bluuebunny/crossref_metadata_2025 huggingface dataset:
Antibiofilm activity of Fmoc-phenylalanine against Gram-positive and Gram-negative bacterial biofilms
Authors: Singh Himanshi , Gahane Avinash Y. , Singh Virender , Ghosh Shreya , Thakur Ashwani Kumar
Published: August 2020

Background

Biofilm associated infections are the major contributor of mortality, morbidity and financial burden in patients with bacterial infection. Molecules with surfactant behaviour are known to show significant antibiofilm effect against these infections. Thus, newly discovered antibacterial Fmoc-phenylalanine (Fmoc-F) and other Fmoc-amino acids (Fmoc-AA) with surfactant properties, could have potential antibiofilm properties.

Objectives

To evaluate and characterise the antibiofilm activity of Fmoc-F and some Fmoc-AA against various clinically relevant bacteria.

Methods

Biofilm inhibition and eradication was evaluated by crystal violet staining procedure along with scanning electron microscopy (SEM). Attenuated Total Reflection - Fourier Transform Infrared Spectroscopy (ATR-FTIR), Biochemical assays and Congo red staining were employed to investigate mechanism of antibiofilm action.

Results

We showed that Fmoc-F not only inhibits the biofilm formation inS. aureusandP. aeruginosa, but also eradicates the already formed biofilms over the surface. Further, Fmoc-F coated glass surface resistsS. aureusandP. aeruginosabiofilm formation and attachment, when biofilm is grown over the surface. The mechanistic investigation suggests that Fmoc-F reduces the ECM components such as proteins carbohydrates and eDNA in the biofilm and affect its stabilityviadirect interactions with ECM components and/ or indirectly through reducing bacterial cell population. Finally, we showed that Fmoc-F treatment in combination with other antibiotics such as vancomycin and ampicillin synergistically inhibit biofilm formation.

Conclusions

Overall, the study demonstrates the potential application of Fmoc-F and other Fmoc-AA molecules individually as well as in combination as antibiofilm agents and antibiofilm coating material for treating biofilm associated infections.
Brain network mechanisms of visual shape completion
Authors: Keane Brian P. , Barch Deanna M. , Mill Ravi D. , Silverstein Steven M. , Krekelberg Bart , Cole Michael W.
Published: August 2020

Visual shape completion represents object shape, size, and number from spatially segregated edges. Despite being extensively investigated, the process’s underlying brain regions, networks, and functional connections are still not well understood. To shed light on the topic, we scanned (fMRI) healthy adults during rest and during a task in which they discriminated pac-man configurations that formed or failed to form visually completed shapes (illusory and fragmented condition, respectively). Task activation differences (illusory-fragmented), resting-state functional connectivity, and multivariate pattern differences were identified on the cortical surface using 360 predefined parcels and 12 functional networks composed of such parcels. Brain activity flow mapping (ActFlow) was used to evaluate the likely involvement of resting-state connections for shape completion. We identified 34 differentially-active parcels including a posterior temporal region, PH, whose activity was consistent across all 20 observers. Significant task regions primarily occupied the secondary visual network but also incorporated the frontoparietal, dorsal attention, default mode, and cingulo-opercular networks. Each parcel’s task activation difference could be modeled via its resting-state connections with the remaining parcels (r=.62,p<10-9), suggesting that such connections undergird shape completion. Functional connections from the dorsal attention network were key in modeling activation differences in the secondary visual network and across all remaining networks. Taken together, these results suggest that shape completion relies upon a distributed but densely interconnected network coalition that is centered in the secondary visual network, coordinated by the dorsal attention network, and inclusive of at least three other networks.

Highlights

Shape completion differentially activates regions distributed across five networks

The secondary visual network plays the clearest role in shape completion

Dorsal attention functional connections likely coordinate activity across networks

Posterior temporal region, PH, played a highly consistent role in completion
RNAlign2D – a rapid method for combined RNA structure and sequence-based alignment using a pseudo-amino acid substitution matrix
Authors: Woźniak Tomasz , Sajek Małgorzata , Jaruzelska Jadwiga , Sajek Marcin Piotr
Published: August 2020

Background

The functions of RNA molecules are mainly determined by their secondary structures. These functions can also be predicted using bioinformatic tools that enable the alignment of multiple RNAs to determine functional domains and/or classify RNA molecules into RNA families. However, the existing multiple RNA alignment tools, which use structural information, are slow in aligning long molecules and/or a large number of molecules. Therefore, a more rapid tool for multiple RNA alignment may improve the classification of known RNAs and help to reveal the functions of newly discovered RNAs.

Results

Here, we introduce an extremely fast Python-based tool called RNAlign2D. It converts RNA sequences to pseudo-amino acid sequences, which incorporate structural information, and uses a customizable scoring matrix to align these RNA molecules via the multiple protein sequence alignment tool MUSCLE.

Conclusions

RNAlign2D produces accurate RNA alignments in a very short time. The pseudo-amino acid substitution matrix approach utilized in RNAlign2D is applicable for virtually all protein aligners.
Homeostatic cerebellar compensation of age-related changes of vestibulo-ocular reflex adaptation: a computational epidemiology study
Authors: Luque Niceto R. , Naveros Francisco , Ros Eduardo , Arleo Angelo
Published: August 2020

The vestibulo-ocular reflex (VOR) stabilizes vision during head motion. Age-related changes of vestibular neuroanatomical properties predict a linear decay of VOR function. Nonetheless, human epidemiological data show a stable VOR function across the life span. In this study, we model cerebellum-dependent VOR adaptation to relate structural and functional changes throughout aging. We consider three neurosynaptic factors that may codetermine VOR adaptation during aging: the electrical coupling of inferior olive neurons, the intrinsic plasticity of Purkinje cell (PC) synapses, and long-term spike timing-dependent plasticity at parallel fiber - PC synapses and mossy fiber - medial vestibular nuclei synapses. Our cross-sectional aging analyses suggest that long-term plasticity acts as a global homeostatic mechanism that underpins the stable temporal profile of VOR function. The results also suggest that the intrinsic plasticity of PC synapses operates as a local homeostatic mechanism that further sustains the VOR at older ages. Importantly, the computational epidemiology approach presented in this study allows discrepancies among human cross-sectional studies to be understood in terms of interindividual variability in older individuals. Finally, our longitudinal aging simulations show that the amount of residual fibers coding for the peak and trough of the VOR cycle constitutes a predictive hallmark of VOR trajectories over a lifetime.
SARS-CoV-2 genome sequences from late April in Stockholm, Sweden reveal a novel mutation in the spike protein
Authors: Soratto Tatiany Aparecida Teixeira , Darban Hamid , Bjerkner Annelie , Coorens Maarten , Albert Jan , Allander Tobias , Andersson Björn
Published: August 2020

Large research efforts are going into characterizing, mapping the spread, and studying the biology and clinical features of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Here, we report four complete SARS-CoV-2 genome sequences obtained from patients confirmed to have the disease in Stockholm, Sweden, in late April. A variant at position 23463 was found for the first time in one genome. It changes an arginine (R) residue to histidine (H) at position 364 in the S1 subunit of the spike protein. The genomes belonged to two different genetic groups, previously reported as two of the three main genetic groups found in Sweden. Three of them are from group B.1/G, corresponding to the Italian outbreak, reported by the Public Health Agency of Sweden to have declined in prevalence by late April, and more investigation is needed in order to ensure that the spread of different types of SARS-CoV-2 is fully characterized.

Highlights

Four near-complete genomes of SARS-CoV-2 were assembled from late April in Stockholm.

A novel mutation in the spike protein were found.

The phylogeny of the strains were discussed.
Temporal experience modifies future thoughts: Manipulation of Libet’s W influences difficulty assessment during a decision-making task
Authors: Isham Eve A.
Published: August 2020

Past studies have employed the subjective experience of decision time (Libet’s W) as an index of consciousness, marking the moment at which the agent first becomes aware of a decision. In the current study, we examined whether the temporal experience of W affects subsequent experience related to the action. Specifically, we tested whether W influenced the perception of difficulty in a decision-making task, hypothesizing that temporal awareness of W might influence the sense of difficulty. Consistent with our predictions, when W was perceived as early or late, participants subsequently rated the decision difficulty to be easy or difficult, respectively (Exp.1). Further investigation showed that perceived difficulty, however, did not influence W (Exp.2). Together, our findings suggest a unidirectional relationship such that W plays a role in the metacognition of difficulty evaluation. The results imply that subjective temporal experience of decision time modifies the consequential sense of difficulty.

Highlights

Perceived timing of decision (W) can bias the metacognition of difficulty evaluation in a decision-making task.

Defined as a temporal index of consciousness, time W’s influence on difficulty evaluation reflects the possibility that the role of consciousness is to modify subsequent thoughts and behaviors.

Explicit attention is necessary for the timing of decision (W) to be consciously experienced and effectively influential on subsequent thoughts.
MiRNA expression profiling and zeatin dynamic changes in a new model system ofin vivoindirect regeneration of tomato
Authors: Cao Huiying , Zhang Xinyue , Ruan Yanye , Zhang Lijun , Cui Zhenhai , Li Xuxiao , Jia Bing
Published: August 2020

Callus formation and adventitious shoot differentiation could be observed on the cut surface of completely decapitated tomato plants. We propose that this process can be used as a model system to investigate the mechanisms that regulate indirect regeneration of higher plants without the addition of exogenous hormones. This study analyzed the patterns of trans-zeatin and miRNA expression duringin vivoregeneration of tomato. Analysis of trans-zeatin revealed that the hormone cytokinin played an important role inin vivoregeneration of tomato. Among 183 miRNAs and 1168 predicted target genes sequences identified, 93 miRNAs and 505 potential targets were selected based on differential expression levels for further characterization. Expression patterns of six miRNAs, including sly-miR166, sly-miR167, sly-miR396, sly-miR397, novel 156, and novel 128, were further validated by qRT-PCR. We speculate that sly-miR156, sly-miR160, sly-miR166, and sly-miR397 play major roles in callus formation of tomato duringin vivoregeneration by regulating cytokinin, IAA, and laccase levels. Overall, our microRNA sequence and target analyses of callus formation duringin vivoregeneration of tomato provide novel insights into the regulation of regeneration in higher plants.
Combinatorial mathematical modelling approaches to interrogate rear retraction dynamics in 3D cell migration
Authors: Hetmanski Joseph H.R. , Jones Matt , Chunara Fatima , Schwartz Jean-Marc , Caswell Patrick T.
Published: August 2020

Cell migration in 3D micro-environments is a complex process which depends on the coordinated activity of leading edge protrusive force and rear retraction in a push-pull mechanism. While the potentiation of protrusions has been widely studied, the precise signalling and mechanical events that lead to forward movement of the cell rear are much less well understood, particularly in physiological 3D extra-cellular matrix (ECM). We previously discovered that rear retraction in fast moving cells is a highly dynamic process involving the precise spatiotemporal interplay of mechanosensing by caveolae and signalling through RhoA. To further interrogate the dynamics of rear retraction, we have adopted three distinct mathematical modelling approaches here based on (i) Boolean logic, (ii) deterministic kinetic ordinary differential equations (ODEs) and (iii) stochastic simulations. The aims of this multi-faceted approach are twofold: firstly to derive new biological insight into cell rear dynamics via generation of testable hypotheses and predictions; and secondly to compare and contrast the distinct modelling approaches when used to describe the same, relatively under-studied system. Whilst Boolean logic was not able to fully recapitulate the complexity of rear retraction signalling completely, our ODE model could make plausible population level predictions. Stochastic simulations added a further level of complexity by accurately mimicking previous experimental findings and acting as a single cell simulator. Our approach has also highlighted the unanticipated potential of targeting CDK1 to abrogate cell movement, a prediction we confirmed experimentally. Moreover, we have made a novel prediction regarding the potential existence of a ‘set point’ in local stiffness gradients that promotes polarisation and rapid rear retraction. Overall, our modelling approaches complement each other, suggesting that such a multi-faceted approach is more informative than methods based on a single modelling technique to interrogate biological systems.
Winners and losers over 35 years of dragonfly and damselfly distributional change in Germany
Authors: Bowler D.E , Eichenberg D. , Conze K.J. , Suhling F. , Baumann K. , Bönsel A. , Bittner T. , Drews A. , Günther A. , Isaac N.J.B. , Petzold F. , Seyring M. , Spengler T. , Trockur B. , Willigalla C. , Bruelheide H. , Jansen F. , Bonn A.
Published: August 2020

Recent studies suggest insect declines in parts of Europe; however, the generality of these trends across different taxa and regions remains unclear. Standardized data are not available to assess large-scale, long-term changes for most insect groups but opportunistic citizen science data is widespread for some taxa. We compiled over 1 million occurrence records of Odonata (dragonflies and damselflies) from different regional databases across Germany. We used occupancy-detection models to estimate annual distributional changes between 1980 and 2016 for each species. We related species attributes to changes in the species’ distributions and inferred possible drivers of change. Species showing increases were generally warm-adapted species and/or running water species while species showing decreases were cold-adapted species using standing water habitats such as bogs. We developed a novel approach using time-series clustering to identify groups of species with similar patterns of temporal change. Using this method, we defined five typical patterns of change for Odonata – each associated with a specific combination of species attributes. Overall, trends in Odonata provide mixed news – improved water quality, coupled with positive impacts of climate change, could explain the positive trend status of many species. At the same time, declining species point to conservation challenges associated with habitat loss and degradation. Our study demonstrates the great value of citizen science data for assessing large-scale distributional change and conservation decision-making.
GigaSOM.jl: High-performance clustering and visualization of huge cytometry datasets
Authors: Kratochvíl Miroslav , Hunewald Oliver , Heirendt Laurent , Verissimo Vasco , Vondrášek Jiří , Satagopam Venkata P. , Schneider Reinhard , Trefois Christophe , Ollert Markus
Published: August 2020

Background

The amount of data generated in large clinical and phenotyping studies that use single-cell cytometry is constantly growing. Recent technological advances allow to easily generate data with hundreds of millions of single-cell data points with more than 40 parameters, originating from thousands of individual samples. The analysis of that amount of high-dimensional data becomes demanding in both hardware and software of high-performance computational resources. Current software tools often do not scale to the datasets of such size; users are thus forced to down-sample the data to bearable sizes, in turn losing accuracy and ability to detect many underlying complex phenomena.

Results

We present GigaSOM.jl, a fast and scalable implementation of clustering and dimensionality-reduction for flow and mass cytometry data. The implementation of GigaSOM.jl in the high-level and high-performance programming language Julia makes it accessible to the scientific community, and allows for efficient handling and processing of datasets with billions of data points using distributed computing infrastructures. We describe the design of GigaSOM.jl, measure its performance and horizontal scaling capability, and showcase the functionality on a large dataset from a recent study.

Conclusions

GigaSOM.jl facilitates utilization of the commonly available high-performance computing resources to process the largest available datasets within minutes, while producing results of the same quality as the current state-of-art software. Measurements indicate that the performance scales to much larger datasets. The example use on the data from an massive mouse phenotyping effort confirms the applicability of GigaSOM.jl to huge-scale studies.

Key points

GigaSOM.jl improves the applicability of FlowSOM-style single-cell cytometry data analysis by increasing the acceptable dataset size to billions of single cells.

Significant speedup over current methods is achieved by distributed processing and utilization of efficient algorithms.

GigaSOM.jl package includes support for fast visualization of multidimensional data.
Assembly defects of the human tRNA splicing endonuclease contribute to impaired pre-tRNA processing in pontocerebellar hypoplasia
Authors: Sekulovski Samoil , Devant Pascal , Panizza Silvia , Gogakos Tasos , Pitiriciu Anda , Heitmeier Katharina , Ramsay Ewan Phillip , Barth Marie , Schmidt Carla , Weitzer Stefan , Tuschl Thomas , Baas Frank , Martinez Javier , Trowitzsch Simon
Published: August 2020

Introns of human transfer RNA precursors (pre-tRNAs) are excised by the tRNA splicing endonuclease TSEN in complex with the RNA kinase CLP1. Mutations in TSEN/CLP1 occur in patients with pontocerebellar hypoplasia (PCH), however, their role in the disease is unclear. Here, we show that intron excision is catalyzed by tetrameric TSEN assembled from inactive heterodimers independently of CLP1. Splice site recognition involves the mature domain and the anticodon-intron base pair of pre-tRNAs. The 2.1-Å resolution X-ray crystal structure of a TSEN15–34 heterodimer and differential scanning fluorimetry analyses show that PCH mutations cause thermal destabilization. While endonuclease activity in recombinant mutant TSEN is unaltered, we observe assembly defects and reduced pre-tRNA cleavage activity resulting in an imbalanced pre-tRNA pool in PCH patient-derived fibroblasts. Our work defines the molecular principles of intron excision in humans and provides evidence that modulation of TSEN stability may contribute to PCH phenotypes.
RAD: a web application to identify region associated differentially expressed genes
Authors: Guo Yixin , Xue Ziwei , Yuan Ruihong , Pastor William A. , Liu Wanlu
Published: August 2020

With the advance of genomic sequencing techniques, chromatin accessible regions, transcription factor binding sites and epigenetic modifications can be identified at genome-wide scale. Conventional analyses focus on the gene regulation at proximal regions; however, distal regions are usually neglected, largely due to the lack of reliable tools to link the distal regions to coding genes. In this study, we introduce RAD (Region Associated Differentially expressed genes), a user-friendly web tool to identify both proximal and distal region associated differentially expressed genes. RAD maps the up- and down-regulated genes associated with any genomic regions of interest (gROI) and helps researchers to infer the regulatory function of these regions based on the distance of gROI to differentially expressed genes. RAD includes visualization of the results and statistical inference for significance.

Availability

RAD is implemented with Python 3.7 and run on a Nginx server. RAD is freely available athttp://labw.org/radas online web service.
Acidic monosaccharides become incorporated into calcite single crystals
Authors: Lang Arad , Mijowska Sylwia , Polishchuk Iryna , Fermani Simona , Falini Giuseppe , Katsman Alexander , Marin Frédéric , Pokroy Boaz
Published: August 2020

Carbohydrates, along with proteins and peptides, are known to represent a major class of biomacromolecules involved in calcium carbonate biomineralization. However, in spite of multiple physical or biochemical characterizations, the explicit role of saccharide macromolecules (long chains of carbohydrate molecules) is not yet understood in mineral deposition. In the present study we investigated the influence of two common acidic monosaccharides (MSs), which are the simplest form of carbohydrates and are represented here by glucuronic and galacturonic acids, on the formation of calcite crystalsin vitro. We show that the size, morphology and microstructure of calcite crystals are altered when they are grown in the presence of these MSs. More importantly, MSs were found to become incorporated into the calcite crystalline lattice and induce anisotropic lattice distortions, a widely studied phenomenon in other biomolecules related to CaCO3biomineralization but never before reported in the case of single MSs. Changes in the calcite lattice induced by MS incorporation were precisely determined by the technique of high-resolution synchrotron powder X-ray diffraction. We believe that the results of this research may deepen our understanding of the interaction of saccharide polymers with an inorganic host and shed light on the implications of carbohydrates for biomineralization processes.
Performance, but not size, of hindleg weaponry is sexually dimorphic in the giant mesquite bug (Thasus neocalifornicus)
Authors: Graham Zackary A. , Kaiser Nicole , Palaoro Alexandre V.
Published: August 2020

In many species, males possess specialized weaponry that have evolved to confer a benefit during aggressive interactions. Because male weaponry is typically an exaggerated or extreme version of pre-existing body parts, females often possess reduced or weaponry. Although much research has investigated sexual dimorphism in the sizes of such weapons, other weapon components, such as weapon performance or alternative weapon forms can also explain the evolution of weapon sexual dimorphisms. Here, we investigated the allometry and variation of multiple weapon components of hindleg weaponry in the male and female giant mesquite bugs,Thasus necalifornicus. Despite theory predicating greater allocation in male weaponry, we found that females allocated more into the lengths of their hindlegs compared to males. Despite this allocation, males possess relatively wider hindlegs, which likely increase area of muscle mass. Indeed, the squeezing performance of male hindlegs was much greater than that of female hindlegs. Lastly, we also described the allometry and variation in a male weapon component, prominent tibial spines, which likely are used to damage competitors during aggressive interaction. Overall, our findings highlight the intricacies of weapon sexual dimorphism and demonstrate the importance of measuring multiple weapon components and not a single measure.
Climate risk to European fisheries and coastal communities
Authors: Payne Mark R. , Kudahl Manja , Engelhard Georg H. , Peck Myron A. , Pinnegar John K.
Published: August 2020

With the majority of the global human population living in coastal regions, correctly characterising the climate risk that ocean-dependent communities and businesses are exposed to is key to prioritising the finite resources available to support adaptation. We apply a climate risk analysis across the European fisheries sector for the first time to identify the most at-risk fishing fleets and coastal regions and then link the two analyses together. We employ a novel approach combining biological traits with physiological metrics to differentiate climate hazards between 556 populations of fish and use these to assess the relative climate risk for 380 fishing fleets and 105 coastal regions in Europe. Countries in southeast Europe as well as the UK have the highest risks to both fishing fleets and coastal regions overall while, in other countries, the risk-profile is greater at either the fleet level or at the regional level. European fisheries face a diversity of challenges posed by climate change and climate adaptation, therefore, needs to be tailored to each country, region and fleet’s specific situation. Our analysis supports this process by highlighting where and what adaptation measures might be needed and informing where policy and business responses could have the greatest impact.

Significance Statement

We present a novel climate risk analysis for i) 105 ocean-dependent communities and ii) 380 fishing fleets in Europe. Our unique approach provides a perspective over the climate risks in this diverse and populous continent that is unprecedented in both its breadth and detail. We show that countries in southeast Europe as well as the UK have the highest climate risk overall, both in terms of fishing fleets and coastal communities. Substantial variation in climate risk is seen even within countries, emphasizing that climate adaptation interventions need to be tailored to the specific characteristics of the fleet or community. A focus on sustainable fisheries management and diversification of fish portfolios can reduce climate risks across the board.
Equal performance but distinct behaviors:Astatotilapia burtonisex differences in a novel object recognition task and spatial maze
Authors: Wallace Kelly J. , Hofmann Hans A.
Published: August 2020

Sex differences in behavior and cognition can be driven by differential selection pressures from the environment and in the underlying neuromolecular mechanisms of decision-making. The highly social cichlid fishAstatotilapia burtoniexhibits dynamic and complex social hierarchies, yet explicit cognitive testing (outside of social contexts) and investigations of sex differences in cognition have yet to be fully explored. Here we assessed male and femaleA. burtoniin two cognitive tasks: a novel object recognition task and a spatial task. We hypothesized that males outperform females in a spatial learning task and exhibit more neophilic/exploratory behavior in across both tasks. In the present study we find that both sexes prefer the familiar object in a novel object recognition task, but the time at which they exhibit this preference differs between the sexes. Females more frequently learned the spatial task, exhibiting longer decision latencies and quicker error correction, suggesting a potential speed-accuracy tradeoff.

Furthermore, the sexes differ in space use in both tasks and in a principal component analysis of the spatial task. A model selection analysis finds that preference, approach, and interaction duration in the novel object recognition task that reach a threshold of importance averaged across all models. This work highlights the need to explicitly test for sex differences in cognition to better understand how individuals navigate dynamic social environments.
Bioconcentration of glyphosate in wetland biofilms
Authors: Beecraft Laura , Rooney Rebecca
Published: August 2020

Wetland biofilms were exposed to the herbicide glyphosate viain situfield exposures and controlled microcosm experiments to measure bioconcentration and metabolism of glyphosate by biofilm organisms. Glyphosate concentrations in biofilms were orders of magnitude higher than the surrounding water, bioconcentration factors averaged 835 and 199 in field- and lab-exposed biofilms, respectively. Glyphosate in water where it had been detected in biofilms at field-exposed sites ranged from below detection (<0.001 ppm) up to 0.13 ppm. Glyphosate bioconcentration in biofilms was inversely proportional to levels in the surrounding water, and the retention kinetics were similar to both adsorption and enzymatic models. Microorganisms present in both the water and biofilms metabolized glyphosate to its primary breakdown product aminomethyl phosphonic acid (AMPA), with increased rates of breakdown in and around the biofilms. Photosynthetic efficiency of the algae within the biofilms was not affected by 24 h glyphosate controlled exposures. Our results demonstrate the role of biofilms in improving wetland water quality by removing contaminants like glyphosate, but also as a potential exposure route to higher trophic levels via consumption. Due to bioconcentration of pesticides, exposure risk to organisms consuming or living in biofilms may be much higher than indicated by concentrations in ambient water samples.
Repeat Exposure to Hypercapnic Seawater Modifies Performance and Oxidative Status in a Tolerant Burrowing Clam
Authors: Gurr Samuel J. , Trigg Shelly A. , Vadopalas Brent , Roberts Steven B. , Putnam Hollie M.
Published: August 2020

Moderate oxidative stress is a hypothesized driver of enhanced stress tolerance and lifespan. Whereas thermal stress, irradiance, and dietary restriction show evidence of dose-dependent benefits for many taxa, stress acclimation remains understudied in marine invertebrates, despite being threatened by climate change stressors such as ocean acidification. To test for life-stage and stress-intensity dependence in eliciting enhanced tolerance under subsequent stress encounters, we initially conditioned pediveliger Pacific geoduck (Panopea generosa) larvae to (i) ambient and moderately elevatedpCO2(920 μatm and 2800 μatm, respectively) for 110 days, (ii) secondarily applied a 7-day exposure to ambient, moderate, and severely elevatedpCO2(750 μatm, 2800 μatm, and 4900 μatm, respectively), followed by 7 days in ambient conditions, and (iii) implemented a modified-reciprocal 7-day tertiary exposure to ambient (970 μatm) and moderatepCO2(3000 μatm). Initial conditioning to moderatepCO2stress followed by secondary and tertiary exposure to severe and moderatepCO2stress increased respiration rate, organic biomass, and shell size suggesting a stress-intensity-dependent effect on energetics. Additionally, stress-acclimated clams had lower antioxidant capacity compared to clams under initial ambient conditions, supporting the hypothesis that stress over postlarval-to-juvenile development affects oxidative status later in life. We posit two subcellular mechanisms underpinning stress-intensity-dependent effects on mitochondrial pathways and energy partitioning: i) stress-induced attenuation of mitochondrial function and ii) adaptive mitochondrial shift under moderate stress. Time series and stress intensity-specific approaches can reveal life-stages and magnitudes of exposure, respectively, that may elicit beneficial phenotypic variation.

Summary statement

Hypercapnic conditions during postlarval development improves physiological performance and oxidative status. This novel investigation of adaptive stress acclimation highlights the plasticity of bioenergetic and subcellular responses inPanopea generosa.
Melting dsDNA donor molecules potentiates precision genome editing inC. elegans
Authors: Ghanta Krishna S. , Mello Craig C.
Published: August 2020

CRISPR genome editing has revolutionized genetics in many organisms. In the nematodeCaenorhabditis elegansone injection into each of the two gonad arms of an adult hermaphrodite exposes hundreds of meiotic germ cells to editing mixtures, permitting the recovery of multiple indels or small precision edits from each successfully injected animal. Unfortunately, particularly for long insertions, editing efficiencies can vary widely, necessitating multiple injections, and often requiring co-selection strategies. Here we show that melting double stranded DNA (dsDNA) donor molecules prior to injection increases the frequency of precise homology-directed repair (HDR) by several fold for longer edits. We describe troubleshooting strategies that enable consistently high editing efficiencies resulting, for example, in up to 100 independent GFP knock-ins from a single injected animal. These efficiencies makeC. elegansby far the easiest metazoan to genome edit, removing barriers to the use and adoption of this facile system as a model for understanding animal biology.
Modeling the evolutionary architectures of human enhancer sequences reveals distinct origins, functions, and associations with human-trait variation
Authors: Fong Sarah L. , Capra John A.
Published: August 2020

Motivation

Despite the importance of gene regulatory enhancers in human biology and evolution, we lack a comprehensive evolutionary model of enhancer sequence architecture and function. This substantially limits our understanding of the genetic basis for divergence between species and our ability to interpret the effects of non-coding variants on human traits.

Results

To explore enhancer sequence evolution and its relationship to regulatory function, we traced the evolutionary origins of human sequences with enhancer activity defined by eRNA from diverse tissues and cellular contexts. The majority of enhancers are sequences of a single evolutionary age (“simple” enhancer architectures), likely indicating constraint against genomic rearrangements. A minority of enhancers are composites of sequences of multiple evolutionary ages (“complex” enhancer architectures). Compared to simple enhancers, complex enhancers are older, more pleiotropic, and more active across species. Genetic variants within complex enhancers are also less likely to have effects on human traits and biochemical activity. Transposable-element-derived sequences have made diverse contributions to enhancer architectures; some have nucleated enhancers with simple architectures, while others have remodeled older sequences to create complex regulatory architectures.

Conclusions

Based on these results, we propose a framework for modeling enhancer sequence architecture and evolution. Applying this framework to human enhancer sequences reveals multiple, distinct trajectories of human regulatory sequence evolution. Considering these evolutionary histories can aid interpretation of the effects of variants on enhancer function.
KH domain containing RNA-binding proteins coordinate with microRNAs to regulateCaenorhabditis elegansdevelopment
Authors: Haskell D , Zinovyeva A
Published: August 2020

microRNAs (miRNAs) and RNA binding proteins (RBPs) regulate gene expression at the post-transcriptional level, but the extent to which these key regulators of gene expression coordinate and the precise mechanisms of their coordination are not well understood. RNA binding proteins often have recognizable RNA binding domains that correlate with specific protein function. Recently, several RBPs containing K Homology (KH) RNA binding domains were shown to work with miRNAs to regulate gene expression, raising the possibility that KH domains may be important for coordinating with miRNA pathways in gene expression regulation. To ascertain whether additional KH domain proteins functionally interact with miRNAs duringCaenorhabditis elegansdevelopment, we knocked down twenty-four genes encoding KH-domain proteins in several miRNA sensitized genetic backgrounds. Here, we report that a majority of the KH domain-containing genes genetically interact with multiple miRNAs and Argonautealg-1. Interestingly, two KH domain genes, predicted splicing factorssfa-1andasd-2, genetically interacted with all of the miRNA mutants tested, while other KH domain genes exhibited functional interactions only with specific miRNAs. Our domain architecture and phylogenetic relationship analyses of theC. elegansKH domain-containing proteins revealed potential groups that may share both structure and function. Collectively, we show that manyC. elegansKH domain RBPs functionally interact with miRNAs, suggesting direct or indirect coordination between these two classes of post-transcriptional gene expression regulators.
Robotic High-Throughput Biomanufacturing and Functional Differentiation of Human Pluripotent Stem Cells
Authors: Tristan Carlos A. , Ormanoglu Pinar , Slamecka Jaroslav , Malley Claire , Chu Pei-Hsuan , Jovanovic Vukasin M. , Gedik Yeliz , Bonney Charles , Barnaeva Elena , Braisted John , Mallanna Sunil K. , Dorjsuren Dorjbal , Iannotti Michael J. , Voss Ty C. , Michael Sam , Simeonov Anton , Singeç Ilyas
Published: August 2020

Efficient translation of human induced pluripotent stem cells (hiPSCs) depends on implementing scalable cell manufacturing strategies that ensure optimal self-renewal and functional differentiation. Currently, manual culture of hiPSCs is highly variable and labor-intensive posing significant challenges for high-throughput applications. Here, we established a robotic platform and automated all essential steps of hiPSC culture and differentiation under chemically defined conditions. This streamlined approach allowed rapid and standardized manufacturing of billions of hiPSCs that can be produced in parallel from up to 90 different patient-and disease-specific cell lines. Moreover, we established automated multi-lineage differentiation to generate primary embryonic germ layers and more mature phenotypes such as neurons, cardiomyocytes, and hepatocytes. To validate our approach, we carefully compared robotic and manual cell culture and performed molecular and functional cell characterizations (e.g. bulk culture and single-cell transcriptomics, mass cytometry, metabolism, electrophysiology, Zika virus experiments) in order to benchmark industrial-scale cell culture operations towards building an integrated platform for efficient cell manufacturing for disease modeling, drug screening, and cell therapy. Combining stem cell-based models and non-stop robotic cell culture may become a powerful strategy to increase scientific rigor and productivity, which are particularly important during public health emergencies (e.g. opioid crisis, COVID-19 pandemic).
Developing Cyclic Peptomers as Broad-Spectrum Gram negative Bacterial Type III Secretion System Inhibitors
Authors: Lam Hanh N. , Lau Tannia , Lentz Adam , Sherry Jessica , Cabrera-Cortez Alejandro , Hug Karen , Engel Joanne , Lokey R. Scott , Auerbuch Victoria
Published: August 2020

Antibiotic resistant bacteria are an emerging global health threat. New antimicrobials are urgently needed. The injectisome type III secretion system (T3SS), required by dozens of Gram-negative bacteria for virulence but largely absent from non-pathogenic bacteria, is an attractive antimicrobial target. We previously identified synthetic cyclic peptomers, inspired by the natural product phepropeptin D, that inhibit protein secretion through theYersiniaYsc andPseudomonas aeruginosaPsc T3SSs, but do not inhibit bacterial growth. Here we describe identification of an isomer, 4EpDN, that is two-fold more potent (IC504 μM) than its parental compound. Furthermore, 4EpDN inhibited theYersiniaYsa and theSalmonellaSPI-1 T3SSs, suggesting that this cyclic peptomer has broad efficacy against evolutionarily distant injectisome T3SSs. Indeed, 4EpDN strongly inhibited intracellular growth ofChlamydia trachomatisin HeLa cells, which requires the T3SS. 4EpDN did not inhibit the unrelated Twin arginine translocation (Tat) system, nor did it impact T3SS gene transcription. Moreover, although the injectisome and flagellar T3SSs are evolutionarily and structurally related, the 4EpDN cyclic peptomer did not inhibit secretion of substrates through theSalmonellaflagellar T3SS, indicating that cyclic peptomers broadly but specifically target the injestisome T3SS. 4EpDN reduced the number of T3SS basal bodies detected on the surface ofY. enterocolitica, as visualized using a fluorescent derivative of YscD, an inner membrane ring with low homology to flagellar protein FliG. Collectively, these data suggest that cyclic peptomers specifically inhibit the injectisome T3SS from a variety of Gram-negative bacteria, possibly by preventing complete T3SS assembly.

IMPORTANCE

Traditional antibiotics target both pathogenic and commensal bacteria, resulting in a disruption of the microbiota, which in turn is tied to a number of acute and chronic diseases. The bacterial type III secretion system (T3SS) is an appendage used by many bacterial pathogens to establish infection, but is largely absent from commensal members of the microbiota. In this study, we identify a new derivative of the cyclic peptomer class of T3SS inhibitors. These compounds inhibit the T3SS of the nosocomial ESKAPE pathogenPseudomonas aeruginosaand enteropathogenicYersiniaandSalmonella. The impact of cyclic peptomers is specific to the T3SS, as other bacterial secretory systems are unaffected. Importantly, cyclic peptomers completely block replication ofChlamydia trachomatis, the causative agent of genital, eye, and lung infections, in human cells, a process that requires the T3SS. Therefore, cyclic peptomers represent promising virulence blockers that can specifically disarm a broad spectrum of Gram-negative pathogens.
Fitting to the UK COVID-19 outbreak, short-term forecasts and estimating the reproductive number
Authors: Keeling Matt J. , Dyson Louise , Guyver-Fletcher Glen , Holmes Alex , Semple Malcolm G ,   ISARIC4C Investigators, Tildesley Michael J. , Hill Edward M.
Published: August 2020

The COVID-19 pandemic has brought to the fore the need for policy makers to receive timely and ongoing scientific guidance in response to this recently emerged human infectious disease. Fitting mathematical models of infectious disease transmission to the available epidemiological data provides a key statistical tool for understanding the many quantities of interest that are not explicit in the underlying epidemiological data streams. Of these, the effective reproduction number, R, has taken on special significance in terms of the general understanding of whether the epidemic is under control (R < 1). Unfortunately, none of the epidemiological data streams are designed for modelling, hence assimilating information from multiple (often changing) sources of data is a major challenge that is particularly stark in novel disease outbreaks.

Here, focusing on the dynamics of the first-wave (March-June 2020), we present in some detail the inference scheme employed for calibrating the Warwick COVID-19 model to the available public health data streams, which span hospitalisations, critical care occupancy, mortality and serological testing. We then perform computational simulations, making use of the acquired parameter posterior distributions, to assess how the accuracy of short-term predictions varied over the timecourse of the outbreak. To conclude, we compare how refinements to data streams and model structure impact estimates of epidemiological measures, including the estimated growth rate and daily incidence.
Hospital Admission Rates, Length of Stay and In-hospital Mortality for Common Acute Care Conditions in COVID-19 vs. Pre-COVID-19 Era
Authors: Butt Adeel A. , Kartha Anand B. , Masoodi Naseer A. , Azad Aftab Mohammad , Asaad Nidal Ahmad , Alhomsi Mohamad Ussama , Saleh Huda A. H. , Bertollini Roberto , Abou-Samra Abdul-Badi
Published: August 2020

Background

Impact of COVID-19 upon acute care admission rates and patterns are unknown. We sought to determine the change in rates and types of admissions to tertiary and specialty care hospitals in the COVID-19 era compared with pre-COVID-19 era.

Methods

Acute care admissions to the largest tertiary care referral hospital, designated national referral centers for cardiac, cancer and maternity hospital in the State of Qatar during March 2020 (COVID-19 era) and January 2020 and March 2019 (pre-COVID-19 era) were compared. We calculated total admissions, and admissions for eight specific acute care conditions, in-hospital mortality rate and length of stay at each hospital.

Results

A total of 18,889 hospital admissions were recorded. A sharp decline ranging from 9%-75% was observed in overall admissions. A decline in both elective and non-elective surgeries was observed. A decline of 9%-58% was observed in admissions for acute appendicitis, acute coronary syndrome, stroke, bone fractures, cancer and live births, while an increase in admissions due to respiratory tract infections was observed. Overall length of stay was shorter in the COVID-19 period possibly suggesting lesser overall disease severity, with no significant change in in-hospital mortality. Unadjusted mortality rate for Qatar showed marginal increase in the COVID-19 period.

Conclusions

We observed a sharp decline in acute care hospital admissions, with a significant decline in admissions due to seven out of eight acute care conditions. This decline was associated with a shorter length of stay, but not associated with a change in in-hospital mortality rate.
Differential Brain Atrophy Patterns and Neurogenetic Profiles in Cognitively-Defined Alzheimer’s Disease Subgroups
Authors: Groot Colin , Grothe Michel J. , Mukherjee Shubhabrata , Jelistratova Irina , Jansen Iris , van Loenhoud Anna Catharina , Risacher Shannon L. , Saykin Andrew J. , Mac Donald Christine L. , Mez Jesse , Trittschuh Emily H. , Gryglewski Gregor , Lanzenberger Rupert , Pijnenburg Yolande A.L. , Barkhof Frederik , Scheltens Philip , van der Flier Wiesje M. , Crane Paul K. , Ossenkoppele Rik
Published: August 2020

Elucidating mechanisms underlying the clinical heterogeneity observed among individuals with Alzheimer’s disease (AD) is key to facilitate personalized treatments. We categorized 679 individuals with AD into subgroups based on a relative impairment in one cognitive domain (i.e. AD-Memory, AD-Executive-Functioning, AD-Language and AD-Visuospatial-Functioning). We compared atrophy patterns derived from MRI and identified patterns that closely matched the respective cognitive profiles, i.e. medial temporal lobe atrophy in AD-Memory, fronto-parietal in AD-Executive-Functioning, asymmetric left-temporal in AD-Language, and posterior in AD-Visuospatial-Functioning. We then determined spatial correlations between subgroup-specific atrophy and a transcriptomic atlas of gene expression, which revealed both shared (e.g. mitochondrial respiration and synaptic function/plasticity) and subgroup-specific (e.g. cell-cycle for AD-Memory, protein metabolism in AD-Language, and modification of gene expression in AD-Visuospatial-Functioning) biological pathways associated with each subgroup’s atrophy patterns. We conclude that cognitive heterogeneity in AD is related to neuroanatomical differences, and specific biological pathways may be involved in their emergence.