bluuebunny/crossref_metadata_2025 huggingface dataset:
rECHOmmend: an ECG-based machine-learning approach for identifying patients at high-risk of undiagnosed structural heart disease detectable by echocardiography
Authors: Ulloa-Cerna Alvaro E. , Jing Linyuan , Pfeifer John M. , Raghunath Sushravya , Ruhl Jeffrey A. , Rocha Daniel B. , Leader Joseph B. , Zimmerman Noah , Lee Greg , Steinhubl Steven R. , Good Christopher W. , Haggerty Christopher M. , Fornwalt Brandon K. , Chen Ruijun
Published: October 2021

Background

Early diagnosis of structural heart disease improves patient outcomes, yet many remain underdiagnosed. While population screening with echocardiography is impractical, electrocardiogram (ECG)-based prediction models can help target high-risk patients. We developed a novel ECG-based machine learning approach to predict multiple structural heart conditions, hypothesizing that a composite model would yield higher prevalence and positive predictive values (PPVs) to facilitate meaningful recommendations for echocardiography.

Methods

Using 2,232,130 ECGs linked to electronic health records and echocardiography reports from 484,765 adults between 1984-2021, we trained machine learning models to predict the presence of any of seven echocardiography-confirmed diseases within one year. This composite label included: moderate or severe valvular disease (aortic/mitral stenosis or regurgitation, tricuspid regurgitation), reduced ejection fraction <50%, or interventricular septal thickness >15mm. We tested various combinations of input features (demographics, labs, structured ECG data, ECG traces) and evaluated model performance using 5-fold cross-validation, multi-site validation trained on one clinical site and tested on 11 other independent sites, and simulated retrospective deployment trained on pre-2010 data and deployed in 2010.

Findings

Our composite “rECHOmmend” model using age, sex and ECG traces had an area under the receiver operating characteristic curve (AUROC) of 0.91 and a PPV of 42% at 90% sensitivity at a prevalence of 17.9% for our composite label. Individual disease models had AUROCs ranging from 0.86-0.93 and lower PPVs from 1%-31%. The AUROC for models using different input features ranged from 0.80-0.93, increasing with additional features. Multi-site validation showed similar results to the cross-validation, with an aggregate AUROC of 0.91 across our independent test set of 11 clinical sites after training on a separate site. Our simulated retrospective deployment showed that for ECGs acquired in patients without pre-existing known structural heart disease in a single year, 2010, 11% were classified as high-risk, of which 41% developed true, echocardiography-confirmed disease within one year.

Interpretation

An ECG-based machine learning model using a composite endpoint can predict previously undiagnosed, clinically significant structural heart disease while outperforming single disease models and improving practical utility with higher PPVs. This approach can facilitate targeted screening with echocardiography to improve under-diagnosis of structural heart disease.
Global Dynamics as Communication Sensors in Peptide Synthetase Cyclization Domains
Authors: Mishra Subrata H. , Kancherla Aswani K. , Marincin Kenneth A. , Bouvignies Guillaume , Nerli Santrupti , Sgourakis Nikolaos , Dowling Daniel P. , Frueh Dominique P.
Published: October 2021

Structural biology is the foundation for deriving molecular mechanisms, where snapshots of macromolecules and binding partners inform on mutations that test or modify function. However, frequently, the impact of mutations violates the underpinnings of structural models, and mechanisms become cryptic. This conundrum applies to multidomain enzymatic systems called nonribosomal peptide synthetases (NRPSs), which assemble simple substrates into complex metabolites often with pharmaceutical properties. Engineering NRPSs can generate new pharmaceuticals1-3but a dynamic domain organization challenges rational design.4-8Using nuclear magnetic resonance (NMR), we determined the solution structure of a 52 kDa cyclization domain and demonstrate that global intra-domain dynamics enable sensing of substrates tethered to partner domains and draw an allosteric response encompassing the enzyme’s buried active site and two binding sites 40 Å apart. We show that a point-site mutation that impedes the domain dynamics globally hampers the allosteric response. We demonstrate this mechanism through NMR experiments that provide atomic-level read-outs of allosteric responses during biochemical transformationsin situ. Our results establish global structural dynamics as sensors of molecular events that can remodel domain interactions and illustrate the need for integrating structural dynamics explicitly when deriving molecular mechanisms through mutagenesis and structural biology.
Uncovering the distinct properties of a bacterial type I-E CRISPR activation system
Authors: Kcam Maria Claudia Villegas , Tsong Annette J. , Chappell James
Published: October 2021

Synthetic gene regulators based upon CRISPR-Cas systems offer highly programmable technologies to control gene expression in bacteria. Bacterial CRISPR activators (CRISPRa) have been developed that use engineered type II CRISPR-dCas9 to localize transcription activation domains near promoter elements to activate transcription. However, several reports have demonstrated distance-dependent requirements and periodical activation patterns that overall limit the flexibility of these systems. Here, we demonstrate the potential of using an alternative type I-E CRISPR-Cas system to create a CRISPRa with distinct and expanded regulatory properties. We create the first bacterial CRISPRa system based upon a type I-E CRISPR-Cas, and demonstrate differences in the activation range of this system compared to type II CRISPRa systems. Furthermore, we characterize the distance-dependent activation patterns of type I-E CRISPRa to reveal a distinct and more frequent periodicity of activation.
Mycobacterium tuberculosis canonical virulence factors interfere with a late component of the TLR2 response.
Authors: Hinman Amelia E. , Jani Charul , Pringle Stephanie C. , Zhang Wei R. , Jain Neharika , Martinot Amanda J. , Barczak Amy K.
Published: October 2021

For many intracellular pathogens, the phagosome is the site of events and interactions that shape infection outcome. Phagosomal membrane damage, in particular, is proposed to benefit invading pathogens. To define the innate immune consequences of this damage, we profiled macrophage transcriptional responses to wild-type Mycobacterium tuberculosis (Mtb) and mutants that fail to damage the phagosomal membrane. We identified a set of genes with enhanced expression in response to the mutants. These genes represented a late component of the TLR2-dependent transcriptional response to Mtb, distinct from an earlier component that included TNF. Expression of the later component was inherent to TLR2 activation, dependent upon endosomal uptake, and enhanced by phagosome acidification. Canonical Mtb virulence factors that contribute to phagosomal membrane damage blunted phagosome acidification and undermined the endosome-specific response. Profiling cell survival and bacterial growth in macrophages demonstrated that the attenuation of these mutants is partially dependent upon TLR2. Further, TLR2 contributed to the attenuated phenotype of one of these mutants in a murine model of infection. These results demonstrate two distinct components of the TLR2 response and identify a component dependent upon endosomal uptake as a point where pathogenic bacteria interfere with the generation of effective inflammation. This interference promotes TB pathogenesis in both macrophage and murine infection models.
A prebiotic basis for ATP as the universal energy currency
Authors: Pinna Silvana , Kunz Cäcilia , Harrison Stuart , Jordan Sean F. , Ward John , Werner Finn , Lane Nick
Published: October 2021

ATP is universally conserved as the principal energy currency in cells, driving metabolism through phosphorylation and condensation reactions. Such deep conservation suggests that ATP arose at an early stage of biochemical evolution. Yet purine synthesis requires six phosphorylation steps linked to ATP hydrolysis. This autocatalytic requirement for ATP to synthesize ATP implies the need for an earlier prebiotic ATP-equivalent, which could drive protometabolism before purine synthesis. Why this early phosphorylating agent was replaced, and specifically with ATP rather than other nucleotide triphosphates, remains a mystery. Here we show that the deep conservation of ATP reflects its prebiotic chemistry in relation to another universally conserved intermediate, acetyl phosphate, which bridges between thioester and phosphate metabolism by linking acetyl CoA to the substrate-level phosphorylation of ADP. We confirm earlier results showing that acetyl phosphate can phosphorylate ADP to ATP at nearly 20 % yield in water in the presence of Fe3+ions. We then show that Fe3+and acetyl phosphate are surprisingly favoured: a panel of other prebiotically relevant ions and minerals did not catalyze ADP phosphorylation; nor did a number of other potentially prebiotic phosphorylating agents. Only carbamoyl phosphate showed some modest phosphorylating activity. Critically, we show that acetyl phosphate does not phosphorylate other nucleotide diphosphates or free pyrophosphate in water. The phosphorylation of ADP monomers seems to be favoured by the interaction between the N6 amino group on the adenine ring with Fe3+coupled to acetyl phosphate. Our findings suggest that the reason ATP is universally conserved across life is that its formation is chemically favoured in aqueous solution under mild prebiotic conditions.
Spatial modelling for population replacement of mosquito vectors at continental scale
Authors: Beeton Nicholas J. , Wilkins Andrew , Ickowicz Adrien , Hayes Keith R. , Hosack Geoffrey R.
Published: October 2021

Malaria is one of the deadliest vector-borne diseases in the world. Researchers are developing new genetic and conventional vector control strategies to attempt to limit its burden. Novel control strategies require detailed safety assessment to ensure responsible and successful deployments. Anopheles gambiae sensu stricto (s.s.) and Anopheles coluzzii, two closely related subspecies within the species complex Anopheles gambiae sensu lato (s.l.), are among the dominant malaria vectors in sub-Saharan Africa. These two subspecies readily hybridise and compete in the wild and are also known to have distinct niches, each with spatially and temporally varying carrying capacities driven by precipitation and land use factors.

We model the spread and persistence of a population-modifying gene drive system in these subspecies across sub-Saharan Africa by simulating introductions of genetically modified mosquitoes across the African mainland and its offshore islands. We explore transmission of the gene drive between the two subspecies that arise from different hybridisation mechanisms, the effects of both local dispersal and potential wind-aided migration to the spread, and the development of resistance to the gene drive. Given the best current available knowledge on the subspecies’ life histories, we find that an introduced gene drive system with typical characteristics can plausibly spread from even distant offshore islands to the African mainland with the aid of wind-driven migration, with resistance taking over within a decade. Our model accounts for regional to continental scale mechanisms, and demonstrates a range of realistic dynamics including the effect of prevailing wind on spread and spatio-temporally varying carrying capacities for subspecies. As a result, it is well-placed to answer future questions relating to mosquito gene drives as important life history parameters become better understood.
Geosmin suppresses defensive behaviour and elicits unusual neural responses in honey bees
Authors: Scarano Florencia , Suresh Mukilan Deivarajan , Tiraboschi Ettore , Cabirol Amélie , Nouvian Morgane , Nowotny Thomas , Haase Albrecht
Published: October 2021

Geosmin is an odorant produced by bacteria in moist soil. It has been found to be extraordinarily relevant to some insects, but the reasons for this are not yet fully understood. Here we report the first tests of the effect of geosmin on honey bees. A stinging assay showed that the defensive behaviour elicited by the bee’s alarm pheromone is strongly suppressed by geosmin. Surprisingly, the suppression is, however, only present at very low geosmin concentrations, and completely disappears at higher concentrations. We investigated the underlying mechanisms of the behavioural change at the level of the olfactory receptor neurons by means of electroantennography and at the level of the antennal lobe output via calcium imaging. Unusual effects were observed at both levels. The responses of the olfactory receptor neurons to mixtures of geosmin and the alarm pheromone component isoamyl acetate (IAA) were lower than to pure IAA, suggesting an interaction of both compounds at the olfactory receptor level. In the antennal lobe, the neuronal representation of geosmin showed a glomerular activation that decreased with increasing concentration, correlating well with the concentration dependence of the behaviour. Computational modelling of odour transduction and odour coding in the antennal lobe suggests that a broader than usual activation of different olfactory receptor types by geosmin in combination with lateral inhibition in the antennal lobe could lead to the observed non-monotonic increasing-decreasing responses to geosmin and thus underlie the specificity of the behavioural response to low geosmin concentrations.
A Novel and Functionally Diverse Class of Acetylcholine-gated Ion Channels
Authors: Hardege Iris , Morud Julia , Courtney Amy , Schafer William R
Published: October 2021

Fast cholinergic neurotransmission is mediated by acetylcholine-gated ion channels; in particular, excitatory nicotinic acetylcholine receptors play well established roles in virtually all nervous systems. Acetylcholine-gated inhibitory channels have also been identified in some invertebrate phyla, yet their roles in the nervous system are less well understood. We report the existence of multiple new inhibitory acetylcholine-gated ion channels with diverse ligand binding properties in C. elegans. We identify three channels, LGC-40, LGC-57 and LGC-58, whose primary ligand is choline rather than acetylcholine, as well as the first evidence of a truly polymodal channel, LGC-39, which is activated by both cholinergic and aminergic ligands. Using our newly deorphanised channel evidence we uncover the surprising extent to which a single neuron expresses both excitatory and inhibitory channels, not only for acetylcholine but also the other major neurotransmitters. The results presented in this study offer a new insight into the potential evolutionary benefit of a vast and diverse repertoire of LGICs to generate complexity in an anatomically compact nervous system.
Genetic determinants of antibiotic resistance and the evolution of trade-offs during adaptation in a single patient
Authors: Woods Robert J. , Barbosa Camilo , Koepping Laura , Raygoza Garay Juan A. , Mwangi Michael , Read Andrew F.
Published: October 2021

The processes by which pathogens evolve within single hosts dictate the efficacy of treatment strategies designed to slow antibiotic resistance evolution and influence the population-wide resistance levels. The aim of this study is to describe the underlying genetic and phenotypic changes leading to antibiotic resistance within a single patient who died as resistance evolved to available antibiotics. We assess whether robust patterns of collateral sensitivity and response to combinations exist that might have been leveraged to improve therapy. Whole-genome sequencing was completed for nine isolates taken from this patient over 279 days of chronic infection withEnterobacter hormaechei, along with systematic measurements of changes in resistance against five of the most relevant drugs considered for treatment. The entirety of the genetic change is consistent withde novomutations and plasmid loss events, without the acquisition of foreign genetic material via horizontal gene transfer. The isolates formed three genetically distinct lineages, with early evolutionary trajectories being supplanted by previously unobserved multi-step evolutionary trajectories. Importantly, no single isolate evolved resistance to all of the antibiotics considered for treatment againstE. hormaechei(i.e., none was pan-resistant). Patterns of collateral sensitivity and response to combination therapy revealed contrasting patterns across this diversifying population. Translating antibiotic resistance management strategies from theoretical and laboratory data to clinical situations, such as this, may require managing diverse populations with unpredictable resistance trajectories.
Developmental cell death of cortical projection neurons is controlled by a Bcl11a/Bcl6-dependent pathway
Authors: Wiegreffe C. , Wahl T. , Joos N. S. , Bonnefont J. , Vanderhaeghen P. , Liu P. , Britsch S.
Published: October 2021

Developmental neuron death plays a pivotal role in refining organization and wiring during neocortex formation. Aberrant regulation of this process results in neurodevelopmental disorders including impaired learning and memory. Underlying molecular pathways are incompletely determined. Loss of Bcl11a in cortical projection neurons induces pronounced cell death in upper-layer cortical projection neurons during postnatal corticogenesis. We used this genetic model to explore genetic mechanisms by which developmental neuron death is controlled. Unexpectedly, we found Bcl6, previously shown to be involved in transition of cortical neurons from progenitor to postmitotic differentiation state to provide a major check point regulating neuron survival during late cortical development. We show that Bcl11a is a direct transcriptional regulator of Bcl6. Deletion of Bcl6 exerts death of cortical projection neurons. In turn, reintroduction of Bcl6 into Bcl11a mutants prevents induction of cell death in these neurons. Together, our data identify a novel Bcl11a/Bcl6-dependent molecular pathway in regulation of developmental cell death during corticogenesis.
Travelling wave and asymptotic analysis of a multiphase moving boundary model for engineered tissue growth
Authors: Jepson Jacob M. , Fadai Nabil T. , O’Dea Reuben D.
Published: October 2021

We derive a multiphase, moving boundary model to represent the development of tissue in vitro in a porous tissue engineering scaffold. We consider a cell, extra-cellular liquid and a rigid scaffold phase, and adopt Darcy’s law to relate the velocity of the cell and liquid phases to their respective pressures. Cell-cell and cell-scaffold interactions which can drive cellular motion are accounted for by utilising relevant constitutive assumptions for the pressure in the cell phase. We reduce the model to a nonlinear reaction-diffusion equation for the cell phase, coupled to a moving boundary condition for the tissue edge, the diffusivity being dependent on the cell and scaffold volume fractions, cell and liquid viscosities, and parameters that relate to cellular motion. Numerical simulations reveal that the reduced model admits three regimes for the evolution of the tissue edge at large-time: linear, logarithmic and stationary. Employing travelling wave and asymptotic analysis, we characterise these regimes in terms of parameters related to cellular production and motion. The results of our investigation allow us to suggest optimal values for the governing parameters, so as to stimulate tissue growth in an engineering scaffold.
Inter-species microbiota transplantation recapitulates microbial acquisition and persistence in mosquitoes
Authors: Coon Kerri L. , Hegde Shivanand , Hughes Grant L.
Published: October 2021

Background

Mosquitoes harbor microbial communities that play important roles in their growth, survival, reproduction, and ability to transmit human pathogens. Microbiome transplantation approaches are often used to study host-microbe interactions and identify microbial taxa and assemblages associated with health or disease. However, no such approaches have been developed to manipulate the microbiota of mosquitoes.

Results

Here, we developed an approach to transfer entire microbial communities between mosquito cohorts. We undertook transfers between (Culex quinquefasciatustoAedes aegypti)and within (Ae. aegypti to Ae. aegypti) species to validate the approach and determine the number of mosquitoes required to prepare donor microbiota. After the transfer, we monitored mosquito development and microbiota dynamics throughout the life cycle. Typical holometabolous lifestyle-related microbiota structures were observed, with higher dynamics of microbial structures in larval stages, including the larval water, and less diversity in adults. Microbiota diversity in recipient adults was also more similar to the microbiota diversity in donor adults.

Conclusions

This study provides the first evidence for successful microbiome transplantation in mosquitoes. Our results highlight the value of such methods for studying mosquito-microbe interactions and lay the foundation for future studies to elucidate the factors underlying microbiota acquisition, assembly, and function in mosquitoes under controlled conditions.
Progesterone supplementation in mice leads to microbiome alterations and weight gain in a sex-specific manner
Authors: Nuriel-Ohayon Meital , Belogovski Anna , Komissarov Sharon , Izhak Meirav Ben , Shtossel Oshrit , Neuman Hadar , Ziv Oren , Turjeman Sondra , Bel Shai , Louzoun Yoram , Koren Omry
Published: October 2021

Background

Progesterone is a steroid hormone produced by the ovaries, involved in pregnancy progression and necessary for successful gestation. We have previously shown that progesterone affects gut microbiota composition and leads to increased relative abundance of Bifidobacterium.

Results

In non-pregnant female GF mice, levels of progesterone were significantly higher than in SPF mice of the same status. However, no significant differences were observed between GF and SPF males. Females treated with progesterone gained more weight than females treated with a placebo. In contrast to female mice, males treated with progesterone did not gain significantly more weight than males treated with a placebo. Progesterone supplementation led to microbial changes in females but not in males (16S rRNA sequencing). Accordingly, the weight gain observed in female mice treated with progesterone was fully transferable to both male and female germ-free mice via fecal transplantation.

Conclusions

We demonstrate that bacteria play a role in regulating progesterone levels in a female-specific manner. Furthermore, weight gain and metabolic changes associated with progesterone may be mediated by the gut microbiota.
SynTracker: a synteny based tool for tracking microbial strains
Authors: Enav Hagay , Ley Ruth E.
Published: October 2021

In the human gut microbiome, specific strains emerge due to within-host evolution and can occasionally be transferred to or from other hosts. Phenotypic variance among such strains can have implications for strain transmission and interaction with the host. Surveilling strains of the same species, within and between individuals, can further our knowledge about the way in which microbial diversity is generated and maintained in host populations. Existing methods to estimate the biological relatedness of similar strains usually rely on either detection of single nucleotide polymorphisms (SNP), which may include sequencing errors, or on the analysis of pangenomes, which can be limited by the requirement for extensive gene databases. To complement existing methods, we developed SynTracker. This strain-comparison tool is based on synteny comparisons between strains, or the comparison of the arrangement of sequence blocks in two homologous genomic regions in pairs of metagenomic assemblies or genomes. Our method is executed in a species-specific manner, has a low sensitivity to SNPs, does not require a pre-existing database, and can correctly resolve strains using complete or draft genomes and metagenomic samples using <5% of the genome length. When applied to metagenomic datasets, we detected person-specific strains with an average sensitivity of 97% and specificity of 99%, and strain-sharing events in mother-infant pairs. SynTracker can be used to study the population structure of specific microbial species between and within environments, to identify evolutionary trajectories in longitudinal datasets, and to further understanding of strain sharing networks.
A systematic genotype-phenotype map for missense variants in the human intellectual disability-associated geneGDI1
Authors: Silverstein Rachel A. , Sun Song , Verby Marta , Weile Jochen , Wu Yingzhou , Gebbia Marinella , Fotiadou Iosifina , Kitaygorodsky Julia , Roth Frederick P.
Published: October 2021

Next generation sequencing has become a common tool in the diagnosis of genetic diseases. However, for the vast majority of genetic variants that are discovered, a clinical interpretation is not available. Variant effect mapping allows the functional effects of many single amino acid variants to be characterized in parallel. Here, we combine multiplexed functional assays with machine learning to assess the effects of amino acid substitutions in the human intellectual disability-associated gene,GDI1. We show that the resulting variant effect map can be used to discriminate pathogenic from benign variants. Our variant effect map recovers known biochemical and structural features ofGDI1and reveals additional aspects ofGDI1function. We explore how our functional assays can aid in the interpretation of novelGDI1variants as they are discovered, and to re-classify previously observed variants of unknown significance.
Membrane-assisted assembly and selective autophagy of enteroviruses
Authors: Dahmane Selma , Kerviel Adeline , Morado Dustin R. , Shankar Kasturika , Ahlman Björn , Lazarou Michael , Altan-Bonnet Nihal , Carlson Lars-Anders
Published: October 2021

Enteroviruses are non-enveloped positive-sense RNA viruses that cause diverse diseases in humans. Their rapid multiplication depends on remodeling of cytoplasmic membranes for viral genome replication. It is unknown how virions assemble around these newly synthesized genomes and how they are then loaded into autophagic membranes for release through secretory autophagy. Here, we use cryo-electron tomography of infected cells to show that poliovirus assembles directly on replication membranes. Pharmacological untethering of capsids from membranes abrogates RNA encapsidation. Our data directly visualize a membrane-bound half-capsid as a prominent virion assembly intermediate. Assembly progression past this intermediate depends on the class III phosphatidylinositol 3-kinase VPS34, a key host-cell autophagy factor. On the other hand, the canonical autophagy initiator ULK1 is shown to restrict virion production since its inhibition leads to increased accumulation of virions in vast intracellular arrays, followed by an increased vesicular release at later time points. Finally, we identify multiple layers of selectivity in virus-induced autophagy, with a strong selection for RNA-loaded virions over empty capsids and the segregation of virions from other types of autophagosome contents. These findings provide an integrated structural framework for multiple stages of the poliovirus life cycle.
Structure of the stress-related LHCSR1 complex determined by an integrated computational strategy
Authors: Prandi Ingrid Guarnetti , Sláma Vladislav , Pecorilla Cristina , Cupellini Lorenzo , Mennucci Benedetta
Published: October 2021

Light-harvesting complexes (LHCs) are pigment-protein complexes whose main function is to capture sunlight and transfer the energy to reaction centers of photosystems. In response to varying light conditions, LH complexes also play photoregulation and photoprotection roles. In algae and mosses, a sub-family of LHCs, Light-Harvesting complex stress related (LHCSR), is responsible for photoprotective quenching. Despite their functional and evolutionary importance, no direct structural information on LHCSRs is available that can explain their unique properties. In this work we propose a structural model of LHCSR1 from the moss P. Patens, obtained through an integrated computational strategy that combines homology modeling, molecular dynamics, and multiscale quantum chemical calculations. The model is validated by reproducing the spectral properties of LHCSR1. Our model reveals the structural specificity of LHCSR1, as compared with the CP29 LH complex, and poses the basis for understanding photoprotective quenching in mosses.
Tracking the fates of iron-labeled tumor cells in vivo using Magnetic Particle Imaging
Authors: Makela Ashley V. , Schott Melissa A. , Sehl Olivia C. , Gevaert Julia J. , Foster Paula J. , Contag Christopher H.
Published: October 2021

The use of imaging to detect and monitor the movement and accumulation of cells in living subjects can provide significant insights that can improve our understanding of metastasis and guide therapeutic development. For cell tracking using Magnetic Resonance Imaging (MRI), cells are labeled with iron oxides and the effects of the iron on water provides contrast. However, due to low specificity and difficulties in quantification with MRI, other modalities and approaches need to be developed. Magnetic Particle Imaging (MPI) is an emerging imaging technique which directly detects magnetic iron, allowing for a specific, quantitative and sensitive readout. Here, we use MPI to image iron-labeled tumor cells longitudinally, from implantation and growth at a primary site to movement to distant anatomic sites. In vivo bioluminescent imaging (BLI) was used to localize tumor metastases and computed tomography (CT) allowed for correlation of these signals to anatomic locations. These three imaging modalities provide information on immune escape and metastasis of iron-labeled, and unlabeled, tumor cells, and the accumulation of cell-free iron contrast over time. We identified iron signals by MPI and tumor cells via BLI, and correlated these positive contrast images with CT scans to reveal the anatomic sites with cancer cells; histologic analysis confirmed the presence of iron-labeled tumor cells in the tissues, suggesting that the metastatic cells retained enough iron for MPI detection. The use of multi-modality cell tracking reveals the movement, accumulation and fates of labeled cells that will be helpful understanding cancer progression and guiding the development of targeted therapies.
NN-RNALoc: neural network-based model for prediction of mRNA sub-cellular localization using distance-based sub-sequence profiles
Authors: Babaiha Negin Sadat , Aghdam Rosa , Eslahchi Changiz
Published: October 2021

Localization of messenger RNAs (mRNA) as a widely observed phenomenon is considered as an efficient way to target proteins to a specific region of a cell and is also known as a strategy for gene regulation. The importance of correct intracellular RNA placement in the development of embryonic and neural dendrites has long been demonstrated in former studies. Improper localization of RNA in the cell, which has been shown to occur due to a variety of reasons, including mutations in trans-regulatory elements, is also associated with the occurrence of some neuromuscular diseases as well as cancer. We propose NN-RNALoc, a neural network-based model to predict the cellular location of mRNAs. The features extracted from mRNA sequences along with the information gathered from their proteins are fed to this prediction model. We introduce a novel distance-based sub-sequence profile for representation of RNA sequences which is more memory and time efficient and comparying to the k-mer frequencies, can possibly better encode sequences when the distance k increases. The performance of NN-RNALoc on the following benchmark datsets CeFra-seq and RNALocate, is compared to the results achieved by two powerful prediction models that were proposed in former studies named as mRNALoc and RNATracker The results reveal that the employment of protein-protein interaction information, which plays a crucial role in many biological functions, together with the novel distance-based sub-sequence profiles of mRNA sequences, leads to a more accurate prediction model. Besides, NN-RNALoc significantly reduces the required computing time compared to previous studies. Source code and data used in this study are available at: https://github.com/NeginBabaiha/NN-RNALoc
Disruption of nucleoid expanded conformation by toxic aberrant proteins synthesized in Escherichia coli
Authors: Tawde Mangala , Bior Abdelaziz , Feiss Michael , Freimuth Paul
Published: October 2021

Aminoglycoside antibiotics interfere with selection of cognate tRNAs during translation, resulting in the production of aberrant proteins that are the ultimate cause of the antibiotic bactericidal effect. To determine if these aberrant proteins are recognized as substrates by the cell’s protein quality control machinery, we studied whether the heat shock (HS) response was activated following exposure of Escherichia coli to the aminoglycoside kanamycin (Kan). Levels of the HS transcription factor σ32 increased about 10-fold after exposure to Kan, indicating that at least some aberrant proteins were recognized as substrates by the molecular chaperone DnaK. To investigate whether toxic aberrant proteins therefore might escape detection by the QC machinery, we studied model aberrant proteins that had a bactericidal effect when expressed in E. coli from cloned genes. As occurred following exposure to Kan, levels of σ32 were permanently elevated following expression of an acutely toxic 48-residue protein (ARF48), indicating that toxic activity and recognition by the QC machinery are not mutually exclusive properties of aberrant proteins, and that the HS response was blocked in these cells at some step downstream of σ32 stabilization. This block could result from halting of protein synthesis or from radial condensation of nucleoids, both of which occurred rapidly following ARF48 induction. Nucleoids were similarly condensed following expression of toxic aberrant secretory proteins, suggesting that transertion of inner membrane proteins, a process that expands nucleoids into an open conformation that promotes growth and gene expression, was disrupted in these cells. The 48-residue ARF48 protein would be well-suited for structural studies to further investigate the toxic mechanism of aberrant proteins.
Structure of the thin filament in native skeletal muscles reveals its interaction with nebulin and two distinct conformations of myosin
Authors: Wang Zhexin , Grange Michael , Pospich Sabrina , Wagner Thorsten , Kho Ay Lin , Gautel Mathias , Raunser Stefan
Published: October 2021

Nebulin is a major structural protein of skeletal sarcomeres and is essential for proper assembly and contraction of skeletal muscle1. It stabilises and regulates the length of thin filaments,2 but the structural mechanism remains nebulous. Using electron cryotomography and sub-tomogram averaging, we present the first structure of native nebulin bound to thin filaments within the A-band and I-band of intact sarcomeres. This in-situ reconstruction reveals unprecedented detail of interaction at pseudo-atomic resolution between nebulin and actin, providing the basis for understanding the structural and regulatory roles of nebulin. The position of nebulin on the thin filament indicates that there is no contact to tropomyosin or myosin, but an unexpected interaction with a troponin-T linker, possibly through two binding motifs on nebulin. In addition, our structure of myosin bound to the thin filaments reveals different conformations of the neck domain, both within the same sarcomere and when compared to purified structures, highlighting an inherent structural variability in muscle. We provide a complete description of cross-bridge formation on fully native, nebulin-containing thin filaments at near-atomic scale. Our structures establish the molecular basis for the role of nebulin as a thin filament “molecular ruler” and the impact of nemaline myopathies mutations that will aid future development of therapies.
Uncovering expression signatures of synergistic drug response using an ensemble of explainable AI models
Authors: Janizek Joseph D. , Dincer Ayse B. , Celik Safiye , Chen Hugh , Chen William , Naxerova Kamila , Lee Su-In
Published: October 2021

Complex machine learning models are poised to revolutionize the treatment of diseases like acute myeloid leukemia (AML) by helping physicians choose optimal combinations of anti-cancer drugs based on molecular features. While accurate predictions are important, it is equally important to be able to learn about the underlying molecular basis of anti-cancer drug synergy. Explainable AI (XAI) offers a promising new route for data-driven cancer pharmacology, combining highly accurate models with interpretable insights into model decisions. Due to the highly correlated, high-dimensional nature of cancer transcriptomic data, however, we find that existing XAI approaches are suboptimal when applied naively to large transcriptomic datasets. We show how a novel approach based on model ensembling helps to increase the quality of explanations. We then use our method to demonstrate that a hematopoietic differentiation signature underlies synergy for a variety of anti-AML drug combinations.
Oxytocin regulation of social transmission of fear in zebrafish reveals its evolutionary conserved role in emotional contagion
Authors: Akinrinade Ibukun , Kareklas Kyriacos , Gliksberg Michael , Petri Giovanni , Levkowitz Gil , Oliveira Rui F.
Published: October 2021

Emotional contagion is the most ancestral form of empathy that relies on simple perception-action mechanisms, on top of which more complex forms of empathic behaviors, such as consolation and helping, have evolved. Here we tested to what extent the proximate mechanisms of emotional contagion are evolutionary conserved by assessing the role of oxytocin, known to regulate empathic behaviors in mammals, in social fear contagion in zebrafish, which represents an evolutionary divergent line to that of tetrapods, within vertebrates. Using mutants for the ligand of the fish oxytocin nonapeptide and both of its receptors in zebrafish we showed that oxytocin is necessary for observer zebrafish to copy the distressed behavior of conspecific demonstrators. Exogeneous administration of oxytocin to the ligand mutant rescued the ability of observers to express social fear transmission, indicating that oxytocin is not only necessary but also sufficient for emotional contagion. The brain regions in the ventral telencephalon that are associated with emotional contagion in zebrafish are homologous to those known to be involved in the same process in rodents (e.g. striatum, lateral septum), and receive direct projections from oxytocinergic neurons located in the pre-optic area. Finally, we ruled out the hypothesis that social transmission of fear in zebrafish merely relies on behavior contagion by motor imitation, and we showed that it rather relies on emotion discrimination. Together our results support an evolutionary conserved role for oxytocin as a key regulator of basic empathic behaviors across vertebrates.

One-Sentence Summary

Oxytocin is necessary and sufficient for social fear contagion in zebrafish supporting an evolutionary conserved role for oxytocin in emotional contagion among vertebrates.
Arginine methylation sites on SepIVA help balance elongation and septation of the cell wall inMycobacterium smegmatis
Authors: Freeman Angela H , Tembiwa Karen , Brenner James R , Chase Michael R , Fortune Sarah M , Morita Yasu S , Boutte Cara C
Published: October 2021

Growth of mycobacterial cells requires successful coordination between elongation and septation of the cell wall. However, it is not clear which factors directly mediate this coordination. Here, we studied the function and post-translational modification of an essential division factor, SepIVA, inMycobacterium smegmatis. We find that SepIVA is arginine methylated, and that alteration of these methylation sites affects both septation and polar elongation ofMsmeg. Furthermore, we show that SepIVA regulates the localization of MurG, and that this regulation may impact polar elongation. Finally, we map SepIVA’s two regulatory functions to different sites on the protein: the N-terminus regulates elongation while the C-terminus regulates division. These results establish SepIVA as a regulator of both elongation and division and characterize a physiological role for protein arginine methylation sites for the first time in mycobacteria.
Patient attrition in Molecular Tumour Boards: A Review
Authors: Frost Hannah , Graham Donna M. , Carter Louise , O’Regan Paul , Landers Donal , Freitas Andre
Published: October 2021

Molecular Tumour Boards (MTBs) were created with the purpose of supporting clinical decision making within precision medicine. Though these meetings are in use globally reporting often focuses on the small percentages of patients that receive treatment via this process and are less likely to report on, and assess, patients who do not receive treatment. A literature review was performed to understand patient attrition within MTBs and barriers to patients receiving treatment. A total of 54 papers were reviewed spanning a 6 year period from 11 different countries. 20% of patients received treatment through the MTB process. Of those that did not receive treatment the main reasons were no mutations identified (26%), no actionable mutations (22%) and clinical deterioration (15%). However, the data was often incomplete due to inconsistent reporting of MTBs with only 53% reporting on patients having no mutations, 48% reporting on presence of actionable mutations with no treatment options and 57% reporting on clinical deterioration. As patient attrition in MTBs is an issue which is very rarely alluded to in reporting, more transparent reporting is needed to understand barriers to treatment and integration of new technologies is required to process increasing omic and treatment data.
Characterizing the effective reproduction number during the COVID-19 epidemic: Insights from Qatar’s experience
Authors: Bsat Raghid , Chemaitelly Hiam , Coyle Peter , Tang Patrick , Hasan Mohammad R. , Al Kanaani Zaina , Al Kuwari Einas , Butt Adeel A. , Jeremijenko Andrew , Kaleeckal Anvar Hassan , Latif Ali Nizar , Shaik Riyazuddin Mohammad , Nasrallah Gheyath K. , Benslimane Fatiha M. , Al Khatib Hebah A. , Yassine Hadi M. , Al Kuwari Mohamed G. , Al Romaihi Hamad Eid , Al-Thani Mohamed H. , Al Khal Abdullatif , Bertollini Roberto , Abu-Raddad Laith J. , Ayoub Houssein H.
Published: October 2021

Background

The effective reproduction number,Rt, is a tool to track and understand epidemic dynamics. This investigation ofRtestimations was conducted to guide the national COVID-19 response in Qatar, from the onset of the epidemic until August 18, 2021.

Methods

Real-time “empirical”was estimated using five methods, including the Robert Koch Institute, Cislaghi, Systrom-Bettencourt and Ribeiro, Wallinga and Teunis, and Cori et al. methods.Rwas also estimated using a transmission dynamics model. Uncertainty and sensitivity analyses were conducted. Agreements between differentRtestimates were assessed by calculating correlation coefficients.

Results

captured the evolution of the epidemic through three waves, public health response landmarks, effects of major social events, transient fluctuations coinciding with significant clusters of infection, and introduction and expansion of the B.1.1.7 variant. The various estimation methods produced consistent and overall comparableestimates with generally large correlation coefficients. The Wallinga and Teunis method was the fastest at detecting changes in epidemic dynamics.estimates were consistent whether using time series of symptomatic PCR-confirmed cases, all PCR-confirmed cases, acute-care hospital admissions, or ICU-care hospital admissions, to proxy trends in true infection incidence.correlated strongly withand provided an average.

Conclusions

Rtestimations were robust and generated consistent results regardless of the data source or the method of estimation. Findings affirmed an influential role forRtestimations in guiding national responses to the COVID-19 pandemic, even in resource-limited settings.
Gut microbial communities modulate efficacy of albendazole-ivermectin against soil-transmitted helminthiases
Authors: Schneeberger Pierre H.H. , Gueuning Morgan , Welsche Sophie , Hürlimann Eveline , Dommann Julian , Häberli Cécile , Frey Jürg E. , Sayasone Somphou , Keiser Jennifer
Published: October 2021

Background

Soil-transmitted helminth infections represent a large burden across the globe with over a quarter of the world’s population at risk. The outcome of available treatments is species-specific with a large proportion of unexplained treatment failure. Administration of albendazole is the standard of care, but because of low cure rates (CR) observed in treatingTrichuris trichiurainfections, a significantly more efficacious alternative therapy combining albendazole and ivermectin is being investigated.

Methods

80 patients from the village of Pak-Khan, in Laos, with confirmed STH infections (Trichuris trichiuraand hookworms), received either albendazole (400 mg) or albendazole (400 mg) and ivermectin (200 µg/kg) together. A pre-treatment stool sample was collected as well as daily post-treatment stool samples for up to 28 days to measure treatment efficacy. Taxonomic profiling of pre-treatment stool samples was conducted using 16S rRNA gene sequencing, target-specific and total bacteria qPCR, as well as shotgun sequencing.

Results

Three bacterial communities, or enterotypes (ET) 1-3, were identified. No association with pre-treatment enterotype and treatment outcome of bothTrichuris trichiuraand hookworm were found in the monotherapy arm with overall cure rates (CR) of 7.5% and 50%, respectively. Pre-treatment enterotype was strongly associated with efficacy of the combination therapy for both,T. trichiura(CRoverall= 33.3%; CRET1= 5.8%; CRET2= 16.6%; CRET3= 68.5%) and hookworm (CRoverall= 47.2%; CRET1= 31.2%; CRET2= 16.6%; CRET3= 78.5%) infections. Daily post-treatment egg per gram of stool counts recapitulated these observations and faster and increased egg reduction was observed in ET3 when compared to failure-associated ET1 and ET2. Species-level comparisons of these enterotypes highlighted a set of ten differentially enriched bacterial species.

Conclusion

Taxonomically distinct gut microbiota communities were found in this setting in terms of both, relative and absolute abundances, of specific bacterial taxa. Pre-treatment enterotype was relevant for treatment outcome of the combination therapy, albendazole and ivermectin, forT. trichiuraas well as for hookworm infections. These observations indicate that pre-treatment microbial composition of stool samples should be monitored to ensure evidence-based administration of albendazole-ivermectin to treat these diseases.