bluuebunny/crossref_metadata_2025 huggingface dataset:
Double-layered two-directional somatopleural cell migration during chicken body wall development revealed with local fluorescent tissue labeling
Authors: Sakamoto Nobuyuki , Aoyama Hirohiko , Ikegami Koji
Published: October 2021

The ventral body wall is derived from the somatic layer of the lateral plate mesoderm, somatopleure, and somite. The primary ventral body wall is formed as a result of the lateral growth of the somatopleure. The secondary body wall is generated through the migration of somitic cells into the somatopleure. While it is reported that the cervical somatopleural cells migrate caudally to the thoracic region during body wall development, the migration of the thoracic somatopleural cells has not been elucidated. To investigate the migration behavior of the somatopleural cells in the thorax during chicken ventral body wall development, we labeled the thoracic somatopleural cells of one somite wide by DiI labeling or gene transfection of enhanced green fluorescent protein and observed the three-dimensional distribution of the labeled cells with the tissue-clearing technique FRUIT. Our labeling experiments revealed the rostral migration of the somatopleural cells into a deep part of the thoracic body wall in embryonic day 6.5 chickens. For embryonic day 8.5 chickens, these deep migrating somatopleural cells were found around the sternal ribs. Thus, we identified the double-layered two-directional migrating pathways of the somatopleural cells: the rostral migration of the deep somatopleural cells and the lateral migration of the superficial somatopleural cells. Our findings imply that the rostral migration of deep somatopleural cells and the lateral migration of superficial ones might be associated with the developing sternal ribs and the innervation of the thoracic cutaneous nerves, respectively.

Mini-abstract

Double-layered two-directional migrations of the somatopleural cells in the thoracic body wall during chicken development were revealed by one-somite-wide labeling of the somatopleure.
Genetic features of antimicrobial drug-susceptible extraintestinal pathogenicEscherichia colipandemic sequence type 95
Authors: Allegretti Yuan Hu , Yamaji Reina , Adams-Sapper Sheila , Riley Lee W
Published: October 2021

Extraintestinal pathogenicEscherichia coli(ExPEC) belonging to multilocus sequence type 95 (ST95) is one of the most geographically widespread ExPEC lineages causing bloodstream (BSI) and urinary tract infections (UTI). In contrast to other widespread ExPEC sequence types, a large proportion ST95 strains remains susceptible to all antimicrobial agents used to treat BSI or UTI. We aimed to identify genomic features of ST95 associated with its relatively high drug-susceptible frequency. We analyzed whole genomes of 1749 ST95 isolates, 80 from patients with BSI or UTI in Northern California, and 1669 isolates from the Enterobase database. We first compared whole-genome sequences (WGS) of 887 drug-susceptible strains and 862 strains resistant to one or more drugs (defined genotypically as strains harboring drug-resistance genes annotated in the ResFinder database) to identify genetic features associated with strains devoid of drug-resistance genes. We then conducted a pan-genome-wide association study on human clinical isolates of ST95, which included 553 UTI and BSI ST95 isolates. We found 44 accessory genes to be significantly associated with ST95 strains lacking drug resistance genes. Fifteen of these were not found in any of the WGSs of ST131 ExPEC strains, which are frequently multidrug-resistant. These genes were annotated to encode transporter or transfer systems and DNA repair polymerases. A large proportion of ST95 strains may have evolved to adapt to antibiotic-imposed stresses without acquiring drug-resistance genes.

Importance

Despite the increasing prevalence of antibiotic-resistantEscherichia colistrains that cause urinary tract and bloodstream infections, a major pandemic lineage of extraintestinal pathogenicE. coli(ExPEC) ST95 has a comparatively low frequency of drug resistance. We compared genomes of 1749 ST95 isolates to identify genetic features that may explain why most strains of ST95 resist becoming drug-resistant. Identification of such genomic features could contribute to the development of novel strategies to prevent the spread of antibiotic-resistant genes and devise new measures to control antibiotic-resistant infections.
Evolution of maternal and early zygotic transcript regulation across Drosophila
Authors: Omura Charles S. , Lott Susan E.
Published: October 2021

The complements of mRNAs in early embryonic development are crucial for setting up developmental trajectories across all animals. The earliest stages of development are regulated by mRNAs deposited into the egg by the mother, until the zygote can become competent to transcribe its own genome. Previously, we showed that the set of maternally deposited and early transcribed zygotic mRNAs inDrosophilaare generally conserved across species, but with some notable variation. We also showed that a majority of regulators of these two types of transcripts are shared. In this study, we examine the differences in regulatory motifs associated with maternal deposition and early zygotic transcription across species ofDrosophila. For maternal transcripts, while the regulators are mostly conserved, we find theDrosophila pseudoobscuraspecies subgroup appears to contain numerous novel regulatory motifs unique to these species. These novel motifs are enriched in transposable elements exclusive to this group. As this species group had been previously identified as having an exceptional amount of divergence in early embryonic transcripts, this change in regulation may be responsible. However, transcripts that are present at the maternal stage only in these species are equally enriched in novel (group-specific) and conserved binding sites, so the novel regulation is not the sole cause of regulatory divergence in these species. At the zygotic stage, we observe a wide variety of species-specific motifs. Additionally, at both stages we observe motifs conserved across species having different effects on gene expression in different species, and regulating different sets of genes in different species. By examining changes in motif content across species, we find that changes in motif content alone is generally insufficient to drive gene expression changes across species.
The indoor mycobiome of daycare centers is affected by occupancy and climate
Authors: Estensmo Eva Lena F. , Botnen Synnøve Smebye , Maurice Sundy , Martin-Sanchez Pedro M. , Morgado Luis , Engh Ingeborg Bjorvand , Høiland Klaus , Skrede Inger , Kauserud Håvard
Published: October 2021

Many children spend considerable time in daycare centers and may here be influenced by indoor microorganisms, including fungi. In this study, we investigate the indoor mycobiome of 125 daycare centers distributed along strong environmental gradients throughout Norway. Dust samples were collected from doorframes outside and inside buildings using a citizen science sampling approach. Fungal communities in the dust samples were analyzed using DNA metabarcoding of the ITS2 region. We observed a marked difference between the outdoor and indoor mycobiomes. The indoor mycobiome included considerably more yeasts and molds compared to the outdoor samples, with Saccharomyces, Mucor, Malassezia and Penicillium among the most dominant fungal genera. Changes in the indoor fungal richness and composition correlated to numerous variables related to both outdoor and indoor conditions; there was a clear geographic structure in the indoor mycobiome composition that mirrored the outdoor climate, ranging from humid areas in western Norway to drier and colder areas in eastern Norway. Moreover, the number of children in the daycare centers, as well as various building features, influenced the indoor mycobiome composition. We conclude that the indoor mycobiome in Norwegian daycare centers is structured by multiple factors and is dominated by yeasts and molds. This study exemplifies how citizen science sampling enables DNA-based analyses of a high number of samples covering wide geographic areas.

Importance

With an alarming increase in chronic diseases like childhood asthma and allergies, there is an increased focus on the exposure of young children to indoor biological and chemical air pollutants. Our study of 125 daycares throughout Norway demonstrates that the indoor mycobiome not only reflects co-occurring outdoor fungi but includes a high abundance of yeast and mold fungi with an affinity for indoor environments. A multitude of factors influence the indoor mycobiome in daycares, including building type, inhabitants, as well as the outdoor environment. Many of the detected yeasts and molds are likely associated with the human body, where some have been coupled to allergies and respiratory problems. Our results call for further studies investigating the potential impact of the identified daycare-associated mycobiomes on children health.
Combinatorial viral vector-based and live-attenuated vaccines without an adjuvant to generate broader immune responses to effectively combat pneumonic plague
Authors: Kilgore Paul B. , Sha Jian , Hendrix Emily K. , Motin Vladimir L. , Chopra Ashok K.
Published: October 2021

Mice immunized with a combination of an adenovirus vector (Ad5-YFV) and live-attenuated (LMA)-based vaccines were evaluated for protective efficacy against pneumonic plague. While the Ad5-YFV vaccine harbors a fusion cassette of three genes encodingYscF,F1, andLcrV, LMA represents a mutant of parentalYersinia pestisCO92 deleted for genes encodingLpp,MsbB, andAil. Ad5-YFV and LMA were either administered simultaneously (1-dose regimen) or 21 days apart in various order and route of administration combinations (2-dose regimen). The 2-dose regimen induced robust immune responses to provide full protection to animals against parental CO92 and its isogenic F1 (CAF-)-deletion mutant challenges during both short- and long-term studies. Mice intranasally (i.n.) immunized with Ad5-YFV first followed by LMA (i.n. or intramuscularly [i.m.]) had higher T- and B-cell proliferative responses and LcrV antibody titers than those in mice vaccinated with LMA (i.n. or i.m.) first ahead of Ad5-YFV (i.n.) during the long-term study. Specifically, the needle- and adjuvant-free vaccine combination (i.n.) is ideal for use in plague endemic regions. Conversely, with a 1-dose regimen, mice vaccinated with Ad5-YFV i.n. and LMA by the i.m. route provided complete protection to animals against CO92 and its CAF-mutant challenges, and elicited Th1/Th2, as well as Th17 responses, thus suitable for emergency vaccination during a plague outbreak or bioterrorist attack. This is a first study in which a viral vector-based and live-attenuated vaccines were effectively used in combination representing adjuvant- and/or needle- free immunization, with each vaccine triggering a distinct cellular immune response.

Importance

Yersinia pestis, the causative agent of plague, is a Tier-1 select agent and a re-emerging human pathogen. A 2017 outbreak in Madagascar with >75% of cases being pneumonic and 8.6% causalities emphasized the importance of the disease. The World Health Organization has indicated an urgent need to develop new generation subunit and live-attenuated plague vaccines. We have developed a subunit vaccine including three components (YscF,F1, and LcrV) using an adenovirus platform (Ad5-YFV). In addition, we have deleted virulence genes ofY. pestis(e.g., lpp,msbB, andail) to develop a live-attenuated vaccine (LMA). Both of these vaccines generated robust humoral and cellular immunity and were highly efficacious in several animal models. We hypothesized the use of a heterologous prime-boost strategy or administrating both vaccines simultaneously could provide an adjuvant- and/or a needle- free vaccine(s) which have attributes of both vaccines for use in endemic regions and during an emergency situation.
Estimating dengue transmission intensity from serological data: a comparative analysis using mixture and catalytic models
Authors: Cox Victoria , O’Driscoll Megan , Imai Natsuko , Prayitno Ari , Hadinegoro Sri Rezeki , Taurel Anne-Frieda , Coudeville Laurent , Dorigatti Ilaria
Published: October 2021

Background

Dengue virus (DENV) infection is a global health concern of increasing magnitude. To target intervention strategies, accurate estimates of the force of infection (FOI) are necessary. Catalytic models have been widely used to estimate DENV FOI and rely on a binary classification of serostatus as seropositive or seronegative, according to pre-defined antibody thresholds. Previous work has demonstrated the use of thresholds can cause serostatus misclassification and biased estimates. In contrast, mixture models do not rely on thresholds and use the full distribution of antibody titres. To date, there has been limited application of mixture models to estimate DENV FOI.

Methods

We compare the application of mixture models and time-constant and time-varying catalytic models to simulated data and to serological data collected in Vietnam from 2004 to 2009 (N ≥ 2178) and Indonesia in 2014 (N = 3194).

Results

The simulation study showed greater estimate bias from the time-constant and time-varying catalytic models (FOI bias = 1.3% (0.05%, 4.6%) and 2.3% (0.06%, 7.8%), seroprevalence bias = 3.1% (0.25%, 9.4%) and 2.9% (0.26%, 8.7%), respectively) than from the mixture model (FOI bias = 0.41% (95% CI 0.02%, 2.7%), seroprevalence bias = 0.11% (0.01%, 3.6%)). When applied to real data from Vietnam, the mixture model frequently produced higher FOI and seroprevalence estimates than the catalytic models.

Conclusions

Our results suggest mixture models represent valid, potentially less biased, alternatives to catalytic models, which could be particularly useful when estimating FOI and seroprevalence in low transmission settings, where serostatus misclassification tends to be higher.

Author summary

Characterising the transmission intensity of dengue virus in different geographic areas over time is essential to understand who is at greatest risk of infection, and to inform the implementation of interventions, such as vector control and vaccination. It is therefore important to understand how methodological differences and model choice may influence estimates of transmission intensity. We compared the application of catalytic and mixture models to calculate the force of infection (FOI) of dengue virus from antibody titre data. We observed greater bias in FOI estimates obtained from catalytic models than from mixture models in areas where the transmission intensity was low. In high transmission intensity areas, catalytic and mixture models produced consistent estimates. Our results indicate that in low transmission settings, when antibody titre data are available, mixture models could be preferential to estimate dengue virus FOI.
100,000 lumens to treat seasonal affective disorder: A proof of concept RCT of bright, whole-room, all-day (BROAD) light therapy
Authors: Sandkühler Julia Fabienne , Brochhagen Sarah , Rohde Paul , Muscheidt Rosa Clara , Grömer Teja Wolfgang , Müller Helge , Brauner Jan Markus
Published: October 2021

Background

Seasonal affective disorder (SAD) is common and debilitating. The standard of care includes light therapy provided by a light box; however, this treatment is restrictive and only moderately effective. Advances in LED technology enable lighting solutions that emit vastly more light than traditional light boxes. Here, we assess the feasibility of BROAD (Bright, whole-ROom, All-Day) light therapy and get a first estimate for its potential effectiveness.

Methods

Patients were randomly assigned to a treatment for four weeks; either a very brightly illuminated room in their home for at least six hours per day (BROAD light therapy) or 30 minutes in front of a standard 10,000 lux SAD light box. Feasibility was assessed by monitoring recruitment, adherence, and side effects. SAD symptoms were measured at baseline and after two and four weeks, with the Hamilton Depression Rating Scale-Seasonal Affective Disorders 29-items, self-report version.

Results

All 62 patients who started treatment were available at four-week follow-up and no significant adverse effects were reported. SAD symptoms of both groups improved similarly and considerably, in line with previous results. Exploratory analyses indicate that a higher illuminance (lux) is associated with a larger symptom improvement in the BROAD light therapy group.

Conclusions

BROAD light therapy is feasible and seems similarly effective as the standard of care while not confining the participants to 30 minutes in front of a light box. In follow-up trials, BROAD light therapy could be modified for increased illuminance, which would likely improve its effectiveness.
Prevalence and Clinical Profiling of Dysglycemia and HIV infection in Persons with Pulmonary Tuberculosis in Brazil
Authors: Arriaga María B. , Araújo-Pereira Mariana , Barreto-Duarte Beatriz , Sales Caio , Miguez-Pinto João Pedro , Nogueira Evelyn B. , Nogueira Betânia M. F. , Rocha Michael S. , Souza Alexandra B. , Benjamin Aline , de Oliveira Jamile G. , Moreira Adriana S. R. , Queiroz Artur T. L. , Rodrigues Moreno M. S. , Spener-Gomes Renata , Figueiredo Marina C. , Durovni Betina , Cavalcante Solange , Lapa-e-Silva José R. , Kristki Afrânio L. , Cordeiro-Santos Marcelo , Sterling Timothy R. , Rolla Valeria C. , Andrade Bruno B. ,   the RePORT-Brazil consortium
Published: October 2021

Background

There are scarce data on the prevalence and disease presentation of HIV in patients with tuberculosis (TB) and dysglycemia (diabetes [DM] and prediabetes [PDM]), especially in TB-endemic countries.

Methods

We assessed the baseline epidemiological and clinical characteristics of patients with culture-confirmed pulmonary TB, enrolled in a multicenter prospective cohort in Brazil (RePORT-Brazil) during 2015-2019. Dysglycemia was defined by elevated glycated hemoglobin and stratified as PDM or DM. Additionally, we used data from TB cases obtained through the Brazilian National Notifiable Diseases Information System (SINAN), during 2015-2019. In SINAN, diagnosis of diabetes was based on self-report. Logistic regression models were performed to test independent associations between HIV, dysglycemia status, and other baseline characteristics in both cohorts.

Results

In the RePORT-Brazil cohort, the prevalence of DM and of PDM was 23.7% and 37.8%, respectively. Furthermore, the prevalence of HIV was 21.4% in the group of persons with TB-dysglycemia and 20.5% in that of patients with TBDM. In the SINAN cohort, the prevalence of DM was 9.2%, and among the TBDM group the prevalence of HIV was 4.1%. Logistic regressions demonstrated that aging was independently associated with PDM or DM in both the RePORT-Brazil and SINAN cohorts. In RePORT-Brazil, illicit drug use was associated with PDM, whereas a higher body mass index (BMI) was associated with DM occurrence. Of note, HIV was not associated with an increased risk of PDM or DM in patients with pulmonary TB in both cohorts. Moreover, in both cohorts, the TBDM-HIV group presented with a lower proportion of positive sputum smear and a higher frequency of tobacco and alcohol users.

Conclusion

There is a high prevalence of dysglycemia in patients with pulmonary TB in Brazil, regardless of the HIV status. This reinforces the idea that DM should be systematically screened in persons with TB. Presence of HIV does not substantially impact clinical presentation in persons with TBDM, although it is associated with more frequent use of recreational drugs and smear negative sputum samples during TB screening.
Correlates of COVID-19 Vaccine Hesitancy among People who Inject Drugs in the San Diego-Tijuana Border Region
Authors: Strathdee Steffanie Ann , Abramovitz Daniela , Harvey-Vera Alicia Y. , Vera Carlos , Rangel Gudelia , Artamonova Irina , Patterson Thomas L. , Mitchell Rylie , Bazzi Angela R.
Published: October 2021

Background: People who inject drugs (PWID) are vulnerable to acquiring SARS-CoV-2 but their barriers to COVID-19 vaccination are under-studied. We examined correlates of COVID-19 vaccine hesitancy among PWID in the U.S.-Mexico border region, of whom only 7.6% had received ≥one COVID-19 vaccine dose by September, 2021.

Methods: Between October, 2020 and September, 2021, participants aged ≥18 years from San Diego, California, USA and Tijuana, Baja California, Mexico who injected drugs within the last month completed surveys and SARS-CoV-2, HIV, and HCV serologic testing. Logistic regressions with robust standard error estimation via generalized estimating equations identified factors associated with COVID-19 vaccine hesitancy, defined as being unsure or unwilling to receive COVID-19 vaccines.

Results: Of 393 participants, 127 (32.3%) were vaccine hesitant. Older participants, those with greater food insecurity, and those with greater concern about acquiring SARS-CoV-2 were more willing to be vaccinated. Higher numbers of chronic health conditions, having access to a smart phone or computer, and citing social media as one's most important source of COVID-19 information were independently associated with vaccine hesitancy. COVID-19-related disinformation was independently associated with vaccine hesitancy (adjusted odds ratio: 1.51 per additional conspiracy theory endorsed; 95% confidence interval: 1.31-1.74).

Conclusions: Nearly one third of PWID in the San Diego-Tijuana border region reported COVID-19 vaccine hesitancy, which was significantly influenced by exposure to disinformation. Interventions that improve accurate knowledge and trust in COVID-19 vaccines are needed to increase vaccination in this vulnerable population.
Trends in SARS-CoV-2 seroprevalence in Massachusetts estimated from newborn screening specimens
Authors: Ma Kevin C. , Hale Jaime E. , Grad Yonatan H. , Alter Galit , Luzuriaga Katherine , Eaton Roger B. , Fischinger Stephanie , Kaur Devinder , Brody Robin , Siddiqui Sameed M. , Leach Dylan , Brown Catherine M. , Klevens R. Monina , Madoff Lawrence , Comeau Anne Marie
Published: October 2021

Background

Estimating the cumulative incidence of SARS-CoV-2 is essential for setting public health policies. We leveraged de-identified Massachusetts newborn screening specimens to generate an accessible, retrospective source of maternal antibodies for estimating statewide SARS-CoV-2 seroprevalence in a non-test-seeking population.

Methods

We analyzed 72,117 newborn dried blood spots collected from November 2019 through December 2020, representing 337 towns and cities across Massachusetts. Seroprevalence was estimated for the general Massachusetts population after correcting for imperfect test specificity and nonrepresentative sampling using Bayesian multilevel regression and poststratification.

Results

Statewide seroprevalence was estimated to be 0.03% (90% credible interval (CI) [0.00, 0.11]) in November 2019 and rose to 1.47% (90% CI [1.00, 2.13]) by May 2020, following sustained SARS-CoV-2 transmission in the spring. Seroprevalence plateaued from May onwards, reaching 2.15% (90% CI [1.56, 2.98]) in December 2020. Seroprevalence varied substantially by community and was particularly associated with community percent non-Hispanic Black (β = 0.024, 90% CI [0.004, 0.044]); i.e., a 10% increase in community percent non-Hispanic Black was associated with a 27% higher odds of seropositivity. Seroprevalence estimates had good concordance with reported case counts and wastewater surveillance for most of 2020, prior to the resurgence of transmission in winter.

Conclusions

Cumulative incidence of SARS-CoV-2 protective antibody in Massachusetts was low as of December 2020, indicating that a substantial fraction of the population was still susceptible. Maternal seroprevalence data from newborn screening can inform longitudinal trends and identify cities and towns at highest risk, particularly in settings where widespread diagnostic testing is unavailable.

The measurement of maternal antibodies in dried blood spots collected for newborn screening offers a statewide source of SARS-CoV-2 seroprevalence data independent of case testing limitations. We analyzed 72,117 Massachusetts spots collected November 2019 – December 2020 and estimated longitudinal trends.
Label-Free SARS-CoV-2 Detection on Flexible Substrates
Authors: Paria Debadrita , Kwok Kam Sang , Raj Piyush , Zheng Peng , Gracias David H. , Barman Ishan
Published: October 2021

One of the most important strategies for mitigation and managing pandemics is widespread, rapid and inexpensive testing and isolation of infected patients. In this study, we demonstrate large area, label-free, and rapid testing sensor platforms fabricated on both rigid and flexible substrates for fast and accurate detection of SARS-CoV-2. SERS enhancing metal insulator metal (MIM) nanostructures are modeled using finite element simulations and then fabricated using nanoimprint lithography (NIL) and transfer printing. The SERS signal of various viral samples, including spiked saliva, was analyzed using machine learning classifiers. We observe that our approach can obtain the test results typically within 25 minutes with a detection accuracy of at least 83% for the viral samples. We envision that this approach which features large area nanopatterning, fabrication in both rigid and flexible formats for wearables, SERS spectroscopy and machine learning can enable new types of rapid, label-free biosensors for screening pathogens and managing current and future pandemics.
Multi-ethnic Investigation of Risk and Immune Determinants of COVID-19 Outcomes
Authors: Jun Tomi , Mathew Divij , Sharma Navya , Nirenberg Sharon , Huang Hsin-Hui , Kovatch Patricia , Wherry E. John , Huang Kuan-lin
Published: October 2021

Objectives

To compare risk factors for COVID-19 mortality among hospitalized Hispanic, Non-Hispanic Black, and White patients.

Design

Retrospecitve cohort study

Setting

Five hosptials within a single academic health system

Participants

3,086 adult patients with self-reported race/ethnicity information presenting to the emergency department and hospitalized with COVID-19 up to April 13, 2020.

Main outcome measures

In-hospital mortality

Results

While older age (multivariable OR 1.06, 95% CI 1.05-1.07) and baseline hypoxia (multivariable OR 2.71, 95% CI 2.17-3.36) were associated with increased mortality overall and across all races/ethnicities, Non-Hispanic Black (median age 67, IQR 58-76) and Hispanic (median age 63, IQR 50-74) patients were younger and had different comorbidity profiles compared to Non-Hispanic White patients (median age 73, IQR 62-84; p<0.05 for both comparisons). Among inflammatory markers associated with COVID-19 mortality, there was a significant interaction between the Non-Hispanic Black population and interleukin-1-beta (interaction p-value 0.04).

Conclusions

This analysis of a multi-ethnic cohort highlights the need for inclusion and consideration of diverse popualtions in ongoing COVID-19 trials targeting inflammatory cytokines.
Assessment of the fatality rate and transmissibility taking account of undetected cases during an unprecedented COVID-19 surge in Taiwan
Authors: Yuan Hsiang-Yu , Hossain M. Pear , Wen Tzai-Hung , Wang Ming-Jiuh
Published: October 2021

Background

During the COVID-19 outbreak in Taiwan between May 11 and June 20, 2021, the observed fatality rate (FR) was 5.3%, higher than the global average at 2.1%. The high number of reported deaths suggests that hospital capacity was insufficient. However, many unexplained deaths were subsequently identified as cases, indicating that there were a few undetected cases, hence resulting in a higher estimate of FR. Estimating the number of total infected cases or knowing how to reduce the undetected cases can allow an accurate estimation of the fatality rate (FR) and effective reproduction number (Rt).

Methods

After adjusting for reporting delays, we estimated the number of undetected cases using reported deaths that were and were not previously detected. The daily FR and Rt were calculated using the number of total cases (i.e. including undetected cases). A logistic regression model was developed to predict the detection ratio among deaths using selected predictors from daily testing and tracing data.

Results

The estimated true daily case number at the peak of the outbreak on May 22 was 897, which was 24.3% higher than the reported number, but the difference became less than 4% on June 9 and afterward. After taking account of undetected cases, our estimated mean FR (4.7%) was still high but the daily rate showed a large decrease from 6.5% on May 19 to 2.8% on June 6. Rt reached a maximum value of 6.4 on May 11, compared to 6.0 estimated using the reported case number. The decreasing proportion of undetected cases was associated with the increases in the ratio of the number of tests conducted to reported cases, and the proportion of cases that are contact-traced before symptom onset.

Conclusions

Increasing testing capacity and tracing efficiency can lead to a reduction of hidden cases and hence improvement in epidemiological parameter estimation.
Mispatterned motile cilia beating causes flow blockage in the epileptic brain
Authors: Faubel Regina J. , Santos Canellas Veronica S. , Gaesser Jenna , Beluk Nancy H. , Feinstein Tim N. , Wang Yong , Yankova Maya , Bindu Kalyani , King Stephen M. , Ganapathiraju Madhavi K. , Lo Cecilia W.
Published: October 2021

Beating of motile cilia at the brain ventricular surface generates rapid flow in an evolutionary conserved pattern mediating the transport of cerebrospinal fluid, but its functional importance has yet to be demonstrated. Here we show disturbance of this transport may contribute to seizure susceptibility. Mice haploinsufficient for FoxJ1, transcription factor regulating motile cilia exhibited cilia-driven flow blockage and increased seizure susceptibility. Mutations in two epilepsy-associated kinases, Cdkl5 and Yes1, in mice resulted in similar cilia-driven flow blockage and increased seizure susceptibility. We showed this arises from disorganized cilia polarity associated with disruption in the highly organized basal body anchoring meshwork. Together these findings suggest mispatterning of cilia-generated flow may contribute to epilepsy and thus might account for seizures unresponsive to current seizure medications.

One sentence summary

Epilepsy is associated with disturbance of cilia motion and mispatterning of fluid transport in the brain ventricles.
Dual Recognition of Multiple Signals in Bacterial Outer Membrane Proteins Enhance Assembly and Maintain Membrane Integrity
Authors: Germany Edward M. , Thewasano Nakajohn , Imai Kenichiro , Maruno Yuki , Bamert Rebecca S. , Stubenrauch Christopher J. , Dunstan Rhys A. , Ding Yue , Nakajima Yukari , Lai XiangFeng , Webb Chaille T. , Hidaka Kentaro , Tan Kher Shing , Shen Hsin-Hui , Lithgow Trevor , Shiota Takuya
Published: October 2021

Outer membrane proteins (OMPs) are essential components of the outer membrane of Gram-negative bacteria. In terms of protein targeting and assembly, the current dogma holds that a “β-signal” imprinted in the final β-strand of the OMP engages the β-barrel assembly machinery (BAM complex) to initiate membrane insertion and assembly of the OMP into the outer membrane. Here, we revealed an additional rule, that signals equivalent to the β-signal are repeated in other, internal β-strands within bacterial OMPs, by peptidomimetic and mutational analysis. The internal signal is needed to promote the efficiency of the assembly reaction of these OMPs. BamD, an essential subunit of the BAM complex, recognizes the internal signal and the β-signal, arranging several β-strands and partial folding for rapid OMP assembly. The internal signal-BamD ordering system is not essential for bacterial viability but is necessary to retain the integrity of the outer membrane against antibiotics and other environmental insults.

TEASER

Bacterial outer membrane proteins are recognized and bound by BamD at specific signals located in multiple β-strands at the C-terminus of these proteins.
Orb-dependent polyadenylation contributes to PLP expression and centrosome scaffold assembly
Authors: Fang Junnan , Lerit Dorothy A.
Published: October 2021

As the microtubule-organizing centers (MTOCs) of most cells, centrosomes engineer the bipolar mitotic spindle required for error-free mitosis.DrosophilaPericentrin (PCNT)-like protein (PLP) is a key centrosome component that directs formation of a pericentriolar material (PCM) scaffold required for PCM organization and MTOC function. Here, we investigate the post-transcriptional regulation ofplpmRNA. We identify conserved binding sites for cytoplasmic polyadenylation element binding (CPEB) proteins within theplp3’-untranslated region and examine the role of the CPEB ortholog, oo18 RNA-binding protein (Orb), inplpmRNA regulation. Our data show Orb biochemically interacts withplpmRNA and promotes PLP protein expression. Loss oforb, but notorb2, diminishes PLP levels in embryonic extracts. Consequently, PLP localization to centrosomes and function in PCM scaffolding is compromised inorbmutant embryos, resulting in genome instability and embryonic lethality. Moreover, we find PLP over-expression can restore centrosome scaffolding and rescue the cell division defects caused byorbdepletion. Our data suggest Orb modulates PLP expression at the level ofplpmRNA polyadenylation and showcases the post-transcriptional regulation of core, conserved centrosomal mRNAs as critical for centrosome function.
Blocking chondrocyte hypertrophy in conditional Evc knockout mice does not modify osteoarthritis progression
Authors: Lamuedra Ana , Gratal Paula , Calatrava Lucía , Ruiz-Perez Víctor Luis , Palencia-Campos Adrián , Portal-Núñez Sergio , Mediero Aránzazu , Herrero-Beaumont Gabriel , Largo Raquel
Published: October 2021

Background

Chondrocytes in osteoarthritic (OA) cartilage acquire a hypertrophic-like phenotype, where Hedgehog (Hh) signaling is pivotal. Hh overexpression causes OA-like cartilage lesions, whereas its downregulation prevents articular destruction in mouse models. Mutations in EVC and EVC2 genes disrupt Hh signaling, and are responsible for the Ellis-van Creveld syndrome skeletal dysplasia. Since Ellis-van Creveld syndrome protein (Evc) deletion is expected to hamper Hh target gene expression we hypothesized that it would also prevent OA progression avoiding chondrocyte hypertrophy. Our aim was to study Evc as a new therapeutic target in OA, and whether Evc deletion restrains chondrocyte hypertrophy and prevents joint damage in an Evc tamoxifen induced knockout (EvccKO) model of OA.

Methods

OA was induced by surgical knee destabilization in wild-type (WT) and EvccKO adult mice, and healthy WT mice were used as controls (n=10 knees/group). Hypertrophic markers and Hh genes were measured by qRT-PCR, and metalloproteinases (MMP) levels assessed by western blot. Human OA chondrocytes and cartilage samples were obtained from patients undergoing knee joint replacement surgery. Cyclopamine (CPA) was used for Hh pharmacological inhibition and IL-1β as an inflammatory insult.

Results

Tamoxifen induced inactivation of Evc inhibited Hh overexpression and partially prevented chondrocyte hypertrophy during OA, although it did not ameliorate cartilage damage in DMM-EvccKO mice. Hh pathway inhibition did not modify the expression of proinflammatory mediators induced by IL-1 beta in human OA chondrocytes in culture. Hypertrophic – IHH – and inflammatory – COX-2 – markers co-localized in OA cartilage samples.

Conclusions

Tamoxifen induced inactivation of Evc partially prevented chondrocyte hypertrophy in DMM-EvccKO mice, but it did not ameliorate cartilage damage. Our results suggest that chondrocyte hypertrophy per se is not a pathogenic event in the progression of OA.
Nuclear-injuries by aberrant dynein-forces defeat proteostatic purposes of Lewy Body Inclusions
Authors: Mansuri Shemin , Jain Aanchal , Singh Richa , Rawat Shivali , Mondal Debodyuti , Raychaudhuri Swasti
Published: October 2021

Biogenesis of inclusion bodies (IBs) facilitates protein quality control (PQC). Canonical aggresomes execute degradation of misfolded proteins while non-degradable amyloids quarantine into Insoluble Protein Deposits. Lewy Bodies (LBs) are well-known neurodegenerative IBs of α-Synuclein associated diseases like Dementia with Lewy bodies (DLB) and Parkinson’s disease. Intriguingly, the PQC benefits and drawbacks associated with LBs remain underexplored. Here, we report that the crosstalk between LBs and aggresome-like IBs of α-Synuclein (Syn-aggresomes) buffers amyloidogenic α-Synuclein load in primary neurons and mitotic cell models. Using cellular biochemistry, genetic knockdown, and microscopy tools we find that LBs possess unorthodox PQC-capacities of self-quarantining the Syn-amyloids, and being degradable upon receding fresh amyloidogenesis. Syn-aggresomes equilibrate biogenesis of LBs by facilitating spontaneous and opportunistic turnover of soluble α-Synuclein and Syn-amyloids, respectively. However, LBs overgrow at the perinucleus once amyloidogenesis sets in and are misidentified by cytosolic BICD2 as cargos for motor-protein dynein. Simultaneously, microtubules surrounding the perinuclear LBs are distorted, misbalancing the dynein motor-force on nucleoskeleton leading to lamina injuries. Like typical Laminopathies, nucleocytoplasmic mixing, DNA-damage, and deregulated transcription of stress chaperones defeat the proteostatic purposes of LBs. We confirmed the lamina disintegrities in brain sections of Parkinson’s disease patients. Together, our study provides insights into the intricate complexities of proteostatic possibilities associated with α-Synuclein inclusions and offers understanding on the proteostasis-sensitivity of LB-containing aging neurons via lamina-injuries.

Significance statement

Amyloid inclusions of α-Synuclein called Lewy Bodies (LBs) are hallmark of multiple neurodegenerative diseases like Dementia with Lewy Bodies and Parkinson’s disease. A significant reason for the degeneration of LB-containing aging neurons in these diseases is their sensitivity to proteostasis stresses. We find two distinct inclusions of α-Synuclein in the same neurons/cells. First, the Syn-aggresomes titrate the biogenesis of the other i.e., the LBs, by facilitating degradation of soluble α-Synuclein. Syn-amyloids deposited in LBs remain degradable but LBs overgrow at the perinucleus once the kinetics of amyloid-biogenesis exceeds aggresome-assisted degradation of α-Synuclein. Perinuclear LBs destabilize local tubulin-meshwork and are misidentified as cargo for cytosolic motor dynein. Aberrant cytoskeleton-nucleoskeleton tension disintegrates lamina, deregulates stress-responsive transcription, and triggers proteostasis-sensitivity in LB-containing neurons.
In vitro reconstituted quorum sensing pathways enable rapid evaluation of quorum sensing inhibitors
Authors: Yu Dingchen
Published: October 2021

Quorum sensing, as inner- or inter-species microbial communication process orchestrated by diffusible autoinducers, typically results in collective pathogenic behaviours, being recognized as a promising druggable target for anti-virulence. Here, we reconstituted las and rhl quorum sensing pathways of Pseudomonas aeruginosa, mediated by acyl-homoserine lactones (AHLs) and LuxI/LuxR-family proteins, with fluorescence output in Escherichia coli cell-free expression system, offering a platform to rapidly evaluate quorum sensing inhibitors (QSIs) in vitro. Previously reported small-molecule quorum sensing inhibitors for interfering with P. aeruginosa quorum sensing systems were tested and showed mild to high on-target inhibition as well as off-target toxicity. Of note, quercetin displayed potent on-target inhibition to quorum sensing pathways as well as acceptable off-target toxicity to cell-free expression machinery. Upon our work, cell-free platform is anticipated to further facilitate automated and high-throughput drug screening, bridge in silico and in vivo drug-screening methods, and accelerate the upgrading of antimicrobial arsenal.

GRAPHICAL ABSTRACT
Assassination Tango: An NLR/NLR-ID immune receptors pair of rapeseed co-operates inside the nucleus to activate cell death
Authors: Mermigka Glykeria , Amartolou Argyro , Mentzelopoulou Adriani , Astropekaki Niki , Sarris Panagiotis F.
Published: October 2021

Plant immunity relies on cell-surface receptors and intracellular NLR immune receptors. Some plant NLRs carry integrated domains (IDs) that that mimic authentic pathogens effector targets. We report here the identification in Brassica napus of the genetically linked NLR/NLR-ID pair, BnRPR1 and BnRPR2. The NLR-ID carries two ID fusions and their mode of action conforms to the proposed “integrated sensor/decoy” model. The two NLRs interact and the heterocomplex localizes in the plant-cell nucleus and nucleolus. However, the BnRPRs pair does not operate through a negative regulation as it was previously reported for other NLR-IDs. Cell death is induced only upon co-expression of the two proteins and it is dependent on the helper genes EDS1 and NRG1. Truncations of the IDs of BnRPR1 results in cytoplasmic localization and compromises cell death activation. Expression, using the native promoter in Nicotiana species, led to a conditional cell death induction. However, this was not the case for the transgenic Arabidopsis, where no cell death was observed. In summary, we describe a new pair of NLR-IDs with interesting features in relation to its regulation and the cell death activation.
Cytonemes coordinate asymmetric signaling and organization in the Drosophila muscle progenitor niche
Authors: Patel Akshay , Wu Yicong , Han Xiaofei , Su Yijun , Maugel Tim , Shroff Hari , Roy Sougata
Published: October 2021

Asymmetric signaling and organization in the stem-cell niche determine stem-cell fates. Here, we investigate the basis of asymmetric signaling and stem-cell organization using the Drosophila wing-disc that creates an adult muscle progenitor (AMP) niche. We show that AMPs extend polarized cytonemes to contact the disc epithelial junctions and adhere themselves to the disc/niche. Niche-adhering cytonemes localize FGF-receptor to selectively adhere to the FGF-producing disc and receive FGFs in a contact-dependent manner. Activation of FGF signaling in AMPs, in turn, reinforces disc-specific cytoneme polarity/adhesion, which maintains their disc-proximal positions. Loss of cytoneme-mediated adhesion promotes AMPs to lose niche occupancy and FGF signaling, occupy a disc-distal position, and acquire morphological hallmarks of differentiation. Discrete AMP organization and diversification patterns are determined by localized expression and presentation patterns of two different FGFs in the wing-disc and their polarized target-specific distribution through niche-adhering cytonemes. Thus, cytonemes are essential for asymmetric signaling and niche-specific AMP organization.
Reproducible Propagation of Species-Rich Soil Microbiomes Suggests Robust Underlying Deterministic Principles of Community Formation
Authors: Čaušević Senka , Tackmann Janko , Sentchilo Vladimir , von Mering Christian , van der Meer Jan Roelof
Published: October 2021

Microbiomes are typically characterised by high species diversity but it is poorly understood how such system-level complexity can be generated and propagated. Here, we used soils as a relevant model to study microbiome development. Despite inherent stochastic variation in manipulating species-rich communities, both laboratory-mixed medium complexity (21 soil bacterial isolates in equal proportions) and high-diversity natural top-soil communities followed highly reproducible succession paths, maintaining distinct soil microbiome signatures. Development trajectories and compositional states were different for communities propagated in soils than in liquid suspension. Microbiome states were maintained over multiple renewed growth cycles but could be diverged by short-term pollutant exposure. The different but robust trajectories demonstrated that deterministic taxa-inherent characteristics underlie reproducible development and self-organized complexity of soil microbiomes within their environmental boundary conditions. Our findings also have direct implications for potential strategies to achieve controlled restoration of desertified land.

TEASER

Species-rich soil microbiomes grow and propagate reproducibly despite inherent stochastic complexity, paving the way for soil restoration.
Loss of Prm1 leads to defective chromatin protamination, impaired PRM2 processing, reduced sperm motility and subfertility in male mice
Authors: Merges Gina Esther , Meier Julia , Schneider Simon , Kruse Alexander , Fröbius Andreas Christian , Steger Klaus , Arévalo Lena , Schorle Hubert
Published: October 2021

One of the key events during spermiogenesis is the hypercondensation of chromatin by substitution of the majority of histones by protamines. In humans and mice, protamine 1 (PRM1/Prm1) and protamine 2 (PRM2/Prm2), are expressed in a species-specific ratio. Using CRISPR-Cas9-mediated gene editing we generated Prm1-deficient mice and demonstrate, that Prm1+/- mice are subfertile while Prm1-/- are infertile. Prm1-deficiency was associated with higher levels of 8-OHdG, an indicator for reactive oxygen mediated DNA-damage. While Prm1+/- males displayed moderate increased levels of 8-OHdG virtually all sperm of Prm1-/- males displayed ROS mediated DNA damage. Consequently, DNA integrity was slightly hampered in Prm1+/-, while DNA was completely fragmented in Prm1-/- animals. Interestingly CMA3 staining which indicates protamine-free DNA revealed, that Prm1+/- sperm displayed high levels (93%), compared to Prm2+/- (29%) and WT (2%) sperm. This is not due to increased histone retention as demonstrated by mass spectrometry (MassSpec) of nuclear proteins in Prm1+/- sperm. Further analysis of the MassSpec data from sperm nuclear proteome revealed, that only one protein (RPL31) is significantly higher abundant in Prm1+/- compared to WT sperm. Comparison of the proteome from Prm1-/- and Prm2-/- to WT suggested, that there are a small number of proteins which differ in abundance. However, their function was not linked mechanistically to primary defects seen in Prm1-/- mice and rather represent a general stress response. Interestingly, using acid urea gels we found that sperm from Prm1+/- and Prm1-/- mice contain a high level of unprocessed, full-length PRM2. Prm2 is transcribed as a precursor protein which, upon binding to DNA is successively processed. Further, the overall ratio of PRM1:PRM2 is skewed from 1:2 in WT to 1:5 in Prm1+/- animals. Our results reveal that Prm1 is required for proper processing of PRM2 to produce the mature PRM2 which, together with Prm1 is able to hypercondense DNA. Hence, the species specific PRM1:PRM2 ratio has to be precisely controlled in order to retain full fertility.
A Notch-dependent transcriptional mechanism controls expression of temporal patterning factors in Drosophila medulla
Authors: Ray Alokananda , Li Xin
Published: October 2021

Temporal patterning is an important mechanism for generating a great diversity of neuron subtypes from a seemingly homogenous progenitor pool in both vertebrates and invertebrates. Drosophila neuroblasts are temporally patterned by sequentially expressed Temporal Transcription Factors (TTFs). These TTFs are proposed to form a transcriptional cascade based on mutant phenotypes, although direct transcriptional regulation between TTFs has not been verified in most cases. Furthermore, it is not known how the temporal transitions are coupled with the generation of the appropriate number of neurons at each stage. We use neuroblasts of the Drosophila optic lobe medulla to address these questions and show that the expression of TTFs Sloppy-paired 1/ 2 (Slp1/2) is directly regulated at the transcriptional level by two other TTFs and the cell-cycle dependent Notch signaling through two cis-regulatory elements. We also show that supplying constitutively active Notch can rescue the delayed transition into the Slp stage in cell cycle arrested neuroblasts. Our findings reveal a novel Notch-pathway dependent mechanism through which the cell cycle progression regulates the timing of a temporal transition within a TTF transcriptional cascade.