bluuebunny/crossref_metadata_2025 huggingface dataset:
Exempting low-risk health research from ethics reviews to better serve the interests of the patients and public: a qualitative analysis of survey responses
Authors: Scott Anna Mae , Chalmers Iain , Barnett Adrian , Stephens Alexandre , Kolstoe Simon E. , Clark Justin , Matthews Richard , Glasziou Paul
Published: February 2021

Background

We conducted a survey to identify what types of health research could be exempted from research ethics reviews in Australia.

Methods

We surveyed active Australian health researchers and members of Human Research Ethics Committees (HREC). We presented the respondents with eight hypothetical research scenarios, involving: N of 1 trials, no treatment studies, linked data sets, surplus samples, audits, surveys, interviews with patients, and professional opinion. We asked whether these scenarios should or should not be exempt from ethics review, and to provide (optional) explanations. We analysed the reasons thematically, to identify Top 3 reasons underlying the decisions.

Results

Most frequent reasons for requiring ethics reviews, included: the need for independent oversight, privacy/confidentiality issues, review of scientific rigour, and publishing considerations. Most frequent reasons for exempting scenarios from reviews, included: level of risk, study design, privacy/confidentiality issues, and standard clinical practice. Four research scenarios listed the same Top 3 reasons for requiring ethics reviews: need for independent oversight, review of scientific rigour, privacy/confidentiality. Reasons for exempting were less uniform, but low risk was a Top 3 reason for 7 scenarios, and study design for 4 scenarios. Privacy/confidentiality was given as a Top 3 reason for both requiring and exempting from ethics the same two scenarios.

Conclusions

The most frequently offered reasons in support of requiring ethics reviews for research scenarios are more uniform than those for exempting them. However, considerable disagreement exists about when the risks of research are so minimal that the exemption is appropriate.
How coiled-coil assemblies accommodate multiple aromatic residues
Authors: Rhys Guto G. , Dawson William M. , Beesley Joseph L. , Martin Freddie J. O. , Brady R. Leo , Thomson Andrew R. , Woolfson Derek N.
Published: February 2021

Rational protein design requires understanding the contribution of each amino acid to a targeted protein fold. For a subset of protein structures, namely theα;-helical coiled coils (CCs), knowledge is sufficiently advanced to allow the rationalde novodesign of many structures, including entirely new protein folds. However, current CC design rules center on using aliphatic hydrophobic residues predominantly to drive the folding and assembly of amphipathicαhelices. The consequences of using aromatic residues—which would be useful for introducing structural probes, and binding and catalytic functionalities—into these interfaces is not understood. There are specific examples of designed CCs containing such aromatic residues,e.g., phenylalanine-rich sequences, and the use of polar aromatic residues to make buried hydrogen-bond networks. However, it is not known generally if sequences rich in tyrosine can form CCs, or what CC assemblies these would lead to. Here we explore tyrosine-rich sequences in a general CC-forming background and resolve new CC structures. In one of these, an antiparallel tetramer, the tyrosine residues are solvent accessible and pack at the interface between the core and the surface. In the other more-complex structure, the residues are buried and form an extended hydrogen-bond network.
Stratified neural networks in a time-to-event setting
Authors: Kuruc Fabrizio , Binder Harald , Hess Moritz
Published: February 2021

Deep neural networks are now frequently employed to predict survival conditional on omics-type biomarkers, e.g. by employing the partial likelihood of Cox proportional hazards model as loss function. Due to the generally limited number of observations in clinical studies, combining different data-sets has been proposed to improve learning of network parameters. However, if baseline hazards differ between the studies, the assumptions of Cox proportional hazards model are violated. Based on high dimensional transcriptome profiles from different tumor entities, we demonstrate how using a stratified partial likelihood as loss function allows for accounting for the different baseline hazards in a deep learning framework. Additionally, we compare the partial likelihood with the ranking loss, which is frequently employed as loss function in machine learning approaches due to its seemingly simplicity. Using RNA-seq data from the Cancer Genome Atlas (TCGA) we show that use of stratified loss functions leads to an overall better discriminatory power and lower prediction error compared to their nonstratified counterparts. We investigate which genes are identified to have the greatest marginal impact on prediction of survival when using different loss functions. We find that while similar genes are identified, in particular known prognostic genes receive higher importance from stratified loss functions. Taken together, pooling data from different sources for improved parameter learning of deep neural networks benefits largely from employing stratified loss functions that consider potentially varying baseline hazards. For easy application, we provide PyTorch code for stratified loss functions and an explanatory Jupyter notebook in a GitHub repository.
Differential dropout analysis captures biological variation in single-cell RNA sequencing data
Authors: Bouland Gerard A. , Mahfouz Ahmed , Reinders Marcel J.T.
Published: February 2021

Single-cell RNA sequencing data is characterized by a large number of zero counts, yet there is growing evidence that these zeros reflect biological variation rather than technical artifacts. We propose differential dropout analysis (DDA) to identify the effects of biological variation in single-cell RNA sequencing data. Using 16 publicly available and simulated datasets, we show that DDA accurately detects biological variation and can assess the relative abundance of transcripts more robustly than methods relying on counts. DDA is available athttps://github.com/gbouland/DDA.
Image denoising for fluorescence microscopy by self-supervised transfer learning
Authors: Wang Yina , Pinkard Henry , Khwaja Emaad , Zhou Shuqin , Waller Laura , Huang Bo
Published: February 2021

When using fluorescent microscopy to study cellular dynamics, trade-offs typically have to be made between light exposure and quality of recorded image to balance phototoxicity and image signal-to-noise ratio. Image denoising is an important tool for retrieving information from dim live cell images. Recently, deep learning based image denoising is becoming the leading method because of its promising denoising performance, achieved by leveraging available prior knowledge about the noise model and samples at hand. We demonstrate that incorporating temporal information in the model can further improve the results. However, the practical application of this method has seen challenges because of the requirement of large, task-specific training datasets. In this work, addressed this challenge by combining self-supervised learning with transfer learning, which eliminated the demand of task-matched training data while maintaining denoising performance. We demonstrate its application in fluorescent imaging of different subcellular structures.
Regenerating insulin-producing β-cells ectopically from a mesodermal origin in the absence of endothelial specification
Authors: Liu Ka-Cheuk , Villasenor Alethia , Schmitner Nicole , Radros Niki , Rautio Linn , Reischauer Sven , Stainier Didier Y.R. , Andersson Olov
Published: February 2021

To investigate the role of the vasculature in pancreatic β-cell regeneration, we crossed a zebrafish β-cell ablation model into the avascularnpas4lmutant (i.e.cloche). Surprisingly, β-cell regeneration increased markedly innpas4lmutants owing to the ectopic differentiation of β-cells in the mesenchyme, a phenotype not previously reported in any models. The ectopic β-cells expressed endocrine markers of pancreatic β-cells, and also reduced glucose levels in the β-cell ablation model. Through lineage tracing, we determined that the vast majority of these ectopic β-cells derived from the mesodermal lineage. Notably, ectopic β-cells were found innpas4lmutants as well as following knockdown of the endothelial determinant Etv2. Together, these data indicate that in the absence of endothelial specification, mesodermal cells possess a remarkable plasticity enabling them to form β-cells, which are normally endodermal in origin. Understanding the restriction of this differentiation plasticity will help exploit an alternative source for β-cell regeneration.
Biosynthesis system of Synechan, a sulfated exopolysaccharide, in the model cyanobacteriumSynechocystissp. PCC 6803
Authors: Maeda Kaisei , Okuda Yukiko , Enomoto Gen , Watanabe Satoru , Ikeuchi Masahiko
Published: February 2021

Extracellular polysaccharides of bacteria contribute to biofilm formation, stress tolerance, and infectivity. Cyanobacteria, the oxygenic photoautotrophic bacteria, uniquely and widely have sulfated extracellular polysaccharides and they may utilize the polysaccharides for survival in nature. In addition, sulfated polysaccharides of cyanobacteria and other organisms have been focused as beneficial biomaterial. However, very little is known about their biosynthesis machinery and function in cyanobacteria. Here we found that the model cyanobacterium,Synechocystissp. PCC 6803, formed bloom-like cell aggregates using sulfated extracellular polysaccharides (designated as synechan) and identified whole set of genes responsible for synechan biosynthesis and its transcriptional regulation, thereby suggesting a model for the synechan biosynthesis apparatus. Because similar genes are found in many cyanobacterial genomes with wide variation, our findings may lead elucidation of various sulfated polysaccharides, their functions, and their potential application in biotechnology.
Impact of a human gut microbe onVibrio choleraehost colonization through biofilm enhancement
Authors: Barrasso Kelsey , Chac Denise , Debela Meti D. , Geigel Catherine , Harris Jason B. , LaRocque Regina C. , Midani Firas S. , Qadri Firdausi , Yan Jing , Weil Ana A. , Ng Wai-Leung
Published: February 2021

Recent studies indicate that the human intestinal microbiota could impact the outcome of infection byVibrio cholerae, the etiological agent of the diarrheal disease cholera. A commensal bacterium,Paracoccus aminovorans, was previously identified in high abundance in stool collected from individuals infected withV. choleraewhen compared to stool from uninfected persons. However, if and howP. aminovoransinteracts withV. choleraehas not been experimentally determined; moreover, whether any association between this bacterium alters the behaviors ofV. choleraeto affect the disease outcome is unclear. Here we show thatP. aminovoransandV. choleraetogether form dual-species biofilm structures at the air-liquid interface, with previously uncharacterized novel features. Importantly, the presence ofP. aminovoranswithin the murine small intestine enhancesV. choleraecolonization in the same niche that is dependent on theVibrioexopolysaccharide (VPS) and other major components of matureV. choleraebiofilm. These studies illustrate that dual-species biofilm formation is a plausible mechanism used by a gut microbe to increase the virulence of the pathogen, and this interaction may alter outcomes in enteric infections.

Significance Statement

While ample evidence suggests that the outcome of some enteric infections can be affected by the intestinal microbiota, how specific gut microbes change the behaviors of a pathogen is unclear. Here we characterize the interaction betweenVibrio choleraeandParacoccus aminovorans, a gut microbe known to increase in abundance in the intestines during activeV. choleraeinfection in humans. These two bacteria form a dual-species biofilm structure at the air-liquid interface, and the gut microbe increases the host colonization efficiency ofV. cholerae. Importantly, our study identifies a previously unknown mechanism of gut microbe-pathogen interaction that has the potential to alter the disease outcome.
Neuronal control of maternal provisioning in response to social cues
Authors: Wasson Jadiel A. , Harris Gareth , Keppler-Ross Sabine , Brock Trisha J. , Dar Abdul R. , Butcher Rebecca A. , Fischer Sylvia E.J. , Kagias Konstantinos , Clardy Jon , Zhang Yun , Mango Susan
Published: February 2021

Mothers contribute cytoplasmic components to their progeny in a process called maternal provisioning. Provisioning is influenced by the parental environment, but the molecular pathways that transmit environmental cues from mother to progeny are not well understood. Here we show that in C. elegans, social cues modulate maternal provisioning to regulate gene silencing in offspring. Intergenerational signal transmission depends on a pheromone-sensing neuron and neuronal FMRF (Phe-Met-Arg-Phe)-like peptides. Parental FMRF signaling promotes the deposition of mRNAs for translational components in progeny, which in turn reduces gene silencing. Previous studies had implicated FMRF signaling in short-term responses such as modulated feeding behavior in response to the metabolic state1,2, but our data reveal a broader role, to coordinate energetically expensive processes such as translation and maternal provisioning. This study identifies a new pathway for intergenerational communication, distinct from previously discovered pathways involving small RNAs and chromatin, that links sensory perception to maternal provisioning.
CRISPR targeting of MEIOTIC-TOPOISOMERASE VIB-dCas9 to a recombination hotspot is insufficient to increase crossover frequency in Arabidopsis
Authors: Yelina Nataliya E. , Gonzalez-Jorge Sabrina , Hirsz Dominique , Yang Ziyi , Henderson Ian R.
Published: February 2021

During meiosis, homologous chromosomes pair and recombine, which can result in reciprocal crossovers that increase genetic diversity. Crossovers are unevenly distributed along eukaryote chromosomes and show repression in heterochromatin and the centromeres. Within the chromosome arms crossovers are often concentrated in hotspots, which are typically in the kilobase range. The uneven distribution of crossovers along chromosomes, together with their low number per meiosis, creates a limitation during crop breeding, where recombination can be beneficial. Therefore, targeting crossovers to specific genome locations has the potential to accelerate crop improvement. In plants, meiotic crossovers are initiated by DNA double strand breaks (DSBs) that are catalysed by SPO11 complexes, which consist of two catalytic (SPO11-1 and SPO11-2) and two non-catalytic subunits (MTOPVIB). We used the model plantArabidopsis thalianato target a dCas9-MTOPVIB fusion protein to the3acrossover hotspot via CRISPR. We observed that this was insufficient to significantly change meiotic crossover frequency or pattern within3a. We discuss the implications of our findings for targeting meiotic recombination within plant genomes.
The Collagens DPY-17 and SQT-3 Direct Anterior-Posterior Migration of the Q Neuroblasts inC. elegans
Authors: Lang Angelica E. , Lundquist Erik A.
Published: February 2021

Cell adhesion molecules and their extracellular ligands control morphogenetic events such as directed cell migration. The migration of neuroblasts and neural crest cells establishes the structure of the central and peripheral nervous systems. InC. elegans, the bilateral Q neuroblasts and their descendants undergo long-range migrations with left/right asymmetry. QR and descendants on the right migrate anteriorly, and QL and descendants on the left migrate posteriorly, despite identical patterns of cell division, cell death, and neuronal generation. The initial direction of protrusion of the Q cells relies on the left/right asymmetric function of the transmembrane receptors UNC-40/DCC and PTP-3/LAR in the Q cells. Here we show that Q cell left/right asymmetry of migration is independent of the GPA-16/Gα pathway that regulates other left/right asymmetries including nervous system L/R asymmetry. No extracellular cue has been identified that guides initial Q anterior versus posterior migration. We show that the Collagens DPY-17 and SQT-3 control initial Q direction of protrusion. Genetic interactions with UNC-40/DCC and PTP-3/LAR suggest that DPY-17 and SQT-3 drive posterior migration and might act with both receptors or in a parallel pathway. Analysis of mutants in other Collagens and extracellular matrix components indicated that general perturbation of Collagens and the ECM did not result in directional defects, and that the effect of DPY-17 and SQT-3 on Q direction is specific. DPY-17 and SQT-3 are components of the cuticle, but a role in the basement membrane cannot be excluded. Possibly, DPY-17 and SQT-3 are part of a pattern in the cuticle and/or basement membrane that is oriented to the anterior-posterior axis of the animal and that is deciphered by the Q cells in a left-right asymmetric fashion. Alternatively, DPY-17 and SQT-3 might be involved in the production or stabilization of a guidance cue that directs Q migrations. In any case, these results describe a novel role for the DPY-17 and SQT-3 Collagens in directing posterior Q neuroblast migration.

Graphical Abstract
Antennal transcriptome analysis and identification of candidate chemosensory genes of the harlequin ladybird beetle,Harmonia axyridis(Pallas) (Coleoptera: Coccinellidae)
Authors: Rondoni Gabriele , Roman Alessandro , Meslin Camille , Montagné Nicolas , Conti Eric , Jacquin-Joly Emmanuelle
Published: February 2021

In predatory ladybirds (Coleoptera: Coccinellidae), antennae are important for chemosensory reception used during food and mate location, and for finding a suitable oviposition habitat. Based on NextSeq 550 Illumina sequencing, we assembled the antennal transcriptome of matedHarmonia axyridis(Pallas) (Coleoptera: Coccinellidae) males and females and described the first chemosensory gene repertoire expressed in this species. We annotated candidate chemosensory sequences encoding 26 odorant receptors (including the coreceptor, Orco), 17 gustatory receptors, 27 ionotropic receptors, 31 odorant-binding proteins, 12 chemosensory proteins and 4 sensory neuron membrane proteins. Maximum-likelihood phylogenetic analyses allowed to assign candidateH. axyridischemosensory genes to previously described groups in each of these families. Differential expression analysis between males and females revealed low variability between sexes, possibly reflecting the known absence of relevant sexual dimorphism in the structure of the antennae and in the distribution and abundance of the sensilla. However, we revealed significant differences in expression of three chemosensory genes, namely 2 male-biased odorant-binding proteins and 1 male-biased odorant receptor, suggesting their possible involvement in pheromone detection. Our data pave the way for improving the understanding of the molecular basis of chemosensory reception in Coccinellidae.

The predatory harlequin ladybirdHarmonia axyridis(Pallas) (Coleoptera: Coccinellidae) has been widely released for classical and augmentative biological control programs of insect herbivores and is now distributed worldwide. Because of its invasive behavior and the threat it can pose to local biodiversity, this ladybird has been adopted as a model species for invasive biocontrol predators. A huge existing literature is available on this species. However, little is known about the mechanisms underlyingH. axyridissmell and taste, even though these senses are important in this ladybird for courtship, mating and for locating suitable habitats for feeding and oviposition. Here we describe the first chemosensory gene repertoire that is expressed in the antennae of male and femaleH. axyridis. Our findings would likely represent the basis for future functional studies aiming at increasing the efficacy ofH. axyridisin biological control or at reducing its populations in those areas where the ladybird has become a matter of concern due to its invasiveness.
The ETS Transcription Factor ERF controls the exit from the naïve pluripotent state
Authors: Vega-Sendino M. , Olbrich T. , Tillo D. , Tran A. D. , Domingo C. N. , Franco M. , FitzGerald P. C. , Kruhlak M. J. , Ruiz S.
Published: February 2021

The naïve epiblast undergoes a transition to a pluripotent primed state during embryo implantation. Despite the relevance of the FGF pathway during this period, little is known about the downstream effectors regulating this signaling. Here, we examined the molecular mechanisms coordinating the naïve to primed transition by using inducible ESC to genetically eliminate all RAS proteins. We show that differentiated RASKOESC remain trapped in an intermediate state of pluripotency with naïve-associated features. Elimination of the transcription factor ERF overcomes the developmental blockage of RAS-deficient cells by naïve enhancer decommissioning. Mechanistically, ERF regulates NANOG expression and ensures naïve pluripotency by strengthening naïve transcription factor binding at ESC enhancers. Moreover, ERF negatively regulates the expression of thede novomethyltransferase DNMT3B, which participates in the extinction of the naïve transcriptional program. Collectively, we demonstrated an essential role for ERF controlling the exit from naïve pluripotency during the progression to primed pluripotency.

Teaser

ERF is the MAPK-dependent switch controlling the transition between naïve and primed pluripotency during embryonic development.
Itaconate and its derivatives repress C2C12 myogenesis
Authors: Oh Tae Seok , Hutchins Damian C. , Mainali Rabina , Goslen Kevin , Quinn Matthew A.
Published: February 2021

A Krebs cycle intermediate metabolite, itaconate, has gained attention as a potential antimicrobial and autoimmune disease treatment due to its anti-inflammatory effects. While itaconate and its derivatives pose an attractive therapeutic option for the treatment of inflammatory diseases, the effects outside the immune system still remain limited, particularly in the muscle. Therefore, we endeavored to determine if itaconate signaling impacts muscle differentiation. Utilizing the well-established C2C12 model ofin vitromyogenesis, we evaluated the effects of itaconate and its derivatives on transcriptional and protein markers of muscle differentiation as well as mitochondrial function. We found itaconate and the derivatives dimethyl itaconate and 4-octyl itaconate disrupt differentiation media-induced myogenesis. A primary biological effect of itaconate is a succinate dehydrogenase (SDH) inhibitor. We find the SDH inhibitors dimethyl malonate and harzianopyridone phenocopie the anti-myogenic effects of itaconate. Furthermore, we find treatment with exogenous succinate results in blunted myogenesis. Together our data indicate itaconate and its derivatives interfere within vitromyogenesis, potentially through inhibition of SDH and subsequent succinate accumulation. More importantly, our findings suggest the therapeutic potential of itaconate and its derivatives could be limited due to deleterious effects on myogenesis.
Isoform-specific functions of Numb in breast cancer progression, metastasis and proteome remodeling
Authors: Zhang Yangjing , Dho Sascha E. , Simpson Craig D. , Othman Kamal , Bondoc Andrew , McGlade C. Jane
Published: February 2021

Deregulated alternative splicing of the endocytic adaptorNUMBresulting in high expression of Exon9in (exon 9-containing) isoforms has been reported in several cancer types. However, the role of Numb isoform expression in tumor progression and the underlying mechanisms remain elusive. Here, we report greater exon 9 inclusion in multiple cancer types including all subtypes of breast cancer, and correlation of higher exon 9 inclusion in patients with worse prognosis. Deletion of Exon9in in breast cancer cells leads to reduced cell growth and a significant decrease of lung metastasis in orthotopic xenograft experiments. Quantitative mass spectrometry revealed downregulation of proteins involved in EMT and ECM organization and remodeling of the endocytic protein network in cells lacking the Exon9in Numb isoforms. Exon 9 deletion also results in reduced surface levels of ITGβ5, and downstream signaling to ERK and SRC, consistent with enhance lysosomal targeting mediated by the remaining Exon9sk (exon 9 skipping) Numb isoforms.

SIGNIFICANCE

Expression ofNUMBExon9in protein isoforms correlate with worse progression free survival, particularly in breast cancer. Our findings also reveal that Exon9in isoforms promote breast cancer progression by relieving Numb mediated down regulation of integrins and implicate Numb alternative splicing as a progression factor in multiple cancer types.
Autonomous Wireless System for Robust and Efficient Inductive Power Transmission to Multi-Node Implants
Authors: Feng Peilong , Constandinou Timothy G.
Published: February 2021

A number of recent and current efforts in brain machine interfaces are developing millimetre-sized wireless implants that achieve scalability in the number of recording channels by deploying a distributed ‘swarm’ of devices. This trend poses two key challenges for the wireless power transfer: (1) the system as a whole needs to provide sufficient power to all devices regardless of their position and orientation; (2) each device needs to maintain a stable supply voltage autonomously. This work proposes two novel strategies towards addressing these challenges: a scalable resonator array to enhance inductive networks; and a self-regulated power management circuit for use in each independent mm-scale wireless device. The proposed passive 2-tier resonant array is shown to achieve an 11.9% average power transfer efficiency, with ultra-low variability of 1.77% across the network.

The self-regulated power management unit then monitors and autonomously adjusts the supply voltage of each device to lie in the range between 1.7 V-1.9 V, providing both low-voltage and over-voltage protection.
Mutant SETBP1 enhances NRAS-driven MAPK pathway activation to promote aggressive leukemia
Authors: Carratt Sarah A. , Braun Theodore P. , Coblentz Cody , Schonrock Zachary , Callahan Rowan , Smith Brittany M. , Maloney Lauren , Foley Amy C. , Maxson Julia E.
Published: February 2021

Mutations in SET binding protein 1 (SETBP1) are associated with poor outcomes in myeloid leukemias. In the Ras-driven leukemia, juvenile myelomonocytic leukemia, SETBP1 mutations are enriched in relapsed disease. While some mechanisms for SETBP1-driven oncogenesis have been established, it remains unclear how SETBP1 specifically modulates the biology of Ras-driven leukemias. In this study, we found that when co-expressed with Ras pathway mutations, SETBP1 promoted oncogenic transformation of murine bone marrow in vitro and aggressive myeloid leukemia in vivo. We demonstrate that SETBP1 enhances the NRAS gene expression signature, driving upregulation of mitogen-activated protein kinase (MAPK) signaling and downregulation of differentiation pathways. SETBP1 also enhances NRAS-driven phosphorylation of MAPK proteins. Cells expressing NRAS and SETBP1 are sensitive to inhibitors of the MAPK pathway, and treatment with the MEK inhibitor trametinib conferred a survival benefit in a mouse model of NRAS/SETBP1-mutant disease. Our data demonstrate that despite driving enhanced MAPK signaling, SETBP1-mutant cells remain susceptible to trametinib in vitro and in vivo, providing encouraging pre-clinical data for the use of trametinib in SETBP1-mutant disease.
Chemogenetic dissection of the primate prefronto-subcortical pathways for working memory and decision-making
Authors: Oyama Kei , Hori Yukiko , Nagai Yuji , Miyakawa Naohisa , Mimura Koki , Hirabayashi Toshiyuki , Inoue Ken-ichi , Suhara Tetsuya , Takada Masahiko , Higuchi Makoto , Minamimoto Takafumi
Published: February 2021

The primate prefrontal cortex (PFC) is situated at the core of higher brain functions by linking and cooperating with the caudate nucleus (CD) and mediodorsal thalamus (MD) via neural circuits. However, the distinctive roles of these prefronto-subcortical pathways remain elusive. Combining in vivo neuronal projection mapping with chemogenetic synaptic silencing, we reversibly dissected key pathways from PFC to the CD and MD individually in single monkeys. We found that silencing the bilateral PFC-MD projections, but not the PFC-CD projections, impaired performance in a spatial working memory task. Conversely, silencing the unilateral PFC-CD projection, but not the PFC-MD projection, altered preference in a free-choice task. These results revealed dissociable roles of the prefronto-subcortical pathways in working memory and decision-making, representing the technical advantage of imaging-guided pathway-selective chemogenetic manipulation for dissecting neural circuits underlying cognitive functions in primates.
Slower prefrontal metastable dynamics during deliberation predicts error trials in a distance discrimination task
Authors: Benozzo Danilo , La Camera Giancarlo , Genovesio Aldo
Published: February 2021

Abstract

Previous studies have established the involvement of prefrontal cortex (PFC) neurons in decision processes in many task contexts. Single neurons and populations of neurons have been found to represent stimuli, actions, and internal deliberations. However, it is much less clear which underlying computations are affected during errors. Neural activity during errors can help to disambiguate confounds and clarify which computations are essential during a specific task. Here, we used a hidden Markov model (HMM) to perform a trial-by-trial analysis of ensembles of simultaneously recorded neurons from the dorsolateral prefrontal (PFdl) cortex of two rhesus monkeys performing a distance discrimination task. The HMM segments the neural activity into sequences of metastable states, allowing to link neural ensemble dynamics with task and behavioral features in the absence of external triggers. We report a precise relationship between the modulation of the metastable dynamics and task features. Specifically, we found that errors were made more often when the metastable dynamics slowed down, while trial difficulty influenced the latency of state transitions at a pivotal point during the trial. Both these phenomena occurred during the decision interval and not following the action, with errors occurring in both easy and difficult trials. Thus, modulations of metastable dynamics reflected a state of internal deliberation rather than actions taken or, in the case of error trials, objective trial difficulty. Our results show that temporal modulations of PFdl activity are key determinants of internal deliberations, providing further support for the emerging role of metastable cortical dynamics in mediating complex cognitive functions and behavior.
Molecular mechanism of N-terminal acetylation by the ternary NatC complex
Authors: Deng Sunbin , Gottlieb Leah , Pan Buyan , Supplee Julianna , Wei Xuepeng , Petersson E James , Marmorstein Ronen
Published: February 2021

Protein N-terminal acetylation is predominantly a ribosome-associated modification, with NatA-E serving as the major enzymes. NatC is the most unusual of these enzymes, containing one Naa30 catalytic subunit and two auxiliary subunits, Naa35 and Naa38; and substrate specificity profile that overlaps with NatE. Here, we report the Cryo-EM structure ofS. pombeNatC with a NatE/C-type bisubstrate analogue and inositol hexaphosphate (IP6), and associated biochemistry studies. We find that the presence of three subunits is a prerequisite for normal NatC acetylation activity in yeast and that IP6binds tightly to NatC to stabilize the complex. We also describe the molecular basis for IP6-mediated NatC complex stabilization and the overlapping yet distinct substrate profiles of NatC and NatE.
Working Memory Representations in Visual Cortex Mediate the Effects of Distraction
Authors: Hallenbeck Grace E. , Sprague Thomas C. , Rahmati Masih , Sreenivasan Kartik K. , Curtis Clayton E.
Published: February 2021

Although the contents of working memory (WM) can be decoded from activity in visual cortex, these representations may play a limited role if they are not robust to distraction. Here, we used model-based fMRI to estimate the impact that a distracting visual task had on WM representations in several visual field maps in visual and frontoparietal association cortex. Distraction caused the fidelity of WM representations in all maps to briefly dip when both the memorandum and distractor were jointly encoded by the population activities. Moreover, distraction induced small biases in memory errors which were predicted by biases in neural decoding in early visual cortex, but not other regions. Although distraction briefly disrupts WM representations, the widespread redundancy with which WM information is encoded may protect against catastrophic loss. In early visual cortex, nonetheless, the neural representation of information in WM and behavioral performance were intertwined, solidifying its importance in memory.
Bioprinting transgenic plant cells for production of a recombinant biodefense agent
Authors: Varma Anika , Gemeda Hawi B. , McNulty Matthew J. , McDonald Karen A. , Nandi Somen , Knipe Jennifer M.
Published: February 2021

Transgenic rice cells (Oryza sativa) producing recombinant butyrylcholinesterase (BChE) as a prophylactic/therapeutic against organophosphate nerve agent poisoning, cocaine toxicity, and neurodegenerative diseases like Alzheimer’s were immobilized in a polyethylene glycol-based hydrogel. The cells were sustained for 14 days in the semi-solid matrix, undergoing a growth phase from days 0-6, a BChE production phase in sugar-free medium from days 6-12, and a growth/recovery phase from days 12-14. Throughout this period, the cells maintained similar viability to those in suspension cultures and displayed analogous sugar consumption trends. The rice cells in the bioprintable hydrogel also produced a significant amount of active BChE, comparable to the levels produced in liquid cultures. A considerable fraction of this BChE was secreted into the media, allowing for easier product separation. Overall, we demonstrate a simple, efficient, robust, modular, and potentially field-deployable bioreactor system for the manufacture of biologics.
Phenotypic and genotypic characterization of antibiotic Resistant Gram Negative Bacteria isolated in Tabuk City, Saudi Arabia
Authors: Alnour Tarig M.S. , Elssaig Elmutuz H. , Ahmed-Abakur Eltayib H. , Abuduhier Faisel M. , Alfifi Khalid A. S. , Abusuliman Mohammad S. , Albalawi Tawfiq
Published: February 2021

Antimicrobial surveillance and identifying the genetic basis of antimicrobial resistance provide important information to optimize patient care. The present study was analytical cross sectional study aimed to determine the prevalence of MDR, XDR, PDR and extended-spectrum β-lactamases genes (SHV, CTX-M and TEM) among Gram-negative bacteria isolated in Tabuk, Saudi Arabia. A total number of 386 non-duplicate Gram-negative isolate were collected. Identification and susceptibility testing were done using automation system (BD Phoenix™). The extracted DNA were subjected to multiplex polymerase chain reaction (PCR). The results showed that only 15 (3.9%) of isolates were fully susceptible, the overall prevalence of XDR, MDR, PDR was 129 (33.4%), 113 (29.3%) and 48(12.4%) respectively. High resistant rate was observed against the antibiotic agents of cephalosporins class 79.3% followed by the agents of penicillins class 69.4%. The most dominant gene was bla SHV which detected in 106/386 (27.5%) isolates followed by bla CTX-M 90/386 (23.3%). Bla CTX-M showed significant relation with all used antibiotic except ampicillin/clavulanic acid, aztreonam, cefoxtin, and meropene. The isolates which showed most frequent resistant genes wereKlebsiella pneumoniae 90/124 (72.6%), A. baumanni37/67 (55.2%),and P.mirabilis24/44 (54.5%). These findings underscores the need for optimization of current therapies and prevention of the spread of these organisms.
Outer membrane vesicles derived fromSalmonellaTyphimurium can deliverShigella flexneri2a O-polysaccharide antigen to prevent lethal pulmonary infection in mice
Authors: Tian Huizhen , Li Biaoxian , Chen Yuxuan , Jie Kaiwen , Xu Tian , Song Zifan , Huang Xiaotian , Liu Qiong
Published: February 2021

The threat to health from shigellosis has become quite serious in many developing countries, causing severe diarrhea.Shigella flexneri2a (S. flexneri2a) is the principal species responsible for this endemic disease. Although there have been multiple attempts to design a vaccine against Shigellosis, one that is effective has not yet been developed. Lipopolysaccharide (LPS) is both an essential virulence factor and a protective antigen againstShigella, due to its outer domain, termed O-polysaccharide antigen. In the present study,S. flexneri2a O-polysaccharide antigen was innovatively bio-synthesized inSalmonellaand attached to core-lipid A by the ligase WaaL, and thus purified outer membrane vesicles (OMVs) were used as a vaccine for subsequent research. Here, we identified the expression of the heterologous polysaccharide antigen and described the isolation, characterization, and immune protection efficiency of the OMV vaccine. The expression ofS. flexneri2a did not affect the formation ofSalmonellaOMVs or their cytotoxicity. Furthermore, the results of the animal experiments indicated that immunization of the mice both intranasally and intraperitoneally with the OMV vaccine induced significant specific anti-Shigella LPS antibodies in both vaginal secretions and fluid from bronchopulmonary lavage, in addition to within sera. The OMV vaccine immunized by both routes of administration provided significant protection against virulentS. flexneri2a infection, as judged by a serum bactericidal assay (SBA), opsonization assay, challenge experiment, and pathological analysis. The present study firstly indicates that the proposed vaccination strategy represents a novel and improved approach to control Shigellosis by the combination of bioconjugation ofSalmonellaglycosyl carrier lipid and OMV. In addition, the strategy of genetic manipulation described here is ideally suited for designs based on otherShigellaserotypes, allowing the development of aShigellavaccine with broad-protection.
Mosaic Ends Tagmentation (METa) assembly for extremely efficient construction of functional metagenomic libraries
Authors: Crofts Terence S. , McFarland Alexander G. , Hartmann Erica M.
Published: February 2021

Functional metagenomic libraries, physical bacterial libraries which allow the high-throughput capture and expression of microbiome genes, have been instrumental in the sequence-naïve and cultivation-independent discovery of novel genes from microbial communities. Preparation of these libraries is limited by their high DNA input requirement and their low cloning efficiency. Here, we describe a new method, METa assembly, for extremely efficient functional metagenomic library preparation. We apply tagmentation to metagenomic DNA from soil and gut microbiomes to prepare DNA inserts for high-throughput cloning into functional metagenomic libraries. The presence of mosaic end sequences in the resulting DNA fragments synergizes with homology-based assembly cloning to result in a 300-fold increase in library size compared to traditional blunt cloning based protocols. Compared to published libraries prepared by state-of-the-art protocols we show that METa assembly is on average 23- to 270-fold more efficient and can be effectively used to prepare gigabase-sized libraries with as little as 200 ng of input DNA. We demonstrate the utility of METa assembly to capture novel genes based on their function by discovering novel aminoglycoside (26% amino acid identity) and colistin (36% amino acid identity) resistance genes in soil and goose gut microbiomes. METa assembly provides a streamlined, flexible, and efficient method for preparing functional metagenomic libraries, enabling new avenues of genetic and biochemical research into low biomass or scarce microbiomes.

IMPORTANCE

Medically and industrially important genes can be recovered from microbial communities by high-throughput sequencing but are limited to previously sequenced genes and their relatives. Cloning a metagenomeen masseinto an expression host to produce a functional metagenomic library is a sequence-naïve and cultivation-independent method to discover novel genes. This directly connects genes to functions, but the process of preparing these libraries is DNA greedy and inefficient. Here we describe a library preparation method that is an order of magnitude more efficient and less DNA greedy. This method is consistently efficient across libraries prepared from cultures, a soil microbiome, and from a goose fecal microbiome and allowed us to discover novel antibiotic resistance genes. This new library preparation method will potentially allow for the functional metagenomic exploration of microbiomes that were previously off limits due to their rarity or low microbial biomass, such biomedical swabs or exotic samples.
DEFINING THE DIVERSITY OF HNRNPA1 MUTATIONS IN CLINICAL PHENOTYPE AND PATHOMECHANISM
Authors: Beijer D , Kim HJ , Guo L , O’Donovan K , Mademan I , Deconinck T , Van Schil K , Fare CM , Drake LE , Ford AF , Kochański A , Kabzińska D , Dubuisson N , Van den Bergh P , Voermans NC , Lemmers RJLF , van der Maarel SM , Bonner D , Sampson JB , Wheeler MT , Mehrabyan A , Palmer S , De Jonghe P , Shorter J , Taylor JP , Baets J
Published: February 2021

Mutations in HNRNPA1 encoding heterogeneous nuclear ribonucleoprotein (hnRNP) A1 are a rare cause of amyotrophic lateral sclerosis (ALS) and multisystem proteinopathy (MSP). hnRNPA1 is part of the group of RNA-binding proteins (RBPs) that assemble with RNA to form ribonucleoproteins. hnRNPs are a major subclass of evolutionarily conserved RBPs that are primarily concentrated in the nucleus and are heavily involved in pre-mRNA splicing, mRNA stability and transcriptional/translational regulation. During times of stress, standard translational programming is interrupted, and hnRNPs, mRNA, and other RBPs condense in the cytoplasm, forming liquid-liquid phase separated (LLPS) membraneless organelles termed stress granules (SGs). SGs are central to the pathogenesis of (neuro-)degenerative diseases, including ALS and inclusion body myopathy (IBM). hnRNPs and other RBPs are critical components of SGs. Indeed, the link between SGs, hnRNPs, and neurodegenerative diseases has been established by the identification of additional mutations in RBPs that affect SG biology, including FUS, TDP-43, hnRNPA1, hnRNPA2B1, and TIA1, each of which can directly lead to ALS, IBM and other related neurodegenerative diseases. Here, we report and characterize four novel HNRNPA1 mutations and two known HNRNPA1 mutations, previously reported as being causal for ALS, in a broad spectrum of patients with hereditary motor neuropathy (HMN), ALS, and myopathy. Our results show the different effects of mutations on hnRNPA1 fibrillization, liquid-liquid phase separation, and SG dynamics, indicating the possibility of different underlying pathomechanisms for HNRNPA1 mutations with a possible link to the clinical phenotypes.
First indication of the effect of COVID-19 vaccinations on the course of the outbreak in Israel
Authors: De-Leon H. , Calderon-Margalit R. , Pederiva F. , Ashkenazy Y. , Gazit D.
Published: February 2021

Concomitantly with rolling out its rapid COVID-19 vaccine program, Israel is experiencing its third, and so far largest, surge in morbidity. We aimed to estimate whether the high vaccine coverage among individuals aged over 60 years old creates an observable change in disease dynamics. Using observed and simulated data, we suggest that the shape of the outbreak as measured by daily new moderate and severe cases, and in particular of patients aged over 60, has changed because of vaccination, bringing the decline in new moderate and severe cases earlier than expected, by about a week. Our analyses is consistent with the assumption that vaccination lead to higher than 50% protection in preventing clinical disease and with at least some effectiveness in blocking transmission of elderly population, and supports the importance of prioritizing vulnerable population. This is the first indication of the effectivity of COVID-19 vaccine in changing the course of an ongoing pandemic outbreak.

One Sentence Summary

We show, by data analysis and modelling of the dynamics of COVID-19 pandemic in Israel, that the current nationwide outbreak, that had up to 0.1% of the population confirmed daily, is clearly affected by the vaccination program, that reached a coverage of more than 80% among people ≥ 60 years old.
Timing of convalescent plasma administration and 28-day mortality for COVID-19 pneumonia
Authors: González Soledad E. , Regairaz Lorena , R. Salazar Martín , Ferrando Noelia S. , González Martínez Verónica V. , Carrera Ramos Patricia M. , Pesci Santiago A. , Vidal Juan M. , Kreplak Nicolas , Estenssoro Elisa
Published: February 2021

Convalescent plasma administration (CPA) is widely used to treat Covid-19, but its effectiveness remains controversial. Here we report the results of an Expanded Access Program of CPA in the province of Buenos Aires, Argentina. We evaluated the relationship between the timing of CPA and 28-day mortality in 4719 hospitalized patients with COVID-19 pneumonia. Early (≤3 days from admission) CPA was associated to decreased mortality in patients in the general ward and in the Intensive Care Unit not requiring mechanical ventilation. This suggests that the favorable effect of CPA might be related both to disease acuity and to the therapeutic window.