bluuebunny/crossref_metadata_2025 huggingface dataset:
CAPG is required for Ebola virus infection by controlling virus egress from infected cells
Authors: Mori Hiroyuki , Connell James P , Donahue Callie J , Boytz RuthMabel , Patten Justin J , Leung Daisy , LaCount Douglas J , Davey Robert A
Published: April 2022

Replication of Ebola virus (EBOV) is dependent upon actin functionality, especially at cell entry through macropinocytosis and at release of virus from cells. Previously, major actin-regulatory factors such as Rac1 and ARP2/3, involved in actin nucleation were shown important in both steps. However, downstream of nucleation, many other cell factors, are needed to control actin dynamics. How these regulate EBOV infection remains largely unknown. Here, we identified the actin-regulating protein, CAPG, as important for EBOV replication. Notably, knockdown (KD) of CAPG specifically inhibited viral infectivity and yield of infectious particles. Mechanistic analysis revealed a requirement of CAPG for virus production from infected cells. Proximity ligation and split GFP reconstitution assays revealed strong association of CAPG with VP40 that was mediated through the S1 domain of CAPG. Overall, CAPG is a novel host factor regulating EBOV infection through connecting actin filament stabilization to viral egress from cells.
Intensity and longevity of SARS-CoV-2 vaccination response and efficacy of adjusted vaccination schedules in patients with immune-mediated inflammatory disease
Authors: Simon David , Tascilar Koray , Fagni Filippo , Kleyer Arnd , Krönke Gerhard , Meder Christine , Dietrich Peter , Orlemann Till , Mößner Johanna , Taubmann Julia , Mutlu Melek Yalcin , Knitza Johannes , Kemenes Stephan , Liphardt Anna-Maria , Schönau Verena , Bohr Daniela , Schuster Louis , Hartmann Fabian , Leppkes Moritz , Ramming Andreas , Pachowsky Milena , Schuch Florian , Ronneberger Monika , Kleinert Stefan , Hueber Axel J. , Manger Karin , Manger Bernhard , Atreya Raja , Berking Carola , Sticherling Michael , Neurath Markus F. , Schett Georg
Published: April 2022

Objectives

To investigate the intensity and longevity of SARS-CoV-2 vaccination response in patients with immune-mediated inflammatory disease (IMID) by diagnosis, treatment and adapted vaccination schedules.

Methods

SARS-CoV-2 IgG antibody response after SARS-CoV-2 vaccination was measured longitudinally in a large prospective cohort of healthy controls (HC) and IMID patients between December 2020 and 2021. Demographic and disease-specific data were recorded. Humoral response was compared across treatment and disease groups, and with respect to receipt of booster vaccinations. Age and sex adjusted SARS-CoV-2 antibody response was modelled over time. Marginal mean antibody levels and marginal risks of poor response were calculated at weekly intervals starting from week-8 after the first vaccination up to week 40.

Results

Among 5076 individuals registered, 2535 IMID patients and 1198 HC were eligible for this analysis. Mean antibody levels were higher in HC compared to IMIDs at all-time points, with peak antibody response in HC more than twice that in IMIDs (12.48 (11.52-13.52) vs. 5.71 (5.46-5.97)). Poor response to vaccination was observed in IMID patients treated with agents affecting B- and T-cell functions. Mean differences in antibody response between IMID diseases were small. After additional vaccinations, IMID patients could achieve higher antibody levels than HC vaccinated according to the two-dose schedule, even-though initial antibody levels were lower.

Conclusions

IMID patients show a lower and less durable SARS-CoV-2 vaccination response and are at risk to lose humoral immune protection. Adjusted vaccination schedules with earlier boosters and/or more frequent re-doses could better protect IMID patients.
Ribo-macs derived from nucleoli: big ribosome clusters in the cytoplasm of naïve stem cells
Authors: Qin Kezhou , Sun Lei , Wu Xinyi , Wen Jitao , Xing Zhuanzhuan
Published: April 2022

Primed stem cells and naïve stem cells are important for understanding early development, but their ribosomes have not been focused on. In this study, we find that big ribosome clusters named Ribo-macs exist in the cytoplasm of naïve stem cells. Then, we prove that Ribo-macs are dynamic and physiological in the cytoplasm, and can synthesize proteins associated with biogenesis of endoplasmic reticulum and mitochondria. We also discover and demonstrate that Ribo-macs are the nucleoli, which of significance is promoting us to rethink our understanding of nucleoli. Besides, we reveal that Ribo-macs have a compatible relation with P-bodies and stress granules. In a word, all the results about Ribo-macs provide us with a new insight to understand how cells adapt quickly to environment.
Housekeeping gene gyrA, a potential molecular marker for Bacillus ecology study
Authors: Liu Yan , Štefanič Polonca , Miao Youzhi , Xue Yansheng , Xun Weibing , Shen Qirong , Xu Zhihui , Zhang Ruifu , Mandic-Mulec Ines
Published: April 2022

Bacillus is a ubiquitous microorganism and is one of the most commercially important species widely used in industry, agriculture and healthcare. Bacillus is relatively well understood at the single-cell level; however, molecular tools that determine diversity and ecology of Bacillus community are limited, which limits our understanding of how the Bacillus community works. In the present study, we investigated the potential of the housekeeping gene gyrA as a molecular marker for determining the diversity of Bacillus species. The amplification efficiency for Bacillus species diversity could be greatly improved by primer design. Therefore, we designed a novel primer pair gyrA3 that can detect at least 92 Bacillus species and related species. For Bacillus amyloliquefaciens, Bacillus pumilus, and Bacillus megaterium, we observed that the high variability of the gyrA gene allows for more detailed clustering at the subspecies level that cannot be achieved by the 16S rRNA gene. Since gyrA provides better phylogenetic resolution than 16S rRNA and informs on the diversity of the Bacillus community, we propose that gyrA gene may have broad application prospects in the study of Bacillus ecology.
Outside-in: intracellular vesicles in giant sulfur bacteria contain peptidoglycan
Authors: Flood Beverly E. , Leprich Dalton J. , Hunter Ryan C. , Delherbe Nathalie , MacGregor Barbara , Nieuwenhze Michael Van , Bailey Jake V.
Published: April 2022

Until recently, the cellular envelopes of bacteria were regarded as static and rigid relative to those of eukaryotes. While investigating peptidoglycan synthesis in populations of giant sulfur bacteria, Candidatus Thiomargarita spp., we observed internal vesicle-like features (VLFs). VLFs, as imaged following the active incorporation of D-amino acids, appear to begin as invaginations and delaminations of the cellular envelope. Staining with wheat germ agglutinin confirmed the presence of peptidoglycan in VLFs, while polymyxin B revealed that the outer membrane is present in some VLFs. Transmission electron microscopy revealed a complex network of interconnected VLFs. Genomes of Ca. Thiomargarita nelsonii lack a canonical divisome, while possessing homologs to genes such as actin, membrane scaffolding proteins, and dynamins that are associated with phagocytosis in eukaryotes. The physiological role of VLFs remains unclear, but the presence of sulfur globules in some suggests compartmentalization of metabolism and energy production. This is the first report of peptidoglycan and outer membrane bound intracellular vesicles within prokaryotic cells. These findings transform the canonical view of the inflexible bacterial cell envelope and further narrow the divide between prokaryotes and eukaryotes.
Measures for infection prevention and control of SARS-CoV-2 in Belgian schools between December 2020 and June 2021: a prospective cohort study
Authors: Callies Milena , Kabouche Ines , Desombere Isabelle , Merckx Joanna , Roelants Mathieu , Vermeulen Melissa , Duysburgh Els
Published: April 2022

Introduction

As the role of school-aged children was unclear at the onset of the COVID-19 pandemic, public health authorities recommended to implement infection prevention and control (IPC) measures in school settings. Few studies evaluated the implementation of these measures and their effect on SARS-CoV-2 infection rates among pupils and staff.

Aim

To describe the implementation of IPC measures in Belgian primary and secondary schools and assess its relation to the prevalence of anti-SARS-CoV-2 antibodies among pupils and staff.

Methods

We conducted a prospective cohort study in a representative sample of primary and secondary schools in Belgium. Implementation of IPC measures in schools was assessed using an online questionnaire. Saliva samples were collected from pupils and staff to determine the SARS-CoV-2 seroprevalence.

Results

A variety of IPC measures (ventilation, hygiene and physical distancing) was implemented by more than 60% of primary and secondary schools with most attention for hygiene measures. Almost no differences in implementation coverage were observed between primary and secondary schools or the Dutch and French language network. Poor implementation of IPC measures was associated with an increased anti-SARS-CoV-2 antibody prevalence among pupils from 8.6% (95% CI: 4.5 - 16.6) to 16.7% (95% CI: 10.2 - 27.4) and staff from 11.5% (95% CI: 8.1 - 16.4) to 17.6% (95% CI: 11.5 - 27.0). This association was statistically significant for all IPC measures and pupils and staff combined.

Conclusion

Belgian schools were relatively compliant with recommended IPC measures at the school level. Poor implementation of IPC measures was associated with higher SARS-CoV-2 seroprevalence among pupils and staff.

Trial registration number

Trial registration number: NCT04613817
Blue turns to grey - Palaeogenomic insights into the evolutionary history and extinction of the blue antelope (Hippotragus leucophaeus)
Authors: Hempel Elisabeth , Bibi Faysal , Faith J. Tyler , Koepfli Klaus-Peter , Klittich Achim M. , Duchêne David A. , Brink James S. , Kalthoff Daniela C. , Dalén Love , Hofreiter Michael , Westbury Michael V.
Published: April 2022

The blue antelope (Hippotragus leucophaeus) is the only large African mammal species to have become extinct in historical times, yet no nuclear genomic information is available for this species. A recent study showed that many alleged blue antelope museum specimens are either roan (H. equinus) or sable (H. niger) antelopes, further reducing the possibilities for obtaining genomic information for this extinct species. While the blue antelope has a rich fossil record from South Africa, climatic conditions in the region are unfavourable to the preservation of ancient DNA. Nevertheless, we recovered two blue antelope draft genomes, one at 3.4x mean coverage from a historical specimen (~200 years old) and one at 2.1x mean coverage from a fossil specimen dating to 9,800–9,300 cal BP, making it currently the oldest palaeogenome from Africa. Phylogenomics show that blue and sable antelope are sister species, confirming previous mitogenomic results, and demonstrate ancient gene flow from roan into blue antelope. We show that blue antelope genomic diversity was much lower than in roan and sable antelopes, indicative of a low population size since at least the early Holocene. This supports observations from the fossil record documenting major decreases in the abundance of blue antelope after the Pleistocene-Holocene transition. Finally, the persistence of this species throughout the Holocene despite low population size suggests that colonial-era human impact was likely a decisive factor in the blue antelope’s extinction.
Human and murine Cryptococcus neoformans infection selects for common genomic changes in an environmental isolate
Authors: Sephton-Clark Poppy , McConnell Scott A. , Grossman Nina , Baker Rosanna , Dragotakes Quigly , Fan Yunfan , Fu Man Shun , Gerbig Gracen , Greengo Seth , Hardwick J. Marie , Kulkarni Madhura , Levitz Stuart M. , Nosanchuk Joshua D. , Shoham Shmuel , Smith Daniel , Stempinski Piotr , Wear Maggie , Cuomo Christina A. , Casadevall Arturo
Published: April 2022

A pet cockatoo was the suspected source of Cryptococcus neoformans recovered from the cerebral spinal fluid (CSF) of an immunocompromised patient with cryptococcosis based on the molecular analyses available in 2000. Here we report whole genome sequence analysis of the clinical and cockatoo strains. Both are closely related MATα strains belonging to the VNII lineage, confirming that the human infection likely originated from pet bird exposure. The two strains differ by 61 single nucleotide polymorphisms, including 8 nonsynonymous changes involving 7 genes. To ascertain whether changes in these genes are selected during mammalian infection, we passaged the cockatoo strain in mice. Remarkably, isolates obtained from mouse tissue possess a frame-shift mutation in one of the seven genes altered in the human sample, a gene predicted to encode a SWI-SNF chromatin-remodeling complex protein. Both cockatoo and patient strains as well as mouse passaged isolates obtained from brain tissue had a premature stop codon in a homolog of ZFC3, a predicted single-zinc finger containing protein, which is associated with larger capsules when deleted and appears to have reverted to a full-length protein in the mouse passaged isolates obtained from lung tissue. The patient strain and mouse passaged isolates show variability in the expression of virulence factors, with differences in capsule size, melanization, and rates on non-lytic expulsion from macrophages observed. Our results establish that environmental strains undergo genomic and phenotypic changes during mammalian passage, suggesting that animal virulence can be a mechanism for genetic change and that the genomes of clinical isolates may provide a readout of mutations acquired during infection.
Deep Brain Magnetothermal Silencing of Dopaminergic Neurons via Endogenous TREK1 Channels Abolishes Place Preference in Mice
Authors: Liu Junting , Munshi Rahul , He Muye , Parker Sara D. , Pralle Arnd
Published: April 2022

Remote neuromodulation techniques have revolutionized our understanding of brain circuits and their role in behavior. The reversible silencing of specific neuronal populations has emerged as a powerful tool to investigate the necessity and sufficiency of these populations in behavioral responses. Here, we apply magnetothermal silencing using endogenous TREK-1 channels to selectively suppress dopaminergic reward in the ventral tegmental area (VTA) to prove that activation of this specific reward circuit is required for place preference in mice. Magnetothermal silencing entails the application of alternating magnetic fields that penetrate tissue, leading to the heating of superparamagnetic nanoparticles at the target cells, without causing any attenuation or adverse effects. The resultant slight, rapid, and reversible elevation in temperature effectively suppresses neuronal firing, without necessitating genetic modification of the neurons. We demonstrate that two-pore potassium channels, TREK-1, are responsible for this thermal neuronal silencing. Using fiber-based optogenetics we measured both the heating and neuronal silencing in the VTA brain of the animals. We show that in a place preference assay, magnetothermal neuronal silencing of the dopaminergic neurons in the VTA is sufficient to abolish the place preference. Notably, TREK1 knock-out mice exhibit immunity to magnetothermal silencing, behaving as if the magnetic field was not applied. These results underscore the critical role of dopaminergic neuronal activity in the VTA for the establishment of place preference and highlight the dependency on functional TREK1 channels in this magnetothermal silencing approach.

Highlights

TREK1 is a highly efficient, thermally activated neuronal silencer

First magnetothermal neuronal silencing in behaving mice

Fiber photometry quantification of local heating and silencing of target neurons in the ventral tegmental area

Magnetothermal suppression of dopaminergic reward response in the ventral tegmental area is sufficient to abolish place preference
Supramolecular architecture of the ER-mitochondria encounter structure in its native environment
Authors: Wozny Michael R. , Di Luca Andrea , Morado Dustin R. , Picco Andrea , Hoffmann Patrick C. , Miller Elizabeth A. , Vanni Stefano , Kukulski Wanda
Published: April 2022

The endoplasmic reticulum and mitochondria are main hubs of eukaryotic membrane biogenesis which rely on lipid exchange via membrane contact sites, but the underpinning mechanisms remain poorly understood. In yeast, tethering and lipid transfer between the two organelles is mediated by the ER-mitochondria encounter structure ERMES, a four-subunit complex of unclear stoichiometry and architecture. We determined the molecular organization of ERMES within cells using integrative structural biology, combining quantitative live-imaging, cryo-correlative microscopy, subtomogram averaging and molecular modeling. ERMES assembles into approximately 25 discrete bridge-like complexes distributed irregularly across a contact site. Each bridge consists of three lipid-binding SMP domains arranged in zig-zag fashion. Our molecular model of ERMES reveals an unconventional restrained pathway for lipids. These findings resolve a supramolecular architecture controlling interorganelle lipid fluxes.
Inflammation induced Vascular Smooth Muscle Cell expressing Angiopoietin-like 2 to promote the development of abdominal aortic aneurysm
Authors: Yang Guangcan , Guo Jie , Wu Shuang , Yu Hongyou
Published: April 2022

Objective

The objective of this study is to investigate the expression of angiopoietin-like protein 2 (Angptl2) in abdominal aortic aneurysm (AAA) and the expression of Angptl2 in vascular smooth muscle cells (VSMC) under inflammation stimuli.

Methods

The mouse AAA model was induced by applying calcium chloride method based the literature and the expression of Angptl2 in AAA was investigated by immunohistochemical staining. The primary VSMCs were cultured and identified following with inflammatory stimuli by Escherichia coli lipopolysaccharide (LPS) for 30 minutes and 24 hours. The expression of Angptl2 were assessed by RT-qPCR and ELISA.

Results

The mouse AAA model was successfully established after being induced by calcium chloride. The inflammatory cell infiltration in the arterial tissue of the mice in the experimental group was obvious, and the elastic fiber layer was thinned and broken. Immunohistochemical staining showed that the expression of Angptl2 in AAA was up-regulated; After LPS treatment, both the mRNA and protein expressions of Angptl2 were significantly up-regulated in VSMCs in the experimental group compared with control group.

Conclusion

Angptl2 expressed in VSMCs promotes the development of calcium chloride induced AAA.
Goldilocks calcium and the mitochondrial respiratory chain: too much, too little, just right
Authors: Vilas-Boas Eloisa A. , Cabral-Costa João Victor , Ramos Vitor M. , Caldeira da Silva Camille C. , Kowaltowski Alicia J.
Published: April 2022

Calcium (Ca2+) is a key regulator in diverse intracellular signaling pathways, and has long been implicated in metabolic control and mitochondrial function. Mitochondria can actively take up large amounts of Ca2+, thereby acting as important intracellular Ca2+buffers and affecting cytosolic Ca2+transients. Excessive mitochondrial matrix Ca2+is known to be deleterious due to opening of the mitochondrial permeability transition pore (mPTP) and consequent membrane potential dissipation, leading to mitochondrial swelling, rupture, and cell death. Moderate Ca2+within the organelle, on the other hand, can directly or indirectly activate mitochondrial matrix enzymes, possibly impacting on ATP production. Here, we aimed to determine in a quantitative manner if extra or intramitochondrial Ca2+modulate oxidative phosphorylation in mouse liver mitochondria and intact hepatocyte cell lines. To do so, we monitored the effects of more modest versus supra-physiological increases in cytosolic and mitochondrial Ca2+on oxygen consumption rates. Isolated mitochondria present increased respiratory control ratios (a measure of oxidative phosphorylation efficiency) when incubated with low (2.4 ± 0.6 μM) and medium (22.0 ± 2.4 μM) Ca2+concentrations in the presence of complex I-linked substrates pyruvate plus malate and α-ketoglutarate, respectively, but not complex II-linked succinate. In intact cells, both low and high cytosolic Ca2+led to decreased respiratory rates, while ideal rates were present under physiological conditions. High Ca2+decreased mitochondrial respiration in a substrate-dependent manner, mediated by mPTP. Overall, our results uncover a Goldilocks effect of Ca2+on liver mitochondria, with specific “just right” concentrations that activate oxidative phosphorylation.
Optimal enzyme utilization suggests concentrations and thermodynamics favor condition-specific saturations and binding mechanisms
Authors: Sahin Asli , Weilandt Daniel Robert , Hatzimanikatis Vassily
Published: April 2022

Understanding the dynamic responses of living cells upon genetic and environmental perturbations is crucial to decipher the metabolic functions of organisms. The rates of enzymatic reactions and their evolution are key to this understanding, as metabolic fluxes are limited by enzymatic activity. In this work, we investigate the optimal modes of operations for enzymes with regard that the evolutionary pressure drives enzyme kinetics toward increased catalytic efficiency. We use an efficient mixed-integer formulation to decipher the principles of optimal catalytic properties at various operating points. Our framework allows assessing the distribution of the thermodynamic forces and enzyme states, providing detailed insight into the mode of operation. Our results confirm earlier theoretical studies on the optimal kinetic design using a reversible Michaelis-Menten mechanism. The results further explored the optimal modes of operation for random-ordered multi-substrate mechanisms. We show that optimal enzyme utilization is achieved by unique or alternative modes of operations depending on the reactant’s concentrations. Our novel formulation allows investigating the optimal catalytic properties of all enzyme mechanisms with known elementary reactions. We propose that our novel framework provides the means to guide and evaluate directed evolution studies and estimate the limits of the direct evolution of enzymes.
Heterotypic Influenza Infections Mitigate Susceptibility to Secondary Bacterial Infection
Authors: Cipolla Ellyse M. , Yue Molin , Nickolich Kara L. , Huckestein Brydie R. , Antos Danielle E. , Chen Wei , Alcorn John F.
Published: April 2022

Influenza associated bacterial super-infections have devastating impacts on the lung and can result in increased risk of mortality. New strains of influenza circulate throughout the population yearly promoting the establishment of immune memory. Nearly all individuals have some degree of influenza memory prior to adulthood. Due to this we sought to understand the role of immune memory during bacterial super-infections. An influenza heterotypic immunity model was established using influenza A/PR/8/34 and A/X31. We report here that influenza experienced mice are more resistant to secondary bacterial infection with methicillin-resistant Staphylococcus aureus as determined by wasting, bacterial burden, pulmonary inflammation, and lung leak, despite significant ongoing lung remodeling. Multidimensional flow cytometry and lung transcriptomics revealed significant alterations in the lung environment in influenza-experienced mice compared with naïve animals. These include changes in the lung monocyte and T cell compartments, characterized by increased expansion of influenza tetramer specific CD8+ T cells. The protection that was seen in memory experienced mouse model is associated with the reduction in inflammatory mechanisms making the lung less susceptible to damage and subsequent bacterial colonization. These findings provide insight into how influenza heterotypic immunity re-shapes the lung environment and the immune response to a re-challenge event, which is highly relevant to the context of human infection.
The C-type Lectin Receptor Dectin-2 is a receptor for Aspergillus fumigatus galactomannan
Authors: Reedy Jennifer L. , Crossen Arianne J. , Negoro Paige E. , Brown Hannah E. , Ward Rebecca A. , Blanco Diego A. Vargas , Timmer Kyle D. , Mansour Michael K. , Wüthrich Marcel , Fontaine Thierry , Latgé Jean-Paul , Vyas Jatin M.
Published: April 2022

Aspergillus fumigatus is a ubiquitous environmental mold that causes significant mortality particularly amongst immunocompromised patients. The detection of the Aspergillus-derived carbohydrate galactomannan in patient sera and bronchoalveolar lavage fluid is the major biomarker used to detect A. fumigatus infection in clinical medicine. Despite the clinical relevance of this carbohydrate, we lack a fundamental understanding of how galactomannan is recognized by the immune system and its consequences. Galactomannan is composed of a linear mannan backbone with galactofuranose sidechains and is found both attached to the cell surface of Aspergillus and as a soluble carbohydrate in the extracellular milieu. In this study, we utilized fungal-like particles composed of highly purified Aspergillus galactomannan to identify a C-type lectin host receptor for this fungal carbohydrate. We identified a novel and specific interaction between Aspergillus galactomannan and the C-type lectin receptor Dectin-2. We demonstrate that galactomannan bound to Dectin-2 and induced Dectin-2 dependent signaling including activation of spleen tyrosine kinase and potent TNFα production. Deficiency of Dectin-2 increased immune cell recruitment to the lungs but was dispensable for survival in a mouse model of pulmonary aspergillosis. Our results identify a novel interaction between galactomannan and Dectin-2 and demonstrate that Dectin-2 is a receptor for galactomannan which leads to a pro-inflammatory immune response in the lung.

IMPORTANCE

Aspergillus fumigatus is a fungal pathogen that causes serious and often fatal disease in humans. The surface of Aspergillus is composed of complex sugar molecules. Recognition of these carbohydrates by immune cells by carbohydrate lectin receptos can lead to clearance of the infection or, in some cases, benefit the fungus by dampening the host response. Galactomannan is a carbohydrate that is part of the cell surface of Aspergillus but is also released during infection and is found in patient lungs as well as their bloodstreams. The significance of our research is that we have identified a mammalian immune cell receptor that recognizes, binds, and signals in response to galactomannan. These results enhance our understanding of how this carbohydrate interacts with the immune system at the site of infection and will lead to broader understanding of how release of galactomannan by Aspergillus effects the immune response in infected patients.
Karyorelict ciliates use an ambiguous genetic code with context-dependent stop/sense codons
Authors: Seah Brandon Kwee Boon , Singh Aditi , Swart Estienne Carl
Published: April 2022

Abstract

In ambiguous stop/sense genetic codes, the stop codon(s) not only terminate translation but can also encode amino acids. Such codes have evolved at least four times in eukaryotes, twice among ciliates (Condylostoma magnum and Parduczia sp.). These have appeared to be isolated cases whose next closest relatives use conventional stop codons. However, little genomic data have been published for the Karyorelictea, the ciliate class that contains Parduczia sp., and previous studies may have overlooked ambiguous codes because of their apparent rarity. We therefore analyzed single-cell transcriptomes from four of the six karyorelict families to determine their genetic codes. Reassignment of canonical stops to sense codons was inferred from codon frequencies in conserved protein domains, while the actual stop codon was predicted from full-length transcripts with intact 3’-untranslated regions (3’-UTRs). We found that all available karyorelicts use the Parduczia code, where canonical stops UAA and UAG are reassigned to glutamine, and UGA encodes either tryptophan or stop. Furthermore, a small minority of transcripts may use an ambiguous stop-UAA instead of stop-UGA. Given the ubiquity of karyorelicts in marine coastal sediments, ambiguous genetic codes are not mere marginal curiosities but a defining feature of a globally distributed and diverse group of eukaryotes.
Tuning aromatic contributions by site-specific encoding of fluorinated phenylalanine residues in bacterial and mammalian cells
Authors: Galles Grace D. , Infield Daniel T. , Clark Colin J. , Hemshorn Marcus L. , Manikandan Shivani , Fazan Frederico , Rasouli Ali , Tajkhorshid Emad , Galpin Jason D. , Cooley Richard B. , Mehl Ryan A. , Ahern Christopher A.
Published: April 2022

The aromatic side-chains of phenylalanine, tyrosine, and tryptophan interact with their environments via both hydrophobic and electrostatic interactions. Determining the extent to which these contribute to protein function and stability is not possible with conventional mutagenesis. Serial fluorination of a given aromatic is a validated method in vitro and in silico to specifically alter electrostatic characteristics, but this approach is restricted to a select few experimental systems. Here, we report a new group of pyrrolysine-based aminoacyl-tRNA synthetase/tRNA pairs that enable the site-specific encoding of a varied spectrum of fluorinated phenylalanine amino acids in E. coli and mammalian (HEK 293T) cells. By allowing the cross-kingdom expression of proteins bearing these unnatural amino acids at biochemical scale, these tools will enable deconstruction of biological mechanisms which utilize aromatic-pi interactions in structural and cellular contexts.

Statement of Significance

The aromatic side-chains of phenylalanine, tyrosine, and tryptophan are crucial for protein function and pharmacology due to their hydrophobic and electrostatic contributions to catalytic centers and ligand-binding pockets. However, few experimental approaches can chemically assess the functional roles of aromatics in cellular environments. The accepted computational method for aromatic interrogation is via serial fluorination, which lacks an experimental correlate in bacterial or mammalian cell systems. We have identified a family of synthetases to encode multiple different types of fluorinated phenylalanine residues in E. coli and HEK cells via nonsense suppression. The efficiency of these synthetases is sufficient to support biochemical characterization and structural determination of proteins with site-specific incorporation of unnatural phenylalanine analogs.
Physiological insight into the conserved properties ofCaenorhabditis elegansacid-sensing DEG/ENaCs
Authors: Kaulich Eva , McCubbin Patrick T. N. , Schafer William R. , Walker Denise S.
Published: April 2022

Acid sensing ion channels (ASICs) are members of the diverse family of degenerin/epithelial sodium channels (DEG/ENaCs). They perform a wide range of physiological roles in healthy organisms, including in gut function and synaptic transmission, but also play important roles in disease, as acidosis is a hallmark of painful inflammatory and ischaemic conditions. We performed a screen for acid-sensitivity on all 30 subunits of theC. elegansDEG/ENaC family using Two-Electrode Voltage Clamp (TEVC) inXenopusoocytes. We found two groups of acid-sensing DEG/ENaCs characterised by being inhibited or activated by increasing proton concentrations. Three of these acid-sensitiveC. elegansDEG/ENaCs were activated by acidic pH, making them functionally similar to the vertebrate ASICs. We also identified four new members of the acid-inhibited DEG/ENaC group, giving a total of seven additional acid-sensitive channels. We observed sensitivity to the anti-hypertensive drug amiloride as well as modulation by the trace element zinc. Acid-sensitive DEG/ENaCs were found to be expressed in both neurons and non-neuronal tissue, highlighting the likely functional diversity of these channels. Our findings provide a framework to exploit theC. eleganschannels as models to study the function of these acid-sensing channelsin vivo, as well as to study them as potential targets for anti-helminthic drugs.
A Joint Subspace Mapping Between Structural and Functional Brain Connectomes
Authors: Ghosh Sanjay , Raj Ashish , Nagarajan Srikantan S.
Published: April 2022

Understanding the connection between the brain’s structural connectivity and its functional connectivity is of immense interest in computational neuroscience. Although some studies have suggested that whole brain functional connectivity is shaped by the underlying structure, the rule by which anatomy constraints brain dynamics remains an open question. In this work, we introduce a computational framework that identifies a joint subspace of eigenmodes for both functional and structural connectomes. We found that a small number of those eigenmodes are sufficient to reconstruct functional connectivity from the structural connectome, thus serving as low-dimensional basis function set. We then develop an algorithm that can estimate the functional eigen spectrum in this joint space from the structural eigen spectrum. By concurrently estimating the joint eigenmodes and the functional eigen spectrum, we can reconstruct a given subject’s functional connectivity from their structural connectome. We perform elaborate experiments and demonstrate that the proposed algorithm for estimating functional connectivity from the structural connectome using joint space eigenmodes gives competitive performance as compared to the existing benchmark methods with better interpretability.
3D-equivariant graph neural networks for protein model quality assessment
Authors: Chen Chen , Chen Xiao , Morehead Alex , Wu Tianqi , Cheng Jianlin
Published: April 2022

Motivation

Quality assessment of predicted protein tertiary structure models plays an important role in ranking and using them. With the recent development of deep learning end-to-end protein structure prediction techniques of generating highly confident tertiary structures for most proteins, it is important to explore corresponding quality assessment strategies to evaluate and select the structural models predicted by them since these models have better quality and different properties than the models predicted by traditional tertiary structure prediction methods.

Results

We develop EnQA, a novel graph-based 3D-equivariant neural network method that is equivariant to rotation and translation of 3D objects to estimate the accuracy of protein structural models by leveraging the structural features acquired from the state-of-the-art tertiary structure prediction method - AlphaFold2. We train and test the method on both traditional model datasets (e.g., the datasets of the Critical Assessment of Techniques for Protein Structure Prediction (CASP)) and a new dataset of high-quality structural models predicted only by AlphaFold2 for the proteins whose experimental structures were released recently. Our approach achieves state-of-the-art performance on protein structural models predicted by both traditional protein structure prediction methods and the latest end-to-end deep learning method - AlphaFold2. It performs even better than the model quality assessment scores provided by AlphaFold2 itself. The results illustrate the 3D-equivariant graph neural network is a promising approach to the evaluation of protein structural models. AlphaFold2 features are important for improving protein model quality assessment and are complimentary with the geometric property features extracted from structural models.

Availability

The source code is available at https://github.com/BioinfoMachineLearning/EnQA.

Contact

chengji@missouri.edu

Supplementary information

Supplementary data are available.
Mutation of Arabidopsis SME1 and Sm core assembly improves oxidative stress resilience
Authors: Willems Patrick , Van Ruyskensvelde Valerie , Maruta Takanori , Pottie Robin , Fernández-Fernández Álvaro Daniel , Pauwels Jarne , Hannah Matthew A. , Gevaert Kris , Van Breusegem Frank , Van der Kelen Katrien
Published: April 2022

Alternative splicing is a key posttranscriptional gene regulatory process, acting in diverse adaptive and basal plant processes. Splicing of precursor-messenger RNA (pre-mRNA) is catalyzed by a dynamic ribonucleoprotein complex, designated the spliceosome. In a suppressor screen, we identified a nonsense mutation in the Sm protein SME1 to alleviate photorespiratory H2O2-dependent cell death in catalase deficient plants. Similar attenuation of cell death was observed upon chemical inhibition of the spliceosome, suggesting pre-mRNA splicing inhibition to be responsible for the observed cell death alleviation. Furthermore, the sme1-2 mutants showed increased tolerance to the reactive oxygen species inducing herbicide methyl viologen. Both an mRNA-seq and shotgun proteomic analysis in sme1-2 mutants displayed a constitutive molecular stress response, together with extensive alterations in pre-mRNA splicing of transcripts encoding metabolic enzymes and RNA binding proteins, even under unstressed conditions. Using SME1 as a bait to identify protein interactors, we provide experimental evidence for almost 50 homologs of mammalian spliceosome-associated protein to reside in the Arabidopsis thaliana spliceosome complexes and propose roles in pre-mRNA splicing for four uncharacterized plant proteins. Furthermore, like in sme1-2, a mutant in the Sm core assembly protein ICLN resulted in a decreased sensitivity to methyl viologen. Taken together, these data show that both a perturbed Sm core composition and assembly results in the activation of a defense response and enhanced resilience to oxidative stress.
Integration of Xeno-Free Single-cell Cloning in CRISPR-mediated DNA Editing of Human iPSCs Improves Homogeneity and Methodological Efficiency of Cellular Disease Modelling
Authors: Namipashaki Atefeh , Pugsley Kealan , Liu Xiaodong , Abrehart Kirra , Lim Sue Mei , Sun Guizhi , Herold Marco J. , Polo Jose M. , Bellgrove Mark A. , Hawi Ziarih
Published: April 2022

The capability to generate induced pluripotent stem cell (iPSC) lines, in tandem with CRISPR-Cas9 DNA editing, offers great promise to understand the underlying genetic mechanisms of human disease. The low efficiency of available methods for homogeneous expansion of singularised CRISPR-transfected iPSCs necessitates the coculture of transfected cells in mixed populations and/or on feeder layers. Consequently, edited cells must be purified using labour-intensive screening and selection, culminating in inefficient editing. Here, we provide a xeno-free method for single-cell cloning of CRISPRed iPSCs achieving a clonal survival of up to 70% within 7-10 days. This was accomplished through improved viability of the transfected cells, paralleled with provision of enriched environment for the robust establishment and proliferation of singularised iPSC clones. Enhanced cell survival was accompanied by a high transfection efficiency exceeding 97%, and editing efficiencies of 50-65% for NHEJ and 10% for HDR, indicative of the method’s utility in stem cell disease modelling.
DNA damage response signaling is crucial for effective Chikungunya virus replication
Authors: Chatterjee Sanchari , Kumar Sameer , Mamidi Prabhudutta , Datey Ankita , Sengupta Soumya , Mahish Chandan , Laha Eshna , De Saikat , Keshry Supriya Suman , Nayak Tapas Kumar , Ghosh Soumyajit , Singh Sharad , Subudhi Bharat Bhusan , Chattopadhyay Subhasis , Chattopadhyaya Soma
Published: April 2022

Viruses utilize a plethora of strategies to manipulate the host pathways and hijack its machineries for efficient replication. Several DNA as well as handful of RNA viruses are reported to interact with proteins involved in DNA damage responses (DDR). As the DDR pathways have never been explored in Alphaviruses, this investigation intended to determine the importance of the DDR pathways in CHIKV infection through in vitro,in vivoandex vivomodels. The study reveals that CHIKV infection activates the Chk2 and Chk1 proteins associated with DDR signaling pathways and increases DNA damage by 95%. Inhibition of both ATM-ATR kinases by ATM/ATR kinase inhibitor (AAKi) shows drastic reduction in viral particle formation in vitro. Next, the treatment of mice with this drug has been shown to reduce the disease score substantially in CHIKV-infected C57BL/6 mice with 71% decrement in the viral copy and the same has been established in hPBMC-derived monocyte-macrophage populations. Additionally, gene silencing of Chk2 and Chk1 reduces viral progeny formation around 73.7% and 78% respectively. Moreover, it has been demonstrated that CHIKV-nsP2 interacts with Chk2 and Chk1 during CHIKV infection and docking analysis depicts the specific amino acids responsible for these interactions. Further, the data suggests that CHIKV infection induces cell cycle arrest in G1 and G2 phases.

In conclusion, this work demonstrated for the first time the mechanistic insight of the induction of DDR pathways by CHIKV that might contribute to the designing of effective therapeutics for the control of this virus infection in future.

IMPORTANCE

Viruses being intra-cellular parasite, need several host cell machineries so as to achieve effective replication of their own genome, along with virus-encoded enzymes. One of the strategies is to hijack the DDR pathways. Several DNA as well as handful of RNA viruses interact with the cellular proteins involved in DDR pathways, however, reports with respect to the association of Chk2 and Chk1 in alphavirus infection are scanty. Hence, this study is amongst the first to report that modulation of DDR pathways is crucial for effective CHIKV infection. This work also shows that there is interaction of CHIKV-nsP2 with two crucial host factors, Chk2 and Chk1 for efficient viral infection. Interestingly, CHIKV infection was found to cause DNA damage and arrest cell cycle in G1 and G2 phases to facilitate viral infection. This information might facilitate to develop effective therapeutics for the control of the CHIKV infection in future.
Associations of genetic and infectious risk factors with coronary heart disease
Authors: Hodel Flavia , Xu Zhi Ming , Thorball Christian W. , de La Harpe Roxane , Letang-Mathieu Prunelle , Brenner Nicole , Butt Julia , Bender Noemi , Waterboer Tim , Marques-Vidal Pedro , Vollenweider Peter , Vaucher Julien , Fellay Jacques
Published: April 2022

Background and Purpose

Coronary heart disease (CHD) is one of the most pressing health problems of our time and a major cause of preventable death. CHD results from complex interactions between genetic and environmental factors. Using multiplex serological testing for persistent or frequently recurring infections and genome-wide analysis in a prospective population study, we delineate the respective and combined influences of genetic variation, infections, and low-grade inflammation on the risk of incident CHD.

Participants and Methods

Study participants are enrolled in the CoLaus|PsyCoLaus study, a longitudinal, population-based cohort with baseline assessments from 2003 through 2008 and follow-up visits every five years. We analyzed a subgroup of 3’459 individuals with available genome-wide genotyping data and immunoglobulin G levels for 22 persistent or frequently recurring pathogens. All reported CHD events were evaluated by a panel of specialists. We identified independent associations with incident CHD using univariable and multivariable stepwise Cox proportional hazards regression analyses.

Results

Of the 3’459 study participants, 210 (6.07%) had at least one CHD event during the 12 years of follow-up. Multivariable stepwise Cox regression analysis, adjusted for known cardiovascular risk factors, socioeconomic status and statin intake, revealed that high polygenic risk (hazard ratio (HR) 1.31, 95% CI 1.10–156, P = 2.64e-03) and infection withFusobacterium nucleatum(HR 1.63, 95% CI 1.08–2.45, P = 1.99e-02) were independently associated with incident CHD.

Conclusion

In a prospective, population-based cohort, high polygenic risk and infection withFusobacterium nucleatumhave a small, yet independent impact on CHD risk.
Proteomic study of differentially expressed proteins in seeds between parents and offspring of castor bean (Ricinus communis L.)
Authors: Liang Xiaotian , Luo Rui , Zhang Yanxin , Yin Mingda , Wen Yanpeng , Hu Xuemei , Wang Zhiyan , Huo Yumiao , Huang Fenglan
Published: April 2022

Castor bean (Ricinus communis L.), one of the top 10 oilseed crops in the world, has high economic value. Hybridization is the most direct and effective method to breed new varieties with high yield, high oil content, and strong stress resistance. Therefore, prediction of desired traits in castor hybrid offspring is particularly important. In this study, proteomic analysis was performed to identify differentially expressed proteins (DEPs) in seeds between castor hybrid offspring and their female (Lm female line aLmAB2) and male parents (CSR•181). Among the DEPs upregulated in the seeds of hybrid offspring, the majority were related to seed yield and stress resistance, while some were related to oil synthesis and fatty acid synthesis and metabolism in seeds. In other words, the hybrid offspring showed heterosis for seed yield, stress resistance, oil synthesis, and fatty acid synthesis and metabolism when compared with their parents. Further, real-time quantitative polymerase chain reaction assays were performed on 12 genes encoding DEPs involved in oil synthesis, pollen abortion, yield, and stress resistance of seeds. The results showed that the expression levels of the 12 genes were consistent with those of the DEPs.
Islamic banking and economic growth: fresh insights from Nigeria using autoregressive distributed lags (ARDL) approach
Authors: Tabash Mosab I. , Abdulkarim Fatima Muhammad , Akinlaso Mustapha Ishaq , Dhankar Raj S.
Published: April 2022

Purpose

The paper examines the relationship between Islamic banking and the growth of the economy in Nigeria in both the short run and long run.

Design/methodology/approach

The study employs quarterly secondary time series data for Islamic banking as well as major macroeconomic variables to study the contribution of Islamic banking to the economy of Nigeria. It employs autoregressive distributed lags (ARDL) and error correction model (ECM) approaches from 2013 quarter 1 up to 2020 quarter 2.

Findings

The results show that Islamic banking has a positive contribution to Nigeria's economy in both short run and long run, but this contribution is insignificant.

Practical implications

Policymakers should endeavor to redesign the country's financial architecture and come up with policies that can support the growth of Islamic finance sector. This will significantly strengthen Nigeria's position as one of the leading Islamic finance hubs in Africa.

Originality/value

This is the first study to examine the contribution of Islamic banking to the Nigerian economy according to the best knowledge of the authors.