bluuebunny/crossref_metadata_2025 huggingface dataset:
Vaccine Effectiveness against COVID-19 among Symptomatic Persons Aged ≥12 Years with Reported Contact with COVID-19 Cases, February – September 2021
Authors: Chung Jessie R , Kim Sara S , Belongia Edward A , McLean Huong Q , King Jennifer P , Nowalk Mary Patricia , Zimmerman Richard K , Geffel Krissy Moehling , Martin Emily T , Monto Arnold S , Lamerato Lois E , Gaglani Manjusha , Hoffman Eric , Volz Marcus , Jackson Michael L , Jackson Lisa A , Patel Manish M , Flannery Brendan
Published: January 2022

Individuals in contact with persons with COVID-19 are at high risk of developing COVID-19, but protection offered by COVID-19 vaccines in the context of known exposure is unknown. Symptomatic outpatients reporting acute onset of COVID-19-like illness and tested for SARS-CoV-2 infection were enrolled. Among 2,229 participants, 283/451 (63%) of those reporting contact and 331/1778 (19%) without known contact tested SARS-CoV-2 positive. Using the test-negative design, adjusted vaccine effectiveness was 71% (95% confidence interval, 49%-83%) among fully vaccinated participants reporting contact versus 80% (95% CI, 72%-86%) among those without. This study supports COVID-19 vaccination and highlights the importance of efforts to increase vaccination coverage.
Urinary Biomarkers and Attainment of Cefepime Therapeutic Targets in Critically Ill Children
Authors: Downes Kevin J. , Sharova Anna , Gianchetti Lauren , Himebauch Adam S. , Fitzgerald Julie C. , Zuppa Athena F.
Published: January 2022

INTRODUCTION

The recommended therapeutic target for cefepime (FEP) is the time above MIC (fT>MIC). The frequency of target attainment and risk factors for sub-therapeutic concentrations in children have not been extensively studied.

METHODS

We performed a prospective observational pilot study in children in our PICU receiving standard dosing of FEP for suspected sepsis (≥2 SIRS criteria). Three FEP concentrations were measured per subject and a urine sample was collected prior to PK sampling for measurement of urinary biomarkers. We used log linear regression to calculate the fT>MIC for each subject across a range of MIC values (1-16 µg/mL). We compared clinical factors/biomarkers between patients who did and did not achieve 100% fT>MIC for 8 µg/mL (cut-point for Pseudomonas) and tested the correlation between covariates and FEP troughs.

RESULTS

21 subjects were enrolled (median SIRS criteria: 3). PK sampling occurred after a median of 5 doses (range: 3-9). 43% of subjects achieved 100% fT>MIC for an MIC of 8 µg/mL. Younger age (p=.005), higher estimated GFR (p=.03), and lower urinary NGAL (p=.006) and KIM-1 (.03) were associated with failure to attain 100% fT>8 µg/mL. Age (r = 0.53), eGFR (r = - 0.58), urinary NGAL (r = 0.42) and KIM-1 (r = 0.50) were significantly correlated with FEP troughs.

CONCLUSIONS

A significant proportion of critically ill children failed to attain target concentrations for treatment of Pseudomonas aeruginosa with FEP. Younger patients and those with good kidney function (high GFR, low urinary biomarkers) may be at highest risk for subtherapeutic FEP concentrations.
Waning of SARS-CoV-2 Antibody levels response to inactivated cellular vaccine over 6 months among healthcare workers
Authors: Taminato Monica , Chaves Ana Paula Cunha , Morais Richarlisson Borges de , Moreira Luiz Vinicius Leão , Conte Danielle Dias , Faico Filho Klinger Soares , Gabrielloni Maria Cristina , de Medeiros Eduardo Alexandrino , Bellei Nancy
Published: January 2022

Background

Health Care workers (HCW) are an important group affected by this pandemic and COVID-19 has presented substantial challenges for health professionals and health systems in many countries. The Brazilian vaccination plan implemented in October, so that third dose for HCW. However, the persistence of CoronaVac vaccine-induced immunity is unknown, and immunogenicity according to age cohorts may differ among individuals.

Objective

Evaluate the post vaccination immune humoral response and the relationship between post-vaccination seropositivity rates and demographic data among Healthcare Workers over 6 months after CoronaVac immunization.

Methods

A cross section study including Healthcare professionals vaccinated with CoronaVac for 6 months or more. The study was carried with the analysis of post-vaccination serological test to assess the levels of humoral response after vaccination.

Results

329 participants were included. Among them, 76% were female. Overall, 18.5% were positive quantitative titles (IQR 42.87-125.5) and the negative group was 80%, quantitative titles (IQR 5.50-13.92).

Conclusion

It was possible to identify a group with positive quantitative titles in serological test for IgG antibody against the SARS-CoV-2. Further investigation is required to determine the durability of post-vaccination antibodies and how serological tests can be determine the ideal timing of vaccine booster doses.
Preferential expansion upon boosting of cross-reactive “pre-existing” switched memory B cells that recognize the SARS-CoV-2 Omicron variant Spike protein
Authors: Perugino Cory A. , Liu Hang , Feldman Jared , Hauser Blake M. , Jacob-Dolan Catherine , Nathan Anusha , Zhou Zezhou , Kaseke Clarety , Tano-Menka Rhoda , Getz Matthew A. , Senjobe Fernando , Berrios Cristhian , Ofoman Onosereme , Lemieux Jacob E. , Goldberg Marcia B. , Nundel Kerstin , Moormann Ann , Marshak-Rothstein Ann , Iafrate John A. , Gaiha Gaurav , Charles Richelle , Balazs Alejandro B. , Naranbhai Vivek , Schmidt Aaron G. , Pillai Shiv
Published: January 2022

In previously unvaccinated and uninfected individuals, non-RBD SARS-CoV-2 spike-specific B cells were prominent in two distinct, durable, resting, cross-reactive, “pre-existing” switched memory B cell compartments. While pre-existing RBD-specific B cells were extremely rare in uninfected and unvaccinated individuals, these two pre-existing switched memory B cell compartments were molded by vaccination and infection to become the primary source of RBD-specific B cells that are triggered by vaccine boosting. The frequency of wild-type RBD-binding memory B cells that cross-react with the Omicron variant RBD did not alter with boosting. In contrast, after a boost, B cells recognizing the full-length Omicron variant spike protein expanded, with pre-existing resting memory B cells differentiating almost quantitatively into effector B cell populations. B cells derived from “ancient” pre-existing memory cells and that recognize the full-length wild-type spike with the highest avidity after boosting are the B cells that also bind the Omicron variant spike protein.

Abstract Figure
Effectiveness of COVID-19 vaccines against Omicron or Delta symptomatic infection and severe outcomes
Authors: Buchan Sarah A. , Chung Hannah , Brown Kevin A. , Austin Peter C. , Fell Deshayne B. , Gubbay Jonathan B. , Nasreen Sharifa , Schwartz Kevin L. , Sundaram Maria E. , Tadrous Mina , Wilson Kumanan , Wilson Sarah E. , Kwong Jeffrey C.
Published: January 2022

Background

The incidence of SARS-CoV-2 infection, including among those who have received 2 doses of COVID-19 vaccines, increased substantially following the emergence of Omicron in Ontario, Canada.

Methods

Applying the test-negative study design to linked provincial databases, we estimated vaccine effectiveness (VE) against symptomatic infection and severe outcomes (hospitalization or death) caused by Omicron or Delta between December 6 and 26, 2021. We used multivariable logistic regression to estimate the effectiveness of 2 or 3 COVID-19 vaccine doses by time since the latest dose, compared to unvaccinated individuals.

Results

We included 16,087 Omicron-positive cases, 4,261 Delta-positive cases, and 114,087 test-negative controls. VE against symptomatic Delta infection declined from 89% (95%CI, 86-92%) 7-59 days after a second dose to 80% (95%CI, 74-84%) after ≥240 days, but increased to 97% (95%CI, 96-98%) ≥7 days after a third dose. VE against symptomatic Omicron infection was only 36% (95%CI, 24-45%) 7-59 days after a second dose and provided no protection after ≥180 days, but increased to 61% (95%CI, 56-65%) ≥7 days after a third dose. VE against severe outcomes was very high following a third dose for both Delta and Omicron (99% [95%CI, 98-99%] and 95% [95%CI, 87-98%], respectively).

Conclusions

In contrast to high levels of protection against both symptomatic infection and severe outcomes caused by Delta, our results suggest that 2 doses of COVID-19 vaccines only offer modest and short-term protection against symptomatic Omicron infection. A third dose improves protection against symptomatic infection and provides excellent protection against severe outcomes for both variants.
The individual and combined associations of depression and socioeconomic status with risk of major cardiovascular events: a prospective cohort study
Authors: Prigge Regina , Wild Sarah H. , Jackson Caroline A.
Published: January 2022

Objective

We aimed to investigate the individual and combined associations of depression and low socioeconomic status (SES) with risk of major cardiovascular events (MCVE), defined as first-ever fatal or non-fatal stroke or myocardial infarction, in a large prospective cohort study.

Methods

We used data from 466,238 UK Biobank participants, aged 40 – 69 years without cardiovascular disease, bipolar disorder or schizophrenia at baseline. We performed Cox proportional hazard models to estimate adjusted hazard ratios (HR) and 95% confidence intervals (CI) of the individual and combined associations of depression and each of educational attainment, area-based deprivation and income with risk of MCVE. We assessed effect modification and explored interaction on the additive and multiplicative scale.

Results

Depression, low education, high area-based deprivation and low income were individually associated with increased risks of MCVE (adjusted HR, 95% CI: 1.28, 1.19 – 1.38; 1.20, 1.14 – 1.27; 1.17, 1.11 – 1.23; and 1.22, 1.16 – 1.29, respectively). Depression was associated with increased risks of MCVE among individuals with high and low SES. Individuals with depression and each of low education, high area-based deprivation and low income were at particularly high risk of MCVE (HR, 95% CI: 1.50, 1.38 – 1.63; 1.63, 1.46 – 1.82; 1.31, 1.23 – 1.40, respectively). There was interaction between depression and area-based deprivation on multiplicative and additive scales but no interaction with education or income.

Conclusion

Depression was associated with increased risks of MCVE among individuals with high and low SES, with particularly high risks among those living in areas of high deprivation.
Global Perspective of COVID-19 Vaccine Nationalism
Authors: Basak Palash , Abir Tanvir , Mamun Abdullah Al , Zainol Noor Raihani , Khanam Mansura , Haque Md. Rashidul , Milton Abul Hasnat , Agho Kingsley Emwinyore
Published: January 2022

This study aimed to explore the global perspective of the association between GDP of various countries and progress of COVID-19 vaccinations; to explore how the global pattern holds in the continents, and investigate the spatial distribution pattern of COVID-19 vaccination progress for all countries. We have used consolidated data on COVID-19 vaccination and GDP from Our World in Data, an open-access data source. Data analysis and visualization were performed in R-Studio. There was a strong linear association between per capita income and the proportion of people vaccinated in countries with one million or more populations. GDP per capita accounts for a 50% variation in the vaccination rate across the nations. Our assessments revealed that the global pattern holds in every continent. Rich European and North-American countries are most protected against COVID-19. Less developed African countries barely initiated the vaccination program. There is a significant disparity among Asian countries. The security of wealthier nations (vaccinated their citizens) cannot be guaranteed unless adequate vaccination covers the less-endowed countries. Therefore, the global community should take initiatives to speed up the COVID-19 vaccination program in all countries of the world, irrespective of their wealth.
Improving air quality and health in Northern Italy: limits and perspectives
Authors: Robotto Angelo , Barbero Secondo , Cremonini Roberto , Brizio Enrico
Published: January 2022

A better air quality has led to a significant reduction of premature deaths over the past decade in Europe, as emissions of many pollutants declined considerably in the EU-27 Member States: SOx emissions by 76%, NOx by 42%, NMVOCs by 29% and PM2.5 by 29%. The present paper reports an in-depth analysis of the reasons why the regions of the Po valley, Northern Italy, still have difficulties to comply with EU air quality standards, in particular for PM10 and NO2, in spite of strong emission reductions carried out through careful Air Quality Plans put in practice during the last 2 decades. The analysis includes a consistent comparison of emission inventories for different European regions in Italy, Germany and Poland, the measured air quality trends and PM source apportionment in these areas, and, most of all, a thorough investigation of meteorological parameters influencing atmospheric pollutant dispersion and transport. The study reports that in the colder seasons, wind speed, PBL height and atmospheric pressure occurring in the Po basin are three to five times less efficient in diluting and dispersing pollutant if compared to regions north of the Alps. Due to the extremely disadvantageous orographic and climatic configuration of the Po Valley, only radical emission reductions could bring air quality into EU limit values with a questionable cost-benefit ratio of due policies. Provided that air quality standards (particularly for PM10 and PM2.5) aim at protecting people from adverse health effects arising from air pollution, it is however necessary to also consider the toxicity of atmospheric particulate in addition to PM10/PM2.5 mass concentration as a limit value. Based on existing toxicological studies and reports, a discussion is reported about PM toxicity factor depending on toxicity scores for source-specific aerosols and PM composition determined by Source Apportionment. Provided that PM components’ profiles are strongly different across Europe, the obtained PM toxicity factors range from 0.3 (for areas where the main PM contribution is referable to sea salts or inorganic matter) to 3.5 (where Elemental and Organic Carbon prevail), suggesting that, even at the same mass concentration, the effects of PM10/2.5 on human health are significantly variable and limit values should take into account differential toxicity.

Modern PM Source Apportionment techniques, along with reliable toxicity and epidemiological analyses, represent the right tools to overcome the shortcomings of the current regulation standard and build a new consistent health metric for ambient PM in the future, helping policy makers impose effective air quality measures to protect people health.
The adverse impact of COVID-19 pandemic on cardiovascular disease prevention and management in England, Scotland and Wales: A population-scale analysis of trends in medication data
Authors: Dale Caroline E , Takhar Rohan , Carragher Ray , Torabi Fatemeh , Katsoulis Michalis , Duffield Stephen , Kent Seamus , Mueller Tanja , Kurdi Amanj , McTaggart Stuart , Abbasizanjani Hoda , Hollings Sam , Scourfield Andrew , Lyons Ronan , Griffiths Rowena , Lyons Jane , Davies Gareth , Harris Dan , Handy Alex , Mizani Mehrdad Alizadeh , Tomlinson Chris , Ashworth Mark , Denaxas Spiros , Banerjee Amitava , Sterne Jonathan , Lovibond Kate , Brown Paul , Bullard Ian , Priedon Rouven , Mamas Mamas A , Slee Ann , Lorgelly Paula , Pirmohamed Munir , Khunti Kamlesh , Sattar Naveed , Morris Andrew , Sudlow Cathie , Akbari Ashley , Bennie Marion , Sofat Reecha
Published: January 2022

Objectives

To estimate the impact of the COVID-19 pandemic on cardiovascular disease (CVD) and CVD management using routinely collected medication data as a proxy.

Design

Descriptive and interrupted time series analysis using anonymised individual-level population-scale data for 1.32 billion records of dispensed CVD medications across 15.8 million individuals in England, Scotland and Wales.

Setting

Community dispensed CVD medications with 100% coverage from England, Scotland and Wales, plus primary care prescribed CVD medications from England (including 98% English general practices).

Participants

15.8 million individuals aged 18+ years alive on 1stApril 2018 dispensed at least one CVD medicine in a year from England, Scotland and Wales.

Main outcome measures

Monthly counts, percent annual change (1stApril 2018 to 31stJuly 2021) and annual rates (1stMarch 2018 to 28thFebruary 2021) of medicines dispensed by CVD/ CVD risk factor; prevalent and incident use.

Results

Year-on-year change in dispensed CVD medicines by month were observed, with notable uplifts ahead of the first (11.8% higher in March 2020) but not subsequent national lockdowns. Using hypertension as one example of the indirect impact of the pandemic, we observed 491,203 fewer individuals initiated antihypertensive treatment across England, Scotland and Wales during the period March 2020 to end May 2021 than would have been expected compared to 2019. We estimated that this missed antihypertension treatment could result in 13,659 additional CVD events should individuals remain untreated, including 2,281 additional myocardial infarctions (MIs) and 3,474 additional strokes. Incident use of lipid-lowering medicines decreased by an average 14,793 per month in early 2021 compared with the equivalent months prior to the pandemic in 2019. In contrast, the use of incident medicines to treat type-2 diabetes (T2DM) increased by approximately 1,642 patients per month.

Conclusions

Management of key CVD risk factors as proxied by incident use of CVD medicines has not returned to pre-pandemic levels in the UK. Novel methods to identify and treat individuals who have missed treatment are urgently required to avoid large numbers of additional future CVD events, further adding indirect cost of the COVID-19 pandemic.
The hidden structural variability in avian genomes
Authors: Peona Valentina , Blom Mozes P. K. , Frankl-Vilches Carolina , Milá Borja , Ashari Hidayat , Thébaud Christophe , Benz Brett W. , Christidis Les , Gahr Manfred , Irestedt Martin , Suh Alexander
Published: January 2022

Structural variants (SVs) are DNA mutations that can have relevant effects at micro- and macro-evolutionary scales. The detection of SVs is largely limited by the type and quality of sequencing technologies adopted, therefore genetic variability linked to SVs may remain undiscovered, especially in complex repetitive genomic regions. In this study, we used a combination of long-read and linked-read genome assemblies to investigate the occurrence of insertions and deletions across the chromosomes of 14 species of birds-of-paradise and two species of estrildid finches including highly repetitive W chromosomes. The species sampling encompasses most genera and representatives from all major clades of birds-of-paradise, allowing comparisons between individuals of the same species, genus, and family. We found the highest densities of SVs to be located on the microchromosomes and on the female-specific W chromosome. Genome assemblies of multiple individuals from the same species allowed us to compare the levels of genetic variability linked to SVs and single nucleotide polymorphisms (SNPs) on the W and other chromosomes. Our results demonstrate that the avian W chromosome harbours more genetic variability than previously thought and that its structure is shaped by the continuous accumulation and turnover of transposable element insertions, especially endogenous retroviruses.
Post-Translational Tubulin Modifications in Differentiated Human Neural Stem Cells
Authors: Knight V. Bleu , Jogalekar Manasi P. , Serrano Elba E.
Published: January 2022

The tubulin protein fulfills a variety of cellular functions that range from chromosomal separation to locomotion. Functional diversity is achieved through the expression of specific tubulin isotypes in different cell types or developmental time periods. Post-translational modifications (PTMs) of tubulin also are vital for specific intracellular tasks, such as binding and recruiting motor proteins. In neurons, the isotypic expression profile for tubulin is well characterized, and the importance of PTMs for proper neuronal function has gained recent attention due to their implication in neurodegenerative disorders. In contrast, the role of tubulin specializations in the specification of neural cell fate has received minimal attention and studies of tubulin PTMs and isotypes in neuroglia such as astrocytes are relatively few. To bridge this knowledge gap, we undertook an analysis of PTMs in neurons and astrocytes derived from the federally approved H9 hESC-derived human neural stem cell (hNSC) line. In hNSCs, basal cells can be directed to assume neural fate as neurons or astrocytes by specifying different media growth conditions. Immunocytochemical methods, fluorescent antibody probes, and confocal microscopy facilitated image acquisition of fluorescent signals from class III β-tubulin (βIII-tubulin), acetylated tubulin, and polyglutamylated tubulin. Fluorescent probe intensities were assessed with the ‘EBImage’ package for the statistical programming language R, and compared using Student’s t-tests. Qualitative analysis indicated that βIII-tubulin, acetylated tubulin, and polyglutamylated tubulin were expressed to some degree in basal hNSCs and their media-differentiated hNSC neuronal and astroglial progeny. In media-differentiated hNSC astrocyte progeny, quantification and statistical analysis of fluorescence probe intensity showed that acetylated tubulin/ βIII-tubulin ratios were greater than the ratio for polyglutamylated tubulin/ βIII-tubulin. These findings represent a snapshot of the dynamic and varied changes in the tubulin expression profile during the specification of neural cell fate. Results imply that investigations of tubulin PTMs have the potential to advance our understanding of the generation and regeneration of nervous tissue.
Apoplastic CBM1-interacting proteins bind conserved carbohydrate binding module 1 motifs in fungal hydrolases to counter pathogen invasion
Authors: Takeda Takumi , Takahashi Machiko , Shimizu Motoki , Sugihara Yu , Saitoh Hiromasa , Fujisaki Koki , Ishikawa Kazuya , Utsushi Hiroe , Kanzaki Eiko , Sakamoto Yuichi , Abe Akira , Terauchi Ryohei
Published: January 2022

When infecting plants, fungal pathogens secrete cell wall degrading enzymes (CWDEs) that break down cellulose and hemicellulose, the primary components of plant cell walls. Some fungal CWDEs contain a unique domain, named the carbohydrate binding module (CBM), that facilitates their access to polysaccharides. However, little is known about how plants counteract pathogen degradation of their cell walls. Here, we show that the rice cysteine-rich repeat secretion protein OsCBMIP binds to and inhibits xylanase MoCel10A of the blast fungus pathogen Magnaporthe oryzae, interfering with its access to the rice cell wall and degradation of rice xylan. We found binding of OsCBMIP to various CBM1-containing enzymes, suggesting it has a general role in inhibiting the catalytic activities of fungal enzymes. OsCBMIP is localized to the apoplast, and its expression is strongly induced in leaves infected with M. oryzae. Remarkably, knockdown of OsCBMIP reduced rice defense against M. oryzae, demonstrating that inhibition of CBM1-containing fungal enzymes by OsCBMIP is crucial for rice defense. We also identified additional CBMIP-related proteins from Arabidopsis thaliana and Setaria italica, indicating that a wide range of plants counteract pathogens through this mechanism.

Plants have evolved various activity-inhibiting proteins as a defense against fungal cell wall degrading enzymes (CWDEs), but how plants counteract the function of fungal enzymes containing carbohydrate binding modules (CBMs) remains unknown. Here, we demonstrate that OsCBMIP, a member of the cysteine-rich repeat secretion protein family, interacts with fungal CBM1. OsCBMIP binding to CBM1 of a blast fungal xylanase blocks access to cellulose, resulting in the inhibition of xylanase enzymatic activity. Our study provides significant insights into plant countermeasure against CWDEs in the apoplastic space during plant–fungal pathogen interactions. It also reveals a molecular function of the DUF26 domain widely distributed in plant proteins.
Adjunctive inhibition of the integrated stress response pathway accelerates bacterial clearance in a mouse model of tuberculosis
Authors: Krug Stefanie , Prasad Pankaj , Xiao Shiqi , Lun Shichun , Ruiz-Bedoya Camilo A. , Klunk Mariah , Ordonez Alvaro A. , Jain Sanjay K. , Srikrishna Geetha , Kramnik Igor , Bishai William R.
Published: January 2022

Tuberculosis (TB) is a devastating infectious disease that continues to cause millions of human deaths every year. Even though most cases of TB can be cured with a 6-month antibiotic combination therapy, these long treatment durations have led to the emergence of multi-drug resistance and pose a major hurdle to global TB control. Despite numerous advances in TB drug development, a substantially shortened treatment time has yet to be achieved. Given the rise in antibiotic resistance, an alternative strategy to the direct targeting of M. tuberculosis (M.tb) is the development of host-directed therapies (HDTs) that promote bacterial clearance and/or lung health when given adjunctive to standard TB antibiotics. We recently discovered that a small molecule inhibitor of the Integrated Stress Response (ISR), which is abnormally activated in TB and associated with the formation of necrotic granulomas, reduced M.tb numbers and lung inflammation in mice. Here, we evaluated the therapeutic potential of adjunctive ISR inhibition in the context of standard TB therapy. Throughout the course of treatment, ISR inhibition robustly lowered bacterial burdens compared to standard TB therapy alone and accelerated the time-to-sterility in mice, as demonstrated by significantly reduced relapse rates after 4 months of treatment. In addition, mice receiving adjunctive ISR inhibition tended to have reduced lung necrosis and inflammation. Together, our findings identify the ISR pathway as a promising therapeutic target with the potential of shortening TB treatment durations and improving lung health.
Liquid condensate is a common state of proteins and polypeptides at the regime of high intermolecular interactions
Authors: Poudyal Manisha , Patel Komal , Sawner Ajay Singh , Gadhe Laxmikant , Kadu Pradeep , Datta Debalina , Mukherjee Semanti , Ray Soumik , Navalkar Ambuja , Maiti Siddhartha , Chatterjee Debdeep , Bera Riya , Gahlot Nitisha , Padinhateeri Ranjith , Maji Samir K.
Published: January 2022

Liquid-liquid phase separation (LLPS) has emerged as a crucial biological mechanism for sequestering macromolecules (such as proteins and nucleic acids) into membraneless organelles in cells. Unstructured and intrinsically disordered domains are known to facilitate multivalent interactions driving protein LLPS. We hypothesized that LLPS could be an intrinsic property of proteins/polypeptides at their high intermolecular interaction regime. To examine this, we studied many (a total of 23) proteins/polypeptides with different structures and sequences for LLPS study using molecular crowder polyethylene glycol (PEG-8000). We showed that all proteins and even highly charged polypeptides (under study) can undergo liquid condensate formation, however with different phase space and conditions. Using a single component and combinations of protein multicomponent (co-LLPS) systems, we establish that a variety of intermolecular interactions can drive proteins/polypeptides LLPS.
Region-specific alterations of perineuronal net expression in postmortem autism brain tissue
Authors: Brandenburg Cheryl , Blatt Gene J.
Published: January 2022

Genetic variance in ASD is often associated with mechanisms that broadly fall into the category of neuroplasticity. Parvalbumin positive neurons and their surrounding perineuronal nets (PNNs) are important factors in critical period plasticity and have both been implicated in ASD. PNNs are found in high density within output structures of the cerebellum and basal ganglia, two regions that are densely connected to many other brain areas and have the potential to participate in the diverse array of symptoms present in an ASD diagnosis. The dentate nucleus and globus pallidus were therefore assessed for differences in PNN expression in human postmortem ASD brain tissue. While Purkinje cell loss is a consistent neuropathological finding in ASD, in this cohort, the Purkinje cell targets within the dentate nucleus did not show differences in number of cells with or without a PNN. However, the density of parvalbumin positive neurons with a PNN were significantly reduced in the globus pallidus internus and externus of ASD cases, which was not dependent on seizure status. It is unclear whether these alterations manifest during development or are a consequence of activity-dependent mechanisms that lead to altered network dynamics later in life.
Isoforms of the transcriptional cofactor SIN3 differentially regulate genes necessary for energy metabolism and cell survival
Authors: Mitra Anindita , Vo Linh , Soukar Imad , Chaubal Ashlesha , Greenberg Miriam L. , Pile Lori A.
Published: January 2022

The SIN3 scaffolding protein is a conserved transcriptional regulator known to fine-tune gene expression. In Drosophila, there are two major isoforms of SIN3, SIN3 220 and SIN3 187, which each assemble into multi-subunit histone modifying complexes. The isoforms have distinct developmental expression patterns and non-redundant functions. Gene regulatory network analyses indicate that both isoforms affect genes encoding proteins in pathways such as the cell cycle and cell morphogenesis. Interestingly, the SIN3 187 isoform uniquely regulates a subset of pathways including post-embryonic development, phosphate metabolism and apoptosis. Target genes in the phosphate metabolism pathway include nuclear-encoded mitochondrial genes coding for proteins responsible for oxidative phosphorylation. Here, we investigate the physiological effects of SIN3 isoforms on energy metabolism and cell survival. We find that ectopic expression of SIN3 187 represses expression of several nuclear-encoded mitochondrial genes affecting production of ATP and generation of reactive oxygen species (ROS). Forced expression of SIN3 187 also activates several pro-apoptotic and represses a few anti-apoptotic genes. In the SIN3 187 expressing cells, these gene expression patterns are accompanied with an increased sensitivity to paraquat-mediated oxidative stress. These findings indicate that SIN3 187 influences the regulation of mitochondrial function, apoptosis and oxidative stress response in ways that are dissimilar from SIN3 220. The data suggest that the distinct SIN3 histone modifying complexes are deployed in different cellular contexts to maintain homeostasis.
Interplay between LHCSR proteins and state transitions governs the NPQ response in intact cells of Chlamydomonas during light fluctuations
Authors: Steen Collin J. , Burlacot Adrien , Short Audrey H. , Niyogi Krishna K. , Fleming Graham R.
Published: January 2022

Photosynthetic organisms use sunlight as the primary energy source to fix CO2. However, in the environment, light energy fluctuates rapidly and often exceeds saturating levels for periods ranging from seconds to hours, which can lead to detrimental effects for cells. Safe dissipation of excess light energy occurs primarily by non-photochemical quenching (NPQ) processes. In the model green microalga Chlamydomonas reinhardtii, photoprotective NPQ is mostly mediated by pH-sensing light-harvesting complex stress-related (LHCSR) proteins and the redistribution of light-harvesting antenna proteins between the photosystems (state transition). Although each component underlying NPQ has been documented, their relative contributions to the dynamic functioning of NPQ under fluctuating light conditions remains unknown. Here, by monitoring NPQ throughout multiple high light-dark cycles with fluctuation periods ranging from 1 to 10 minutes, we show that the dynamics of NPQ depend on the frequency of light fluctuations. Mutants impaired in the accumulation of LHCSRs (npq4, lhcsr1, and npq4lhcsr1) showed significantly less quenching during illumination, demonstrating that LHCSR proteins are responsible for the majority of NPQ during repetitive exposure to high light fluctuations. Activation of NPQ was also observed during the dark phases of light fluctuations, and this was exacerbated in mutants lacking LHCSRs. By analyzing 77K chlorophyll fluorescence spectra and chlorophyll fluorescence lifetimes and yields in a mutant impaired in state transition, we show that this phenomenon arises from state transition. Finally, we quantified the contributions of LHCSRs and state transition to the overall NPQ amplitude and dynamics for all light periods tested and show that both processes interact to facilitate NPQ during light fluctuations. We further assess the role of LHCSRs in cell growth under various periods of fluctuating light. These results highlight the dynamic functioning of photoprotection under light fluctuations and open a new way to systematically characterize the photosynthetic response to an ever-changing light environment.

One sentence summary

The roles of LHCSR and STT7 in NPQ vary with the light fluctuation period and duration of light fluctuation.
High Speed Visual Insect Swarm Tracker (Hi-VISTA) used to identify the effects of confinement on individual insect flight
Authors: Ahmed Ishriak , Faruque Imraan A.
Published: January 2022

Individual insects flying in crowded assemblies perform complex aerial maneuvers by sensing and feeding back neighbor measurements to small changes in their wing motions. To understand the individual feedback rules that permit these fast, adaptive behaviors in group flight, a high-speed tracking system is needed capable of tracking both body motions and more subtle wing motion changes for multiple insects in simultaneous flight. This capability extends tracking beyond the previous focus on individual insects to multiple insects. This paper presents Hi-VISTA, which provides a capability to track wing and body motions of multiple insects using high speed cameras (9000 fps). Processing steps consist of automatic background identification, data association, hull reconstruction, segmentation, and feature measurement. To improve the biological relevance of laboratory experiments and develop a platform for interaction studies, this paper applies the Hi-VISTA measurement system toApis melliferaforagers habituated to transit flights through a transparent tunnel. Binary statistical analysis (Welch’s t-test, Cohen’s d effect size) of 95 flight trajectories is presented, quantifying the differences between flights in an unobstructed tunnel and in a confined tunnel volume. The results indicate that body pitch angle, heading rate, flapping frequency, and vertical speed (heave) are all affected by confinement, and other flight variables show minor or statistically insignificant changes. These results form a baseline as swarm tracking and analysis begins to isolate the effects of neighbors from environment.
Abnormal larval neuromuscular junction morphology and physiology in Drosophila Prickle isoform mutants with defective axonal transport and adult seizure behavior
Authors: O’Harrow Tristan , Ueda Atsushi , Xing Xiaomin , Ehaideb Salleh , Manak J. Robert , Wu Chun-Fang
Published: January 2022

Previous studies have demonstrated that mutations of the Drosophila planar cell polarity gene prickle (pk) result in altered microtubule-mediated vesicular transport in larval motor axons, as well as adult neuronal circuit hyperexcitability and epileptic behavior. It is also known that mutant alleles of the prickle-prickle (pkpk) and prickle-spiny-legs (pksple) isoforms differ in phenotype but display isoform counterbalancing effects in heteroallelic pkpk/pksple flies to ameliorate adult motor circuit and behavioral hyperexcitability. We have further investigated the larval neuromuscular junction (NMJ) and uncovered robust phenotypes in both pkpk and pksple alleles (heretofore referred to as pk and sple alleles, respectively), including synaptic terminal overgrowth, as well as irregular motor axon terminal excitability, poor vesicle release synchronicity, and altered efficacy of synaptic transmission. We observed significant increase in whole-cell excitatory junctional potential (EJP) in pk homozygotes, which was restored to near WT level in pk/sple heterozygotes. We further examined motor terminal excitability sustained by presynaptic Ca2+ channels, under the condition of pharmacological blockade of Na+ and K+ channel function. Such manipulation revealed extreme Ca2+ channel-dependent nerve terminal excitability in both pk and sple mutants. However, when combined in pk/sple heterozygotes, such terminal hyper-excitability was restored to nearly normal. Focal recording from individual synaptic boutons revealed asynchronous vesicle release in both pk and sple homozygotes, which nevertheless persisted in pk/sple heterozygotes without indications of isoform counter-balancing effects. Similarly, the overgrowth at NMJs was not compensated in pk/sple heterozygotes, exhibiting an extremity comparable to that in pk and sple homozygotes. Our observations uncovered differential roles of the pk and sple isoforms and their distinct interactions in the various structural and functional aspects of the larval NMJ and adult neural circuits.
Correlative cryogenic montage electron tomography for comprehensive in-situ whole-cell structural studies
Authors: Yang Jie E. , Larson Matthew R. , Sibert Bryan S. , Kim Joseph Y. , Parrell Daniel , Sanchez Juan C. , Pappas Victoria , Kumar Anil , Cai Kai , Thompson Keith , Wright Elizabeth R.
Published: January 2022

Imaging large fields of view while preserving high-resolution structural information remains a challenge in low-dose cryo-electron tomography. Here, we present robust tools for montage electron tomography tailored for vitrified specimens. The integration of correlative cryo-fluorescence microscopy, focused-ion beam milling, and micropatterning produces contextual three-dimensional architecture of cells. Montage tilt series may be processed in their entirety or as individual tiles suitable for sub-tomogram averaging, enabling efficient data processing and analysis.
Structure determination of protein-peptide complexes from NMR chemical shift data using MELD
Authors: Mondal Arup , Swapna G.V.T. , Hao Jingzhou , Ma LiChung , Roth Monica J. , Montelione Gaetano T. , Perez Alberto
Published: January 2022

Intrinsically disordered regions of proteins often mediate important protein-protein interactions. However, the folding upon binding nature of many polypeptide-protein interactions limits the ability of modeling tools to predict structures of such complexes. To address this problem, we have taken a tandem approach combining NMR chemical shift data and molecular simulations to determine structures of peptide-protein complexes. Here, we demonstrate this approach for polypeptide complexes formed with the extraterminal (ET) domain of bromo and extraterminal domain (BET) proteins, which exhibit a high degree of binding plasticity. This system is particularly challenging as the binding process includes allosteric changes across the ET receptor upon binding, and the polypeptide binding partners can form different conformations (e.g., helices and hairpins) in the complex. In a blind study, the new approach successfully modeled bound-state conformations and binding poses, using only backbone chemical shift data, in excellent agreement with experimentally-determined structures. The approach also predicts relative binding affinities of different peptides. This hybrid MELD-NMR approach provides a powerful new tool for structural analysis of protein-polypeptide complexes in the low NMR information content regime, which can be used successfully for flexible systems where one polypeptide binding partner folds upon complex formation.
SpotLink enables sensitive and precise identification of site non-specific cross-links at the proteome scale
Authors: Zhang Weijie , Gong Pengyun , Shan Yichu , Zhao Lili , Hu Hongke , Wei Qiushi , Liang Zhen , Liu Chao , Zhang Lihua , Zhang Yukui
Published: January 2022

We developed SpotLink software for identifying site non-specific cross-links at the proteome scale. Contributed by the dual pointer dynamic pruning (DPDP) algorithm and the quality control of cross-linking sites, SpotLink identified more than 3000 cross-links from human proteome database with rich site information in a few days. We demonstrated that SpotLink outperformed other approaches in terms of sensitivity and precision on a simulated dataset and a protein complexes dataset with known structures. Additionally, we discovered some valuable protein-protein interaction (PPI) information contained in the protein complexes dataset and HeLa dataset, indicating the unique identification advantages of site non-specific cross-linking. The excellent performance of SpotLink will increase the usage of site non-specific cross-linking in the near future. SpotLink is publicly available on GitHub [https://github.com/DICP1810/SpotLink].
Pachytene karyotypes of 17 species of birds
Authors: Slobodchikova Anastasia Y. , Malinovskaya Lyubov P. , Grishko Ekaterina O. , Pristyazhnyuk Inna E. , Torgasheva Anna A. , Borodin Pavel M.
Published: January 2022

Karyotypes of less than 10% of bird species are known. Using immunolocalization of the synaptonemal complex, the core structure of meiotic chromosomes at the pachytene stage, and centromere proteins we described male pachytene karyotypes of seventeen species of birds. This method enables higher resolution than the conventional analyses of metaphase chromosomes. We provided the first descriptions of the karyotypes of three species (Rook, Blyth’s reed warbler and European pied flycatcher), corrected the published data on the karyotypes of ten species and confirmed them for four species. All passerine species examined have highly conservative karyotypes, 2n=80-82 with seven pairs of macrochromosomes and 33-34 pairs of microchromosomes. In all of them but not in the Common cuckoo we revealed single copies of the germline restricted chromosomes varying in size and morphology even between closely related species. This indicates a fast evolution of this additional chromosome. The interspecies differences concern the sizes of the macrochromosomes, morphology of the microchromosomes and sizes of the centromeres. The pachytene cells of the Gouldian finch, Brambling and Common linnet contained heteromorphic synaptonemal complexes indicating heterozygosity for inversions or centromere shifts. The European pied flycatcher, Gouldian finch and Domestic canary have extended centromeres in several macro- and microchromosomes.
Concerted expansion and contraction of immune receptor gene repertoires in plant genomes
Authors: Man Ngou Bruno Pok , Heal Robert , Wyler Michele , Schmid Marc W , Jones Jonathan DG
Published: January 2022

Recent reports suggest that cell-surface and intracellular immune receptors function synergistically to activate robust defence against pathogens, but whether or not they co-evolve is unclear. Here we determined the copy numbers of cell-surface and intracellular immune receptors in 208 species. Surprisingly, these receptor gene families contract and/or expand together in plant genomes, suggesting the mutual potentiation of immunity initiated by cell-surface and intracellular receptors is reflected in the concerted co-evolution of the size of their repertoires across plant species.
A simple island biodiversity model is robust to trait dependence in diversification and colonization rates
Authors: Xie Shu , Valente Luis , Etienne Rampal S.
Published: January 2022

The application of state-dependent speciation and extinction (SSE) models to phylogenetic trees has revealed an important role for traits in diversification. However, this role remains comparatively unexplored on islands, which can include multiple independent clades resulting from different colonization events. Here, we perform a robustness study to identify how trait-dependence in rates of island colonization, extinction and speciation (CES rates) affects the estimation accuracy of a phylogenetic model that assumes no rate variation between trait states. We extend the DAISIE (Dynamic Assembly of Islands through Speciation, Immigration and Extinction) simulation model to include state-dependent rates, and evaluate the robustness of the DAISIE inference model using simulated data. Our results show that when the CES rate differences between trait states are moderate, DAISIE shows negligible error for a variety of island diversity metrics. However, for large differences in speciation rates, we find large errors when reconstructing clade size variation and non-endemic species diversity through time. We conclude that for many biologically realistic scenarios with trait-dependent speciation and colonization, island diversity dynamics can be accurately estimated without the need to explicitly model trait dynamics. Nonetheless, our new simulation model may provide a useful tool for studying patterns of trait variation.
oca2targeting using CRISPR/Cas9 in the Malawi cichlidAstatotilapia calliptera
Authors: Clark Bethan , Elkin Joel , Marconi Aleksandra , Turner George F. , Smith Alan M. , Joyce Domino , Miska Eric A. , Juntti Scott A. , Santos M. Emília
Published: January 2022

Identifying genetic loci underlying trait variation provides insights into the mechanisms of diversification, but demonstrating causality and characterising the role of genetic loci requires testing candidate gene function, often in non-model species. Here we establish CRISPR/Cas9 editing inAstatotilapia calliptera, a generalist cichlid of the remarkably diverse Lake Malawi radiation. By targeting the geneoca2required for melanin synthesis in other vertebrate species, we show efficient editing and germline transmission. Gene edits include indels in the coding region, likely a result of non-homologous end joining, and a large deletion in the 3′ UTR due to homology-directed repair. We find thatoca2knock-outA. callipteralack melanin, which may be useful for developmental imaging in embryos and studying colour pattern formation in adults. AsA. callipteraresembles the presumed generalist ancestor of the Lake Malawi cichlids radiation, establishing genome editing in this species will facilitate investigating speciation, adaptation and trait diversification in this textbook radiation.