bluuebunny/crossref_metadata_2025 huggingface dataset:
The effect of geographical variation in income measures on Measles-Mumps-Rubella uptake and coverage in England; a protocol for an ecological study
Authors: Ghazal Salma , Soyiri Ireneous N.
Published: December 2022

3.

Measles is a vaccine-preventable disease whose vaccine was introduced in the United Kingdom in 1988, however, Measles outbreaks are still occurring in England. Consequently, the World Health Organization (WHO) removed the UK’s elimination status of Measles in 2019.

Noticeably, MMR vaccination coverage in England is below the recommended threshold with geographical variations across local authorities (LA). The research into the effect of income disparities on MMR vaccine coverage was insufficiently examined. Therefore, an ecological study will be conducted aiming at determining whether there is a relationship between income deprivation measures and MMR vaccine coverage in upper-tier local authorities in England, using 2019 publicly available data. The effect of spatial clustering of income level on vaccination coverage will also be assessed.

Vaccination coverage data will be obtained from “Cover of Vaccination Evaluated Rapidly (COVER)”. Income deprivation score, Deprivation gap, and Income Deprivation Affecting Children Index will be obtained from Office for National Statistics and Moran’s Index will be generated using RStudio.

Rural/urban LA classification and mothers’ education will be included as possible confounding factors. Additionally, the live births rate per mothers’ age group will be included as a proxy for the mothers’ age variation in different LA. Multiple linear regression will be used after testing the relevant assumptions, using SPSS software. Moran’s I together with income deprivation score will be analysed through regression and mediation analysis.

This study will help in determining whether income level is a determinant of MMR vaccination uptake and coverage in LA in England which would help policymakers in designing targeted campaigns, thus preventing measles outbreaks in the future.
Is it possible to flatten-the-curve after the initial outbreak of Covid-19? A data-driven modeling analysis for Omicron pandemic in China
Authors: Sun Jiaqi , Li Yusi , Shao Ning-Yi , Liu Miao
Published: December 2022

In the current coronavirus disease 2019 (COVID-19) pandemic, the Omicron variant of severe acute respiratory syndrome coronavirus 2 has become the predominant strain circulating worldwide. In China, enormous controversies exist regarding the “dynamic zero tolerance” (DZT) and “totally no inventions” (TNI) strategies for preventing the spread of the Omicron variant. Currently, China is gradually relaxing the COVID-19 measures from DZT level. In such situations, the “flatten-the-curve” (FTC) strategy, which decreases and maintains the low rate of infection to avoid overwhelming the healthcare system by adopting relaxed nonpharmaceutical interventions (NPIs) after the initial outbreak, has been perceived as most appropriate and effective method to prevent the spread of the Omicron variant. Hence, we established a data-driven model of Omicron transmission based on the pandemic data of Macau, Hong Kong, and Singapore in 2022 to deduce the overall prevention effect throughout China. In the current immunity level without any NPI applied, more than 12.7 billion (including asymptomatic individuals) were infected with the Omicron variant within 90 days, but the daily new infections sharply declined; moreover, Omicron outbreak would result to 1.49 million deaths within 180 days. The application of FTC could decrease the deaths by 36.91% within 360 days. Age-stratified analyses showed that the NPI application among individuals aged >60 years would also result in 0.81 million deaths within 360 days, and the application of FTC strategy through treatment with anti-COVID drugs can reduce the number of deaths to 0.40 million. In a model of completed vaccination, the application of TNI strategy would also result in 0.56 million deaths and slightly decrease the infection numbers. The strict implementation of FTC policy combined with completed vaccination and drug use, which only resulted in 0.19 million deaths in an age-stratified model, will help end the pandemic within about 240 days. The pandemic would be terminated within a shorter period of time without resulting in a high fatality rate; therefore, the FTC policy could be strictly implemented through enhancement of immunity and drug use.
Antiviral treatments lead to the rapid accrual of hundreds of SARS-CoV-2 mutations in immunocompromised patients
Authors: Fountain-Jones Nicholas M. , Vanhaeften Robert , Williamson Jan , Maskell Janelle , Chua I-Ly J , Charleston Michael , Cooley Louise
Published: December 2022

The antiviral Molnupiravir (Lageviro) is widely used across the world to treat SARS-CoV-2 infection. Molnupiravir reduces viral replication by inducing mutations throughout the genome, yet in patients that do not clear the infection, the longer-term impact of the drug on virus evolution is unclear. Here, we used a case-control approach to monitor SARS-CoV-2 genomes through time in nine immunocompromised -patients with five treated with Molnupiravir. Within days of treatment, we detected a large number of low-frequency mutations in patients and that these new mutations could persist and, in some cases, were fixed in the virus population. All patients treated with the drug accrued new mutations in the spike protein of the virus, including non-synonymous mutations that altered the amino acid sequence. Our study demonstrates that this commonly used antiviral can ‘supercharge’ viral evolution in immunocompromised patients, potentially generating new variants and prolonging the pandemic.
Understanding the quality of life of people living with HIV in rural and urban areas in Indonesia
Authors: Fauk Nelsensius Klau , Gesesew Hailay Abrha , Mwanri Lillian , Hawke Karen , Ward Paul Russell
Published: December 2022

Human Immunodeficiency Virus (HIV) is a major global public health issue that affects the quality of life (QoL) of people living with HIV (PLHIV) globally and in Indonesia. As a part of a large-scale qualitative study investigating HIV risk factors and impacts on PLHIV and facilitators of and barriers to their access to HIV care services in Yogyakarta and Belu, Indonesia, this paper describes their in-depth views and experiences of the influence of HIV on their QoL. 92 participants were recruited using the snowball sampling technique. Data were collected using in-depth interviews. In addition, the World Health Organisation Quality of Life questionnaire (WHOQOL – HIV BREF) was also distributed to each of them to fill out prior to the interviews. Chi-Square analysis was used to analyse data from the survey and qualitative data analysis was guided by a framework analysis. The findings reported several factors affecting the QoL of the participants. These included (i) environmental factors, such as living in rural areas, the unavailability of HIV care services and public transport, and long-distance travel to healthcare facilities; (ii) personal beliefs associated with HIV; (iii) sexual and social relationships and their influence of the QoL of participants; and (iv) level of independence and physical health condition following HIV diagnosis. The findings indicate the need for intervention programs that address the availability and accessibility of HIV care services to PLHIV within rural communities, and support various physical, psychological, and financial needs of PLHIV. These can be implemented through the provision of supplements and nutritious food, HIV counselling and door-to-door/community-based ART service delivery to PLHIV which may increase their engagement in and adherence to the treatment and improve their physical and psychological condition and QoL.
CIRCUST: a novel methodology for temporal order reconstruction of molecular rhythms; validation and application towards a daily rhythm gene expression atlas in humans
Authors: Larriba Yolanda , Mason Ivy C. , Saxena Richa , Scheer Frank A.J.L. , Rueda Cristina
Published: December 2022

Abstract

The circadian system drives near-24-h oscillations in behaviors and biological processes. The underlying core molecular clock regulates the expression of other genes, and it has been shown that the expression of more than 50 percent of genes in mammals displays 24-h rhythmic patterns, with the specific genes that cycle varying from one tissue to another. Determining rhythmic gene expression patterns in human tissues sampled as single timepoints has several challenges, including the reconstruction of temporal order of highly noisy data. Previous methodologies have attempted to address these challenges in one or a small number of tissues for which clock gene evolutionary conservation is assumed to be preserved. Here we introduce CIRCUST, a novel CIRCular-robUST methodology for analyzing molecular rhythms, that relies on circular statistics, is robust against noise, and requires fewer assumptions than existing methodologies. Next, we validated the method against two controlled experiments in which sampling times were known, and finally, CIRCUST was applied to 34 tissues from the Genotype-Tissue Expression (GTEx) dataset with the aim towards building a comprehensive daily rhythm gene expression atlas in humans. The validation and application shown here indicate that CIRCUST provides a flexible framework to formulate and solve the issues related to the analysis of molecular rhythms in human tissues. CIRCUST methodology is publicly available athttps://github.com/yolandalago/CIRCUST/.
Genetic inactivation of the USP19 deubiquitinase regulates a-synuclein ubiquitination and inhibits accumulation of Lewy body like aggregates in mice
Authors: Schorova Lenka , Bedard Nathalie , Khayachi Anouar , Bolivar-Pedroso Joao , Ho Hung-Hsiang , Huynh Julie , Piccirelli Mikaela , Wang Yifei , Plourde Marie , Luo Wen , Cid-Pellitero Esther del , Shlaifer Irina , Ye Yihong , Durcan Thomas M. , Wing Simon S.
Published: December 2022

The USP19 deubiquitinase is found in a locus associated with Parkinson’s Disease (PD), interacts with heat shock proteins and promotes secretion of a-synuclein (a-syn) through the misfolding associated protein secretion (MAPS) pathway. Since these processes might modulate the processing of a-syn aggregates during the progression of PD, we tested the effect of USP19 knockout (KO) in mice expressing the A53T mutation of a-syn and in whom a-syn preformed fibrils (PFF) had been injected in the striatum. Compared to WT, KO brains showed decreased accumulation of phospho-synuclein (pSyn) positive aggregates. The improved pathology was associated with less activation of microglia, higher levels of synaptic marker proteins and improved performance in a tail suspension test. Exposure of primary neurons from WT and KO mice to PFF in vitro also led to decreased accumulation of pSyn aggregates. KO did not affect uptake of PFF in the cultured neurons. It also did not affect the propagation of aggregates as assessed by exposing WT or KO neurons to PFF and measuring pSyn positive aggregates in non-exposed adjacent neurons separated using a microfluidics device. We conclude that USP19 instead modulates intracellular dynamics of aggregates. Indeed, at the early time following PFF injection when the number of pSyn positive neurons were similar in WT and KO brains, the KO neurons contained less aggregates. KO brain aggregates stained more intensely with anti-ubiquitin antibodies. Immunoprecipitation of soluble proteins from primary neurons exposed to PFF with antibodies to ubiquitin or pSyn showed higher levels of ubiquitinated a-syn oligomeric species in the KO neurons. We propose that the improved pathology in USP19 KO brains may arise from decreased formation or enhanced clearance of the more ubiquitinated aggregates and/or enhanced disassembly towards more soluble oligomeric species. USP19 inhibition may represent a novel therapeutic approach that targets the intracellular dynamics of a-syn complexes.
Hepatic mTORC2 compensates for loss of adipose mTORC2 in mediating energy storage and glucose homeostasis
Authors: Frei Irina C. , Weissenberger Diana , Müller Christoph , Hall Michael N. , Shimobayashi Mitsugu
Published: December 2022

Mammalian target of rapamycin complex 2 (mTORC2) is a protein kinase complex that plays an important role in energy homeostasis. Loss of adipose mTORC2 reduces lipogenic enzyme expression andde novolipogenesis in adipose tissue. Adipose-specific mTORC2 knockout mice also displays triglyceride accumulation in the liver. However, the mechanism and physiological role of hepatic triglyceride accumulation upon loss of adipose mTORC2 are unknown. Here, we show that loss of adipose mTORC2 increases expression ofde novolipogenic enzymes in the liver, thereby causing accumulation of hepatic triglyceride and hypertriglyceridemia. Simultaneous inhibition of lipogenic enzymes in adipose tissue and liver by ablating mTORC2 in both tissues prevented accumulation of hepatic triglycerides and hypertriglyceridemia. However, loss of adipose and hepatic mTORC2 caused severe insulin resistance and glucose intolerance. Thus, our findings suggest that increased hepatic lipogenesis is a compensatory mechanism to cope with loss of lipogenesis in adipose tissue, and further suggest that mTORC2 in adipose tissue and liver plays a crucial role in maintaining whole-body energy homeostasis.

Graphical abstract
CHESS 3: an improved, comprehensive catalog of human genes and transcripts based on large-scale expression data, phylogenetic analysis, and protein structure
Authors: Varabyou Ales , Sommer Markus J. , Erdogdu Beril , Shinder Ida , Minkin Ilia , Chao Kuan-Hao , Park Sukhwan , Heinz Jakob , Pockrandt Christopher , Shumate Alaina , Rincon Natalia , Puiu Daniela , Steinegger Martin , Salzberg Steven L. , Pertea Mihaela
Published: December 2022

The original CHESS database of human genes was assembled from nearly 10,000 RNA sequencing experiments in 53 human body sites produced by the Genotype-Tissue Expression (GTEx) project, and then augmented with genes from other databases to yield a comprehensive collection of protein-coding and noncoding transcripts. The construction of the new CHESS 3 database employed improved transcript assembly algorithms, a new machine learning classifier, and protein structure predictions to identify genes and transcripts likely to be functional and to eliminate those that appeared more likely to represent noise. The new catalog contains 41,356 genes on the GRCh38 reference human genome, of which 19,839 are protein-coding, and a total of 158,377 transcripts. These include 14,863 novel protein-coding transcripts. The total number of transcripts is substantially smaller than earlier versions due to improved transcriptome assembly methods and to a stricter protocol for filtering out noisy transcripts. Notably, CHESS 3 contains all of the transcripts in the MANE database, and at least one transcript corresponding to the vast majority of protein-coding genes in the RefSeq and GENCODE databases. CHESS 3 has also been mapped onto the complete CHM13 human genome, which gives a more-complete gene count of 43,773 genes and 19,968 protein-coding genes. The CHESS database is available athttp://ccb.jhu.edu/chess.
Whole genome assemblies ofZophobas morioandTenebrio molitor
Authors: Kaur Sabhjeet , Stinson Sydnie A , diCenzo George C
Published: December 2022

Zophobas morio(=Zophobas atratus) andTenebrio molitorare darkling beetles with industrial importance due to their use as feeder insects, their potential for use in aquafeed and human food products, and their apparent ability to biodegrade various plastic polymers. We report draft genome assemblies forZ. morioandT. molitorgenerated from Nanopore and Illumina data. Following scaffolding against published genomes, haploid assemblies of 462 Mb (scaffold N90 of 16.8 Mb) and 258 Mb (scaffold N90 of 5.9 Mb) were produced forZ. morioandT. molitor, respectively. Gene prediction led to the prediction of 28,544 and 19,830 genes forZ. morioandT. molitor, respectively. BUSCO analyses suggested both assemblies have a high level of completeness; 91.5% and 89.0% of the BUSCO endopterygota marker genes were complete in theZ. morioassembly and proteome, respectively, while 99.1% and 92.8% were complete in theT. molitorassembly and proteome, respectively. Phylogenomic analyses of four genera from the family Tenebrionidae yielded phylogenies consistent with those previously constructed based on mitochondrial genomes. Synteny analyses revealed large stretches of macrosynteny across the family Tenebrionidae, as well as numerous within-chromosome rearrangements. Finally, orthogroup analysis identified ∼28,000 gene families across the family Tenebrionidae, of which 8,185 were identified in all five of the analyzed species, and 10,837 were conserved betweenZ. morioandT. molitor. We expect that the availability of multiple whole genome sequences forZ. morioandT. molitorwill facilitate population genetics studies to identify genetic variation associated with industrially relevant phenotypes.
Mean amplitude of low frequency fluctuations measured by fMRI at 11.7T in the aging brain of mouse lemur primate
Authors: Garin Clément M. , Dhenain Marc
Published: December 2022

Non-human primates are a critical species for the identification of key biological mechanisms in normal and pathological aging. One of these primates, the mouse lemur, has been widely studied as a model of cerebral aging or Alzheimer’s disease. The amplitude of low-frequency fluctuations of blood oxygenation level-dependent (BOLD) can be measured with functional MRI. Within specific frequency bands (e.g. the 0.01–0.1 Hz), these amplitudes were proposed to indirectly reflect neuronal activity as well as glucose metabolism. Here, we first created whole brain maps of the mean amplitude of low frequency fluctuations (mALFF) in middle-aged mouse lemurs. Then, we extracted mALFF in old lemurs to identify age-related changes. A high level of mALFF was detected in the temporal cortex (Brodmann area 20), somatosensory areas (Brodmann area 5), insula (Brodmann area 13-6) and the parietal cortex (Brodmann area 7) of healthy middle-aged mouse lemurs. Aging was associated with alteration of mALFF in somatosensory areas (area 5) and the parietal cortex (area 7).

Graphical abstract

Highlights

We characterized mean amplitude of fluctuation at low frequencies (mALFF) in mouse lemurs.

mALFF was the highest in regions involved in visuo-somatosensory-motor function (Brodmann areas 5, 7, 20) and in more integrative functions (area 13-16).

mALFF was affected by aging in regions involved in visuo-somatosensory-motor function (parietal areas 5 and 7).

mALFF is a useful marker to investigate age-related cerebral dysfunction in animals.

Significance Statement

The amplitude of low-frequency fluctuations (ALFF) is expected to reflect neuronal activity. It has been proposed as an MRI-based method to evaluate brain function.

ALFF has been used to investigate different cerebral pathologies in animal models but the regional differences of ALFF signal and the impact of cerebral aging on ALFF has never been characterized.

Here, we highlight for the first time regional difference of ALFF. High signal was detected in regions involved in visuo-somatosensory-motor function as well as in more integrative functions. ALFF was reduced in regions involved in visuo-somatosensory-motor function during aging. ALFF is thus a useful marker to investigate age-related cerebral dysfunction.
O-GlcNAc glycosylation orchestrates fate decision and niche function of bone marrow stromal progenitors
Authors: Zhang Zengdi , Huang Zan , Awad Mohamed , Elsalanty Mohammed , Cray James , Ball Lauren E. , Maynard Jason C. , Burlingame Alma L. , Zeng Hu , Mansky Kim C. , Ruan Hai-Bin
Published: December 2022

In mammals, interactions between the bone marrow (BM) stroma and hematopoietic progenitors contribute to bone-BM homeostasis. Perinatal bone growth and ossification provide a microenvironment for the transition to definitive hematopoiesis; however, mechanisms and interactions orchestrating the development of skeletal and hematopoietic systems remain largely unknown. Here, we establish intracellular O-linked β-N-acetylglucosamine (O-GlcNAc) modification as a posttranslational switch that dictates the differentiation fate and niche function of early BM stromal cells (BMSCs). By modifying and activating RUNX2, O-GlcNAcylation promotes osteogenic differentiation of BMSCs and stromal IL-7 expression to support lymphopoiesis. In contrast, C/EBPβ-dependent marrow adipogenesis and expression of myelopoietic stem cell factor (SCF) is inhibited by O-GlcNAcylation. Ablating O-GlcNAc transferase (OGT) in BMSCs leads to impaired bone formation, increased marrow adiposity, as well as defective B-cell lymphopoiesis and myeloid overproduction in mice. Thus, the balance of osteogenic and adipogenic differentiation of BMSCs is determined by reciprocal O-GlcNAc regulation of transcription factors, which simultaneously shapes the hematopoietic niche.
ROCK and the actomyosin network control biomineral growth and morphology during sea urchin skeletogenesis
Authors: Hijaze Eman , Gildor Tsvia , Seidel Ronald , Layous Majed , Winter Mark , Bertinetti Luca , Politi Yael , de-Leon Smadar Ben-Tabou
Published: December 2022

Biomineralization had apparently evolved independently in different phyla, using distinct minerals, organic scaffolds and gene regulatory networks (GRNs). However, diverse eukaryotes from unicellular organisms, through echinoderms to vertebrates, use the actomyosin network during biomineralization. Specifically, the actomyosin remodeling protein, Rho-associated coiled-coil kinase (ROCK) regulates cell differentiation and gene expression in vertebrates’ biomineralizing cells, yet, little is known on ROCK’s role in invertebrates’ biomineralization. Here we reveal that ROCK controls the formation, growth and morphology of the calcite spicules in the sea urchin larva. ROCK expression is elevated in the sea urchin skeletogenic cells downstream of the Vascular Endothelial Growth Factor (VEGF) signaling. ROCK inhibition leads to skeletal loss and disrupts skeletogenic gene expression. ROCK inhibition after spicule formation reduces spicule elongation rate and induces ectopic spicule branching. Similar skeletogenic phenotypes are observed when ROCK is inhibited in a skeletogenic cell culture, indicating that these phenotypes are due to ROCK activity specifically in the skeletogenic cells. Reduced skeletal growth and enhanced branching are also observed under direct perturbations of the actomyosin network. We propose that ROCK and the actomyosin machinery were employed independently, downstream of distinct GRNs, to regulate biomineral growth and morphology in Eukaryotes.
Optimal parameters for Rapid Invisible Frequency Tagging using MEG
Authors: Minarik Tamas , Berger Barbara , Jensen Ole
Published: December 2022

Frequency tagging has been demonstrated to be a useful tool for identifying representational-specific neuronal activity in the auditory and visual domains. However, the slow flicker (<30Hz) applied in conventional frequency tagging studies is highly visible and might entrain endogenous neuronal oscillations. Hence, stimulation at faster frequencies that is much less visible and does not interfere with endogenous brain oscillatory activity is a promising new tool. In this study, we set out to examine the optimal stimulation parameters ofrapid invisible frequency tagging (RFT/RIFT)with magnetoencephalography (MEG) by quantifying the effects of stimulation frequency, size and position of the flickering patch.Rapid frequency tagging (RFT)using flickers above 50 Hz results in almost invisible stimulation which does not interfere with slower endogenous oscillations; however, the signal is weaker as compared to tagging at slower frequencies so the optimal parameters of stimulation delivery are crucial. The here presented results examining the frequency range between 60Hz and 96Hz suggest that RFT induces brain responses with decreasing strength up to about 84Hz. In addition, even at the smallest flicker patch (2°) focally presented RFT induces a significant oscillatory brain signal at the stimulation frequency (66Hz); however, the elicited response increases with patch size. While focal RFT presentation elicits the strongest response, off-centre presentations do generally mainly elicit a measureable response if presented below the horizontal midline. The results also revealed considerable individual differences in the neuronal responses of to RFT stimulation. Finally, we discuss the comparison of oscillatory measures (coherence and power) and sensor types (planar gradiometers and magnetometers) in order to achieve optimal outcomes. Based on our extensive findings we set forward concrete recommendations for using rapid frequency tagging in human cognitive neuroscience investigations.
Electrophysiological indices of distractor processing in visual search are shaped by target expectations
Authors: van Moorselaar Dirk , Huang Changrun , Theeuwes Jan
Published: December 2022

Although in many cases salient stimuli capture attention involuntarily, it has been proposed recently that under certain conditions the bottom-up signal generated by such stimuli can be proactively suppressed. In support of this signal suppression hypothesis, ERP studies have demonstrated that salient stimuli that do not capture attention elicit a distractor positivity (PD),a putative neural index of suppression. At the same time, it is becoming increasingly clear that regularities across preceding search episodes have a large influence on attentional selection. Yet to date, studies in support of the signal suppression hypothesis have largely ignored the role of selection history on the processing of distractors. The current study addressed this issue by examining how electrophysiological markers of attentional selection (N2pc) and suppression (PD) elicited by targets and distractors respectively were modulated when the search target randomly varied instead of being fixed across trials. Results showed that while target selection was unaffected by this manipulation, both in terms of manual response times, as well as in terms of the N2pc component, the PDcomponent was reliably attenuated when the target features varied randomly across trials. This result demonstrates that the distractor PD, which is typically considered the marker of selective distractor processing cannot unequivocally be attributed to suppression only, as it also, at least in part, reflects the upweighting of target features.
Variability of Phenylalanine side chain conformations facilitates promiscuity of Fatty acid binding in Cockroach milk proteins
Authors: Santhakumari Partha Radhakrishnan , Dhanabalan KanagaVijayan , Virani Saniya , Hopf-Jannasch Amber S. , Benoit Joshua B. , Chopra Gaurav , Subramanian Ramaswamy
Published: December 2022

The pacific beetle cockroach,Diploptera punctata, is a viviparous cockroach that produces a milk-like substance to support the growing embryo with a brood sac. The structure of thein vivogrown crystals present in the gut of the embryo showed that the milk-derived crystals are heterogenous and are made of three proteins (called Lili-Mips). Multiple fatty acids could be modeled into the active site, and we hypothesized that each of the three isoforms of the protein bound to a different fatty acid. We previously reported that the recombinantly expressed Lili-Mip2 has a structure similar to the structure of the protein determined fromin vivocrystals, and this single isoform also binds to several fatty acids. In this study, we aimed to probe the specificity and affinity of fatty acid binding and test the stability of different isoforms. We show that all the isoforms can bind to different fatty acids with very similar affinities, and the local abundance of a fatty acid determined bound fatty acid ratios. Lili-Mips’ thermostability is pH dependent, where stability is highest at acidic pH and declines as the pH increases to physiological levels near 7.0. The measurement of the pH in the gut lumen and the gut cells suggests that the pH in the gut is acidic and the pH inside the gut cells is closer to neutral pH. We propose that the protein has evolved to be highly stable in the acidic gut lumen and, when absorbed inside the gut cells, becomes less stable to enable the breakdown of the glycosylated lipo-protein complex to provide essential metabolites for survival and development of the embryo. The different orientations of Phe-98 and Phe-100 control the binding pocket volume and allow the binding of different chain-length fatty acids to bind with similar affinities.
Crosstalk between regulatory elements in the disordered TRPV4 N-terminus modulates lipid-dependent channel activity
Authors: Goretzki Benedikt , Wiedemann Christoph , McCray Brett A. , Schäfer Stefan L. , Jansen Jasmin , Tebbe Frederike , Mitrovic Sarah-Ana , Nöth Julia , Donohue Jack K. , Jeffries Cy M. , Steinchen Wieland , Stengel Florian , Sumner Charlotte J. , Hummer Gerhard , Hellmich Ute A.
Published: December 2022

Intrinsically disordered regions (IDRs) are essential for membrane receptor regulation but often remain unresolved in structural studies. TRPV4, a member of the TRP vanilloid channel family involved in thermo- and osmosensation, has a large N-terminal IDR of approximately 150 amino acids. With an integrated structural biology approach, we analyze the structural ensemble of the TRPV4 IDR and identify a network of regulatory elements that modulate channel activity in a hierarchical lipid-dependent manner through transient long-range interactions. A highly conserved autoinhibitory patch acts as a master regulator by competing with PIP2binding to attenuate channel activity. Molecular dynamics simulations show that loss of the interaction between the PIP2-binding site and the membrane reduces the force exerted by the IDR on the structured core of TRPV4. This work demonstrates that IDR structural dynamics are coupled to TRPV4 activity and highlights the importance of IDRs for TRP channel function and regulation.
A Spatiotemporal Notch Interaction Map from Membrane to Nucleus
Authors: Martin Alexandre P. , Bradshaw Gary A. , Eisert Robyn J. , Egan Emily D. , Tveriakhina Lena , Rogers Julia M. , Dates Andrew N. , Scanavachi Gustavo , Aster Jon C. , Kirchhausen Tom , Kalocsay Marian , Blacklow Stephen C.
Published: December 2022

Notch signaling relies on ligand-induced proteolysis to liberate a nuclear effector that drives cell fate decisions. The location and timing of individual steps required for proteolysis and movement of Notch from membrane to nucleus, however, remain unclear. Here, we use proximity labeling with quantitative multiplexed mass spectrometry to monitor the microenvironment of endogenous Notch2 after ligand stimulation in the presence of a gamma secretase inhibitor and then as a function of time after inhibitor removal. Our studies show that gamma secretase cleavage of Notch2 occurs in an intracellular compartment and that formation of nuclear complexes and recruitment of chromatin-modifying enzymes occurs within 45 minutes of inhibitor washout. This work provides a spatiotemporal map of unprecedented detail tracking the itinerary of Notch from membrane to nucleus after activation and identifies molecular events in signal transmission that are potential targets for modulating Notch signaling activity.
Promoting Axon Regeneration By Inhibiting RNA N6-methyladenosine Demethylase ALKBH5
Authors: Wang Dong , Zheng Tiemei , Zhou Songlin , Liu Mingwen , Liu Yaobo , Gu Xiaosong , Mao Susu , Yu Bin
Published: December 2022

A key limiting factor of successful axon regeneration is the intrinsic regenerative ability in both the peripheral (PNS) and central nervous system (CNS). Previous studies have identified axon regeneration regulators that act on gene expression in injured neurons. However, it is less known if RNA modifications play a role in this process. Here, we systematically screened the functions of all common m6A modification-related enzymes in axon regeneration and report ALKBH5, an evolutionarily conserved RNA m6A demethylase, as a regulator of axonal regeneration. In PNS, knockdown of ALKBH5 enhanced sensory axonal regeneration, whereas overexpressing ALKBH5 impaired axonal regeneration in an m6A-dependent manner. Mechanistically, ALKBH5 increased the stability of Lpin2 mRNA and thus limited regenerative growth associated lipid metabolism in DRG neurons. Moreover, in CNS, knockdown of ALKBH5 enhanced the survival and axonal regeneration of retinal ganglion cells after optic nerve injury. Together, our results suggest a novel mechanism regulating axon regeneration and point ALKBH5 as a potential target for promoting axon regeneration in both PNS and CNS.
Detection of horizontal sequence transfer in microorganisms in the genomic era
Authors: Tall Mamadou Lamine , Mbogning Maxime Descartes , Kuete Yimagou Edmond , Raoult Didier , Levasseur Anthony
Published: December 2022

Sequence transfer and genome remodeling are very frequent events in microorganisms, especially prokaryotes. This is due to the mosaic structure of the genomes, which calls into question the correct classification of genomes in terms of a single gene or a group of genes. We started here, as a first step, the inventory of bioinformatics tools applied to the detection of horizontal sequence transfers in microorganisms in the genomic era by applying bibliometric survey. Our bibliographic analysis allowed us to identify 17 main tools for the detection of chimeras. The first Bellerophon developed in 2004, followed by CCode and Pintail in 2005; Mallard in 2006; Mothur in 2009; Blackbox Chimera in 2010; Perseus, ChimeraSlayer, UCHIME 1 and UCHIME2, and ChimeraScan in 2011; Decipher in 2012; EBARDenovo and FunFrame in 2013; CATCh in 2015; Uchime 2 in 2016 and ChimeraMiner in April 2019. We then described each of these tools, highlighting their operating principles as well as the advantages and limitations of each (specificities, sensitivity, rapidity and frequent updates). The number of articles citing these tools has increased over the years especially for Mothur, Uchime, VSEARCH and ChimeraSlayer, thus demonstrating the interest of researchers in these tools and the need to decipher chimeras in genomic era.
Integrating pharmacogenomics and cheminformatics with diverse disease phenotypes for cell type-guided drug discovery
Authors: Halu Arda , Decano Julius L. , Matamalas Joan , Whelan Mary , Asano Takaharu , Kalicharran Namitra , Singh Sasha A. , Loscalzo Joseph , Aikawa Masanori
Published: December 2022

Large-scale pharmacogenomic resources, such as the Connectivity Map (CMap), have greatly assisted computational drug discovery. However, despite their widespread use, CMap-based methods have thus far been agnostic to the biological activity of drugs, as well as to the genomic effects of drugs in multiple disease contexts. Here, we present a network-based statistical approach, Pathopticon, that uses CMap to build cell type-specific gene-drug perturbation networks and integrates these networks with cheminformatic data and diverse disease phenotypes for a nested prioritization of cell lines and drugs. Pathopticon demonstrates a better prediction performance than solely cheminformatic measures and state-of-the-art methods that rely exclusively on pharmacogenomic data. Top predictions made by Pathopticon have high chemical structural diversity, suggesting their potential for building compound libraries. In a proof-of-concept application on vein graft disease, we validate the predicted drugsin vitroand demonstrate that Pathopticon helps pinpoint the shared intermediate phenotypes targeted by each prediction. Overall, our analytical framework integrating pharmacogenomics and cheminformatics provides a feasible blueprint for a cell typespecific drug discovery and repositioning platform with broad implications for the efficiency and success of drug development.
Salmonellasuccinate utilisation is inhibited by multiple regulatory systems
Authors: Wenner Nicolas , Zhu Xiaojun , Rowe Will P. M. , Händler Kristian , Hinton Jay C. D.
Published: December 2022

Succinate is a potent immune signalling molecule that is present in the mammalian gut and within macrophages. Both of these niches are colonised by the pathogenic bacteriumSalmonella entericaserovar Typhimurium during infection. Succinate is a C4-dicarboyxlate that can serve as a source of carbon for bacteria. When succinate is provided as the sole carbon source forin vitrocultivation,Salmonellaand other enteric bacteria exhibit a slow growth rate and a long lag phase. This growth inhibition phenomenon was known to involve the sigma factor RpoS, but the genetic basis of the repression of bacterial succinate utilisation was poorly understood. Here, we used an experimental evolution approach to isolate fast-growing mutants during growth ofS. Typhimurium on succinate containing minimal medium.

Our approach reveals novel RpoS-independent systems that inhibit succinate utilisation. The CspC RNA binding protein restricts succinate utilisation, an inhibition that is antagonised by high levels of the small regulatory RNA (sRNA) OxyS. We discovered that the Fe-S cluster regulatory protein IscR inhibits succinate utilisation by repressing the C4-dicarboyxlate transporter DctA.

The RNA chaperone Hfq, the exoribonuclease PNPase and their cognate sRNAs function together to repress succinate utilisationviaRpoS induction. Furthermore, the ribose operon repressor RbsR is required for the complete RpoS-driven repression of succinate utilisation, suggesting a novel mechanism of RpoS regulation.

Our discoveries shed light on redundant regulatory systems that tightly regulate the utilisation of succinate. We propose that the control of central carbon metabolism by multiple regulatory systems inSalmonellagoverns the infection niche-specific utilisation of succinate.
Rapid and collective determination of the complete “hot-spring frog” mitochondrial genome containing long repeat regions using Nanopore sequencing
Authors: Asaeda Yuka , Shiraga Kento , Suzuki Makoto , Sambongi Yoshihiro , Ogino Hajime , Igawa Takeshi
Published: December 2022

The mitochondrial genome (mt-genome) is one of the promising molecular markers for phylogenetics and population genetics. Recently, various mt-genomes have been determined rapidly by using massively parallel sequencers. However, the control region (CR, also called D-loop) in mt-genomes remain difficult to precisely determine due to the presence of repeat regions. Here, using Nanopore sequencing, we succeeded in rapid and collective determination of complete mt-genome of the hot-spring frog,Buergeria japonica, and found that its mt-genome size was 22,274 bp including CR (6,929 bp) with two types of tandem repeat motifs forming repeat regions. Comparison of assemble strategies revealed that the long- and short-read data combined together enabled efficient determination of the CR, but the short-read data alone did not. TheB. japonicaCR was longer than that of a congenic species inhabiting cooler climate areas,Buergeria buergeri, because of the long repeat regions in the former. During the thermal adaptation ofB. japonica, the longer repeat regions in its CR may have accumulated within a short period after divergence fromB. buergeri.
Category-induced global effects of feature-based attention in human visual system
Authors: Huang Ling , Wang Jingyi , He Qionghua , Li Chu , Sun Yueling , Seger Carol A. , Zhang Xilin
Published: December 2022

Global effects of FBA are generally limited to stimuli sharing the same or similar features, as hypothesized in the “feature-similarity gain model”. Visual perception, however, often reflects categories acquired via experience; whether the global-FBA effect can be induced by the categorized features remains unclear. Here human subjects were trained to classify motion-directions into two discrete categories and performed a classical motion-based attention task. We found a category-induced global-FBA effect in both the MT+ and frontoparietal areas, where attention to a motion-direction globally spread to unattended motion-directions within the same category, but not to those in a different category. Effective connectivity analysis showed that the category-induced global-FBA effect in MT+ was derived by feedback from the IFJ. Altogether, our results reveal for the first time a category-induced global-FBA effect and identify a source for this effect in human prefrontal cortex, implying that FBA is of greater ecological significance than previously thought.
CRAM compression: practical across-technologies considerations for large-scale sequencing projects
Authors: Al Ali Ayesha , Kandavel Palani Kannan , Al Mabrazi Hakeem , Carvalho George , Kusuma Vinay , Katagi Gurunath , Elavalli Santosh , Yousif Ayman , Akhter Mohammad Riyaz , Mafofo Joseph , Magalhaes Tiago , Quilez Javier
Published: December 2022

CRAM is an efficient format to store high-throughput sequencing data and it has been widely adopted. We thus plan to use CRAM for the Emirati Genome Program, which aims to sequence the genomes of ~1 million nationals in the United Arab Emirates using short- and long-read sequencing technologies (Illumina, MGI and Oxford Nanopore Sequencing). We conducted a pilot study on the three technologies before start using CRAM at scale. We found CRAM achieved 40–70% compression depending on the sequencing platform. As expected, CRAM compression was data lossless and did not alter variant calls. In our cloud, we observed compression speeds 0.7–1.4 GB per minute, varying on the sequencing platform too. This translates into ~1–2 hours using a single CPU to compress a ~30X human whole-genome sequencing sample. Despite its wide use, we found little publicly available information about CRAM compression rate, speed, losslessness and parallelization, especially across many sequencing platforms. This work will have direct application for Emirati Genome Program and provide practical considerations for other large-scale sequencing efforts.
ATG9A regulates dissociation of recycling endosomes from microtubules leading to formation of influenza A virus liquid condensates
Authors: Vale-Costa Sílvia , Etibor Temitope Akhigbe , Brás Daniela , Sousa Ana Laura , Ferreira Mariana , Martins Gabriel G. , Mello Victor Hugo , Amorim Maria João
Published: December 2022

It is now established that many viruses that threaten public health establish condensates via phase transitions to complete their lifecycles, and knowledge on such processes may offer new strategies for antiviral therapy. In the case of influenza A virus (IAV), liquid condensates known as viral inclusions, concentrate the 8 distinct viral ribonucleoproteins (vRNPs) that form IAV genome and are viewed as sites dedicated to the assembly of the 8-partite genomic complex. Despite not being delimited by host membranes, IAV liquid inclusions accumulate host membranes inside as a result of vRNP binding to the recycling endocytic marker Rab11a, a driver of the biogenesis of these structures. We lack molecular understanding on how Rab11a-recycling endosomes condensate specifically near the endoplasmic reticulum (ER) exit sites upon IAV infection. We show here that liquid viral inclusions interact with the ER to fuse, divide and slide. We uncover that, contrary to previous indications, the reported reduction in recycling endocytic activity is a regulated process rather than a competition for cellular resources involving a novel role for the host factor ATG9A. In infection, ATG9A mediates the removal of Rab11a-recycling endosomes carrying vRNPs from microtubules. We observe that the recycling endocytic usage of microtubules is rescued when ATG9A is depleted, which prevents condensation of Rab11a endosomes near the ER. The failure to produce viral inclusions accumulates vRNPs in the cytosol, reduces genome assembly and the release of infectious virions. We propose that the ER supports the dynamics of liquid IAV inclusions, with ATG9A facilitating their formation. This work advances our understanding on how epidemic and pandemic influenza genomes are formed. It also reveals the plasticity of recycling pathway endosomes to undergo condensation in response to infection, disclosing new roles for ATG9A beyond its classical involvement in autophagy.
Taxonomic and metabolic diversity of Actinobacteria isolated from faeces of a 28,000-year-old mammoth
Authors: van Bergeijk Doris A. , Augustijn Hannah E. , Elsayed Somayah S. , Willemse Joost , Carrión Victor J. , Urem Mia , Grigoreva Lena V. , Cheprasov Maksim Y. , Grigoriev Semyon , Wintermans Bas , Budding Andries E. , Spaink Herman P. , Medema Marnix H. , van Wezel Gilles P.
Published: December 2022

Ancient microbial communities of permafrost soils and frozen animal remains represent an archive that has barely been explored. This yet unexplored microbial world is a vast resource that can provide us with new evolutionary insights, metabolic pathways and novel chemistry. Here, we reveal that Actinobacteria isolated from a faecal sample from the intestinal tract of a 28,000-year-old Siberian mammoth are phylogenetically and metabolically distinct from currently known modern siblings. AncientMicromonospora, Oerskovia, Saccharopolyspora, SanguibacterandStreptomycesspecies were successfully revived and their genome sequences resolved. Surprisingly, the genomes of the ancestors show a large phylogenetic distance to strains isolated today and harbour many novel biosynthetic gene clusters that may well represent uncharacterised biosynthetic potential. Metabolic profiles of the strains display production of known molecules like antimycin, conglobatin and macrotetrolides, but the majority of the mass features could not be dereplicated. Our work provides a snapshot into Actinobacteria of the past, yielding unexplored genomic information that is not yet present in current databases.
Coupling of Coastal Activity with Tidal Cycles is Stronger in Tool-using Capuchins (Cebus capucinus imitator)
Authors: Goldsborough Zoë , Crofoot Margaret C. , Alavi Shauhin E. , Garza Sylvia F. , Del Rosario-Vargas Evelyn , Tiedeman Kate , Monteza-Moreno Claudio M. , Barrett Brendan J.
Published: December 2022

Terrestrial mammals exploiting coastal resources must cope with the challenge that resource availability and accessibility fluctuate with tidal cycles. Tool use can improve foraging efficiency and provide access to structurally protected resources that are otherwise unavailable (e.g., mollusks and fruits). To understand how variable accessibility of valuable resources shapes behavioral patterns, and whether tool use aids in the efficient exploitation of intertidal resources, we compared the relationship between tidal cycles and activity patterns of tool-using vs. non-tool-using groups of white-faced capuchin monkeys on Jicarón Island in Coiba National Park, Panama. Although only a single group of capuchins on Jicarón uses tools, all coastal groups forage on intertidal resources. Using data from >3 years of camera trapping at varying distances from the coast, we found that capuchins on Jicarón showed increased coastal activity during specific parts of the tidal cycle, and that this relationship differed between tool-using and non-tool-using groups, as well as between seasons. Activity patterns of tool-using capuchins were more strongly and consistently tied to tidal cycles compared to non-tool-users, indicating that tool use might allow for more efficient exploitation of tidal resources. Our findings highlight the potential of tool use to aid niche expansion.