bluuebunny/crossref_metadata_2025 huggingface dataset:
Interrogating COVID-19 Vaccine Hesitancy in the Philippines with a Nationwide Open-Access Online Survey
Authors: Caple Alexandria , Dimaano Arnie O. , Sagolili Marc Martin C. , Uy April Anne M. , Aguirre Panjee Mariel G. , Alano Dean Lotus C. , Camaya Giselle Sophia M. , Ciriaco Brent John A. , Clavo Princess Jerah S. , Cuyugan Dominic G. , Fermo Cleinne Florence Geeseler V. , Lanete Paul Jeremy C. , La Torre Ardwayne Jurel D. , Loteyro Thomas Albert T. , Lua Raisa Mikaela , Manansala Nicole Gayle R. , Mosquito Raphael Willard M. , Octaviano Alexa Marie C. , Orfanel Alexandra Erika T. , Pascual Gheyanna Merly U. , Sale Aubrey Joy S. , Tendenilla Sophia Lorraine S. , Trinidad Maria Sofia Lauren R. , Trinidad Nicole Jan S. , Verano Daphne Louise V. , Austriaco Nicanor
Published: September 2021

To mitigate the unprecedented health, social, and economic damage of COVID-19, the Philippines is undertaking a nationwide vaccination program to mitigate the effects of the global pandemic. In this study, we interrogated COVID-19 vaccine hesitancy in the country by deploying a nationwide open-access online survey, two months before the rollout of the national vaccination program. The Health Belief Model (HBM) posits that people are likely to adopt disease prevention behaviors and to accept medical interventions like vaccines if there is sufficient motivation and cues to action. A majority of our 7,193 respondents (62.5%) indicated that they were willing to be vaccinated against COVID-19. Moreover, multivariable analysis revealed that HBM constructs were associated with vaccination intention in the Philippines. Perceptions of high susceptibility, high severity, and significant benefits were all good predictors for vaccination intent. We also found that external cues to action were important. Large majorities of our respondents would only receive the COVID-19 vaccines after many others had received it (72.8%) or after politicians had received it (68.2%). Finally, our study revealed that most (21%) were willing to pay an amount of PHP1,000 [USD20] for the COVID-19 vaccines with an average willing-to-pay amount of PHP1,892 [USD38].
Early life predictors of late life cerebral small vessel disease in four prospective cohort studies
Authors: Backhouse Ellen V , Shenkin Susan D , McIntosh Andrew M , Bastin Mark E , Whalley Heather C , Hernandez Maria Valdez , Maniega Susana Muñoz , Harris Mat , Stolicyn Aleks , Campbell Archie , Steele Douglas , Waiter Gordon D , Sandu Anca-Larisa , Waymont Jennifer MJ , Murray Alison D , Cox Simon R , de Rooij Susanne R. , Roseboom Tessa J. , Wardlaw Joanna M
Published: September 2021

Development of cerebral small vessel disease, a major cause of stroke and dementia, may be influenced by early life factors. It is unclear whether these relationships are independent of each other, of adult socioeconomic status or of vascular risk factor exposures.

We examined associations between factors from birth (ponderal index, birth weight), childhood (IQ, education, socioeconomic status), adult small vessel disease, and brain volumes, using data from four prospective cohort studies: STratifying Resilience And Depression Longitudinally (STRADL) (n=1080; mean age=59 years); The Dutch Famine Birth cohort (n=118; mean age=68 years); the Lothian Birth Cohort 1936 (LBC1936; n=617; mean age=73 years), and the Simpson’s cohort (n=110; mean age=78 years). We analysed each small vessel disease feature individually and summed to give a total small vessel disease score (range 1-4) in each cohort separately, then in meta-analysis, adjusted for vascular risk factors and adult socioeconomic status.

Higher birth weight was associated with fewer lacunes (OR per 100g, 0.93 95%CI=0.88-0.99), fewer infarcts (OR=0.94 95%CI=0.89-0.99), and fewer perivascular spaces (OR=0.95 95%CI=0.91-0.99). Higher childhood IQ was associated with lower white matter hyperintensity burden (OR per IQ point=0.99 95%CI 0.98-0.998), fewer infarcts (OR=0.98, 95%CI=0.97-0.998), fewer lacunes (OR=0.98, 95%CI=0.97-0.999), and lower total small vessel disease burden (OR=0.98, 95%CI=0.96-0.999). Low education was associated with more microbleeds (OR=1.90 95%CI=1.33-2.72) and lower total brain volume (MD=-178.86cm3, 95%CI=-325.07- -32.66). Low childhood socioeconomic status was associated with fewer lacunes (OR=0.62, 95%CI=0.40-0.95).

Early life factors are associated with worse small vessel disease in later life, independent of each other, vascular risk factors and adult socioeconomic status. Risk for small vessel disease may originate in early life and provide a mechanistic link between early life factors and risk of stroke and dementia. Policies investing in early child development may contribute to improve lifelong brain health to prevent dementia and stroke in older age.
Efficacy of two doses of COVID-19 vaccine against severe COVID-19 in those with risk conditions and residual risk to the clinically extremely vulnerable: the REACT-SCOT case-control study
Authors: McKeigue Paul M , McAllister David A , Robertson Chris , Hutchinson Sharon , McGurnaghan Stuart , Stockton Diane , Colhoun Helen M ,   for the PHS COVID-19 Epidemiology and Research Cell
Published: September 2021

Objectives

To determine whether COVID-19 efficacy varies with clinical risk category and to investigate risk factors for severe COVID-19 in those who have received two doses of vaccine.

Design

Matched case-control study (REACT-SCOT).

Setting

Population of Scotland from 1 December 2020 to 8 September 2021.

Main outcome measure

Severe COVID-19, defined as cases with entry to critical care or fatal outcome.

Results

Efficacy against severe COVID-19 of two doses of vaccine was 94% (95 percent CI 93% to 96%) in those without designated risk conditions, 89% (95 percent CI 86% to 91%) in those with moderate risk conditions, but only 73% (95 percent CI 64% to 79%) in those designated as clinically extremely vulnerable (CEV) and eligible for shielding. Of the 641 cases of severe COVID-19 in double-vaccinated individuals, 47% had moderate risk conditions and 38% were CEV. In the double-vaccinated CEV group, the rate ratio for severe disease (with no risk condition as reference category) was highest in solid organ transplants at 101 (95% CI 47 to 214) but even in this subgroup the absolute risk of severe COVID-19 was low (35 cases in 23678 person-months of follow-up).

Conclusions

Two doses of vaccine protect against severe COVID-19 in CEV individuals but the residual risk in double-vaccinated individuals remains far higher in those who are CEV than in those who are not. These results lay a basis for determining eligibility for additional measures including passive immunization to protect those at highest risk.
Visual Processing During the Interictal Period Between Migraines: A Meta-Analysis
Authors: Sezai Timucin , Nguyen Vinh , Riddell Nina , Murphy Melanie J. , Crewther Sheila G.
Published: September 2021

Migraine is a poorly understood neurological disorder and a leading cause of disability in young adults. Migraines are characterized by severe pulsating unilateral headache and visual symptoms. Whether visual function is also impaired in the interictal period between migraines remains controversial. Thus, this meta-analysis investigated the evidence for altered visual function as measured electrophysiologically via pattern-reversal visual evoked potential (VEP) amplitudes and habituation in adult migraineurs with or without visual aura and control in the interictal period. Twenty-three studies were selected for random effects meta-analysis, demonstrating slightly diminished VEP amplitudes and substantially reduced habituation in the early P100 component in migraineurs without aura and with aura compared to controls. No differences were found between migraineurs with and without aura. Although heterogeneity between studies and insufficient published data for VEP latencies and the earlier N75 VEP component data was observed and require further testing, P100 anomalies may indicate abnormal functioning of the fast-conducting magnocellular visual pathway, in episodic migraineurs.
The Paradox of the Plankton: Coexistence of Structured Microbial Communities
Authors: Scarampi Alberto
Published: September 2021

In the framework of resource-competition models, it has been argued that the number of species stably coexisting in an ecosystem cannot exceed the number of shared resources. However, plankton seems to be an exception of this so-called “competitive-exclusion principle”. In planktic ecosystems, a large number of different species stably coexist in an environment with limited resources. This contradiction between theoretical expectations and empirical observations is often referred to as “The Paradox of the Plankton”. This project aims to investigate biophysical models that can account for the large biodiversity observed in real ecosystems in order to resolve this paradox. A model is proposed that combines classical resource competition models, metabolic trade-offs and stochastic ecosystem assembly. Simulations of the model match empirical observations, while relaxing some unrealistic assumptions from previous models.

Paradox: from Greek para: “distinct from”, and doxa: opinion. Sainsbury (1995) defines a paradox as “an apparently unacceptable conclusion derived by apparently acceptable reasoning from apparently acceptable premises”. Paradoxes are useful research tools as they suggest logical inconsistencies. In order to spot the flaw, the validity of all the premises has to be carefully assessed.

Plankton: refers to the collection of organisms that spend part or all of their lives in suspension in water (Reynolds 2006). Plankton, or plankters, are “organisms that have velocities significantly smaller than oceanic currents and thus are considered to travel with the water parcel they occupy” (Lombard et al. 2019). Phytoplankters refer to the members of the plankton that perform photosynthesis.
Installation and imaging of thousands of minirhizotrons to phenotype root systems of field-grown plants
Authors: Rajurkar Ashish B. , McCoy Scott M. , Ruhter Jeremy , Mulcrone Jessica , Freyfogle Luke , Leakey Andrew D. B.
Published: September 2021

Background

Roots are vital to plant performance because they acquire resources from the soil and provide anchorage. However, it remains difficult to assess root system size and distribution because roots are inaccessible in the soil. Existing methods to phenotype entire root systems range from slow, often destructive, methods applied to relatively small numbers of plants in the field to rapid methods that can be applied to large numbers of plants in controlled environment conditions. Much has been learned recently by extensive sampling of the root crown portion of field-grown plants. But, information on large-scale genetic and environmental variation in the size and distribution of root systems in the field remains a key knowledge gap. Minirhizotrons are the only established, non-destructive technology that can address this need in a standard field trial. Prior experiments have used only modest numbers of minirhizotrons, which has limited testing to small numbers of genotypes or environmental conditions. This study addressed the need for methods to install and collect images from thousands of minirhizotrons and thereby help break the phenotyping bottleneck in the field.

Results

Over three growing seasons, methods were developed and refined to install and collect images from up to3038 minirhizotrons per experiment. Modifications were made to four tractors and hydraulic soil corers mounted to them. High quality installation was achieved at an average rate of up to 84.4 minirhizotron tubes per tractor per day. A set of four commercially available minirhizotron camera systems were each transported by wheelbarrow to allow collection of images of mature maize root systems at an average rate of up to 65.3 tubes per day per camera. This resulted in over 300,000 images being collected in as little as 11 days for a single experiment.

Conclusion

The scale of minirhizotron installation was increased by two orders of magnitude by simultaneously using four tractor-mounted, hydraulic soil corers with modifications to ensure high quality, rapid operation. Image collection can be achieved at the corresponding scale using commercially available minirhizotron camera systems. Along with recent advances in image analysis, these advances will allow use of minirhizotrons at unprecedented scale to address key knowledge gaps regarding genetic and environmental effects on root system size and distribution in the field.
Genome-wide association mapping within a single Arabidopsis thaliana population reveals a richer genetic architecture for defensive metabolite diversity
Authors: Gloss Andrew D. , Vergnol Amélie , Morton Timothy C. , Laurin Peter J. , Roux Fabrice , Bergelson Joy
Published: September 2021

A paradoxical finding from genome-wide association studies (GWAS) in plants is that variation in metabolite profiles typically maps to a small number of loci, despite the complexity of underlying biosynthetic pathways. This discrepancy may partially arise from limitations presented by geographically diverse mapping panels. Properties of metabolic pathways that impede GWAS by diluting the additive effect of a causal variant, such as allelic and genic heterogeneity and epistasis, would be expected to increase in severity with the geographic range of the mapping panel. We hypothesized that a population from a single locality would reveal an expanded set of associated loci. We tested this in a French Arabidopsis thaliana population (< 1 km transect) by profiling and conducting GWAS for glucosinolates, a suite of defensive metabolites that have been studied in depth through functional and genetic mapping approaches. For two distinct classes of glucosinolates, we discovered more associations at biosynthetic loci than previous GWAS with continental-scale mapping panels. Candidate genes underlying novel associations were supported by concordance between their observed effects in the TOU-A population and previous functional genetic and biochemical characterization. Local populations complement geographically diverse mapping panels to reveal a more complete genetic architecture for metabolic traits.
Quantitative measurement of antibiotic resistance in Mycobacterium tuberculosis reveals genetic determinants of resistance and susceptibility in a target gene approach
Authors:   The CRyPTIC Consortium, Carter Joshua J
Published: September 2021

The World Health Organization goal of universal drug susceptibility testing for patients with tuberculosis is most likely to be achieved through molecular diagnostics; however, to date these have focused largely on first-line drugs, and always on predicting binary susceptibilities. Here, we used whole genome sequencing and a quantitative microtiter plate assay to relate genomic mutations to minimum inhibitory concentration in 15,211 Mycobacterium tuberculosis patient isolates from 27 countries across five continents.

This work identifies 449 unique MIC-elevating genetic determinants across thirteen drugs, as well as 91 mutations resulting in hypersensitivity for eleven drugs. Our results provide a guide for further implementation of personalized medicine for the treatment of tuberculosis using genetics-based diagnostics and can serve as a training set for novel approaches to predict drug resistance.
Land use change through the lens of macroecology: insights from Azorean arthropods and the Maximum Entropy Theory of Ecology
Authors: Brush Micah , Matthews Thomas J. , Borges Paulo A.V. , Harte John
Published: September 2021

Human activity and land management practices, in particular land use change, have resulted in the global loss of biodiversity. These types of disturbance affect the shape of macroecological patterns, and therefore analyzing these patterns can provide insights into how ecosystems are affected by land use change. We here use arthropod census data from 96 sites at Terceira Island in the Azores archipelago across four different land uses of increasing management intensity: native forest, exotic forest, semi-natural pasture, and intensive pasture, to examine the effects of land use type on three macroecological patterns: the species abundance distribution, the metabolic rate distribution of individuals, and the species–area relationship. The Maximum Entropy Theory of Ecology (METE) has successfully predicted these patterns across habitats and taxa in undisturbed ecosystems, and thus provides a null expectation for their shapes. Across these patterns, we find that the forest habitats are the best fit by METE predictions, while the semi-natural pasture is consistently the worst fit, and the intensive pasture is intermediately well fit. We show that the direction of failure of the METE predictions at the pasture sites is likely due to the hyper-dominance of introduced spider species present there. We hypothesize that the particularly poor fit for the semi-natural pasture is due to the mix of arthropod communities out of equilibrium, leading to greater heterogeneity in composition and complex dynamics that violate METE’s assumption of static state variables. The comparative better fit for the intensive pasture plausibly results from more homogeneous arthropod communities that are well adapted to intensive management, and thus whose state variables are less in flux. Analyzing deviations from theoretical predictions across land use type provides useful information about how land use and disturbance affect ecosystems, and such comparisons could be useful across other habitats and taxa.
Bacterial composition reflects fine-scale salinity changes while phylogenetic diversity exhibits a strong salt divide
Authors: Peralta Ariane L. , Muscarella Mario E. , Stucy Alexandra , Werba Jo A. , McCoy Michael W.
Published: September 2021

Climate change induced salinization events are predicted to intensify and lead to increased salt stress in freshwater aquatic ecosystems. As a consequence, formerly distinct abiotic conditions and associated biotic communities merge, and the emergence, loss, and persistence of microbial taxa modify the types and rates of ecosystem processes. This study examined how bacterial taxonomic and phylogenetic diversity and ecosystem function respond to acute salinization events where freshwater and estuarine communities and environments coalesce. We hypothesized that when the salinity change outpaces microbial adaptation or saline microbial populations are not yet established in formerly freshwater conditions, then these aquatic communities will exhibit diminished carbon cycling rates, decreased microbial diversity, and altered composition of microbial communities compared to historically freshwater communities. We used an experimental mesocosm approach to determine how salinity and the merging of distinct communities influenced resultant bacterial community structure and function. Each mesocosm represented different salinities (0, 5, 9, 13 psu). Two dispersal treatments, representing aquatic communities sourced from brackish 13 psu ponds and a mix of 13 psu and freshwater ponds, were added to all salinity levels and replicated four times. Results revealed that salinity, but not dispersal, decreased bacterial taxonomic and phylogenetic diversity. Carbon mineralization rates were highest in freshwater conditions and associated to bacterial taxa represented in low relative abundance. Acute salinity changes, such as localized flooding due to storm surge, will more negatively affect freshwater aquatic communities compared to chronic exposure to salinization where the communities have had time to adapt or turnover.

IMPORTANCE STATEMENT

Climate change induced salinization results in the mixing of formerly distinct environmental conditions and aquatic communities. This study examined the consequence of short-term, acute salinity stress on aquatic bacterial taxonomic and phylogenetic diversity and ecosystem function using an experimental approach. Results revealed that salinity, but not the source of aquatic communities, decreased bacterial taxonomic and phylogenetic diversity. Carbon mineralization rates, which represented ecosystem function, were highest in freshwater conditions and also associated with indicator bacterial taxa in low abundance relative to the total microbial community. Taken together, acute salinity changes will more negatively affect freshwater aquatic communities compared to chronic exposure to salinization where the communities have had time to adapt or turnover resulting in recovered biogeochemical functions.
3D Microenvironment-Specific Mechanosensing Regulates Neural Stem Cell Lineage Commitment
Authors: Baek Jieung , Lopez Paola A. , Lee Sangmin , Kim Taek-Soo , Kumar Sanjay , Schaffer David V.
Published: September 2021

While extracellular matrix (ECM) mechanics strongly regulate stem cell commitment, the field’s mechanistic understanding of this phenomenon largely derives from simplified two-dimensional (2D) culture substrates. Here we found a three-dimensional (3D) matrix-specific mechanoresponsive mechanism for neural stem cell (NSC) differentiation. NSC lineage commitment in 3D is maximally stiffness-sensitive in the range of 0.1-1.2 kPa, a narrower and more brain-mimetic range than we had previously identified in 2D (0.75 – 75 kPa). Transcriptomics revealed stiffness-dependent upregulation of early growth response 1 (Egr1) in 3D but not in 2D. Egr1 knockdown enhanced neurogenesis in stiff ECMs by driving β-catenin nuclear localization and activity in 3D, but not in 2D. Mechanical modeling and experimental studies under osmotic pressure indicate that stiff 3D ECMs are likely to stimulate Egr1 via increases in confining stress during cell volumetric growth. To our knowledge, Egr1 represents the first 3D-specific stem cell mechanoregulatory factor.
Evolution of degrees of carnivory and dietary specialization across Mammalia and their effects on speciation
Authors: Pollard Matthew D. , Puckett Emily E.
Published: September 2021

Abstract

Conflation between omnivory and dietary generalism limits ecological and evolutionary analyses of diet, including estimating contributions to speciation and diversification. Additionally, categorizing species into qualitative dietary classes leads to information loss in these analyses. Here, we constructed two continuous variables – degree of carnivory (i.e., the position along the continuum from complete herbivory to complete carnivory) and degree of dietary specialization (i.e., the number and variety of food resources utilized) – to elucidate their histories across Mammalia, and to tease out their independent contributions to mammalian speciation. We observed that degree of carnivory significantly affected speciation rate across Mammalia, whereas dietary specialization did not. We further considered phylogenetic level in diet-dependent speciation and saw that degree of carnivory significantly affected speciation in ungulates, carnivorans, bats, eulipotyphlans, and marsupials, while the effect of dietary specialization was only significant in carnivorans. Across Mammalia, omnivores had the lowest speciation rates. Our analyses using two different categorical diet variables led to contrasting signals of diet-dependent diversification, and subsequently different conclusions regarding diet’s macroevolutionary role. We argue that treating variables such as diet as continuous instead of categorical reduces information loss and avoids the problem of contrasting macroevolutionary signals caused by differential discretization of biologically continuous traits.
Non-enzymatic assembly of active chimeric ribozymes from aminoacylated RNA oligonucleotides
Authors: Radakovic Aleksandar , DasGupta Saurja , Wright Tom H. , Aitken Harry R.M. , Szostak Jack W.
Published: September 2021

Aminoacylated tRNAs, which harbor a covalent linkage between amino acids and RNA, are a universally conserved feature of life. Because they are essential substrates for ribosomal translation, aminoacylated oligonucleotides must have been present in the RNA World prior to the evolution of the ribosome. One possibility we are exploring is that the aminoacyl ester linkage served another function before being recruited for ribosomal protein synthesis. The nonenzymatic assembly of ribozymes from short RNA oligomers under realistic conditions remains a key challenge in demonstrating a plausible pathway from prebiotic chemistry to the RNA World. Here, we show that aminoacylated RNAs can undergo template-directed assembly into chimeric amino acid-RNA polymers that are active ribozymes. We demonstrate that such chimeric polymers can retain the enzymatic function of their all-RNA counterparts by generating chimeric hammerhead, RNA ligase, and aminoacyl transferase ribozymes. Amino acids with diverse side chains form linkages that are well tolerated within the RNA backbone, potentially bringing novel functionalities to ribozyme catalysis. Our work suggests that aminoacylation chemistry may have played a role in primordial ribozyme assembly. Increasing the efficiency of this process provides an evolutionary rationale for the emergence of sequence and amino acid specific aminoacyl-RNA synthetase ribozymes, which could then have generated the substrates for ribosomal protein synthesis.

Significance Statement

The emergence of the primordial ribosome from the RNA World would have required access to aminoacylated RNA substrates. The spontaneous generation of such substrates without enzymes is inefficient, and it remains unclear how they could be selected for in a prebiotic milieu. In our study we identify a role for aminoacylated RNA in ribozyme assembly, a longstanding problem in the origin of life research. We show that aminoacylated RNAs, but not unmodified RNAs, rapidly assemble into chimeric amino acid-bridged ribozymes that retain their native enzymatic activity. Our work therefore addresses two key challenges within the origin-of-life field: we demonstrate assembly of functional ribozymes and we identify a potential evolutionary benefit for RNA aminoacylation that is independent of coded peptide translation.
Intact reading ability in spite of a spatially distributed visual word form ‘area’ in an individual born without the left superior temporal lobe
Authors: Li Jin , Kean Hope , Fedorenko Evelina , Saygin Zeynep
Published: September 2021

The visual word form area (VWFA) is an experience-dependent region in the left ventral temporal cortex (VTC) of literate adults that responds selectively to visual words. Why does it emerge in this stereotyped location? Past research shows the VWFA is preferentially connected to the left-lateralized frontotemporal language network. However, it remains unclear whether the presence of a typical language network and its connections with VTC are critical for the VWFA’s emergence, and whether alternative functional architectures may support reading ability. We explored these questions in an individual (EG) born without the left superior temporal lobe but exhibiting normal reading ability. We recorded fMRI activation to visual words, objects, faces, and scrambled words in EG and neurotypical controls. We did not observe word selectivity either in EG’s right homotope of the VWFA (rVWFA)—the most expected location given that EG’s language network is right-lateralized—or in her spared left VWFA (lVWFA), despite typical face selectivity in both the right and left fusiform face area (rFFA, lFFA). We replicated these results across scanning sessions (5 years apart). Moreover, in contrast with the idea that the VWFA is simply part of the language network that responds to general linguistic information, no part of EG’s VTC showed selectivity to higher-level linguistic processing. Interestingly, multivariate pattern analyses revealed sets of voxels in EG’s rVWFA and lVWFA that showed 1) higher within- than between-category correlations for words (e.g., Words-Words>Words-Faces), and 2) higher within-category correlations for words than other categories (e.g., Words-Words>Faces-Faces). These results suggest that a typical left-hemisphere language network may be necessary for the emergence of focal word selectivity within the VTC, and that orthographic processing can be supported by a distributed neural code.
The copper resistome of group B Streptococcus reveals insight into the genetic basis of cellular survival during metal ion stress
Authors: Goh Kelvin G. K. , Sullivan Matthew J. , Ulett Glen C.
Published: September 2021

In bacteria, copper (Cu) can support metabolic processes as an enzymatic cofactor but can also cause cell damage if present in excess, leading to intoxication. In group B Streptococcus (GBS) a system for control of Cu efflux based on the canonical cop operon supports survival during Cu stress. In some other bacteria, genetic systems additional to the cop operon are engaged during Cu stress and also contribute to Cu management. Here, we examined genetic systems beyond the cop operon in GBS for regions that contribute to survival of GBS in Cu stress using a forward genetic screen and probe of the entire bacterial genome. A high-density mutant library, generated using pGh9-ISS1, was used to expose GBS to Cu stress and compared to non-exposed controls en masse. Nine genes were identified as essential for GBS survival in Cu stress, whereas five genes constrained GBS growth in Cu stress. The genes encode varied factors including enzymes for metabolism, cell wall synthesis, transporters and global transcriptional regulators. Targeted mutation of the genes validated their roles in GBS resistance to Cu stress. Notably, several genes, including stp1, yceG, plyB and rfaB were also essential for resistance to Zn stress. Excepting copA, the genes identified are new to the area of bacterial metal ion intoxication. We conclude that a discrete and limited suite of genes beyond the cop operon in GBS contribute to a repertoire of mechanisms used to survive Cu stress in vitro and achieve cellular homeostasis.

Significance Statement

Genetic systems for copper (Cu) homeostasis in bacteria, including Streptococci, are vital to survive metal ion stress. Genetic systems that underpin survival of GBS during Cu stress, beyond for the archetypal cop operon for Cu management, are undefined. We show that Streptococcus resists Cu intoxication by utilizing a discrete and limited suite of genes beyond the cop operon, including several genes that are new to the area of bacterial cell metal ion homeostasis. The Cu resistome of GBS defined here enhances our understanding of metal ion homeostasis in GBS.
Angiocrine IGFBP3 Spatially Coordinates IGF Signaling During Neonatal Cardiac Regeneration
Authors: Ali Shah R. , Elhelaly Waleed , Nguyen Ngoc Uyen Nhi , Li Shujuan , Menendez-Montes Ivan , Wang Zhaoning , Cui Miao , Elnwasany Abdallah , Xiao Feng , Thet Suwannee , Lam Nicholas T. , Cardoso Alisson , Pereira Ana Helena , Goodarzi Mohammad , Kinter Michael T. , Lemoff Andrew , Szweda Luke I. , Shelton John , Kimura Wataru , Sadek Hesham A.
Published: September 2021

To identify non-cell-autonomous effectors of cardiomyocyte mitosis, we analyzed a transcriptomic screen of regenerating and non-regenerating neonatal hearts for differentially-expressed secreted proteins – which we hypothesized could include candidate mitogens. We identified and validated IGFBP3, which has a Janus-like stabilizing and sequestering effect on IGF growth factors, as a neonatal injury-associated secreted protein. IGFBP3 is expressed by and secreted from vascular cells in the neonatal heart after cardiac injury, notably in the infarct border zone. We found that global deletion of IGFBP3 blunted neonatal regeneration, while gain-of-function experiments using recombinant IGFBP3 and a transgenic mouse model uncovered a pro-mitotic effect of IGFBP3 on cardiomyocytes in vitro and in the adult heart. We show that site-specific expression of an IGFBP3 protease (PAPP-A2) and its inhibitor (STC2) coordinate the spatial release of IGF2 in the infarct zone to regio-selectively activate the INSR-ERK-AKT cell growth pathways in cardiomyocytes. Collectively, our work highlights the spatiotemporal orchestration of endothelial-cardiomyocyte interactions that are required for neonatal cardiac regeneration.
Epicardial HDAC3 promotes myocardial growth through a novel microRNA pathway
Authors: Jang Jihyun , Song Guang , Li Qinshan , Song Xiaosu , Cai Chenleng , Kaushal Sunjay , Li Deqiang
Published: September 2021

Rational

Establishment of the myocardial wall requires proper growth cues from nonmyocardial tissues. During heart development, the epicardium and epicardium-derived cells (EPDCs) instruct myocardial growth by secreting essential factors including fibroblast growth factor 9 (FGF9) and insulin-like growth factor 2 (IGF2). However, it is poorly understood how the epicardial secreted factors are regulated, in particular by chromatin modifications for myocardial formation.

Objective

To understand whether and how histone deacetylase 3 (HDAC3) in the developing epicardium regulates myocardial growth.

Methods and Results

We deleted Hdac3 in the developing murine epicardium and mutant hearts showed ventricular myocardial wall hypoplasia with reduction of EPDCs. The cultured embryonic cardiomyocytes with supernatants from Hdac3 knockout (KO) mouse epicardial cells (MECs) also showed decreased proliferation. Genome-wide transcriptomic analysis revealed that Fgf9 and Igf2 were significantly down-regulated in Hdac3 KO MECs. We further found that Fgf9 and Igf2 expression is dependent on HDAC3 deacetylase activity. The supplementation of FGF9 or IGF2 can rescue the myocardial proliferation defects treated by Hdac3 KO supernatant. Mechanistically, we identified that microRNA (miR)-322 and miR-503 were upregulated in Hdac3 KO MECs and Hdac3 epicardial KO hearts. Overexpression of miR-322 or miR-503 repressed FGF9 and IGF2 expression, while knockdown of miR-322 or miR-503 restored FGF9 and IGF2 expression in Hdac3 KO MECs.

Conclusions

Our findings reveal a critical signaling pathway in which epicardial HDAC3 promotes compact myocardial growth by stimulating FGF9 and IGF2 through repressing miR-322/miR-503, providing novel insights in elucidating etiology of congenital heart defects, and conceptual strategies to promote myocardial regeneration.
Mechanism of R-loop formation and conformational activation of Cas9
Authors: Pacesa Martin , Loeff Luuk , Querques Irma , Muckenfuss Lena M. , Sawicka Marta , Jinek Martin
Published: September 2021

Cas9 is a CRISPR-associated endonuclease capable of RNA-guided, site-specific DNA cleavage1–3. The programmable activity of Cas9 has been widely utilized for genome editing applications4–6, yet its precise mechanisms of target DNA binding and off-target discrimination remain incompletely understood. Here we report a series of cryo-EM structures of Streptococcus pyogenes Cas9 capturing the directional process of target DNA hybridization. In the early phase of R-loop formation, the Cas9 REC2 and REC3 domains form a positively charged cleft that accommodates the distal end of the target DNA duplex. Guide-target hybridization past the seed region induces rearrangements of the REC2/3 domains and relocation of the HNH nuclease domain to assume a catalytically incompetent checkpoint conformation. Completion of the guide-target heteroduplex triggers conformational activation of the HNH nuclease domain, enabled by distortion of the guide-target heteroduplex, and complementary REC2/3 domain rearrangements. Together, these results establish a structural framework for target DNA-dependent activation of Cas9 that sheds light on its conformational checkpoint mechanism and may facilitate the development of novel Cas9 variants and guide RNA designs with enhanced specificity and activity.
Proteomic Characterization of Isolated Arabidopsis Clathrin-Coated Vesicles Reveals Evolutionarily Conserved and Plant Specific Components
Authors: Dahhan Dana A. , Reynolds Gregory D. , Cárdenas Jessica J. , Eeckhout Dominique , Johnson Alexander , Yperman Klaas , Kaufmann Walter A. , Vang Nou , Yan Xu , Hwang Inhwan , Heese Antje , De Jaeger Geert , Friml Jiri , Van Damme Daniel , Pan Jianwei , Bednarek Sebastian Y.
Published: September 2021

In eukaryotes, clathrin-coated vesicles (CCVs) facilitate the internalization of material from the cell surface as well as the movement of cargo in post-Golgi trafficking pathways. This diversity of functions is partially provided by multiple monomeric and multimeric clathrin adaptor complexes that provide compartment and cargo selectivity. The adaptor- protein AP-1 complex operates as part of the secretory pathway at the trans-Golgi network, while the AP-2 complex and the TPLATE complex (TPC) jointly operate at the plasma membrane to execute clathrin-mediated endocytosis. Key to our further understanding of clathrin-mediated trafficking in plants will be the comprehensive identification and characterization of the network of evolutionarily conserved and plant- specific core and accessory machinery involved in the formation and targeting of CCVs. To facilitate these studies, we have analyzed the proteome of enriched trans-Golgi network/early endosome-derived and endocytic CCVs isolated from dividing and expanding suspension-cultured Arabidopsis cells. Tandem mass spectrometry analysis results were validated by differential chemical labeling experiments to identify proteins co-enriching with CCVs. Proteins enriched in CCVs included previously characterized CCV components and cargos such as the vacuolar sorting receptors in addition to conserved and plant-specific components whose function in clathrin-mediated trafficking has not been previously defined. Notably, in addition to AP-1 and AP-2, all subunits of the AP-4 complex, but not AP-3 or AP-5, were found to be in high abundance in the CCV proteome. The association of AP-4 with suspension-cultured Arabidopsis CCVs is further supported via additional biochemical data.
The beta-tubulin isotype TUBB6 controls microtubule and actin dynamics in osteoclasts
Authors: Maurin Justine , Morel Anne , Guérit David , Cau Julien , Urbach Serge , Blangy Anne , Bompard Guillaume
Published: September 2021

Osteoclasts are bone resorbing cells that participate in the maintenance of bone health. Pathological increase in osteoclast activity causes bone loss eventually resulting in osteoporosis. Actin cytoskeleton of osteoclasts organizes into a belt of podosomes, which sustains the bone resorption apparatus and is maintained by microtubules. Better understanding of the molecular mechanisms regulating osteoclast cytoskeleton is key to understand the mechanisms of bone resorption, in particular to propose new strategies against osteoporosis. We reported recently that β-tubulin isotype TUBB6 is key for cytoskeleton organization in osteoclasts and for bone resorption. Here, using an osteoclast model CRISPR/Cas9 KO for Tubb6, we show that TUBB6 controls both microtubule and actin dynamics in osteoclasts. Osteoclasts KO for Tubb6 have reduced microtubule growth speed with longer growth life time, higher levels of acetylation and smaller EB1-caps. On the other hand, lack of TUBB6 increases podosome life time while the belt of podosomes is destabilized. Finally, we performed proteomic analyses of osteoclast microtubule-associated protein enriched fractions. This highlighted ARHGAP10 as a new microtubule-associated protein, which binding to microtubules appears to be negatively regulated by TUBB6. ARHGAP10 is a negative regulator of CDC42 activity, which participates in actin organization in osteoclasts. Our results suggest that TUBB6 plays a key role in the control of microtubule and actin cytoskeleton dynamics in osteoclasts. Moreover, by controlling ARHGAP10 association with microtubules, TUBB6 may participate in the local control CDC42 activity to ensure efficient bone resorption.
C-type natriuretic peptide facilitates autonomic Ca2+ entry in growth plate chondrocytes for stimulating bone growth
Authors: Miyazaki Yuu , Ichimura Atsuhiko , Kitayama Ryo , Okamoto Naoki , Yasue Tomoki , Liu Feng , Ueda Yohei , Yamauchi Ichiro , Hakata Takuro , Nakao Kazumasa , Kakizawa Sho , Nishi Miyuki , Mori Yasuo , Akiyama Haruhiko , Nakao Kazuwa , Takeshima Hiroshi
Published: September 2021

The growth plates are cartilage tissues found at both ends of developing bones, and vital proliferation and differentiation of growth plate chondrocytes are primarily responsible for bone growth. C-type natriuretic peptide (CNP) stimulates bone growth by activating natriuretic peptide receptor 2 (NPR2) which is equipped with guanylate cyclase on the cytoplasmic side, but its signaling pathway is unclear in growth plate chondrocytes. We previously reported that transient receptor potential melastatin-like 7 (TRPM7) channels mediate intermissive Ca2+ influx in growth plate chondrocytes, leading to activation of Ca2+/calmodulin-dependent protein kinase II (CaMKII) for promoting bone growth. In this report, we provide experimental evidence indicating a functional link between CNP and TRPM7 channels. Our pharmacological data suggest that CNP-evoked NPR2 activation elevates cellular cGMP content and stimulates big-conductance Ca2+-dependent K+ (BK) channels as a substrate for cGMP-dependent protein kinase (PKG). BK channel-induced hyperpolarization likely enhances the driving force of TRPM7-mediated Ca2+ entry and seems to accordingly activate CaMKII. Indeed, ex vivo organ culture analysis indicates that CNP-facilitated bone growth is abolished by chondrocyte-specific Trpm7 gene ablation. The defined CNP signaling pathway, the NPR2-PKG-BK channel-TRPM7 channel-CaMKII axis, likely pinpoints promising target proteins for developing new therapeutic treatments for divergent growth disorders.
The nuts and bolts of SARS-CoV-2 Spike Receptor Binding Domain heterologous expression
Authors: Maffei Mariano , Montemiglio Linda Celeste , Vitagliano Grazia , Fedele Luigi , Sellathurai Shaila , Bucci Federica , Compagnone Mirco , Chiarini Valerio , Exertier Cécile , Muzi Alessia , Roscilli Giuseppe , Vallone Beatrice , Marra Emanuele
Published: September 2021

COVID-19 is a highly infectious disease caused by a newly emerged coronavirus (SARS-CoV-2) that has rapidly progressed into a pandemic. This unprecedent emergency has stressed the significance of developing effective therapeutics to fight current and future outbreaks. The receptor-binding domain (RBD) of the SARS-CoV-2 surface Spike protein is the main target for vaccines and represents a helpful “tool” to produce neutralizing antibodies or diagnostic kits. In this work, we provide a detailed characterization of the native RBD produced in three major model systems: Escherichia coli, insect and HEK-293 cells. Circular dichroism, gel filtration chromatography and thermal denaturation experiments indicated that recombinant SARS-CoV-2 RBD proteins are stable and correctly folded. In addition, their functionality and receptor-binding ability were further evaluated through ELISA, flow cytometry assays and bio-layer interferometry.
Perception and adaptation of agricultural households to climate change in the semi-arid regions of Rajasthan – a gender perspective study
Authors: Mohapatra Geetilaxmi , George Meera
Published: September 2021

Purpose

The study aims to analyze the gender-wise perception of the agricultural households toward climate change and the adaption measures taken by these households, especially women, to mitigate climate changes.

Design/methodology/approach

Purposive random sampling technique is used to collect primary data from a pilot survey conducted in two semi-arid districts of Rajasthan, India. Data mainly focused on analyzing the gender-based perception and adaptation strategies undertaken toward climate change. And descriptive statistics are used for analysis.

Findings

The study found that both the gender are aware of the climatic changes. Deforestation increased population, change in living standards, urbanization and industrialization contribute to climate changes. The women are employing limited adaptation strategies to mitigate the climatic stress compared to males.

Research limitations/implications

This is a pilot study; hence, it has an insufficient sample size for the detailed statistical analysis. Further, it is only limited to two semi-arid districts of Rajasthan.

Originality/value

This pioneering study highlights gender-wise differences in perception and adaptation strategies undertaken in this region. The study suggests raising awareness about climate change and providing credit facilities for undertaking adaptation measures to reduce agricultural households' vulnerability, particularly enhancing women's adaptive capacity to climate change.
Future of work: a systematic literature review and evolution of themes
Authors: Singh Anjali , Jha Sumi , Srivastava Dinesh Kumar , Somarajan Abheesh
Published: September 2021

Purpose

Concerned with the rising social, economic and technological disruption in the world, the impact of the technological disruption had a significant impact on the future of work and it has been tremendously increased in past five years. Further, with the rising uncertainties and COVID-19 in the picture, the trends suggested by earlier literature might not hold. The purpose of this paper is to understand the evolution of technology in the workplace in the past five years, how does it stand during COVID-19, will the trend continue in light of disruption caused by COVID-19, the impact of COVID-19 on the future of work.

Design/methodology/approach

The paper uses bibliometric techniques to identify the conceptual and intellectual structure of the studies. The programming language named after authors Robert and Ross (R) software and Biblioshiny were used to identify the structures and the themes underlying those structures, which further helped in forecasting the trends of the studies.

Findings

The paper shows the drastic evolution of the studies in past few years and different technologies implemented at the workplace in the same period. It further identified the influential papers, authors, journals in the area with an emphasis on the various collaboration network among authors and countries. It also paints a picture of the impact of COVID-19 on the future of work. The paper finally concluded with future directions for the emerging trends and themes in the area in aftermath of COVID-19.

Originality/value

This paper takes the microscopic view of the studies carried out in the past five years as during the past five years, the studies related to this topic have grown tremendously and accordingly many trends have been identified but with the COVID-19 pandemic in the picture, the trend is likely to get accelerated. This paper takes this view and identifies the trends in the future by identifying the themes based on periods and at different levels – organizational, managerial, individual.