bluuebunny/crossref_metadata_2025 huggingface dataset:
The origin of phagocytosis in Earth history
Authors: Mills Daniel B.
Published: June 2020

Phagocytosis, or ‘cell eating’, is a eukaryote-specific process where particulate matter is engulfed via invaginations of the plasma membrane. The origin of phagocytosis has been central to discussions on eukaryogenesis for decades­, where it is argued as being either a prerequisite for, or consequence of, the acquisition of the ancestral mitochondrion. Recently, genomic and cytological evidence has increasingly supported the view that the pre-mitochondrial host cell—abona fidearchaeon branching within the ‘Asgard’ archaea—was incapable of phagocytosis and used alternative mechanisms to incorporate the alphaproteobacterial ancestor of mitochondria. Indeed, the diversity and variability of proteins associated with phagosomes across the eukaryotic tree suggest that phagocytosis, as seen in a variety of extant eukaryotes, may have evolved independently several times within the eukaryotic crown-group. Since phagocytosis is critical to the functioning of modern marine food webs (without it, there would be no microbial loop or animal life), multiple late origins of phagocytosis could help explain why many of the ecological and evolutionary innovations of the Neoproterozoic Era (e.g. the advent of eukaryotic biomineralization, the ‘Rise of Algae’ and the origin of animals) happened when they did.
CTX-M-type ESBL-mediated resistance to third-generation cephalosporins and conjugative transfer of resistance in Gram-negative bacteria isolated from hospitals in Tamil Nadu, India
Authors: Nachimuthu Ramesh , Kannan Velu Rajesh , Bozdogan Bulent , Krishnakumar Vaithilingam , S Karutha Pandian , Manohar Prasanth
Published: June 2020

Clinical pathogens, especially Gram-negative bacteria developing resistance to third-generation cephalosporins, are making clinical outcomes more complicated and serious. This study was undertaken to evaluate the distribution of CTX-M-type extended-spectrum β-lactamases (ESBLs) in Tamil Nadu, India. For this study, clinical samples were collected from five different hospitals located in Tamil Nadu and the ESBL-producing Gram-negative isolates were characterized. MIC was performed using cefotaxime and ceftazidime. The bla
ESBL-producing genes were screened using multiplex PCR for the genes, CTX-M group-1, -2, -8, -9, -26. The conjugation studies were performed using

Escherichia coli

AB1157 as a recipient for the isolates harbouring plasmid-borne resistance following broth-mating experiment. In total, 1500 samples were collected and 599 Gram-negative bacteria were isolated that included

E. coli

(n=233),

Klebsiella pneumoniae

(n=182),

Pseudomonas aeruginosa

(n=79),

Citrobacter

spp. (n=30),

Proteus mirabilis

(n=28),

Salmonella

spp. (n=21),

Acinetobacter baumannii

(n=12), Serratia spp. (n=6),

Shigella

spp. (n=4),

Morganella morganii

(n=3) and

Providencia

spp. (n=1). MIC results showed that 358 isolates were resistant to cefotaxime and ceftazidime. Further, ESBL gene-amplification results showed that 19 isolates had CTX-M group-1 gene including

E. coli

(n=16), K. pneumoniae (n=2) and

P. aeruginosa

(n=1) whereas one

M. morganii

isolate had CTX-M group-9, which was plasmid-borne. Through conjugation studies, 12/20 isolates were found to be involved in the transformation of its plasmid-borne resistance gene. Our study highlighted the importance of horizontal gene transfer in the dissemination of plasmid-borne bla
CTX-M-type resistance genes among the clinical isolates.
ICTV Virus Taxonomy Profile: Alphaflexiviridae
Authors: Kreuze Jan F. , Vaira Anna Maria , Menzel Wulf , Candresse Thierry , Zavriev Sergey K. , Hammond John , Hyun Ryu Ki , Report Consortium ICTV
Published: June 2020

The family Alphaflexiviridae includes viruses with flexuous filamentous virions that are 470–800 nm in length and 12–13 nm in diameter. Alphaflexiviruses have a single-stranded, positive-sense RNA genome of 5.5–9 kb. They infect plants and plant-infecting fungi. They share a distinct lineage of alphavirus-like replication proteins that is unusual in lacking any recognized protease domain. With a single exception, cell-to-cell and long-distance movement is facilitated by triple gene block proteins in plant-infecting genera. This is a summary of the International Committee on Taxonomy of Viruses (ICTV) Report on the family Alphaflexiviridae, which is available at www.ictv.global/report/alphaflexiviridae.
Deciding between one-step and two-step irreversible inhibition mechanisms on the basis of “kobs” data: A statistical approach
Authors: Kuzmič Petr
Published: June 2020

This paper describes an objective statistical approach that can be used to decide between two alternate kinetic mechanisms of covalent enzyme inhibition from kinetic experiments based on the standard “kobs” method. The two alternatives are either a two-step kinetic mechanism, which involves a reversibly formed noncovalent intermediate, or a one-step kinetic mechanism, proceeding in a single bimolecular step. Recently published experimental data [Hopperet al.(2020)J. Pharm. Exp. Therap.372, 331–338] on the irreversible inhibition of Bruton tyrosine kinase (BTK) and tyrosine kinase expressed in hepatocellular carcinoma (TEC) by ibrutinib (PCI-32765) and acalabrutinib are used as an illustrative example. The results show that the kinetic mechanism of inhibition was misdiagnosed in the original publication for at least one of the four enzyme/inhibitor combinations. In particular, based on the availablekobsdata, ibrutinib behaves effectively as a one-step inhibitor of the TEC enzyme, which means that it is not possible to reliably determine either the inhibition constantKior the inactivation rate constantkinact, but only the covalent efficiency constantkeff=kinact/Ki. Thus, the published values ofKiandkinactfor this system are not statistically valid.
SARS-CoV-2 sequence typing, evolution and signatures of selection using CoVa, a Python-based command-line utility
Authors: Ali Farhan , Sharda Mohak , Seshasayee Aswin Sai Narain
Published: June 2020

The current global pandemic COVID-19, caused by SARS-CoV-2, has resulted in millions of infections worldwide in a few months. Global efforts to tackle this situation have produced a tremendous body of genomic data, which can be used for tracing transmission routes, characterization of isolates, and monitoring variants with potential for unusual virulence. Several groups have analyzed these genomes using different approaches. However, as new data become available, the research community needs a pipeline to perform a set of routine analyses, that can quickly incorporate new genome sequences and update the analysis reports. We developed a programmatic tool, CoVa, with this objective. It is a fast, accurate and user-friendly utility to perform a variety of genome analyses on hundreds of SARS-CoV-2 sequences. Using CoVa, we define a modified sequence typing nomenclature and identify sites under positive selection. Further analysis identified some peptides and sites showing geographical patterns of selection. Specifically, we show differences in sequence type distribution between sequences from India and those from the rest of the world. We also show that several sites show signatures of positive selection uniquely in sequences from India. Preliminary evolutionary analysis, using features that will be incorporated into CoVa in the near future, show a mutation rate of 7.4 × 10−4substitutions/site/year, confirm a temporal signal with a November 2019 origin of SARS-CoV-2, and a heterogeneity in the geographical distribution of Indian samples.
A Rare Deletion in SARS-CoV-2 ORF6 Dramatically Alters the Predicted Three-Dimensional Structure of the Resultant Protein
Authors: Riojas Marco A. , Frank Andrew M. , Puthuveetil Nikhita P. , Flores Beth , Parker Michael , King Stephen P. , Peiris Malik , Chu Daniel K. W. , Benton Briana , Bradford Rebecca , Hazbón Manzour Hernando , Rashid Sujatha
Published: June 2020

The function of the SARS-CoV-2 accessory protein p6, encoded by ORF6, is not fully known. Based upon its similarity to p6 from SARS-CoV, it may play a similar role, namely as an antagonist of type I interferon (IFN) signaling. Here we report the sequencing of a SARS-CoV-2 strain passaged six times after original isolation from a clinical patient in Hong Kong. The genome sequence shows a 27 nt in-frame deletion (Δ27,264-27,290) within ORF6, predicted to result in a 9 aa deletion (ΔFKVSIWNLD) from the central portion of p6. This deletion is predicted to result in a dramatic alteration in the three-dimensional structure of the resultant protein (p6Δ22-30), possibly with significant functional implications. Analysis of the original clinical sample indicates that the deletion was not present, while sequencing of subsequent passages of the strain identifies the deletion as a majority variant. This suggests that the deletion originatedab initioduring passaging and subsequently propagated into the majority, possibly due to the removal of selective pressure through the IFN-deficient Vero E6 cell line. The specific function of the SARS-CoV-2 p6 N-terminus, if any, has not yet been determined. However, this deletion is predicted to cause a shift from N-endo to N-ecto in the transmembrane localization of the SARS-CoV-2 p6Δ22-30N-terminus, possibly leading to the ablation of its native function.
Diversification of fungal chitinases and their functional differentiation inHistoplasma capsulatum
Authors: Goughenour Kristie D. , Whalin Janice , Slot Jason C. , Rappleye Chad A.
Published: June 2020

Chitinases enzymatically hydrolyze chitin, a highly abundant biomolecule with many potential industrial and medical uses in addition to their natural biological roles. Fungi are a rich source of chitinases, however the phylogenetic and functional diversity of fungal chitinases are not well understood. We surveyed fungal chitinases from 373 publicly available genomes, characterized domain architecture, and conducted phylogenetic analyses of the glycoside hydrolase family 18 (GH18) domain. This large-scale analysis does not support the previous division of fungal chitinases into three major clades (A, B, C). The chitinases previously assigned to the “C” clade are not resolved as distinct from the “A” clade in this larger phylogenetic analysis. Fungal chitinase diversity was partly shaped by horizontal gene transfer, and at least one clade of bacterial origin occurs among chitinases previously assigned to the “B” clade. Furthermore, chitin binding domains (CBD) including the LysM domain do not define specific clades but instead are found more broadly across clades of chitinase enzymes. To gain insight into biological function diversity, we characterized all eight chitinases (Cts) from the thermally dimorphic fungus,Histoplasma capsulatum:six A clade (3 A-V, 1 A-IV, and two A-II), one B clade (B-I), and one formerly classified C clade (C-I) chitinases. Expression analyses showed variable induction of chitinase genes in the presence of chitin but preferential expression ofCTS3in the mycelial stage. Activity assays demonstrated that Cts1 (B-I), Cts2 (A-V), Cts3 (A-V), Cts4 (A-V) have endochitinase activities with varying degrees of chitobiosidase function. Cts6 (C-I) has activity consistent with N-acetyl-glucosaminidase exochitinase function and Cts8 (A-II) has chitobiase activity. This suggests chitinase activity is variable even within sub-clades and that predictions of functionality require more sophisticated models.
Potent neutralization of clinical isolates of SARS-CoV-2 D614 and G614 variants by a monomeric, sub-nanomolar affinity Nanobody
Authors: Nieto Guillermo Valenzuela , Jara Ronald , Watterson Daniel , Modhiran Naphak , Amarilla Alberto A , Himelreichs Johanna , Khromykh Alexander A. , Salinas Constanza , Pinto Teresa , Cheuquemilla Yorka , Margolles Yago , González del Rey Natalia López , Miranda-Chacon Zaray , Cuevas Alexei , Berking Anne , Deride Camila , González-Moraga Sebastián , Mancilla Héctor , Maturana Daniel , Langer Andreas , Toledo Juan Pablo , Müller Ananda , Uberti Benjamín , Krall Paola , Ehrenfeld Pamela , Blesa Javier , Chana-Cuevas Pedro , Rehren German , Schwefel David , Fernandez Luis Ángel , Rojas-Fernandez Alejandro
Published: June 2020

Despite unprecedented global efforts to rapidly develop SARS-CoV-2 treatments, in order to reduce the burden placed on health systems, the situation remains critical. Effective diagnosis, treatment, and prophylactic measures are urgently required to meet global demand: recombinant antibodies fulfill these requirements and have marked clinical potential. Here, we describe the fast-tracked development of an alpaca Nanobody specific for the receptor-binding-domain (RBD) of the SARS-CoV-2 Spike protein with therapeutic potential applicability. We present a rapid method for nanobody isolation that includes an optimized immunization regimen coupled with VHH library E. coli surface display, which allows single-step selection of high-affinity nanobodies using a simple density gradient centrifugation of the bacterial library. The selected single and monomeric Nanobody, W25, binds to the SARS-CoV-2 S RBD with sub-nanomolar affinity and efficiently competes with ACE-2 receptor binding. Furthermore, W25 potently neutralizes SARS-CoV-2 wild type and the D614G variant with IC50 values in the nanomolar range, demonstrating its potential as antiviral agent.
Prime editing for functional repair in patient-derived disease models
Authors: Schene Imre F. , Joore Indi P. , Oka Rurika , Mokry Michal , van Vugt Anke H.M. , van Boxtel Ruben , van der Doef Hubert P.J. , van der Laan Luc J.W. , Verstegen Monique M.A. , van Hasselt Peter M. , Nieuwenhuis Edward E.S. , Fuchs Sabine A.
Published: June 2020

Prime editing is a novel genome editing technology using fusion proteins of Cas9-nickase and reverse transcriptase, that holds promise to correct the vast majority of genetic defects. We develop prime editing for primary adult stem cells grown in organoid culture models. First, we generate precise in-frame deletions in the gene encoding ß-catenin (CTNNB1) that result in proliferation independent of Wnt-stimuli, mimicking a mechanism of the development of liver cancer. Moreover, prime editing functionally recovers diseasecausing mutations in intestinal organoids from patients with DGAT1-deficiency and liver organoids from a patient with Wilson disease (ATP7B). Prime editing is as efficient in 3D grown organoids as in 2D grown cell lines and offers greater precision than Cas9-mediated homology directed repair (HDR). Base editing remains more reliable than prime editing but is restricted to a subgroup of pathogenic mutations. Whole-genome sequencing of four prime-edited clonal organoid lines reveals absence of genome-wide off-target effects underscoring therapeutic potential of this versatile and precise gene editing strategy.
p53-dependent polyploidisation after DNA damage in G2 phase
Authors: Middleton Anna , Suman Rakesh , O’Toole Peter , Akopyan Karen , Lindqvist Arne
Published: June 2020

Cell cycle progression in the presence of damaged DNA can lead to accumulation of mutations and pose a risk for tumour development. In response to DNA damage in G2 phase, human cells can be forced to exit the cell cycle in a p53-p21- and APC/CCdh1-dependent manner. Cells that exit the cell cycle in G2 phase become senescent, but it is unclear what determines this commitment and whether other cell fates occur. We find that a subset of immortalised RPE-1 cells and primary human fibroblasts spontaneously initiate DNA re-replication several days after forced cell cycle exit in G2 phase. By combining single cell tracking for more than a week with quantitative immunofluorescence, we find that the resulting polyploid cells contain increased levels of damaged DNA and frequently exit the cell cycle again in the next G2 phase. Subsequently, these cells either enter senescence or commit to another round of DNA re-replication, further increasing the ploidy. At least a subset of the polyploid cells show abnormal centrosome numbers or localisation. In conclusion, cells that are forced to exit the cell cycle in G2 phase face multiple choices that lead to various phenotypes, including propagation of cells with different ploidies. Our findings suggest a mechanism by which p53-positive cells can evade senescence that risks genome integrity.

Main points

-Cell cycle exit from G2 phase does not necessarily lead to senescence

-Resumption of proliferation after G2 phase cell cycle exit starts with DNA replication

-Successive cell cycle exits lead to propagation of cells with different ploidies

-A p53-dependent mechanism allows eventual proliferation after DNA damage
Directed information exchange between cortical layers in macaque V1 and V4 and its modulation by selective attention
Authors: Ferro Demetrio , van Kempen Jochem , Boyd Michael , Panzeri Stefano , Thiele Alexander
Published: June 2020

Achieving behavioral goals requires integration of sensory and cognitive information, across cortical laminae and cortical regions. How this computation is performed remains unknown. Using local field potential recordings and spectrally resolved conditional Granger causality (cGC) analysis, we mapped visual information flow, and its attentional modulation, between cortical layers within and between macaque areas V1 and V4. Stimulus induced inter-laminar information flow within V1 dominated upwardly, channeling information towards supragranular cortico-cortical output layers. Within V4, information flow dominated from granular to supragranular layers, but interactions between supragranular and infragranular layers dominated downwardly. Low-frequency across-area communication was stronger from V4 to V1, with little layer specificity. Gamma-band communication was stronger in the feedforward V1 to V4 direction. Attention to the receptive field of V1 decreased communication between all V1 layers, except for granular to supragranular layers interactions. Communication within V4, and from V1 to V4, increased with attention across all frequencies. While communication from V4 to V1 was stronger in lower frequency bands (4-25 Hz), attention modulated cGCs from V4 to V1 across all investigated frequencies. Our data show that top down cognitive processes result in reduced communication within cortical areas, increased feedforward communication across all frequency bands and increased gamma band feedback communication.
Connecting conformational stiffness of the protein with energy landscape by a single experiment
Authors: Chakraborty Soham , Chaudhuri Deep , Chaudhuri Dyuti , Singh Vihan , Banerjee Souradeep , Haldar Shubhasis
Published: June 2020

Proteins are versatile biopolymers whose functions are determined by their structures. Understanding the structural dynamicity, with respect to energy landscape, is essential to describe their biological functions. The ability to study the dynamical properties of a single protein molecule is thus crucial, but ensuring that multiple physical properties can be simultaneously extracted within a single experiment on the exact same protein molecule in real-time has hitherto been infeasible.

Here, we present magnetic tweezers technology that surmounts this limitation, providing real-time dynamic information about changes in several molecular properties (ΔG0, conformation, and mean first passage time of unfolding and refolding) from a single experiment, byremeasuring the very same protein moleculein varying chemical condition. We illustrate the versatility of the method by studying electrolyte-dependent conformational flexibility and the energy landscape of substrate protein L under force. Changing salt concentrations reshapes the energy landscape by two specific ways: it speeds-up refolding kinetics while slowing down unfolding kinetics. From the same trajectory, we calculate the stiffness of the protein polymer, a quantity that varies with salt concentration. The data is described within the framework of a modified ‘electrolyte FJC model’ that we propose and study here. The observed correlation betweenΔG0, kinetics and polymer elasticity connect protein chain physics and the energy landscape, while the experimental methodology we describe of getting energy landscape from a single experiment could have wide-ranging applications.
Efficient detection of transposable element insertion polymorphisms between genomes using short-read sequencing data
Authors: Baduel P. , Quadrana L. , Colot V.
Published: June 2020

Transposable elements (TEs) are powerful generators of major-effect mutations, most of which are deleterious at the species level and maintained at very low frequencies within populations. As reference genomes can only capture a minor fraction of such variants, methods were developed to detect TE insertion polymorphisms (TIPs) in non-reference genomes from short-read sequencing data, which are becoming increasingly available. We present here a bioinformatic framework combining an improved version of the SPLITREADER and TEPID pipelines to detect non-reference TE presence and reference TE absence variants, respectively. We benchmark our method on ten non-referenceArabidopsis thalianagenomes and demonstrate its high specificity and sensitivity in the detection of TIPs between genomes.
Excess histone H3 is a Chk1 inhibitor that controls embryonic cell cycle progression
Authors: Shindo Yuki , Amodeo Amanda A.
Published: June 2020

The early embryos of many species undergo a switch from rapid, reductive cleavage divisions to slower, cell fate-specific division patterns at the Mid-Blastula Transition (MBT). The maternally loaded histone pool is used to measure the increasing ratio of nuclei to cytoplasm (N/C ratio) to control MBT onset, but the molecular mechanism of how histones regulate the cell cycle has remained elusive. Here, we show that excess histone H3 inhibits the DNA damage checkpoint kinase Chk1 to promote cell cycle progression in theDrosophilaembryo. We find that excess H3-tail that cannot be incorporated into chromatin is sufficient to shorten the embryonic cell cycle and reduce the activity of Chk1in vitroandin vivo. Removal of the Chk1 phosphosite in H3 abolishes its ability to regulate the cell cycle. Mathematical modeling quantitatively supports a mechanism where changes in H3 nuclear concentrations over the final cell cycles leading up to the MBT regulate Chk1-dependent cell cycle slowing. We provide a novel mechanism for Chk1 regulation by H3, which is crucial for proper cell cycle remodeling during early embryogenesis.
Speeding up the detection of invasive aquatic species using environmental DNA and nanopore sequencing
Authors: Egeter Bastian , Veríssimo Joana , Lopes-Lima Manuel , Chaves Cátia , Pinto Joana , Riccardi Nicoletta , Beja Pedro , Fonseca Nuno A.
Published: June 2020

Traditional detection of aquatic invasive species, via morphological identification is often time-consuming and can require a high level of taxonomic expertise, leading to delayed mitigation responses. Environmental DNA (eDNA) detection approaches of multiple species using Illumina-based sequencing technology have been used to overcome these hindrances, but sample processing is often lengthy. More recently, portable nanopore sequencing technology has become available, which has the potential to make molecular detection of invasive species more widely accessible and to substantially decrease sample turnaround times. However, nanopore-sequenced reads have a much higher error rate than those produced by Illumina platforms, which has so far hindered the adoption of this technology. We provide a detailed laboratory protocol and bioinformatic tools to increase the reliability of nanopore sequencing to detect invasive species, and we test its application using invasive bivalves. We sampled water from sites with pre-existing bivalve occurrence and abundance data, and contrasting bivalve communities, in Italy and Portugal. We extracted, amplified and sequenced eDNA with a turnaround of 3.5 days. The majority of processed reads were ≥ 99 % identical to reference sequences. There were no taxa detected other than those known to occur. The lack of detections of some species at some sites could be explained by their known low abundances. This is the first reported use of MinION to detect aquatic invasive species from eDNA samples. The approach can be easily adapted for other metabarcoding applications, such as biodiversity assessment, ecosystem health assessment and diet studies.
Ancient bacterial genomes reveal a formerly unknown diversity ofTreponema pallidumstrains in early modern Europe
Authors: Majander Kerttu , Pfrengle Saskia , Neukamm Judith , Kocher Arthur , du Plessis Louis , Pla-Díaz Marta , Arora Natasha , Akgül Gülfirde , Salo Kati , Schats Rachel , Inskip Sarah , Oinonen Markku , Valk Heiki , Malve Martin , Kriiska Aivar , Onkamo Päivi , González-Candelas Fernando , Kühnert Denise , Krause Johannes , Schuenemann Verena J.
Published: June 2020

Sexually transmitted (venereal) syphilis marked European history with a devastating epidemic at the end of the 15thcentury, and is currently re-emerging globally. Together with non-venereal treponemal diseases, like bejel and yaws, found in subtropical and tropical regions, it poses a prevailing health threat worldwide. The origins and spread of treponemal diseases remain unresolved, including syphilis’ potential introduction into Europe from the Americas. Here, we present the first genetic data from archaeological human remains reflecting a previously unknown diversity ofTreponema pallidumin historical Europe. Our study demonstrates that a variety of strains related to both venereal syphilis and yaws were already present in Northern Europe in the early modern period. We also discovered a previously unknownT. pallidumlineage recovered as a sister group to yaws and bejel. These findings imply a more complex pattern of geographical prevalence and etiology of early treponemal epidemics than previously understood.
Self-renewal of double negative 3 (DN3) early thymocytes allows for thymus autonomy but compromises the β-selection checkpoint
Authors: Paiva Rafael A. , Sousa António G. G. , Ramos Camila V. , Ávila Mariana , Lilue Jingtao , Paixão Tiago , Martins Vera C.
Published: June 2020

T lymphocyte differentiation in the thymus relies on high cellular turnover, and cell competition enforces thymocyte replenishment. If deprived of competent progenitors, the thymus can maintain thymopoiesis autonomously for several weeks but this bears a high risk of leukemia. Here we show that double negative 3 early (DN3e) thymocytes can acquire stem cell like properties, which enables them to maintain thymopoiesis. Specifically, DN3e proved to be long-lived, they proliferated and differentiatedin vivo, were necessary for autonomous thymopoiesis, and included DNA-label-retaining cells. Single cell RNAseq revealed a transcriptional program of thymopoiesis similar in autonomy and the controls. Nevertheless, a new population was identified in thymus autonomy that was enriched for an aberrant Notch target gene signature and bypassed the β−selection checkpoint. In sum, DN3e have the potential to self-renew and differentiatein vivoif cell competition is compromised but this enables the accumulation of atypical cells, probably leading to leukemia.
Epigenome-wide change and variation in DNA methylation from birth to late adolescence
Authors: Mulder Rosa H. , Neumann Alexander , Cecil Charlotte A. M. , Walton Esther , Houtepen Lotte C. , Simpkin Andrew J. , Rijlaarsdam Jolien , Heijmans Bastiaan T. , Gaunt Tom R. , Felix Janine F. , Jaddoe Vincent W. V. , Bakermans-Kranenburg Marian J. , Tiemeier Henning , Relton Caroline L. , van IJzendoorn Marinus H. , Suderman Matthew
Published: June 2020

DNA methylation (DNAm) is known to play a pivotal role in childhood health and development, but a comprehensive characterization of genome-wide DNAm trajectories across this age period is currently lacking. We have therefore performed a series of epigenome-wide association studies in 5,019 blood samples collected at multiple time-points from birth to late adolescence from 2,348 participants of two large independent cohorts. DNAm profiles of autosomal CpG sites (CpGs) were generated using the Illumina Infinium HumanMethylation450 BeadChip. Change over time was widespread, observed at over one-half (53%) of CpGs. In most cases DNAm was decreasing (36% of CpGs). Inter-individual variation in linear trajectories was similarly widespread (27% of CpGs). Evidence for nonlinear change and inter-individual variation in nonlinear trajectories was somewhat less common (11% and 8% of CpGs, respectively). Very little inter-individual variation in change was explained by sex differences (0.4% of CpGs) even though sex-specific DNAm was observed at 5% of CpGs. DNAm trajectories were distributed non-randomly across the genome. For example, CpGs with decreasing DNAm were enriched in gene bodies and enhancers and were annotated to genes enriched in immune-developmental functions. By contrast, CpGs with increasing DNAm were enriched in promoter regions and annotated to genes enriched in neurodevelopmental functions. These findings depict a methylome undergoing widespread and often nonlinear change throughout childhood. They support a developmental role for DNA methylation that extends beyond birth into late adolescence and has implications for understanding life-long health and disease. DNAm trajectories can be visualized athttp://epidelta.mrcieu.ac.uk.
NMDA receptors require multiple pre-opening gating steps for efficient synaptic activity
Authors: Amin Johansen , Gochman Aaron , He Miaomiao , Certain Noele , Wollmuth Lonnie P.
Published: June 2020

NMDA receptors (NMDAR) are glutamate-gated ion channels that mediate the majority of fast excitatory synaptic transmission in the nervous system. A central feature of NMDAR physiology is the opening of the ion channel driven by presynaptically-released glutamate. Using glutamate applications to outside-out patches containing a single NMDAR in the continuous presence of the co-agonist glycine, we find that agonist-bound receptors transition to the open state via two conformations, an ‘unconstrained pre-active’ state that can rapidly transition to the open state and contributes to synaptic events, and a ‘constrained pre-active’ state that requires more energy and hence time to open and does not contribute to fast signaling. To define how agonist binding might drive these conformations, we decoupled the ligand-binding domains from specific transmembrane segments for the GluN1 and GluN2A subunits. Displacements of the central pore-forming M3 segments define the energy of fast channel opening. However, to enter the unconstrained conformation and contribute to fast signaling, a peripheral helix, the GluN2 pre-M1, must be displaced before the M3 segments move. This pre-M1 displacement is facilitated by the flexibility of another nearby peripheral element, the GluN1 and GluN2A S2-M4. We conclude that peripheral structural elements – pre-M1 and S2-M4 – work in concert to remove constraints and prime the channel for rapid opening, thus facilitating fast synaptic transmission.
Extensive transfer of genes for edible seaweed digestion from marine to human gut bacteria
Authors: Pudlo Nicholas A. , Pereira Gabriel Vasconcelos , Parnami Jaagni , Cid Melissa , Markert Stephanie , Tingley Jeffrey P. , Unfried Frank , Ali Ahmed , Campbell Austin , Urs Karthik , Xiao Yao , Adams Ryan , Martin Duña , Bolam David N. , Becher Dörte , Schmidt Thomas M. , Abbott D. Wade , Schweder Thomas , Hehemann Jan Hendrik , Martens Eric C.
Published: June 2020

Humans harbor numerous species of colonic bacteria that digest the fiber polysaccharides in commonly consumed terrestrial plants. More recently in history, regional populations have consumed edible macroalgae seaweeds containing unique polysaccharides. It remains unclear how extensively gut bacteria have adapted to digest these nutrients and use these abilities to colonize microbiomes around the world, especially outside Asia. Here, we show that the ability of gut bacteria to digest seaweed polysaccharides is more pervasive than previously appreciated. Using culture-based approaches, we show that knownBacteroidesgenes involved in seaweed degradation have mobilized into many members of this genus. We also identify several previously unknown examples of marine bacteria-derived genes, and their corresponding mobile DNA elements, that are involved in degrading seaweed polysaccharides. Some of these genes reside in gut-resident, Gram-positive Firmicutes, for which phylogenetic analysis suggests an origin in theEpulopisciumgut symbionts of marine fishes. Our results are important for understanding the metabolic plasticity of the human gut microbiome, the global exchange of genes in the context of dietary selective pressures and identifying new functions that can be introduced or engineered to design and fill orthogonal niches for a future generation of engineered probiotics.
Mechanisms Coordinating Ribosomal Protein Gene Transcription in Response to Stress
Authors: Zencir Sevil , Dilg Daniel , Rueda Maria Paula , Shore David , Albert Benjamin
Published: June 2020

While expression of ribosomal protein genes (RPGs) in the budding yeastSaccharomyces cerevisiaehas been extensively studied, a longstanding enigma persists regarding their co-regulation under fluctuating nutrient and stress conditions. Most (<90%) of RPG promoters display one of two distinct arrangements of a core set of transcription factors (TFs; Rap1, Fhl1 and Ifh1) and are further differentiated by the presence or absence of the HMGB box protein Hmo1. However, a third group of promoters appears not to bind any of these proteins, raising the question of how the whole suite of genes is co-regulated. We demonstrate that all RPGs are regulated by two distinct, but complementary mechanisms driven by the TFs Ifh1 and Sfp1, both of which are required for maximal expression in optimal conditions and coordinated down-regulation upon stress. At the majority of RPG promoters Ifh1-dependent regulation predominates, whereas Sfp1 plays the major role at all other genes. We also uncovered an unexpected, protein homeostasis-dependent binding property of Hmo1 at a large subset of RPG promoters. Finally, we show that the Ifh1 paralog Crf1, previously described as a transcriptional repressor, can act as a constitutive RPG activator in the W303 strain background when overexpressed. Our study thus provides a more complete picture of RPG regulation and may serve as a paradigm for unravelling RPG regulation in multicellular eukaryotes.
SC-GAN: 3D self-attention conditional GAN with spectral normalization for multi-modal neuroimaging synthesis
Authors: Lan Haoyu ,   the Alzheimer Disease Neuroimaging Initiative, Toga Arthur W , Sepehrband Farshid
Published: June 2020

Image synthesis is one of the key applications of deep learning in neuroimaging, which enables shortening of the scan time and/or improve image quality; therefore, reducing the imaging cost and improving patient experience. Given the multi-modal and large-scale nature of neuroimaging data, the synthesis task is computationally challenging. 2D image synthesis networks do not take advantage of multi-dimensional spatial information and the 3D implementation has dimensionality problem, negatively affecting the network reliability. These limitations hinder the research and clinical applicability of deep learning-based neuroimaging synthesis. In this paper, we proposed a new network that is designed and optimized for the application of multi-modal 3D synthesis of neuroimaging data. The network is based on 3D conditional generative adversarial network (GAN), and employs spectral normalization and feature matching to stabilize the training process and ensure optimization convergence. We also added a self-attention module to model relationships between widely separated voxels. The performance of the network was evaluated by predicting positron emission tomography (PET) images, Fractional anisotropy (FA) and mean diffusivity (MD) maps from multi-modal magnetic resonance images (MRI) of 265 and 497 individuals correspondingly. The proposed network, called self-attention conditional GAN (SC-GAN), significantly outperformed conventional 2D conditional GAN and the 3D implementation, enabling robust 3D deep learning-based neuroimaging synthesis.
Sound generation in zebrafish with Bio-Opto-Acoustics (BOA)
Authors: Favre-Bulle Itia A. , Taylor Michael A. , Marquez-Legorreta Emmanuel , Vanwalleghem Gilles , Poulsen Rebecca E. , Rubinsztein-Dunlop Halina , Scott Ethan K.
Published: June 2020

Hearing is a crucial sense in underwater environments for communication, hunting, attracting mates, and detecting predators. However, the tools currently used to study hearing are limited, as they cannot controllably stimulate specific parts of the auditory system. To date, the contributions of hearing organs have been identified through lesion experiments that inactivate an organ, but this makes it difficult to gauge the specific stimuli to which each organ is sensitive, or the ways in which inputs from multiple organs are combined during perception. Here, we introduce Bio-Opto-Acoustic (BOA) stimulation, using optical forces to generate localized sound in vivo, and demonstrate stimulation of the auditory system of zebrafish larvae with unprecedented control. We use a rapidly oscillated optical trap to generate vibrations in individual otolith organs that are perceived as sound, while adjacent otoliths are either left unstimulated or similarly stimulated with a second optical laser trap. The resulting brain-wide neural activity is characterized using fluorescent calcium indicators, thus linking each otolith organ to its individual neuronal network in a way that would be impossible using traditional sound delivery methods. The results reveal integration and cooperation of the utricular and saccular otoliths, which were previously described as having separate biological functions, during hearing.
A potent synthetic nanobody targets RBD and protects mice from SARS-CoV-2 infection
Authors: Li Tingting , Cai Hongmin , Yao Hebang , Zhou Bingjie , Zhang Ning , Gong Yuhuan , Zhao Yapei , Shen Quan , Qin Wenming , Hutter Cedric A.J. , Lai Yanling , Kuo Shu-Ming , Bao Juan , Lan Jiaming , Seeger Markus A. , Wong Gary , Bi Yuhai , Lavillette Dimitri , Li Dianfan
Published: June 2020

SARS-CoV-2, the causative agent of COVID-191, recognizes host cells by attaching its receptor-binding domain (RBD) to the host receptor ACE22–7. Neutralizing antibodies that block RBD-ACE2 interaction have been a major focus for therapeutic development8–18. Llama-derived single-domain antibodies (nanobodies, ∼15 kDa) offer advantages including ease of production and possibility for direct delivery to the lungs by nebulization19, which are attractive features for bio-drugs against the global respiratory disease. Here, we generated 99 synthetic nanobodies (sybodies) by in vitro selection using three libraries. The best sybody, MR3 bound to RBD with high affinity (KD = 1.0 nM) and showed high neutralization activity against SARS-CoV-2 pseudoviruses (IC50 = 0.40 μg mL−1). Structural, biochemical, and biological characterization of sybodies suggest a common neutralizing mechanism, in which the RBD-ACE2 interaction is competitively inhibited by sybodies. Various forms of sybodies with improved potency were generated by structure-based design, biparatopic construction, and divalent engineering. Among these, a divalent MR3 conjugated with the albumin-binding domain for prolonged half-life displayed highest potency (IC50 = 12 ng mL−1) and protected mice from live SARS-CoV-2 challenge. Our results pave the way to the development of therapeutic nanobodies against COVID-19 and present a strategy for rapid responses for future outbreaks.
Mathematical estimation of COVID-19 prevalence in Latin America
Authors: Matabuena Marcos , Rodríguez-Mier Pablo , Meijide-García Carlos , Leborán Víctor , Gude Francisco
Published: June 2020

After the rapid spread with severe consequences in Europe and China, the SARS-CoV-2 virus is now manifesting itself in more vulnerable countries, including those in Latin America. In order to guide political decision-making via epidemiological criteria, it is crucial to assess the real impact of the epidemic. However, the use of large-scale population testing is unrealistic or not feasible in some countries. Based on a newly developed mathematical model, we estimated the seroprevalence of SARS-CoV-2 in Latin American countries. The results show that the virus spreads unevenly across countries. For example, Ecuador and Brazil are the most affected countries, with approximately 3% of the infected population. Currently, the number of new infections is increasing in all countries examined, with the exception of some Caribbean countries as Cuba. Moreover, in these countries, the peak of newly infected patients has not yet been reached.
Assessment of Experiences of Preventive Measures Practice including Vaccination History and Health Education among Umrah Pilgrims in Saudi Arabia, 1440H-2019
Authors: Tobaiqy Mansour , Almudarra Sami S. , M.Shams Manal , Amer Samar A. , F.Alcattan Mohamed , H.Alhasan Ahmed
Published: June 2020

Background

Annually, approximately 10 million Umrah pilgrims travel to the Kingdom of Saudi Arabia for Umrah from more than 180 countries. This event presents major challenges for the Kingdom’s public health sector, which strives to decrease the burden of infectious diseases and to adequately control its spread.

Aims of the study

The aims of the study were to assess the experiences of preventive measures practice, including vaccination history and health education, among Umrah pilgrims in Saudi Arabia.

Methods

A cross sectional survey administered to a randomly selected group of pilgrims by the research team members from February to the end of April 2019 at the departure lounge at King Abdul Aziz International airport, Jeddah city. The questionnaire was comprised of questions on the following factors: sociodemographic information, level of education, history of vaccinations and chronic illnesses, whether the pilgrim has received any health education and orientation prior to coming Saudi Arabia or on their arrival, and their experiences with preventive medicine.

Results

Pilgrims (n=1012) of 48 nationalities completed the survey and were reported in this study. Chronic diseases (n=230) were reported among pilgrims, with hypertension being the most reported morbidity (n=124, 53.9%). The majority of pilgrims had taken immunization prior to travel to Saudi Arabia, and the most commonly reported immunizations were meningitis (n=567, 56%), influenza (n=460, 45.5%), and Hepatitis B virus vaccinations (n=324, 32%); however, 223(22%) had not received any vaccinations prior to travel, including meningitis vaccine, which is mandatory in Saudi Arabia. 305 pilgrims (30.1%) had reported never using face masks in crowded areas; however, 63.2% reported lack of availability of these masks.

The majority of participants had received health education on preventive measures, including hygienic aspects (n=799, 78.9%) mostly in their home countries (n=450, 56.3%). A positive association was found between receiving health education and practicing of preventive measures, such as wearing masks in crowded areas (P= 0.04) and other health practice scores (P= 0.02).

Conclusion

Although the experiences of the preventive measures among pilgrims in terms of health education, vaccinations, and hygienic practices were overall positive, this study identified several issues with the following preventive measures: immunizations particularly meningitis vaccine and using face masks in crowded areas.

Further studies are required to develop a health education module to promote comprehensive preventive measures for pilgrims.
Rapid characterization of the propagation of COVID-19 in different countries
Authors: Vargas Patricio , Allende Sebastián , Vogel Eugenio E. , Kobe Sigismund
Published: June 2020

BACKGROUND

COVID-19 has spread rapidly, and there are still many characteristics of this new disease to be unveiled. We propose a simple method to calculate a “figure of merit” FC to provide an early characterization of the disease status in country C.

METHODS

We use mathematical tools to adjust a Gaussian function to the daily increase of infected patients. Maximum value and full width half maximum of the Gaussian are characteristics of the development of the development of the pandemic in each country. These parameters are supplemented by the testing volume and the mortality rate to produce just one characterizing parameter: FC. In addition, the stability of the Gaussian fits was calculated within an entire week towards the end of the study period. Seventeen different countries were fully considered, while others are considered when discussing particular properties. Data employed is publically available.

FINDINGS

Fitted Gaussian functions render effective information about the development of COVID-19. The number of critical days vary between 11 (South Korea) and 52 (Mexico). FC varies between 1 (Australia) and 899 (Mexico). The epidemic appears stabilized in some countries and unstable in others. Some large countries are experiencing fast development of the propagation of the disease with high FC. A correlation between low (high) values of the mortality rate (and to some extent FC) and the presence (absence) of BCG vaccination is exposed.

INTERPRETATION

The adjustment of a Gaussian to daily data of COVID-19 in each country reveals the different propagation dynamics, properly characterized by the parameters proposed here. Testing plays a clear role to control the spread of the disease. Mortality rate spans more than one order of magnitude and is somewhat related to permanent massive BCG vaccination. The figure of merit, FC, introduced here spans more than 2 orders of magnitude which makes it a useful indicator to quickly find out the status of the pandemics in each territory. Geography plays a role: low population density and isolated countries can be efficient in controlling the spread of the disease.

HIGHLIGHTS

An easy-to-evaluate parameter is defined to rapidly establish the status of the evolution of COVID-19 in any given territory. 17 countries in 4 continents are chosen to apply it and compare different evolutions.

The parameter or figure of merit (FC) is dynamic: it combines testing, mortality rate, and characteristics of the Gaussian function that fits the new daily contagions.

FC spans more than two orders of magnitude which makes it a very sensitive indicator to promptly detect second waves or local outbreaks.

It is found that countries with massive BCG vaccination present low COVID-19 mortality rates and low values for FC.