bluuebunny/crossref_metadata_2025 huggingface dataset:
Evolutionary dynamics of sex-biased gene expression in a young XY system: Insights from the brown alga genus Fucus
Authors: Hatchett William J. , Jueterbock Alexander , Kopp Martina , Coyer James A. , Coelho Susana M. , Hoarau Galice , Lipinska Agnieszka P.
Published: August 2021

The sex-dependent regulation of gene expression is considered to be an underlying cause of often extensive, sexually dimorphic traits between males and females. Although the nature and degree of sex-biased gene expression has been well-documented in several animal and plant systems, far less is known about the commonality, conservation, recruitment mechanisms and evolution of sex-biased genes in more distant eukaryotic groups. Brown algae are of particular interest for empirical studies on the evolution of sex-biased gene expression, as they have been evolving independently from animals and plants for over one billion years. Here we focus on two brown algal dioecious species, Fucus serratus and Fucus vesiculosus, where male heterogamety (XX/XY) has recently emerged. Using RNA-seq, we study sex-biased gene expression and discuss different evolutionary forces responsible for the evolution of sex-biased genes. We find that both species evolved masculinized transcriptomes, with sex-biased genes allocated mainly to male reproductive tissue, but virtually absent in vegetative tissues. Conserved male-biased genes were enriched in functions related to gamete production, along with sperm competition and include two flagellar proteins under positive selection. In contrast to female-biased genes, which show high turnover rates, male-biased genes reveal remarkable conservation of bias and expression levels between the two species. As observed in other XY systems, male-biased genes also display accelerated rates of coding sequence evolution compared to female-biased or unbiased genes. Our results imply that evolutionary forces affect male and female sex-biased genes differently on structural and regulatory levels. Similar to evolutionarily distant plant and animal lineages, sex-biased gene expression in Fucus evolved during the transition to dioecy to resolve intra-locus sexual conflict arising from anisogamy.
Predicting Future Cognitive Impairment inDe NovoParkinson’s Disease Using Clinical Data and Structural MRI
Authors: Smith Nicola , Williams Owen , Ricciardi Lucia , Morgante Francesca , Barrick Thomas R , Edwards Mark , Lambert Christian
Published: August 2021

BACKGROUND

Parkinson’s disease is the second most common neurodegenerative condition and associated with increasing cognitive dysfunction as the disease progresses. However, subtle cognitive deficits can be detected at diagnosis in 42% of individuals, suggesting that damage may already be present. Our aim was to determine clinical and structural differences in those recently diagnosed with PD who later develop cognitive impairment, and whether these changes predict future cognitive decline.

METHODS

Clinical and imaging data was acquired from the Parkinson’s Progression Markers Initiative for 318 individuals with a diagnosis of Parkinson’s disease and baseline 3T T1-weighted MRI. The cohort was divided according to cognitive status over follow-up, with 9 individuals developing Parkinson’s disease dementia, 102 developing mild cognitive impairment and 207 remaining cognitively unaffected.

FINDINGS

At baseline, those who went on to develop cognitive impairment (mild cognitive impairment or dementia) wereolder with more severe motor and non-motor symptoms (anosmia, rapid eye movement sleep behaviour disorder, depression). Grey matter loss was present in those destined for Parkinson’s disease dementia in theprecuneus, hippocampi, primary olfactory cortex, lingual gyrus, temporal cortex and cerebellum. Those who later developed mild cognitive impairment had an attenuated but similar pattern ofgrey matter loss in the temporal lobe, lingual gyrus and cerebellum. Using support vector machines with a feature selection step, future cognitive impairment could be predicted using 11 clinical variables (AUC = 0.81), structural imaging (AUC = 0.72) or a combination of these two modalities (AUC = 0.85). These models more accurately predicted those who developed dementia (subgroup sensitivity 100%).

INTERPRETATION

Significant abnormalities in cortical structure is present at least three years before dementia manifests in Parkinson’s disease, with associated differences in clinical profiles. Combining this data provides a technique to accurately identify future cognitive impairment, providing a non-invasive way to stratify individuals early on.
Mitochondrial interactome quantitation reveals structural changes in metabolic machinery in failing murine heart
Authors: Caudal Arianne , Tang Xiaoting , Chavez Juan D. , Keller Andrew , Villet Outi , Zhou Bo , Walker Matthew A. , Tian Rong , Bruce James E.
Published: August 2021

Advancements of cross-linking mass spectrometry (XL-MS) for structural analysis of proteins bridges the gap between purified systems and native tissue environments. Here, isobaric quantitative protein interaction reporter technology (iqPIR) was utilized to further extend XL-MS to the first system-wide comparative study of mitochondrial proteins from healthy and diseased murine hearts. The failing heart interactome includes 602 statistically significant cross-linked peptide pairs altered in the disease condition. Structural insight into ketone oxidation metabolons, OXPHOS machinery, and nucleotide transporter hybrid-conformations, support mitochondrial remodeling in failing heart while bringing forth new hypotheses for pathological mechanisms. Application of quantitative cross-linking technology in tissue provides molecular-level insight to complex biological systems difficult to model in cell culture, thus providing a valuable resource for study of human diseases.
Dynamics of maternal gene expression in Rhodnius prolixus
Authors: Pascual Agustina , Pomar Rolando Rivera
Published: August 2021

The study of the developmental processes in Rhodnius prolixus has recently advanced with the sequencing of the genome. In this work, we study maternal gene expression driving oogenesis and early embryogenesis in R. prolixus. We analyze the transcriptional profile of mRNAs to establish the genes expressed across the ovary, unfertilized eggs and different embryonic stages of R. prolixus until the formation of the germ band anlage (0, 12, 24, and 48 hours post egg laying). We identified 81 putative maternal and ovary-related genes and validated their expression by qRT-PCR. Consistent with a role in oogenesis and early development of R. prolixus, we show that parental RNAi against Rp-BicD results in embryos that did not show any distinguishable embryonic structure. In this framework we propose three hierarchies of maternal genes that affect early and late oogenesis, and embryonic patterning.
Seven-CpG DNA Methylation Age determined by Single Nucleotide Primer Extension and Illumina’s Infinium MethylationEPIC array provide highly comparable results
Authors: Vetter Valentin Max , Kalies Christian Humberto , Sommerer Yasmine , Bertram Lars , Demuth Ilja
Published: August 2021

DNA methylation age (DNAm age, epigenetic clock) is a novel and promising biomarker of aging. It is calculated from the methylation fraction of specific cytosine phosphate guanine sites (CpG sites) of genomic DNA. Several groups have proposed epigenetic clock algorithms and these differ mostly regarding the number and location of the CpG sites considered and the method used to assess the methylation status. Most epigenetic clocks are based on a large number of CpGs, e.g. as measured by DNAm microarrays. We have recently evaluated an epigenetic clock based on the methylation fraction of seven CpGs that were determined by methylation-sensitive single nucleotide primer extension (MS-SNuPE). This method is more cost-effective when compared to array-based technologies as only a few CpGs need to be examined. However, there is only little data on the correspondence in epigenetic age estimation using the 7-CpG clock and other algorithms.

To bridge this gap, in this study we measured the 7-CpG DNAm age using two methods, via MS-SNuPE and via the MethylationEPIC array, in a sample of 1,058 participants of the Berlin Aging Study II (BASE-II), assessed as part of the GendAge study. On average, participants were 75.6 years old (SD: 3.7, age range: 64.9 – 90.0, 52.6% female). Agreement between methods was assessed by Bland-Altman plots. DNAm age was highly correlated between methods (Pearson’s r=0.9) and Bland-Altman plots showed a difference of 3.1 years. DNAm age by the 7-CpG formula was 71.2 years (SD: 6.9 years, SNuPE) and 68.1 years (SD: 6.4 years, EPIC array). The mean of difference in methylation fraction between methods for the seven individual CpG sites was between 0.7 and 13 percent. To allow direct conversion between methods we developed an adjustment formula with a randomly selected training set of 529 participants using linear regression. After conversion of the Illumina data in a second and independent validation set, the adjusted DNAm age was 71.44 years (SD: 6.1 years, n=529). In summary, we found the results of DNAm clocks to be highly comparable. Furthermore, we developed an adjustment formula that allows for direct conversion of estimates between methods and enables one singular clock to be used in studies that employ either the Illumina or the SNuPE method.
The first chromosome-level gecko genome reveals dynamic sex chromosomes in Neotropical leaf-litter geckos (Sphaerodactylidae:Sphaerodactylus)
Authors: Pinto Brendan J. , Keating Shannon E. , Nielsen Stuart V. , Scantlebury Daniel P. , Daza Juan D. , Gamble Tony
Published: August 2021

Sex chromosomes have evolved many times across eukaryotes, indicating both their importance and their evolutionary flexibility. Some vertebrate groups, such as mammals and birds, have maintained a single, conserved sex chromosome system across long evolutionary time periods. By contrast, many reptiles, amphibians, and fish have undergone frequent sex chromosome transitions, most of which remain to be catalogued. Among reptiles, gecko lizards (infraorder Gekkota) have shown an exceptional lability with regard to sex chromosome transitions and may possess the majority of transitions within squamates (lizards and snakes). However—across geckos—information about sex chromosome linkage is expressly lacking, leaving large gaps in our understanding of the evolutionary processes at play in this system. To address this gap, we assembled the first chromosome-level genome for a gecko and use this linkage information to survey sixSphaerodactylusspecies using a variety of genomic data, including whole-genome re-sequencing, RADseq, and RNAseq. Previous work has identified XY systems in two species ofSphaerodactylusgeckos. We expand upon that work to identify between two and four sex chromosomecis-transitions (XY to XY) within the genus. Interestingly, we confirmed two linkage groups as XY sex chromosome systems that were previously unknown to act as sex chromosomes in tetrapods (syntenic withGallus3 andGallus18/30/33). We highlight the increasing evidence that most (if not all) linkage groups will likely be identified as a sex chromosome in future studies given thorough enough sampling.
Maternal γδ T cells shape offspring pulmonary type-2 immunity in a microbiota-dependent manner
Authors: Papotto Pedro H. , Yilmaz Bahtiyar , Pimenta Gonçalo , Mensurado Sofia , Cunha Carolina , Fiala Gina , da Costa Daniel Gomes , Gonçalves-Sousa Natacha , Chan Brian H. K. , Blankenhaus Birte , Carvalho Tânia , Macpherson Andrew J. , Allen Judith E. , Silva-Santos Bruno
Published: August 2021

Immune system development is greatly influenced by vertically transferred cues. However, beyond antibody-producing B cells, little is known about the role of other cell subsets of the maternal immune system in regulating offspring immunity. We reasoned γδ T cells to be attractive candidates based on their tissue distribution pattern: abundant in the skin, mammary glands and female reproductive tract. Here we found that mice born from γδ T cell-deficient (TCRδ-/-) dams display, early after birth, a pulmonary milieu selectively enriched in type-2 cytokines such as IL-33, IL-4, IL-5, and IL-13, and type-2-polarized immune cells, when compared to the progeny of γδ T cell-sufficient dams. In addition, upon helminth infection, mice born from TCRδ-/- dams sustained an increased type-2 inflammatory response. Critically, this was independent of the genotype of the pups. Despite similar levels of circulating antibodies in mothers and progeny, the intestinal microbiota in the offspring of TCRδ-/- and TCRδ+/- dams harbored distinct bacterial communities acquired during birth and fostering. These differences were accompanied by changes in the intestinal short-chain fatty acids (SCFA) profile. Importantly, antibiotic treatment abrogated the differences observed in the pulmonary milieu, and exogenous SCFA supplementation suppressed first-breath- and infection-induced inflammation. In summary, maternal γδ T cells control the establishment of a neonatal gut–lung axis by conditioning the postnatal microbial colonization of the off-spring and bacterial-derived metabolite availability; ultimately impacting on the development of pulmonary type-2 immunity in the offspring.
Maternal control over caste allocation in the ant Cardiocondyla obscurior
Authors: Schultner Eva , Wallner Tobias , Dofka Benjamin , Bruelhart Jeanne , Heinze Jürgen , Freitak Dalial , Pokorny Tamara , Oettler Jan
Published: August 2021

Ant queens and workers commonly engage in conflict over reproductive allocation because they have different fitness optima. How such conflicts are resolved depends on the power that each party of interest holds. Here, we show that queens have control over caste allocation in the ant Cardiocondyla obscurior. With the discovery of crystalline deposits that allow the identification of queens and workers across the entire course of development, we demonstrate that caste fate is irreversibly determined in the egg stage. Comparison of queen and worker-destined eggs and larvae revealed size and weight differences in late development, but no discernible differences in traits that may be used in social interactions, including hair morphology and cuticular odors. In line with this lack of caste-specific traits, adult workers treated developing queens and workers indiscriminately, even in the presence of a fertile queen. Together with previous studies showing queen control over sex allocation, these results provide evidence that conflict over reproductive allocation is absent in this ant.
Overlap of expression and alignment of diurnal and circadian rhythmicity in the human blood transcriptome with organ and tissue specific rhythmicity in a non-human primate
Authors: Möller-Levet Carla S , Laing Emma E , Archer Simon N , Dijk Derk-Jan
Published: August 2021

BACKGROUND

Twenty-four-hour rhythmicity in transcriptomes of tissues and organs is driven by local circadian oscillators, systemic factors, the central circadian pacemaker, and light-dark cycles. This rhythmicity is to some extent organ- and tissue-specific such that the sets of rhythmic transcripts or their timing are different across tissues/organs. Monitoring rhythmicity of tissues and organs holds promise for circadian medicine, but in humans most tissues and organs are not easily accessible. To investigate the extent to which rhythmicity in the human blood transcriptome reflects rhythmicity in tissues and organs, we compared the overlap and timing of rhythmic transcripts in human blood and rhythmic transcripts in 64 tissues/organs of the baboon.

METHODS

Rhythmicity in the transcriptomes of humans and baboons were compared using set logic, circular cross-correlation, circular clustering, functional enrichment analyses and partial least squares regression.

RESULTS

Of the 759 orthologous genes that were rhythmic in human blood, 652 (86%) were also rhythmic in at least one baboon tissue. Most of these genes were associated with basic processes such as transcription and protein homeostasis. 109 (17%) of the 652 overlapping rhythmic genes were reported as rhythmic in only one baboon tissue or organ and several of these genes have tissue/organ-specific functions. Analysis of the alignment between baboon and human transcriptomes showed that in these diurnal species, rhythmicity is aligned with the onset, rather than midpoint or end of light period. In both species, the timing of rhythmic transcripts displayed prominent ‘night’ and ‘day’ clusters, with genes in the dark cluster associated with translation. The timing of human and baboon transcriptomes was significantly correlated in 25 tissue/organs with an average earlier timing of 3.21 h (SD 2.47 h) in human blood.

CONCLUSIONS

The human blood transcriptome contains sets of rhythmic genes that overlap with rhythmic genes of tissues/organs, some of which are tissue/organ-specific, in the baboon. The rhythmic sets vary across tissues/organs but the timing of most rhythmic genes is similar across human blood and baboon tissues/organs. These results have implications for our understanding of the regulation of rhythmicity across tissues/organs and species and development of blood transcriptome-based biomarkers for rhythmicity in tissues and organs.
Responses of Escherichia coli and Listeria monocytogenes to ozone treatment on non-host tomato: Efficacy of intervention and evidence of induced acclimation
Authors: Shu Xiaomei , Singh Manavi , Karampudi Naga Bhushana Rao , Bridges David F. , Kitazumi Ai , Wu Vivian C. H. , De los Reyes Benildo G.
Published: August 2021

Because of the continuous rise of foodborne illnesses caused by the consumption of raw fruits and vegetables, effective post-harvest anti-microbial strategies are needed. This study evaluated the dose × time effects on the anti-microbial action of ozone (O3) gas against the Gram-negative Escherichia coli O157:H7 and Gram-positive Listeria monocytogenes, which are common contaminants in fresh produce. The study on non-host tomato environment correlated the dose × time aspects of xenobiosis by examining the correlation between bacterial survival in terms of log-reduction and defense responses at the level of gene expression. In E. coli, low (1 μg O3/g of fruit) and moderate (2 μg O3/g of fruit) doses caused insignificant reduction in survival, while high dose (3 μg/g of fruit) caused significant reduction in survival in a time-dependent manner. In L. monocytogenes, moderate dose caused significant reduction even with short-duration exposure. Distinct responses to O3 xenobiosis between E. coli and L. monocytogenes are likely related to differences in membrane and cytoplasmic structure and components.

Transcriptome profiling by RNA-Seq showed that primary defenses in E. coli were attenuated after exposure to a low dose, while the responses at moderate dose were characterized by massive upregulation of pathogenesis and stress-related genes, which implied the activation of defense responses. More genes were downregulated during the first hour at high dose, with a large number of such genes getting significantly upregulated after 2 hr and 3 hr. This trend suggests that prolonged exposure led to potential adaptation. In contrast, massive downregulation of genes was observed in L. monocytogenes regardless of dose and exposure duration, implying a mechanism of defense distinct from that of E. coli. The nature of bacterial responses revealed by this study should guide the selection of xenobiotic agents for eliminating bacterial contamination on fresh produce without overlooking the potential risks of adaptation.
FLARIM v2.0, an improved method to quantify transcript-ribosome interactions in vivo in the adult Drosophila brain
Authors: Richer Petra , Speese Sean D. , Logan Mary A.
Published: August 2021

Neural injury triggers striking immune reactions from glial cells, including significant transcriptional and morphological changes, but it is unclear how these events are coordinated to mount an effective immune response. Here, we present a new variant of the Fluorescence assay to detect ribosome interactions with mRNA (FLARIM), which we term FLARIM v2.0, to visualize single immune gene transcripts and association with ribosomes in glia responding to neurodegeneration. Specifically, using an in vivo axotomy assay in Drosophila, we show that matrix metalloproteinase-1 (Mmp-1) mRNAs and associated ribosomes are detected in distal processes of reactive glia where they are actively engulfing degenerating axonal material, suggesting that local translation is an important component of the glial immune response to axotomy. This work also validates our enhanced FLARIM assay as a promising tool to investigate mechanisms of mRNA transport and translation in a wide range of in vitro and in vivo paradigms.
Partial endothelial-to-mesenchymal transition (EndMT) contributes to lumen re-organization after carotid artery ligation
Authors: Yamashiro Yoshito , Ramirez Karina , Nagayama Kazuaki , Tomita Shuhei , Kubota Yoshiaki , Yanagisawa Hiromi
Published: August 2021

Endothelial-to-mesenchymal transition (EndMT) is a fundamental process in vascular remodeling. Carotid artery ligation is commonly used for induction of neointima formation and vessel stenosis; however, the precise regulatory mechanism of vascular remodeling is not entirely understood. In this study, we showed that resident endothelial cells (ECs) are the origin of neointima cells and ECs transiently expressed CD45 in the early stage of neointima formation accompanied by increased expression of EndMT markers. In vitro, CD45-positive EndMT was induced by stabilization of HIF-1α with cobalt chloride or VHL inhibitor in human primary ECs, which mimicked the hypoxic condition of ligated artery, and promoted the formation of integrin α11-SHARPIN complex. Notably, a CD45 phosphatase inhibitor disrupted this complex, thereby destabilizing cell-cell junctions. These results suggest that the CD45 activity is required for the retention of an EC phenotype and cell-cell junctions during EndMT (termed “partial EndMT”). We thus propose a novel mechanism of partial EndMT that contributes to lumen re-organization during vascular injury.
Cortical hyperexcitability drives dying forward ALS symptoms and pathology in mice
Authors: Haidar Mouna , Viden Aida , Cuic Brittany , Wang Taide , Rosier Marius , Tomas Doris , Mills Samuel A. , Govier-Cole Alistair , Djouma Elvan , Luikinga Sophia , Rytova Valeria , Barton Samantha K. , Gonsalvez David G. , Palmer Lucy M. , McLean Catriona , Kiernan Matthew C. , Vucic Steve , Turner Bradley J.
Published: August 2021

Amyotrophic lateral sclerosis (ALS) is a progressive fatal disorder caused by degeneration of motor neurons in the cortex and spinal cord. The origin of ALS in the central nervous system is unclear, however cortical hyperexcitability appears as an early and intrinsic feature of ALS and has been linked to degeneration of spinal motor neurons via a dying-forward mechanism. Here, we implement chemogenetics to validate the dying forward hypothesis of ALS in mice. We show that chronic hyperexcitability of corticomotoneurons induced by excitatory chemogenetics results in motor symptoms and core neuropathological hallmarks of ALS, including corticomotoneuron loss, corticospinal tract degeneration and reactive gliosis. Importantly, corticomotoneuron loss was sufficient to drive degeneration of spinal motor neurons and neuromuscular junctions (NMJs), associated with cytoplasmic TAR DNA binding protein 43 (TDP-43) pathology. These findings establish a cortical origin of ALS mediated by neuronal hyperexcitability, consistent with a dying forward mechanism of neurodegeneration.
Machine-learning-guided library design cycle for directed evolution of enzymes: the effects of training data composition on sequence space exploration
Authors: Saito Yutaka , Oikawa Misaki , Sato Takumi , Nakazawa Hikaru , Ito Tomoyuki , Kameda Tomoshi , Tsuda Koji , Umetsu Mitsuo
Published: August 2021

Machine learning (ML) is becoming an attractive tool in mutagenesis-based protein engineering because of its ability to design a variant library containing proteins with a desired function. However, it remains unclear how ML guides directed evolution in sequence space depending on the composition of training data. Here, we present a ML-guided directed evolution study of an enzyme to investigate the effects of a known “highly positive” variant (i.e., variant known to have high enzyme activity) in training data. We performed two separate series of ML-guided directed evolution of Sortase A with and without a known highly positive variant called 5M in training data. In each series, two rounds of ML were conducted: variants predicted by the first round were experimentally evaluated, and used as additional training data for the second-round prediction. The improvements in enzyme activity were comparable between the two series, both achieving enzyme activity 2.2–2.5 times higher than 5M. Intriguingly, the sequences of the improved variants were largely different between the two series, indicating that ML guided the directed evolution to the distinct regions of sequence space depending on the presence/absence of the highly positive variant in the training data. This suggests that the sequence diversity of improved variants can be expanded not only by conventional ML using the whole training data, but also by ML using a subset of the training data even when it lacks highly positive variants. In summary, this study demonstrates the importance of regulating the composition of training data in ML-guided directed evolution.
NLRP1B and NLRP3 control the host response following colonization with the commensal protist Tritrichomonas musculis
Authors: Chiaranunt Pailin , Burrows Kyle , Ngai Louis , Cao Eric Y. , Liang Helen , Streutker Catherine J. , Girardin Stephen E. , Mortha Arthur
Published: August 2021

Commensal intestinal protozoa, unlike their pathogenic relatives, are neglected members of the mammalian microbiome. These microbes have a significant impact on the host’s intestinal immune homeostasis, typically by elevating anti-microbial host defense. Tritrichomonas musculis (T. mu), a protozoan gut commensal, strengthens the intestinal host defense against enteric Salmonella infections through Asc- and Il1r1-dependent Th1 and Th17 cell activation. However, the underlying inflammasomes mediating this effect remain unknown. Here, we report that colonization with T. mu results in an increase in luminal extracellular ATP, elevated levels of IL-1β, and increased numbers of IL-18 receptor-expressing Th1 and Th17 cells in the colon. Mice deficient in either Nlrp1b or Nlrp3 failed to display these protozoan-driven immune changes and lost resistance to enteric Salmonella infections even in the presence of T. mu. These findings demonstrate that T. mu-mediated host protection requires sensors of extra and intracellular ATP to confer resistance to enteric Salmonella infections.

KEY POINTS

Intestinal colonization with the commensal Tritrichomonas musculis elevates luminal ATP levels

NLRP1B and NLRP3 activation is required for Tritrichomonas musculis-driven Th cell response.
Cardiomyocyte BRAF and type 1 RAF inhibitors promote cardiomyocyte and cardiac hypertrophy in mice in vivo
Authors: Clerk A , Meijles DN , Hardyman MA , Fuller SJ , Chothani SP , Cull JJ , Cooper STE , Alharbi HO , Vanezis K , Felkin LE , Markou T , Leonard SJ , Shaw SW , Rackham OJL , Cook SA , Glennon PE , Sheppard MN , Sembrat JC , Rojas M , McTiernan CF , Barton PJ , Sugden PH
Published: August 2021

The extracellular signal-regulated kinase 1/2 (ERK1/2) cascade promotes cardiomyocyte hypertrophy and is cardioprotective, with the three RAF kinases forming a node for signal integration. Our aims were to determine if BRAF is relevant for human heart failure, if BRAF promotes cardiomyocyte hypertrophy, and if Type 1 RAF inhibitors developed for cancer (that paradoxically activate ERK1/2 at low concentrations: the “RAF paradox”) may have the same effect. BRAF was upregulated in heart samples from patients with heart failure compared with normal controls. We assessed the effects of activated BRAF in the heart using mice with tamoxifen-activated Cre for cardiomyocyte-specific knock-in of the activating V600E mutation into the endogenous gene. We used echocardiography to measure cardiac dimensions/function. Cardiomyocyte BRAFV600E induced cardiac hypertrophy within 10 d, resulting in increased ejection fraction and fractional shortening over 6 weeks. This was associated with increased cardiomyocyte size without significant fibrosis, consistent with compensated hypertrophy. The experimental Type 1 RAF inhibitor, SB590885, and/or encorafenib (a RAF inhibitor used clinically) increased ERK1/2 phosphorylation in cardiomyocytes, and promoted hypertrophy, consistent with a “RAF paradox” effect. Both promoted cardiac hypertrophy in mouse hearts in vivo, with increased cardiomyocyte size and no overt fibrosis. In conclusion, BRAF potentially plays an important role in human failing hearts, activation of BRAF is sufficient to induce hypertrophy, and Type 1 RAF inhibitors promote hypertrophy via the “RAF paradox”. Cardiac hypertrophy resulting from these interventions was not associated with pathological features, suggesting that Type 1 RAF inhibitors may be useful to boost cardiomyocyte function.
Cannabinoids differentially modulate behavioral and developmental responses to ethanol in Drosophila
Authors: He Jianzheng , Ng Si Yun , Tan Alice Mei Xien , Yong Wei Lin , Yu Fengwei
Published: August 2021

Prolonged prenatal or adult exposure to ethanol is detrimental to mental and physical well-being, resulting in developmental abnormalities, progressive addiction and ultimate death. A growing number of studies have shown the therapeutic potential of cannabinoids in ethanol-related behaviors in mammals. However, the potential pharmacological actions of cannabinoids in ethanol responses have not been examined in the model organism Drosophila melanogaster. Here, we systematically investigated the effects of various cannabinoids on ethanol preference, ethanol sensitivity and tolerance, and ethanol-induced developmental defect in Drosophila. We showed that treatment with the phytocannabinoid cannabidiol (CBD) displayed a significant decrease in preference for consuming ethanol in adult flies. Interestingly, cannabinoids exhibited differential roles in short- and long-term ethanol tolerance in flies. Although cannabinoids had no detectable effects on short-term ethanol tolerance, CBD and the endocannabinoid anandamide (AEA) suppressed long-term tolerance to ethanol. Moreover, ethanol exposure delayed larval-to-pupal development and increased larval/pupal size. Unexpectedly, treatment with CBD or endocannabinoids did not attenuate ethanol-induced developmental delay, instead, exacerbated its detrimental effect. Thus, our systematical study reveals, for the first time, a differential role of the cannabinoids in the modulation of ethanol-related responses in Drosophila.
Household transmission of SARS-CoV-2; a prospective longitudinal study showing higher viral load and transmissibility of the Alpha variant compared to previous strains
Authors: Julin Cathinka Halle , Robertson Anna Hayman , Hungnes Olav , Tunheim Gro , Bekkevold Terese , Laake Ida , Aune Idunn Forland , Rykkvin Rikard , Dorenberg Dagny Haug , Stene-Johansen Kathrine , Berg Einar Sverre , Bodin Johanna Eva , Oftung Fredrik , Steens Anneke , Næss Lisbeth Meyer
Published: August 2021

Objectives

We studied the secondary attack rate (SAR), risk factors, and precautionary practices of household transmission in a prospective, longitudinal study. We further compared transmission between the Alpha (B.1.1.7) variant and non-Variant of Concern (non-VOC) viruses.

Methods

We recruited households of 70 confirmed COVID-19 cases with 146 household contacts from May 2020 to May 2021. Participants donated biological samples 8 times over 6 weeks and answered questionnaires. Whole genome sequencing and droplet digital PCR were used to establish the SARS-CoV-2 variant and viral load.

Results

SARS-CoV-2 transmission occurred in 60% of the households, and the overall SAR for household contacts was 50%. The SAR was significantly higher for the Alpha variant (78%) compared with non-VOC viruses (43%) and was associated with a higher viral load. SAR was higher in household contacts aged ≥40 years (69%) than in younger contacts (40-47%), and for contacts of cases with loss of taste/smell. Children had lower viral loads and were more often asymptomatic than adults. Sleeping separately from the primary case reduced the risk of transmission.

Conclusions

We found substantial household transmission, particularly for the Alpha variant. Precautionary practices seem to reduce SAR, but preventing household transmission may become difficult with more contagious variants.
Point of emission air filtration enhances protection of health care workers against skin contamination with virus aerosol
Authors: Landry Shane Anthony , Subedi Dinesh , MacDonald Martin Ian , Dix Samantha , Kutey Donna , Barr Jeremy , Mansfield Darren , Hamilton Garun , Edwards Bradley , Joosten Simon
Published: August 2021

Rationale: We recently demonstrated that a patient hood with a high efficiency particulate air filter eliminates virus aerosol contamination when very large quantities of bacteriophage virus are aerosolised into a clinical room. While this containment method is relatively low cost, it is unclear whether similar efficacy can be achieved with lower cost/commercial grade air purifiers, or if such an approach protects healthcare workers against virus aerosol contamination.

Method: A total of 109 (10 ml of 108) PhiX174 bacteriophages was nebulized into a sealed clinical room. Surface contamination was detected by settle plates left uncovered during exposure. A healthcare worker remained in the room, personal exposure was determined by skin swabs after exiting the room, following doffing of personal protective equipment (PPE). Four skin areas were swabbed: forearms/hands, neck, forehead, under N95 mask. Three conditions were tested, 1) hood with hospital grade air purifier (IQ Air Health Pro 250), 2) hood with commercial air purifier (Philips 1000i), and 3) control (no hood/air-purification).

Findings: The control condition demonstrated extensive environmental and limited skin contamination underneath PPE, which was highest under an N95 mask. The commercial air purifier and hood provided environmental control of virus aerosol and almost zero skin contamination. In comparison, the hospital grade purifier provided complete environmental and skin contamination protection, despite a lower clean air filtration rate (240m3/hr vs 270m3/hr). Virus counts on plates and swabs were significantly lower for both air purifiers and across neck, forehead, and under the N95. There were no statistically significant differences in detected virus counts between air purifiers.

Conclusion: This cheap and scalable method may be an effective way to reduce the spread of COVID-19 in hospitals by enhancing the effectiveness of PPE worn by health care workers who care for COVID-19 patients and who are exposed to virus aerosol.
Seasonal betacoronavirus antibodies expansion post BNT161b2 vaccination associates with reduced SARS-CoV-2 VoCs neutralization
Authors: Dispinseri Stefania , Marzinotto Ilaria , Brigatti Cristina , Pirillo Maria Franca , Tolazzi Monica , Bazzigaluppi Elena , Canitano Andrea , Borghi Martina , Gallinaro Alessandra , Caccia Roberta , Vercesi Riccardo , McKay Paul F , Ciceri Fabio , Piemonti Lorenzo , Negri Donatella , Cinque Paola , Cara Andrea , Lampasona Vito , Scarlatti Gabriella
Published: August 2021

SARS-CoV-2 vaccination is known to induce antibodies that recognize also variants of concerns (VoCs) of the virus. However, epidemiological and laboratory evidences indicate that these antibodies have a reduce neutralization ability against VoCs. We studied binding and neutralizing antibodies against the Spike RBD and S2 domains of the Wuhan-Hu-1 virus and its alpha and beta VoCs and of seasonal betacoronaviruses (HKU1 and OC43) in a cohort of 31 health care workers vaccinated with BNT162b2-Comirnaty and prospectively followed post-vaccination. The study of sequential samples collected up to 64 days post-vaccination showed that serological assays measuring IgG against Wuhan-Hu-1 antigens were a poor proxy for VoCs neutralization. In addition, in subjects who had asymptomatic or mild COVID-19 prior to vaccination the loss of nAbs following disease can be rapid and protection from re-infection post-vaccination is often no better than in naïve subjects. Interestingly, in health care workers naïve for SARS-CoV-2 infection, vaccination induced a rapid and transient reactivation of pre-existing seasonal coronaviruses IgG responses that was associated with a subsequent reduced ability to neutralize some VoCs.
Time needed to perform intermittent catheterization in adults with spinal cord injury: A pilot randomized controlled cross-over study
Authors: Gopalakrishnan Karthik , Nielsen Nick Fabrin , Ramirez Andrea L. , Sørensen Jeppe , Walter Matthias , Krassioukov Andrei V.
Published: August 2021

Background

Intermittent catheterization (IC), considered the gold standard for bladder management for individuals with spinal cord injury (SCI) with sufficient dexterity, is usually performed using hydrophilic (HPC) or non-hydrophilic (non-HPC) catheters. Currently, there is no evidence on the temporal burden associated with IC with either catheter.

Objective

To compare both catheters regarding their time requirement for IC and participant satisfaction.

Design, setting and participants

Twenty individuals with chronic (>1-year) SCI at any spinal segment were randomized to undergo two cross-over assessments within 10 days (i.e., either starting with HPC or non-HPC). We measured time taken to perform IC using a 13 step pre-determined IC protocol (e.g., enter bathroom, wash hands, transfer to toilet, etc.). Furthermore, we assessed user satisfaction of both catheters using a Likert scale (i.e., strongly agree=5, strongly disagree=1).

Outcome measures and statistical analysis

Time (i.e., for each step and in total) to perform IC and participant satisfaction were compared between catheters using non-parametric statistics, i.e., Wilcoxon rank sign tests. Results are presented as median with interquartile range.

Results and limitations

Participants using HPCs spent less time to prepare a catheter [15 s (10-20) vs. 41 (20-69), p=0.002] and overall to perform IC [283 s (242-352) vs. 373 (249-441), p=0.01] compared to non-HPCs. Moreover, participants rated the preparation of HPCs to be easier [5 (4-5) vs. 4 (2-4), p=0.047] compared to non-HPCs. The key limitation of this pilot study was the sample size.

Conclusions

Preparation and usage of HPCs for IC is easier and faster compared to non-HPCs. IC can be a significant temporal burden for SCI individuals.

Patient summary

We compared coated and uncoated catheters on time needed for intermittent catheterization and user satisfaction in individuals with spinal cord injury. Participants can manually empty their bladder quicker and easier with coated compared to uncoated catheters.
Peripheral Artery Disease and COVID-19 Outcomes: Insights from the Yale DOM-CovX Registry
Authors: Smolderen Kim G. , Lee Megan , Arora Tanima , Simonov Michael , Mena-Hurtado Carlos
Published: August 2021

Background

Both COVID-19 infection and peripheral arterial disease (PAD) cause hypercoagulability in patients, and it remains unknown whether PAD predisposes patients to experience worse outcomes when infected with SARS-CoV-2.

Methods

The Yale DOM-CovX Registry consecutively enrolled inpatients for SARS-CoV-2 between March 1, 2020, and November 10, 2020. Adjusted logistic regression models examined associations between PAD and mortality, stroke, myocardial infarction (MI), and major adverse cardiovascular events (MACE, all endpoints combined).

Results

Of the 3,830 patients were admitted with SARS-CoV-2, 50.5% were female, mean age was 63.1 ±18.4 years, 50.7% were minority race, and 18.3% (n = 693) had PAD. PAD was independently associated with increased mortality (OR=1.45, 95% CI 1.11-1.88) and MACE (OR=1.48, 95% CI 1.16-1.87). PAD was not independently associated with stroke (p=0.06) and MI (p=0.22).

Conclusion

Patients with PAD have a >40% odds of mortality and MACE when admitted with a SARS-CoV-2, independent of known risk factors.
DeepSARS: simultaneous diagnostic detection and genomic surveillance of SARS-CoV-2
Authors: Yermanos Alexander , Hong Kai-Lin , Agrafiotis Andreas , Han Jiami , Nadeau Sarah , Valenzuela Cecilia , Azizoglu Asli , Ehling Roy , Gao Beichen , Spahr Michael , Neumeier Daniel , Chang Ching-Hsiang , Dounas Andreas , Petrillo Ezequiel , Nissen Ina , Burcklen Elodie , Feldkamp Mirjam , Beisel Christian , Oxenius Annette , Savic Miodrag , Stadler Tanja , Rudolf Fabian , Reddy Sai T.
Published: August 2021

The continued spread of SARS-CoV-2 and emergence of new variants with higher transmission rates and/or partial resistance to vaccines has further highlighted the need for large-scale testing and genomic surveillance. However, current diagnostic testing (e.g., PCR) and genomic surveillance methods (e.g., whole genome sequencing) are performed separately, thus limiting the detection and tracing of SARS-CoV-2 and emerging variants. Here, we developed DeepSARS, a high-throughput platform for simultaneous diagnostic detection and genomic surveillance of SARS-CoV-2 by the integration of molecular barcoding, targeted deep sequencing, and computational phylogenetics. DeepSARS enables highly sensitive viral detection, while also capturing genomic diversity and viral evolution. We show that DeepSARS can be rapidly adapted for identification of emerging variants, such as alpha, beta, gamma, and delta strains, and profile mutational changes at the population level. DeepSARS sets the foundation for quantitative diagnostics that capture viral evolution and diversity.

Abstract Figure

Graphical abstract

DeepSARS uses molecular barcodes (BCs) and multiplexed targeted deep sequencing (NGS) to enable simultaneous diagnostic detection and genomic surveillance of SARS-CoV-2.
T Cell Predominant Response to AAV-Spike Protects hACE2 Mice from SARS-CoV-2 Pneumonia
Authors: Greer Christopher D. , Kasden Coral M. , Morales Leon , Lundgreen Kendall A. , Hicks Philip D. , Carpenter Lilia J. , Salas-Quinchucua Cristhian , Tichy Elisia D. , Maguire Albert M. , Hoffman Jennifer G. , Bailey Robin J. , Zhou Shangzhen , Luo Angela , Chomistek Steven J. , Kozyak Benjamin W. , Bridges Charles R. , Gordon Gilad S. , Tabin Geoffrey C. , Bates Paul F. , Osorio Jorge E. , Bennett Jean , Stedman Hansell H.
Published: August 2021

Prevention of COVID-19 is widely believed to depend on neutralization of SARS-CoV-2 by vaccine-induced humoral immunity1,2, raising concern that emerging escape variants may perpetuate the pandemic3–6. Here we show that a single intramuscular injection of Adeno-Associated Virus-6 (AAV6) or AAV9 encoding a modified, N-terminal domain deleted (ΔNTD) spike protein induces robust cellular immunity and provides long-term protection in k18-hACE2 transgenic mice from lethal SARS-CoV-2 challenge, associated weight loss and pneumonia independent of vaccine-induced neutralizing humoral immunity. In both mice and macaques, vaccine-induced cellular immunity results in the clearance of transduced muscle fibers coincident with macrophage and CD8+ cytotoxic T cell infiltration at the site of immunization. Additionally, mice demonstrate a strong Type-1 polarized cellular immunophenotype and equivalent ex vivo T cell reactivity to peptides of wt and alpha (B.1.1.7) variant spike. These studies demonstrate not only that AAV6 and AAV9 can function as effective vaccine platforms, but also that vaccines can provide long-term efficacy primarily through the induction of cellular immunity. The findings may provide an alternative approach to containment of the evolving COVID-19 pandemic and have broader implications for the development of variant-agnostic universal vaccines against a wider range of pathogens.
Genome size drives morphological evolution in organ-specific ways
Authors: Itgen Michael W. , Siegel Dustin S. , Sessions Stanley K. , Mueller Rachel Lockridge
Published: August 2021

Morphogenesis is an emergent property of biochemical and cellular interactions during development. Genome size and the correlated trait of cell size can influence these interactions through its effects on developmental rate and tissue geometry, ultimately driving the evolution of morphology. We tested the effects of genome size and body size evolution on heart and liver morphology using nine species of the salamander genus Plethodon (genome sizes 29.3–67 Gb). Our results show that whole organ size is determined by body size, whereas tissue structure changes dramatically with evolutionary increases in genome size. In the heart, increased genome size is correlated with a reduction of myocardia in the ventricle, yielding proportionally less force–producing mass and more empty space. In the liver, increased genome size is correlated with fewer and larger vascular structures, positioning hepatocytes farther from the circulatory vessels that transport key metabolites. Although these structural changes should have obvious impacts on organ function, their effects on organismal performance and fitness are likely negligible because low metabolic rates in salamanders relax selective pressure on key metabolic organ performance. Overall, this study reveals the effects of large genome and cell size on the developmental systems producing the heart and liver.
Distinct stage-specific transcriptional states of B cells in human tonsillar tissue
Authors: Espinoza Diego A. , Le Coz Carole , Romberg Neil , Bar-Or Amit , Li Rui
Published: August 2021

B cells within secondary lymphoid tissues encompass a diverse range of activation states and multiple maturation processes that reflect antigen recognition and transition through the germinal center (GC) reaction, in which mature B cells differentiate into memory and antibody-secreting cells (ASCs). Here, using single-cell RNA-seq, we identify distinct activation and maturation profiles of B cells within and outside the GC reaction in human secondary lymphoid tissue. In particular, we identify a distinct, previously uncharacterizedCCL4/CCL3chemokine-expressing B-cell population with an expression pattern consistent with BCR/CD40 activation. Furthermore, we present a computational method leveraging regulatory network inference and pseudotemporal modeling to identify upstream transcription factor modulation along the GC to ASC maturation axis. Our dataset provides valuable insight into the diverse functional profiles and maturation processes that B cells undergo within secondary lymphoid tissues and will be a useful resource on which to base further studies into the B-cell immune compartment.

Highlights

scRNA-seq of human tonsillar B cells identifies distinct activation and maturation phenotypes.

Identification of a chemokine-expressing B-cell population in the human tonsil with a BCR and CD40 co-stimulatory gene signature.

Transcription factor regulatory network analysis identifies MYC and REL as predicted regulators of chemokine expression in the chemokine-expressing B-cell population.

Trajectory inference with gene and regulatory network modeling implicates novel transcription factors in the GC-to-ASC transition.