). Satisfaction with water services also decreased with every 100-meter increase in distance from a water main pipe (OR: 0.80; 95% CI: 0.69, 0.94). Findings from this study highlight the unequal household access to water and sanitation in urban informal settlements, even within low-income neighborhoods. Describing this heterogeneity of access to water services, sanitation, and satisfaction – and the factors influencing them - can inform stakeholders and guide the development of infrastructural solutions to reduce water access inequities within urban settings.
A longitudinal seroconversion panel shows anti-SARS-CoV-2 antibody levels up to 6.5 months after vaccination with mRNA-1273 (Moderna)
Authors: Belda Francisco , Mora Oscar , Christie Rebecca , Crowley Michael
Published: January 2022

Background

Vaccines have emerged as a crucial tool in combatting the COVID-19 pandemic particularly those based on SARS-CoV-2 S-protein mRNA. A crucial aspect of vaccine efficacy is the duration of antibody responses. In this study, a seroconversion panel was created to assess antibody responses to the mRNA-1273 vaccine over time (6.5 months).

Methods

Blood samples collected from 15 healthy adult participants prior to and up to 6.5 months after vaccination with the mRNA-1273 vaccine (Moderna). Serum from these blood samples were analyzed for anti-SARS-CoV-2 antibody activity by chemiluminescent immunoassay.

Results

The immunoassay results showed that one participant was positive for anti-SARS-CoV- 2 antibodies prior to vaccination indicating a prior infection. All participants showed a positive antibody response after the first vaccination. Highest antibody responses were seen after the second dose (41-45 days from the first dose). Subsequent samples collected at 69-75 days, 130-135 days and 221-229 days after the first vaccination showed positive responses but declining levels of anti-SARS-CoV-2 antibodies.

Conclusions

Declining antibody levels in these participants support the use of booster vaccination to increase antibody levels 4-6 months after the initial vaccine series and continued monitoring to assess the durability of COVID-19 vaccine responses. These results are in agreement with other studies showing antibody persistence but declining the antibody levels in the months after immunization with mRNA-based vaccines.
Automatic Identification of Tinnitus Malingering Based on Overt and Covert Behavioral Responses During Psychoacoustic Testing
Authors: Smalt Christopher J. , Sugai Jenna A. , Koops Elouise , Jahn Kelly N. , Hancock Kenneth E. , Polley Daniel B.
Published: January 2022

Tinnitus, or ringing in the ears, is a prevalent condition that imposes a substantial health and financial burden on the patient and to society. The diagnosis of tinnitus, like pain, relies on patient self-report. Subjective self-report measures can complicate the distinction between actual and fraudulent claims and obscure accurate severity assessments. In this study, we combined tablet-based self-directed hearing assessments with neural network classifiers to objectively determine tinnitus severity, and to differentiate participants with tinnitus (N=24) from a malingering cohort, who were instructed to feign an imagined tinnitus percept (N=28). We identified clear differences between the groups, both in their overt rating of tinnitus severity but also covert differences in their fingertip movement trajectories on the tablet surface as they performed the reporting assay. Using only 10 minutes of data, we achieved 81% accuracy classifying patients vs malingerers (ROC AUC=0.88) with leave-one-participant-out cross validation. Objective measurements of tinnitus will improve estimates of tinnitus prevalence and help to prioritize and direct funds for tinnitus compensation.
Frequency of neutropenia over time in patients on clozapine
Authors: Govind Risha , Jewell Amelia , Whiskey Eromona , Gee Siobhan , Oloyede Ebenezer , Taylor David , MacCabe James H.
Published: January 2022

Background

Clozapine, the only evidence-based drug for treatment-resistant schizophrenia is associated with agranulocytosis. For this reason, all clozapine patients are required to undergo mandatory regular blood monitoring throughout their clozapine treatment. The blood test results are reported using a traffic light system. The clozapine treatment is stopped immediately after a confirmed red result, which is the indication for risk of agranulocytosis. The need for blood tests places a burden on patients and acts as a barrier to clozapine treatment. There is growing evidence that the risk of agranulocytosis falls steeply after the first few months of treatment, raising the possibility that clozapine monitoring could be discontinued after a certain period of treatment.

Aim

To investigate the frequency density of the confirmed red results from clozapine monitoring across clozapine treatment.

Method

By merging electronic health records (EHR) data with clozapine blood monitoring data, we identified the clozapine treatment dates. The EHR data was from South London and Maudsley NHS Foundation Trust (SLAM). The clozapine blood monitoring data was from Zaponex Treatment Access System (ZTAS). ZTAS is one of the mandatory blood monitoring service providers in the United Kingdom. From these data, Kaplan-Meier survival curve was fitted to determine the time to get confirmed red results. At fixed points in the treatment, the future risk of obtaining a red result were calculated.

Results

By merging over 301,000 data points that came from the blood monitoring results and EHR data of 1,362 patients, we identified 1,891 clozapine treatment periods. Of these, 75 treatments were stopped due to confirmed red results. The Kaplan-Meier survival curve and the incidence rates data showed that 56 (74.7%) confirmed red results occur within the first 6 months of clozapine treatment.

Conclusion

We found a contrast between the relatively high density of the confirmed red results at the beginning of clozapine treatment which significantly reduces after 6 months of treatment which remained low thereafter.
Spectral sparsification helps restore the spatial structure at single-cell resolution
Authors: Wang Jingwan , Li Shiying , Chen Lingxi , Li Shuai Cheng
Published: January 2022

Single-cell RNA sequencing thoroughly quantifies the individual cell transcriptomes but renounces the spatial structure. Conversely, recently emerged spatial transcriptomics technologies capture the cellular spatial structure but skimp cell or gene resolutions. Cell-cell affinity estimated by ligand-receptor interactions can partially reconstruct the quasi-structure of cells but falsely include the pseudo affinities between distant or indirectly interacting cells. Here, we develop a software package, STORM, to reconstruct the single-cell resolution quasi-structure from the spatial transcriptome with diminished pseudo affinities. STORM first curates the representative single-cell profiles for each spatial spot from a candidate library, then reduces the pseudo affinities in the intercellular affinity matrix by partial correlation, spectral graph sparsification, and spatial coordinates refinement. STORM embeds the estimated interactions into a low-dimensional space with the cross-entropy objective to restore the intercellular quasi-structures, which facilitates the discovery of dominant ligand-receptor pairs between neighboring cells at single-cell resolution. STORM reconstructed structures achieved shape Pearson correlations ranging from 0.91 to 0.97 on the mouse hippocampus and human organ tumor microenvironment datasets. Furthermore, STORM can solelyde novoreconstruct the quasi-structures at single-cell resolution,i.e., reaching the cell-type proximity correlations 0.68 and 0.89 between reconstructed and immunohistochemistry-informed spatial structures on a human developing heart dataset and a tumor microenvironment dataset, respectively.
Robust, versatile DNA FISH probes for chromosome-specific repeats in Caenorhabditis elegans and Pristionchus pacificus
Authors: Adilardi Renzo S. , Dernburg Abby F.
Published: January 2022

Repetitive DNA sequences are useful targets for chromosomal fluorescence in situ hybridization (FISH). We analyzed recent genome assemblies of Caenorhabditis elegans and Pristionchus pacificus to identify tandem repeats with a unique genomic localization. Based on these findings, we designed and validated sets of oligonucleotide probes for each species targeting at least one locus per chromosome. These probes yielded reliable fluorescent signals in different tissues and can easily be combined with immunolocalization of cellular proteins. Synthesis and labeling of these probes are highly cost-effective and require no hands-on labor. The methods presented here can be easily applied in other model and non-model organisms with a sequenced genome.
Deep Learning Characterization of Brain Tumours With Diffusion Weighted Imaging
Authors: Meaney Cameron , Das Sunit , Colak Errol , Kohandel Mohammad
Published: January 2022

Glioblastoma multiforme (GBM) is one of the most deadly forms of cancer. Methods of characterizing these tumours are valuable for improving predictions of their progression and response to treatment. A mathematical model called the proliferation-invasion (PI) model has been used extensively in the literature to model these tumours, though it relies on known values of two key parameters: the tumour cell diffusivity and proliferation rate. Unfortunately, these parameters are difficult to estimate in a patient-specific manner, making personalized tumour projections challenging. In this paper, we develop and apply a deep learning model capable of making accurate estimates of these key GBM-characterizing parameters while simultaneously producing a full projection of the tumour progression curve. Our method uses two sets of multi sequence MRI imaging in order to make predictions and relies on a preprocessing pipeline which includes brain tumour segmentation and conversion to tumour cellularity. We apply our deep learning model to both synthetic tumours and a dataset consisting of five patients diagnosed with GBM. For all patients, we derive evidence-based estimates for each of the PI model parameters and predictions for the future progression of the tumour. Discussion and implications for future work and clinical relevance are included.
Open science policies of medical and health sciences journals before and during the COVID-19 pandemic: a repeat cross-sectional study
Authors: Gardener Antoni D. , Hicks Ellen J. , Jacklin Chloe , Tan Gifford , Cashin Aidan G. , Lee Hopin , Nunan David , Toomey Elaine C. , Richards Georgia C.
Published: January 2022

Cross-disciplinary openness and transparency of research plays an important role in scientific progress. We evaluated open-science related policies of 19 high ranking health and medical journals before (February 2020) and during (May 2021) the COVID-19 pandemic. The Transparency and Openness Promotion (TOP) guideline and the International Committee of Medical Journal Editors (ICMJE) requirements for disclosing conflicts of interest (COIs) were used to audit journal policies. TOP scores slightly improved during the COVID-19 pandemic, from a median of 5 (IQR: 2-12.5) out of a possible 24 points in February 2020 to 7 (IQR: 4-12) in May 2021. Most journals fulfilled all ICMJE provisions for reporting COIs before (84%; n=16) and during (95%; n=18) the COVID-19 pandemic. The COVID-19 pandemic has highlighted the importance of practising open science, however adherence to open science standards in audited policies was low overall, which may reduce progress in health and medical research.
Social connectedness as a determinant of mental health: A scoping review
Authors: Wickramaratne Priya J. , Yangchen Tenzin , Lepow Lauren , Patra Braja G. , Glicksburg Benjamin , Talati Ardesheer , Adekkanattu Prakash , Ryu Euijung , Biernacka Joanna M. , Charney Alexander , Mann J. John , Pathak Jyotishman , Olfson Mark , Weissman Myrna M.
Published: January 2022

Public health and epidemiologic research have established that social connectedness promotes overall health. Yet there have been no recent reviews of findings from research examining social connectedness as a determinant of mental health. The goal of this review was to evaluate recent longitudinal research probing the effects of social connectedness on depression and anxiety symptoms and diagnoses in the general population. A scoping review was performed of PubMed and PsychInfo databases from January 2015 to December 2020 following PRISMA-ScR guidelines using a defined search strategy. The search yielded 56 articles representing 52 unique studies. In research with other than pregnant women, 84% (16 of 19) studies reported that social support benefited symptoms of depression with the remaining 16% (3 of 19) reporting minimal or no evidence that lower levels of social support predict depression at follow-up. In research with pregnant women, 80% (21 of 26 studies) found that low social support increased postpartum depressive symptoms. Among 3 of 4 studies that focused on loneliness, feeling lonely at baseline was related to adverse outcomes at follow-up including higher risks of major depressive disorder, depressive symptom severity, generalized anxiety disorder, and lower levels of physical activity. In 5 of 7 reports, smaller social network size predicted depressive symptoms or disorder at follow-up. In summary, most recent relevant longitudinal studies have demonstrated that social support protects adults in the general population from depressive symptoms and disorders. The results, which were largely consistent across settings, exposure measures, and populations, support efforts to improve clinical detection of high-risk patients, including adults with low social support and elevated loneliness.
Viral Cultures for Assessing Fomites Transmission of SARS-CoV-2: a Systematic
Authors: Onakpoya Igho J. , Heneghan Carl J. , Spencer Elizabeth A. , Brassey Jon , Rosca Elena C. , Maltoni Susanna , Plüddemann Annette , Evans David H. , Conly John M. , Jefferson Tom
Published: January 2022

This is a protocol for a systematic review to assess fomite transmission in SARS-CoV-2. Our research questions are as follows:

Are fomite samples infectious?

If so, what proportion are infectious, and what is the distance and duration of infectiousness in the air?

What is the relationship between fomites, infectiousness and PCR cycle threshold (Ct)?

Is there evidence of a chain of transmission that establishes an actual instance of fomite transmission of SARS-CoV-2?

We will include studies of any design (and in any setting) that investigate fomite transmission (defined as any inanimate object that, when contaminated with or exposed to infectious agents, can transfer the agent to a new host). We will only include studies that performed viral culture which assessed cytopathic effect and verification techniques to ensure the cultured virus is SARS-CoV-2. We will assess the risk of bias using a checklist modified from the QUADAS-2 criteria.
Supportive Mobility Across the Lifespan in Cerebral Palsy: A Modified Delphi Study to Establish Stakeholder Research Priorities
Authors: Feldner Heather A. , Gaebler-Spira Deborah , Awasthi Varun , Bjornson Kristie
Published: January 2022

Aim

The overarching aim of this research was to 1) Understand the mobility experiences, supported mobility device (SMD) use, and desired participation outcomes of people with cerebral palsy (CP) across the lifespan; and 2) Describe how perspectives of rehabilitation care and professional resources may influence mobility decision-making processes and outcomes. The aim of this study was to co-develop research priorities and identify meaningful research questions with a diverse group of stakeholders representing the CP community for implementation in subsequent research activities.

Methods

A modified, three-round Delphi consensus study was conducted with a stakeholder advisory panel consisting of three adults with CP, two parents of children with CP, and four SMD providers.

Results

The advisory panel identified 13 unique topical categories focused on SMD selection and use, stratified by age group and stakeholder role. Questions or statements within each category were ranked, and top consensus and concordance statements were retained, reviewed, and refined for use in a co-developed focus group guide.

Interpretation

A modified Delphi process was a useful tool for stakeholders in co-developing research priorities related to SMD use across the lifespan. Drawing on the lived expertise of stakeholders is important in facilitating improved research translation in the CP community.

What this Paper Adds

Nine stakeholders from the CP community participated as Stakeholder Advisory Panelists and co-developers of research tools

Stakeholders identified 175 unique responses across 12 SMD related categories

Stakeholders prioritized 38 mobility technology research priorities during consensus-building

Results from consensus-building will be directly implemented into a qualitative focus group protocol
Spatial and molecular anatomy of germ layers in the gastrulating Cynomolgus monkey embryo
Authors: Cui Guizhong , Feng Su , Yan Yaping , Wang Li , He Xiechao , Li Xi , Duan Yanchao , Chen Jun , Tam Patrick P.L. , Tang Ke , Zheng Ping , Si Wei , Jing Naihe , Peng Guangdun
Published: January 2022

During mammalian embryogenesis, spatial regulation of gene expression and cell signaling are functionally coupled with lineage specification, patterning of tissue progenitors and germ layer morphogenesis. While the mouse model has been instrumental for our understanding of mammalian development, comparatively little is known about human and non-human primate gastrulation due to the restriction of both technical and ethical issues. Here, we present a morphological and molecular survey of spatiotemporal dynamics of cell types populating the non-human primate embryos during gastrulation. We performed serial sections of Cynomolgus monkeys (Macaca fascicularis) gastrulating embryos at 1-day temporal resolution from E17 to E21, and reconstructed three-dimensional digital models based on high-resolution anatomical atlas that revealed the dynamic changes in the geography of the mesoderm and primitive streaks. Spatial transcriptomics identified unique gene profiles that correspond to distinct germ layers and cross-species spatiotemporal transcriptome analysis revealed a developmental coordinate of germ layer segregation between mouse and primate. Furthermore, we identified species-specific transcription programs during gastrulation. These results offer important insights into evolutionarily conserved and divergent processes during mammalian gastrulation.

Highlight

A high-resolution anatomical atlas of Cynomolgus gastrulation embryos

Created a three-dimensional digital template from serial sections of five developmental stages

A two-dimensional spatiotemporal transcriptome of the germ layers of gastrulating embryos

Cross-species comparison infers conservation of functional attributes of regulome and signaling activity in germ layer formation
INFLAMMATORY BOWEL DISEASE INDUCES α-SYNUCLEIN AGGREGATION IN GUT AND BRAIN
Authors: Espinosa-Oliva Ana M. , Ruiz Rocío , Soto Manuel Sarmiento , Boza-Serrano Antonio , Rodriguez-Perez Ana I. , Roca-Ceballos María A. , García-Revilla Juan , Santiago Marti , Serres Sébastien , Economopoulus Vasiliki , Carvajal Ana E. , Vázquez-Carretero María D. , García-Miranda Pablo , Klementieva Oxana , Oliva-Martín María J. , Deierborg Tomas , Rivas Eloy , Sibson Nicola R. , Labandeira-García José L. , Machado Alberto , Peral María J. , Herrera Antonio J. , Venero José L. , de Pablos Rocío M.
Published: January 2022

According to Braak’s hypothesis, it is plausible that Parkinsońs disease (PD) starts in the enteric nervous system (ENS) to spread the brain via the vagus nerve. Thus, we were wondering whether human inflammatory bowel diseases (IBD) can progress with appearance of pathogenic α-synuclein (α-syn) in the gastrointestinal tract and midbrain dopaminergic neurons. Analysis of human gastrointestinal tract sections from IBD patients demonstrated the presence of pathogenic phosphorylated α-syn in both myenteric (Auerbach’s) and submucosal (Meissner’s) plexuses. Remarkably, PD subjects exhibit α-syn pathology in identical gastrointestinal locations. Analysis of human midbrain sections from IBD subjects revealed a clear displacement of neuromelanin in some nigral neurons from the ventral mesencephalon, which were inherently associated with presence of α-syn aggregates reminiscent of pale bodies. We also used different dextran sodium sulfate (DSS)-based rat models of gut inflammation (subchronic and chronic) to study the appearance of phosphorylated α-syn inclusions in both Auerbach’s and Meissner’s plexuses (gut), and in dopaminergic neuritic processes (brain) along with degeneration of nigral dopaminergic neurons, which are considered classical hallmarks of PD. Vagotomized DSS-treated animals exhibited pathological α-syn in the gut but failed to show dopaminergic cells degeneration and α-syn aggregation in the ventral mesencephalon. Taken together, these results strongly suggest that Braak’s hypothesis is plausible.
Single mutation makes Escherichia coli an insect mutualist
Authors: Koga Ryuichi , Moriyama Minoru , Onodera-Tanifuji Naoko , Ishii Yoshiko , Takai Hiroki , Mizutani Masaki , Oguchi Kohei , Okura Reiko , Suzuki Shingo , Goto Yasuhiro , Hayashi Tetsuya , Seki Masahide , Suzuki Yutaka , Nishide Yudai , Hosokawa Takahiro , Wakamoto Yuichi , Furusawa Chikara , Fukatsu Takema
Published: January 2022

We report an experimental system in which Escherichia coli evolves into an insect mutualist. When the essential gut symbiont of the stinkbug Plautia stali was replaced by E. coli, a few survivor insects exhibited specific localization and vertical transmission of E. coli. Through trans-generational maintenance with P. stali, several hyper-mutating E. coli lines independently evolved host’s high adult emergence and improved body color. Such “mutualistic” E. coli lines exhibited independent mutations disrupting the carbon catabolite repression (CCR) global transcriptional regulator. Each of the mutations reproduced the mutualistic phenotypes when introduced into wild-type E. coli, confirming that the single CCR mutations instantly make E. coli an insect mutualist. Our discovery uncovers that evolution of elaborate mutualism can proceed more easily and rapidly than conventionally envisaged.
LCK-14-3-3ζ-TRPM8 axis for regulating TRPM8 function/assembly promotes pancreatic cancer malignancy
Authors: Huang Yuan , Li Shi , Wang Zhijie , Liu Qinfeng , Li Shunyao , Liu Lei , Zhao Weiwei , Wang Kai , Zhang Rui , Ali Declan , Michalak Marek , Chen Xing-Zhen , Zhou Cefan , Tang Jingfeng
Published: January 2022

The transient receptor potential melastatin 8 (TRPM8), function as a Ca2+-permeable channel in the plasma membrane (PM). Dysfunction of TRPM8 is associated with human pancreatic cancer and several other diseases in clinical patients, but with unclear underlying mechanisms. Here, we found lymphocyte-specific protein tyrosine kinase (LCK) directly interacts with TRPM8 and potentiates TRPM8 phosphorylation at Y1022. LCK positively regulated channel function characterized by increased TRPM8 currents densities through enhancing TRPM8 multimerization. Furthermore, 14-3-3ζ interacted with TRPM8 and positively modulated channel multimerization. LCK significantly enhanced the binding of 14-3-3ζ and TRPM8, whereas mutant TRPM8-Y1022F impaired TRPM8 multimerization and the binding of TRPM8 and 14-3-3ζ. Knockdown of 14-3-3ζ impaired the regulation of LCK on TRPM8 multimerization. Additionally, TRPM8 phosphotyrosine at Y1022 feedback regulated LCK activity by inhibition of Tyr505 phosphorylation and modulation of LCK ubiquitination. Finally, we revealed the importance of TRPM8 phosphorylation at Y1022 in the proliferation, migration and tumorigenesis of pancreatic cancer cells. Our findings demonstrate that LCK-14-3-3ζ-TRPM8 axis for regulating TRPM8 assembly, channel function, LCK activity and providing potential therapeutic targets for pancreatic cancer.
Steroidogenic factor-1 lineage origin of skin lesions in Carney complex syndrome
Authors: Sahut-Barnola Isabelle , Lefrancois-Martinez A-Marie , Dufour Damien , Botto Jean-Marie , Kamilaris Crystal , Faucz Fabio R. , Stratakis Constantine A. , Val Pierre , Martinez Antoine
Published: January 2022

Carney complex (CNC) is a rare familial multi-neoplastic syndrome predisposing to endocrine and non-endocrine tumors due to inactivating mutations of PRKAR1A leading to perturbations of the cAMP protein kinase A (PKA) signaling pathway. Skin lesions are the most common manifestation of CNC, including lentigines, blue nevi and cutaneous myxomas, in unusual locations such as oral and genital mucosa. Unlike endocrine disorders, the pathogenesis of skin lesions remains unexplained. Here, we show that embryonic invalidation of the Prkar1a gene in Steroidogenic Factor-1-expressing cells, leads to the development of familial skin pigmentation alterations reminiscent of those in patients. Immunohistological and molecular analyses coupled with genetic monitoring of recombinant cell lineages in mouse skin, suggest that familial lentiginosis and myxomas occurs in skin areas specifically enriched in dermal melanocytes. In lentigines and blue nevi-prone areas from mutant mice and patients, Prkar1a/PRKAR1A invalidation occurs in a subset of dermal fibroblasts capable of inducing, under the influence of PKA signaling, the production of pro-melanogenic EDN3 and HGF signals. Our model strongly suggests that the origin of the typical CNC cutaneous lesions is the result of non-cell-autonomous pro-melanogenic activity of a dermal fibroblast population sharing a community of origin with SF-1 lineage.
Microliter spotting and micro-colony observation: a rapid and simple approach for counting bacterial colony forming units
Authors: Bhuyan Shuvam , Yadav Mohit , Giri Shubhra Jyoti , Begum Shuhada , Das Saurav , Phukan Akash , Priyadarshani Pratiksha , Sarkar Sharmilee , Jayswal Anurag , Kabyashree Kristi , Kumar Aditya , Mandal Manabendra , Ray Suvendra Kumar
Published: January 2022

For enumerating viable bacteria, traditional dilution plating to count colony forming units (CFU) has always been the preferred method in microbiology owing to its simplicity, albeit laborious and time-consuming. Similar CFU counts can be obtained by quantifying growing micro-colonies in conjunction with the perks of a microscope. Here, we employed a simple method of five microliter spotting of differently diluted bacterial culture multiple times on a single Petri dish followed by finding out CFU by counting micro-colonies using a phase-contrast microscope. In this method, the CFU of an Escherichia coli culture can be estimated within a four-hour period. Further, within a ten-hour period, CFU in a culture of Ralstonia solanacearum, a bacterium with a generation time of around 2 h, can be estimated. The CFU number determined by micro-colonies observed is comparable with that obtained by the dilution plating method. Micro-colonies number observed in the early hours of growth (2 h in case of E. coli and 8 h in case of R. solanacearum) were found to remain consistent at later hours, though there was a noticeable increase in the size of the colonies. It suggested that micro-colonies observed in the early hours indeed represent the bacterial number in the culture. Practical applications to this counting method were employed in studying the rifampicin-resistant mutation rate as well as performing the fluctuation test in E. coli. The method described here results in a 90% reduction of labour, time and resources. Thus, the method is likely to be adopted by many microbiologists in their routine laboratory research.
Epidermal clock integration and gating of brain signals guarantees skin homeostasis
Authors: Mortimer Thomas , Zinna Valentina M. , Atalay Muge , Laudanna Carmelo , Deryagin Oleg , Smith Jacob G. , García-Lara Elisa , Vaca-Dempere Mireia , Koronowski Kevin B. , Petrus Paul , Greco Carolina M. , Forrow Stephen , Sassone-Corsi Paolo , Welz Patrick-Simon , Muñoz-Cánoves Pura , Aznar Benitah Salvador
Published: January 2022

In mammals, an integrated network of molecular oscillators drives daily rhythms of tissue-specific homeostatic processes. This circadian clock network is required for maintaining health and is compromised by disease and lifestyle choices, such as diet and exercise. However, critical properties of this systemic network, such as which tissues communicate to coordinate their respective programs of daily physiology, and the exact homeostatic processes requiring each communication pathway, remain undefined. To dissect daily inter-tissue communication, we have constructed in mice a minimal clock network comprising only two nodes: the peripheral epidermal clock and the central brain clock. By circadian transcriptomic and functional characterization of this isolated connection, we have identified a previously unknown gatekeeping function of the peripheral tissue clock with respect to systemic inputs. That is, the epidermal clock concurrently integrates and corrects brain signals to ensure timely execution of epidermal daily physiology. Specifying the integrative arm of the clock, we identify that timely cell cycle termination in the epidermal stem cell compartment is dependent upon incorporation of clock-driven signals originating from the brain. Unexpectedly, and in contrast, the epidermal clock corrects potentially disruptive feeding-related signals to ensure that DNA replication occurs at the optimum time of day. Together, we present a novel approach for cataloguing the systemic dependencies of a given tissue, and in turn identify an essential gate-keeping function of peripheral circadian clocks that guarantees tissue homeostasis.
Extinction risk, reconstructed catches, and management of chondrichthyan fishes in the Western Central Atlantic Ocean
Authors: Talwar Brendan S. , Anderson Brooke , Avalos-Castillo Cristopher G. , del Pilar Blanco-Parra María , Briones Alejandra , Cardeñosa Diego , Carlson John K. , Charvet Patricia , Cotton Charles F. , Crysler Zoe , Derrick Danielle H. , Heithaus Michael R. , Herman Katelyn B. , Koubrak Olga , Kulka David W. , Kyne Peter M. , Lasso-Alcalá Oscar M. , Mejía-Falla Paola A. , Morales-Saldaña Jorge Manuel , Naranjo-Elizondo Beatriz , Navia Andrés F. , Pacoureau Nathan , Peréz-Jiménez Juan C. , Pollom Riley A. , Rigby Cassandra L. , Schneider Eric V.C. , Simpson Nikola , Dulvy Nicholas K.
Published: January 2022

Chondrichthyan fishes are among the most threatened vertebrates on the planet because many species have slow life histories that are outpaced by intense fishing. The Western Central Atlantic Ocean, which includes the greater Caribbean, is a hotspot of chondrichthyan biodiversity and abundance, but is historically characterized by extensive shark and ray fisheries and a lack of sufficient data for effective management and conservation. To inform future research and management decisions, we analyzed patterns in chondrichthyan extinction risk, reconstructed catches, and regulations in this region. We summarized the extinction risk of 180 sharks, rays, and chimaeras using contemporary IUCN Red List assessments and found that over one-third (35.6%) were assessed as Vulnerable, Endangered, or Critically Endangered largely due to fishing. Reconstructed catches from 1950 to 2016 reached their peak in 1992, then declined by 40.2% through the end of the series. The United States, Venezuela, and Mexico were responsible for most catches and hosted large proportions of the regional distributions of threatened species; these countries therefore held the greatest responsibility for chondrichthyan management. The abundance and resolution of fisheries landings data were poor in much of the region, and national-level regulations varied widely across jurisdictions. Deepwater fisheries represent an emerging threat, although many deepwater chondrichthyans currently find refuge beyond the depths of most fisheries. Regional collaboration as well as effective and enforceable management informed by more complete fisheries data, particularly from small-scale fisheries, are required to protect and recover threatened species and ensure sustainable fisheries.
Soil fungal communities vary more with soil characteristics than tree diversity at a local scale
Authors: Kutos Steve , Barnes Elle M. , Lewis J.D.
Published: January 2022

Soil fungal communities vary spatially due to factors including variations in plant diversity and soil characteristics; however, the relative influences of these factors on composition and therefore function remain unclear. Small-scale variation in fungal communities may drive local variation in nutrient cycling and decomposition and may respond more to local factors compared with large climatic variations. Clarifying the roles of these factors can improve our predictions of soil fungal community and biogeochemical cycling responses to anthropogenic changes. Therefore, we examined relationships among abiotic and biotic factors and soil fungal communities associated with Quercus rubra and Pinus resinosa saplings and mature trees in a mixed-hardwood woodland. We also compared community composition and fungal enzymatic activity. Fungal community composition was associated with spatial heterogeneity of soil characteristics, while host sapling and tree species identity were poor predictors of community composition. Further, most of the compositional variation was unexplained by measured variables, suggesting stochasticity and other environmental characteristics may drive spatial variation in these communities. Additionally, enzymatic activity did not clearly correlate with fungal community composition. Overall, soil fungal communities and enzymatic activity adjacent to saplings in this woodland are influenced primarily by soil characteristics and stochasticity and not plant identity.
When host populations move north, but disease moves south: counter-intuitive impacts of climate warming on disease spread
Authors: Moran E. Joe , Martignoni Maria M. , Lecomte Nicolas , Leighton Patrick , Hurford Amy
Published: January 2022

Empirical observations and mathematical models show that climate warming can lead to the northern (or, more generally, poleward) spread of host species ranges and their corresponding diseases. Here, we explore an unexpected possibility whereby climate warming induces disease spread in the opposite direction to the directional shift in the host species range. To test our hypothesis, we formulate a reaction-diffusion equation model with a Susceptible-Infected (SI) epidemiological structure for two host species, both susceptible to a disease, but spatially isolated due to distinct thermal niches, and where prior to climate warming the disease is endemic in the northern species only. Previous theoretical results show that species’ distributions can lag behind species’ thermal niches when climate warming occurs. As such, we find that climate warming, by shifting both species’ niches forward, may increase the overlap between northern and southern host species ranges, due to the northern species lagging behind its thermal tolerance limit, thus facilitating a southern disease spread. As our model is general, our findings may apply to viral, bacterial, and prion diseases that do not have thermal tolerance limits and are inextricably linked to their hosts’ distributions, such as the spread of rabies from arctic to red foxes.
WAT3R: Recovery of T-Cell Receptor Variable Regions From 3’ Single-Cell RNA-Sequencing
Authors: Ainciburu Marina , Morgan Duncan M. , DePasquale Erica A. K. , Love J. Christopher , Prósper Felipe , van Galen Peter
Published: January 2022

Diversity of the T-cell receptor (TCR) repertoire is central to adaptive immunity. The TCR is composed of α and β chains, encoded by the TRA and TRB genes, of which the variable regions determine antigen specificity. To generate novel biological insights into the complex functioning of immune cells, combined capture of variable regions and single-cell transcriptomes provides a compelling approach. Recent developments enable the enrichment of TRA and TRB variable regions from widely used technologies for 3’-biased single-cell RNA-sequencing (scRNA-seq). However, a comprehensive computational pipeline to process TCR-enriched data from 3’ scRNA-seq is not available. Here we present an analysis pipeline to process TCR variable regions enriched from 3’ scRNA-seq cDNA. The tool reports TRA and TRB nucleotide and amino acid sequences linked to cell barcodes, enabling the reconstruction of T-cell clonotypes with associated transcriptomes. We demonstrate the software using peripheral blood mononuclear cells (PBMCs) from a healthy donor and detect TCR sequences in a high proportion of single T-cells. Detection of TCR sequences is negligible in non-T-cell populations, demonstrating specificity. Finally, we show that TCR clones are larger in CD8 Memory T-cells than other T-cell types, indicating an association between T-cell clonotypes and differentiation states.

Availability and implementation

The Workflow for Association of T-cell receptors from 3’ single-cell RNA-seq (WAT3R), including test data, is available on GitHub (https://github.com/mainciburu/WAT3R), Docker Hub (https://hub.docker.com/r/mainciburu/wat3r), and a workflow on the Terra platform (https://app.terra.bio). The test dataset is available on GEO (accession number pending).
Preclinical stage abundance and nuclear antigen reactivity of fecal Immunoglobulin A (IgA) varies among males and females of lupus-prone mouse models
Authors: Gudi Radhika , Roy Soumyabrata , Sun Wei , Vasu Chenthamarakshan
Published: January 2022

Systemic lupus erythematosus (SLE) is characterized by the production of pathogenic autoantibodies with nuclear antigen (nAg) specificity. Using (SWRxNZB)F1 (SNF1) mice, we showed higher levels of IgA production in the intestine and the nAg reactivity of fecal IgA under lupus susceptibility. Here, we determined if the fecal IgA abundance and nAg reactivity are higher in, different among, various lupus-prone preclinical models (MRL/lpr, NZBxNZW-F1, SNF1, NZM2410 and NZM2328). We also determined if the fecal IgA nAg reactivity at pre-seropositive ages correlates with the eventual serum autoantibody levels in males and females of these mouse models. We show that age dependent increase in the abundance and nAg reactivity of fecal IgA can vary among different lupus-prone mouse models. Importantly, fecal IgA in these mice show significant levels of nAg reactivity, starting as early as at juvenile age. Furthermore, the pre-seropositive stage nAg reactivity of fecal IgA in most lupus-prone strains correlates well with that of eventual, seropositive stage systemic autoantibody levels. Gender differences in serum autoantibody levels were preceded by similar differences in the fecal IgA abundance and nAg reactivity. These observations suggest that fecal IgA features, nAg reactivity particularly, could serve as a biomarker for early prediction of the eventual systemic autoimmunity in lupus-prone subjects.
Sex-Specific Genes Identified in Sea Urchin Gonads are Expressed Prior to Metamorphosis
Authors: Pieplow Cosmo , Wessel Gary M.
Published: January 2022

A great collaboration between the germline and somatic cells of an organism is the creation of a functional gonad. Here we begin to test this mechanism in a sea urchin by use of RNA-seq, and quantitative mRNA measurements throughout the life cycle of the sea urchin, Lytechinus variegatus (Lv). We found through de novo analyses that the ovary and testis of this echinoderm contains the many transcripts predicted for gamete morphology and function, but we also discovered many uncharacterized gene products unique to each gonad. We found that transcripts involved in glycolysis are highly enriched in the ovary compared to the testis, and that Lv has an expansion of nanos genes not observed in other sequenced echinoderms. We developed a pipeline integrating timepoint RNA-seq data throughout development to identify hallmark gene expression in gonads. We found activation of meiotic genes surprisingly early in development, and observed that candidate genes involved in sex determination are first expressed during larval growth, well before metamorphosis. We further discovered that individual larvae express varying levels of male- or female-hallmark genes before metamorphosis, including factors for the germ line, oocyte, sperm, and meiosis related genes. Together these data support the hypothesis that sex determination in the sea urchin is initiated prior to metamorphosis, from a shared profile of male and female factors, and that the many uncharacterized genes unique to the gonads may reveal unique pathways and mechanisms in echinoderm reproduction.

Highlight

Testis and Ovary of the sea urchin, Lytechinus variegatus, have distinct transcriptome profiles

L. variegatus gonad RNA-seq reveals the expression of 9 nanos genes

The ovary in the sea urchin uniquely expresses genes of the glycolytic pathway, including an ovary-specific transcript of GAPDH

Genes involved in meiosis and in sex determination are expressed early in larval development

From gene expression profiles we conclude here that sex determination is initiated prior to metamorphosis in this echinoderm
Modeling Pulse Dynamics of Juvenile Fish Enables the Short-term Forecasting of Population Dynamics in Japanese Pufferfish: A Latent Variable Approach
Authors: Nishijima Shota , Suzuki Shigenori , Fukuta Ryo , Okada Makoto
Published: January 2022

The time lag between data collection and management implementation is a source of uncertainty and bias in the calculation of acceptable biological catch. Here, we developed a method to use small-scale survey data for juvenile Japanese pufferfish (Takifugu rubripes) to shorten this time lag and achieve accurate short-term forecasting. A survey of juvenile fish at a local sandy beach in Ise-Mikawa Bay, Japan provides data for the strength of year classes before fisheries recruitment; however, it is difficult to use the raw data owing to the small sample size and large observation errors. We found that a random-effect model overcame these problems and more accurately predicted pulse patterns of catch rates to derive a standardized recruitment index compared with a fixed-effect model. We then showed that a stock assessment model using the standardized recruitment index from the random-effect model outperformed models without the standardized recruitment index with respect to retrospective forecasting ability. This study highlights the applicability of a latent-variable approach for standardizing small-scale survey data and thereby for unbiased forecasting of short-term fish dynamics.
Ultramicrobacteria in various fermented cabbages
Authors: Lee Hae-Won , Yoon So-Ra , Dang Yun-Mi , Kang Miran , Lee Kwang Ho , Ha Ji-Hyoung , Bae Jin-Woo
Published: January 2022

Little is known about the ultramicrobial communities of foods. Several bacteria, including pathogenic species, can form ultramicrobial communities when exposed to harsh conditions, making their detection via conventional culture techniques difficult. This study aimed to explore ultramicrobial communities within the microbial communities of fermented cabbage products, such as kimchi, sauerkraut, and suancai, which are produced through specific manufacturing methods based on the laws and culture of respective regions. We used single-molecule real-time sequencing with tangential flow filtration for fermented cabbages after pre-filtration and transmission electron microscopy to confirm the identity of ultramicrobacteria (UMB).To the best of our knowledge, this is the first study to identify the differences between ultramicrobial communities and microbial communities of fermented cabbages. Although the size of the ultramicrobial communities was smaller than that of the latter, their diversity was not lower. In addition, some UMB underwent cell shrinkage due to unfavorable environments, while others maintained their small size regardless. Major pathogens were not detected in the ultramicrobial communities of fermented cabbages. Nevertheless, several suspicious strains were detected. Our method can be used to screen food materials for the presence of UMB undetectable via conventional methods. Ultramicrobial and microbial communities were efficiently separated using tangential flow filtration and analyzed via single-molecule real-time sequencing. The ultramicrobial communities of fermented vegetables were different from conventional microbial communities. This study provides new insights into the ecology of UMB in foods.
Germinal center-derived broadly neutralizing antibodies adapt to SARS-CoV-2 antigenic drift
Authors: Shitaoka Kiyomi , Kawano Yohei , Higashiura Akifumi , Mizoguchi Yoko , Hashiguchi Takao , Nishimichi Norihisa , Huang Shiyu , Ito Ayano , Yamamoto Akima , Ohki Shun , Kanda Miyuki , Taniguchi Tomohiro , Yokosaki Yasuyuki , Okada Satoshi , Sakaguchi Takemasa , Yasuda Tomoharu
Published: January 2022

The outbreak of SARS-CoV-2 variant Omicron which harbors a striking number of mutations in the spike protein has been raising concerns about the effectiveness of vaccines and antibody treatment1. Here, we confirmed a substantial reduction in neutralizing potency against Omicron in all convalescent and vaccinated sera. However, we found that some people infected by the early strain show relatively higher neutralization to Omicron. From those B cells, we developed neutralizing antibodies inhibiting broad variants including Delta and Omicron. Unlike reported antibodies, one had an extremely large interface and widely covered receptor binding motif of spike, thereby interfering with diversified variants. Somatic mutations introduced by long-term germinal center reaction contributed to the key structure of antibodies and the universal interaction with spike variants. Recalling such rare B cells may confer sustainable protection against SARS-CoV-2 variants emerging one after another.