bluuebunny/crossref_metadata_2025 huggingface dataset:
Structure and specialization of mycorrhizal networks in phylogenetically diverse tropical communities
Authors: Perez-Lamarque Benoît , Petrolli Rémi , Strullu-Derrien Christine , Strasberg Dominique , Morlon Hélène , Selosse Marc-André , Martos Florent
Published: May 2022

Background

The root mycobiome plays a fundamental role in plant nutrition and protection against biotic and abiotic stresses. In temperate forests or meadows dominated by angiosperms, the numerous fungi involved in root symbioses are often shared between neighboring plants, thus forming complex plant-fungus interaction networks of weak specialization. Whether this weak specialization also holds in rich tropical communities with more phylogenetically diverse sets of plant lineages remains unknown.

We collected roots of 30 plant species in semi-natural tropical communities including angiosperms, ferns, and lycophytes, in three different habitat types on La Réunion island: a recent lava flow, a wet thicket, and an ericoid shrubland. We identified root-inhabiting fungi by sequencing both the 18S rRNA and the ITS2 variable regions. We assessed the diversity of mycorrhizal fungal taxa according to plant species and lineages, as well as the structure and specialization of the resulting plant-fungus networks.

Results

The 18S and ITS2 datasets are highly complementary at revealing the root mycobiota. According to 18S, Glomeromycotina colonize all plant groups in all habitats forming the least specialized interactions, resulting in nested network structures, while Mucoromycotina (Endogonales) are more abundant in the wetland and show higher specialization and modularity compared to the former. According to ITS2, mycorrhizal fungi of Ericaceae and Orchidaceae, namely Helotiales, Sebacinales, and Cantharellales, also colonize the roots of most plant lineages, confirming that they are frequent endophytes. While Helotiales and Sebacinales present intermediate levels of specialization, Cantharellales are more specialized and more sporadic in their interactions with plants, resulting in highly modular networks.

Conclusions

This study of the root mycobiome in tropical environments reinforces the idea that mycorrhizal fungal taxa are locally shared between co-occurring plants, including phylogenetically distant plants (e.g. lycophytes and angiosperms), where they may form functional mycorrhizae or establish endophytic colonization. Yet, we demonstrate that, irrespectively of the environmental variations, the level of specialization significantly varies according to the fungal lineages, probably reflecting the different evolutionary origins of these plant-fungus symbioses. Frequent fungal sharing between plants questions the roles of the different fungi in community functioning and highlights the importance of considering networks of interactions rather than isolated hosts.
Structures reveal a key mechanism of WAVE Regulatory Complex activation by Rac1 GTPase
Authors: Ding Bojian , Yang Sheng , Schaks Matthias , Liu Yijun , Brown Abbigale , Rottner Klemens , Chowdhury Saikat , Chen Baoyu
Published: May 2022

Rho-family GTPase Rac1 activates the WAVE regulatory complex (WRC) to drive Arp2/3-mediated actin polymerization in many essential processes. Rac1 binds to WRC at two distinct sites—the A and D sites. Precisely how Rac1 binds and how the binding triggers WRC activation remain unknown. Here we report WRC structures by itself, and when bound to single or double Rac1 molecules, at ∼3 Å resolutions by cryogenic-electron microscopy. The structures reveal that Rac1 binds to the two sites by distinct mechanisms, and binding to the A site, but not the D site, drives WRC activation. Activation involves a series of unique conformational changes leading to the release of sequestered WCA (WH2- central-acidic) polypeptide, which stimulates the Arp2/3 complex to polymerize actin. Together with biochemical and cellular analyses, the structures provide a novel mechanistic understanding of how the Rac1-WRC-Arp2/3-actin signaling axis is regulated in diverse biological processes and diseases.
Saccade-related modulation of oscillatory activity in primary auditory cortex
Authors: Barczak Annamaria , O’Connell Monica Noelle , McGinnis Tammy , Mackin Kieran , Schroeder Charles E. , Lakatos Peter
Published: May 2022

The auditory and visual sensory systems are both used by the brain to obtain and organize information from our external environment, yet there are fundamental differences between these two systems. Visual information is acquired using systematic patterns of fixations and saccades, which are controlled by internal motor commands. Sensory input occurs in volleys that are tied to the timing of saccades. In contrast, the auditory system does not use such an overt motor sampling routine so the relationship between sensory input timing and motor activity is less clear. Previous studies of primary visual cortex (V1) in nonhuman primates (NHP) have shown that there is a cyclical modulation of excitability tied to the eye movement cycle and suggests that this excitability modulation stems from the phase reset of neuronal oscillations. We hypothesized that if saccades provide a supramodal temporal context for environmental information then we should also see saccade-related modulation of oscillatory activity in primary auditory cortex (A1) as NHPs shift their gaze around their surroundings. We used linear array multielectrodes to record cortical laminar neuroelectric activity profiles while subjects sat in a dark or dimly lit and silent chamber. Analysis of oscillatory activity in A1 suggests that saccades lead to a phase reset of neuronal oscillations in A1. Saccade-related phase reset of delta oscillations were observed across all layers while theta effects occurred primarily in extragranular layers. Although less frequent, alpha oscillations also showed saccade-related phase reset within the extragranular layers. Our results confirm that saccades provide a supramodal temporal context for the influx of sensory information into A1 and highlight the importance of considering the effects of eye position on auditory processing.

Significance Statement

Using laminar multielectrodes, the current study examined saccade-related neuronal activity during resting state while NHPs sat in a dark or dimly lit room. Our results confirm that saccade-related modulation of delta band oscillatory activity occurs across all layers of A1. Interestingly, our data also show a saccade-related phase reset of theta and alpha bands that preferentially occurs in extragranular layers. These results confirm that saccades provide a supramodal temporal context for the influx of environmental information into A1 and emphasizes the importance of considering eye position when examining auditory processing.
Ghrelin is related to lower brain reward activation during touch
Authors: Pfabigan D.M. , Frogner E.R. , Schéle E. , Thorsby P. M. , Skålhegg B. S , Dickson S. L. , Sailer U.
Published: May 2022

The gut hormone ghrelin drives food motivation and increases food intake, but it is also involved in the anticipation of and response to rewards other than food. This pre-registered study investigated how naturally varying ghrelin concentrations affect the processing of touch as a social reward in humans.

Sixty-seven volunteers received slow caressing touch (so-called CT-targeted touch) as a social reward and control touch on their shins during 3T functional imaging on two test days. On one occasion participants were fasted and on another they received a meal. On each occasion plasma ghrelin was measured at three time points.

All touch was rated as more pleasant after the meal, but there was no association between ghrelin concentrations and pleasantness. CT-targeted touch was rated as most pleasant and activated somatosensory and reward networks (whole-brain). A region-of-interest in the right medial orbitofrontal cortex (mOFC) showed lower activation during all touch the higher ghrelin concentrations were. During CT-targeted touch, a larger satiety response (ghrelin decrease after the meal) was associated with higher mOFC activation, and this OFC activation was associated with higher experienced pleasantness.

Overall, higher ghrelin concentrations appear to be related to lower reward value of touch. Ghrelin may reduce the value of social stimuli, such as touch, to promote food search and intake in a state of low energy. This suggests that the role of ghrelin goes beyond assigning value to food reward.
The fidelity of transcription in human cells
Authors: Chung C. , Verheijen B.M. , Zhang X. , Huang B. , Coakley A. , McGann E. , Wade E. , Dinep-Schneider O. , LaGosh J. , Anagnostou M. , Simpson S. , Thomas K. , Ernst J. M. , Rattray A. , Lynch M. , Kashlev M. , Benayoun B. A. , Li Z. , Strathern J. , Gout J-F. , Vermulst M.
Published: May 2022

Accurate transcription is required for the faithful expression of genetic information. To provide insight into the molecular mechanisms that control the fidelity of transcription, we analyzed the landscape of transcription errors in human embryonic stem cells. These measurements provide the first reasonable estimate of the fidelity of transcription in human cells and identify multiple genetic and epigenetic factors that control its accuracy. In addition, we developed a new reporter mouse to identify cell types and tissues that commit these errors the most. These experiments revealed that CA1 and dentate gyrus neurons are highly sensitive to transcriptional mutagenesis, lending new support to the hypothesis that transcription errors play a role in the progression of Alzheimer’s disease. Taken together, these experiments provide unprecedented insight into the fidelity of gene expression in human cells and the molecular mechanisms that govern the central dogma of life.
High resolution mapping reveals hotspots and sex-biased recombination inPopulus trichocarpa
Authors: Abeyratne Chanaka Roshan , Macaya-Sanz David , Zhou Ran , Barry Kerrie W. , Daum Christopher , Haiby Kathy , Lipzen Anna , Stanton Brian , Yoshinaga Yuko , Zane Matthew , Tuskan Gerald A. , DiFazio Stephen P.
Published: May 2022

Fine-scale meiotic recombination is fundamental to the outcome of natural and artificial selection. Here, dense genetic mapping and haplotype reconstruction were used to estimate recombination for a full factorialPopulus trichocarpacross of seven males and seven females. Genomes of the resulting 49 full-sib families (N=829 offspring) were re-sequenced, and high-fidelity biallelic SNP/INDELs and pedigree information were used to ascertain allelic phase and impute progeny genotypes to recover gametic haplotypes. The fourteen parental genetic maps contained 1820 SNP/INDELs on average that covered 376.7 Mb of physical length across 19 chromosomes. Comparison of parental and progeny haplotypes allowed fine-scale demarcation of cross-over (CO) regions, where 38,846 CO events in 1,658 gametes were observed. CO events were positively associated with gene density and negatively associated with GC content and long terminal repeats. One of the most striking findings was higher rates of COs in males in 8 out of 19 chromosomes. Regions with elevated male CO rates had lower gene density and GC content than windows showing no sex bias. High-resolution analysis identified 67 candidate CO hotspots spread throughout the genome. DNA sequence motifs enriched in these regions showed striking similarity to those of maize, Arabidopsis and wheat. These findings, and recombination estimates, will be useful for ongoing efforts to accelerate domestication of this and other biomass feedstocks, as well as future studies investigating broader questions related to evolutionary history, perennial development, phenology, wood formation, vegetative propagation, and dioecy that cannot be studied using annual plant model systems.
A long non-coding RNA is a key factor in the evolution of insect eusociality
Authors: Cardoso-Junior Carlos A. M. , Tibério Gustavo J. , Lago Denyse C. , Vieira Luiz Carlos , Rosa José C. , Paschoal Alexandre R. , Ronai Isobel , Oldroyd Benjamin P. , Hartfelder Klaus
Published: May 2022

Insect sociality is a major evolutionary transition based on the suppression of worker reproduction in favor of the reproductive monopoly of the queen. In the honey bee (Apis mellifera) model organism, the development of the two female caste phenotypes, queen and worker, is triggered by differences in their larval diets. However, the mechanistic details underlying their respective developmental trajectories, as well as the maintenance of sterility in the adult workers, are still not fully understood. Here we show that the long non-coding RNA lncov1 interacts with the Tudor staphylococcus nuclease (Tudor-SN) protein to form a regulatory module that promotes apoptosis in the ovaries of worker larvae. In adult workers, the lncov1/Tudor-SN module responds positively to environmental cues that suppress reproductive capacity. As lncov1 is considerably conserved in the Apidae, we propose that, by promoting worker sterility, the lncov1/Tudor-SN module has likely played critical roles in the social evolution of bees.
Disease classification for whole blood DNA methylation: meta-analysis, missing values imputation, and XAI
Authors: Kalyakulina Alena , Yusipov Igor , Bacalini Maria Giulia , Franceschi Claudio , Vedunova Maria , Ivanchenko Mikhail
Published: May 2022

Background

DNA methylation has a significant effect on gene expression and can be associated with various diseases. Meta-analysis of available DNA methylation datasets requires development of a specific pipeline for joint data processing.

Results

We propose a comprehensive approach of combined DNA methylation datasets to classify controls and patients. The solution includes data harmonization, construction of machine learning classification models, dimensionality reduction of models, imputation of missing values, and explanation of model predictions by explainable artificial intelligence (XAI) algorithms. We show that harmonization can improve classification accuracy by up to 20% when preprocessing methods of the training and test datasets are different. The best accuracy results were obtained with tree ensembles, reaching above 95% for Parkinson’s disease. Dimensionality reduction can substantially decrease the number of features, without detriment to the classification accuracy. The best imputation methods achieve almost the same classification accuracy for data with missing values as for the original data. Explainable artificial intelligence approaches have allowed us to explain model predictions from both populational and individual perspectives.

Conclusions

We propose a methodologically valid and comprehensive approach to the classification of healthy individuals and patients with various diseases based on whole blood DNA methylation data using Parkinson’s disease and schizophrenia as examples. The proposed algorithm works better for the former pathology, characterized by a complex set of symptoms. It allows to solve data harmonization problems for meta-analysis of many different datasets, impute missing values, and build classification models of small dimensionality.
BigNeuron: A resource to benchmark and predict best-performing algorithms for automated reconstruction of neuronal morphology
Authors: Manubens-Gil Linus , Zhou Zhi , Chen Hanbo , Ramanathan Arvind , Liu Xiaoxiao , Liu Yufeng , Bria Alessandro , Gillette Todd , Ruan Zongcai , Yang Jian , Radojević Miroslav , Zhao Ting , Cheng Li , Qu Lei , Liu Siqi , Bouchard Kristofer E. , Gu Lin , Cai Weidong , Ji Shuiwang , Roysam Badrinath , Wang Ching-Wei , Yu Hongchuan , Sironi Amos , Iascone Daniel Maxim , Zhou Jie , Bas Erhan , Conde-Sousa Eduardo , Aguiar Paulo , Li Xiang , Li Yujie , Nanda Sumit , Wang Yuan , Muresan Leila , Fua Pascal , Ye Bing , He Hai-yan , Staiger Jochen F. , Peter Manuel , Cox Daniel N. , Simonneau Michel , Oberlaender Marcel , Jefferis Gregory , Ito Kei , Gonzalez-Bellido Paloma , Kim Jinhyun , Rubel Edwin , Cline Hollis T. , Zeng Hongkui , Nern Aljoscha , Chiang Ann-Shyn , Yao Jianhua , Roskams Jane , Livesey Rick , Stevens Janine , Liu Tianming , Dang Chinh , Guo Yike , Zhong Ning , Tourassi Georgia , Hill Sean , Hawrylycz Michael , Koch Christof , Meijering Erik , Ascoli Giorgio A. , Peng Hanchuan
Published: May 2022

BigNeuron is an open community bench-testing platform combining the expertise of neuroscientists and computer scientists toward the goal of setting open standards for accurate and fast automatic neuron reconstruction. The project gathered a diverse set of image volumes across several species representative of the data obtained in most neuroscience laboratories interested in neuron reconstruction. Here we report generated gold standard manual annotations for a selected subset of the available imaging datasets and quantified reconstruction quality for 35 automatic reconstruction algorithms. Together with image quality features, the data were pooled in an interactive web application that allows users and developers to perform principal component analysis, t-distributed stochastic neighbor embedding, correlation and clustering, visualization of imaging and reconstruction data, and benchmarking of automatic reconstruction algorithms in user-defined data subsets. Our results show that image quality metrics explain most of the variance in the data, followed by neuromorphological features related to neuron size. By benchmarking automatic reconstruction algorithms, we observed that diverse algorithms can provide complementary information toward obtaining accurate results and developed a novel algorithm to iteratively combine methods and generate consensus reconstructions. The consensus trees obtained provide estimates of the neuron structure ground truth that typically outperform single algorithms. Finally, to aid users in predicting the most accurate automatic reconstruction results without manual annotations for comparison, we used support vector machine regression to predict reconstruction quality given an image volume and a set of automatic reconstructions.
A computational model of fractal interface formation in bacterial biofilms
Authors: Brooks Caelan , Yao Meiyi , McCool Jake T. , Gillman Alan , Süel Gürol M. , Mugler Andrew , Larkin Joseph W.
Published: May 2022

Bacterial colonies benefit from cellular heterogeneity, with cells differentiating into diverse states of physiology and gene expression. As colonies grow, such cells in distinct states arrange into spatial patterns. To uncover the functional role of these emergent patterns, we must understand how they arise from cellular growth, phenotypic inheritance, and mechanical interactions among cells. Here we present a simple, agent-based model to predict patterns formed by motile and extracellular matrix-producing cells in developing populations ofBacillus subtilisbacteria. By incorporating phenotypic inheritance, differential mechanical interactions of the two cell types, and the escape of peripheral motile cells, our model predicts the emergence of a pattern: matrix cells surround a fractal-like population of interior motile cells. We find that, while some properties of the emergent motile-matrix interface depend on the initial cellular arrangement, the distribution of motile cells at large radii are a product solely of the model’s growth mechanism. Using a box-counting analysis, we find that the interface of the two phenotypes exhibits a fractal dimension that increases as biofilms grow but eventually reaches a maximum as the thickness of the peripheral layer of matrix exceeds the capacity of the inner cells to grow and push it out of the way. By systematically varying the model parameters, we find correlations between the fractal dimension of the phenotypic interface and the radial growth of the motile cells within simulated biofilms. We validate several of our findings using experimental data from aB. subtilisbiofilm grown in a microfluidic device. Our model demonstrates how colony-level phenotypes emerge from single cell-level interactions and cells modifying their own environment.
OPUS-Mut: studying the effect of protein mutation through side-chain modeling
Authors: Xu Gang , Wang Qinghua , Ma Jianpeng
Published: May 2022

Predicting the effect of protein mutation is crucial in many applications such as protein design, protein evolution, and genetic disease analysis. Structurally, the mutation is basically the replacement of the side chain of a particular residue. Therefore, accurate side-chain modeling is useful in studying the effect of mutation. Here, we propose a computational method, namely OPUS-Mut, which significantly outperforms other backbone-dependent side-chain modeling methods including our previous method OPUS-Rota4. We evaluate OPUS-Mut by four case studies on Myoglobin, p53, HIV-1 protease, and T4 lysozyme. The results show that the predicted structures of side chains of different mutants are consistent well with their experimentally determined results. In addition, when the residues with significant structural shifts upon the mutation are considered, it is found that the extent of the predicted structural shift of these affected residues can be correlated reasonably well with the functional changes of the mutant measured by experiments. OPUS-Mut can also help one to identify the harmful and benign mutations, and thus may guide the construction of a protein with relatively low sequence homology but with similar structure.
Computer-aided diagnosis of reflectance confocal images to differentiate between lentigo maligna (LM) and atypical intraepidermal melanocytic proliferation (AIMP)
Authors: Mandal Ankita , Priyam Siddhaant , Chan Hsien Herbert , Gouveia Bruna Melhoranse , Guitera Pascale , Song Yang , Baker Matthew Arthur Barrington , Vafaee Fatemeh
Published: May 2022

Lentigo maligna (LM), a form of melanoma in situ that predominantly affects sun-exposed areas such as the face, has an ill-defined clinical border and has a high rate of recurrence. Atypical Intraepidermal Melanocytic Proliferation (AIMP) is a term used to describe the melanocytic proliferation of an uncertain malignant potential. Clinically and histologically, AIMP can be difficult to distinguish from LM, and indeed AIMP may in some cases progress to LM. Reflectance Confocal Microscopy (RCM) is often used to investigate these lesions non-invasively, however, RCM is often not readily available nor is the associated expertise for RCM image interpretation. Here, we demonstrate machine learning architectures that can correctly classify lesions between LM and AIMP on stacks of RCM images. Overall, our methods showcase the potential for computer-aided diagnosis in dermatology, which in conjunction with the remote acquisition, can expand the range of diagnostic tools in the community.
Bacterial strain-dependent dissociation of cell recruitment and cell-to-cell spread in earlyM. tuberculosisinfection
Authors: Zha B. Shoshana , Desvignes Ludovic , Fergus Tawania J. , Cornelius Amber , Cheng Tan-Yun , Moody D. Branch , Ernst Joel D.
Published: May 2022

In the initial stage of respiratory infection,Mycobacterium tuberculosistraverses from alveolar macrophages to phenotypically diverse monocyte-derived phagocytes and neutrophils in the lung parenchyma. Here, we compare thein vivokinetics of early bacterial growth and cell-to-cell spread of two strains ofM. tuberculosis: a lineage 2 strain, 4334, and the widely studied lineage 4 strain H37Rv. Using flow cytometry, live cell sorting of phenotypic subsets, and quantitation of bacteria in cells of the distinct subsets, we found that 4334 induces less leukocyte influx into the lungs but demonstrates earlier population expansion and cell-to-cell spread. The earlier spread of 4334 to recruited cells, including monocyte-derived dendritic cells, is accompanied by earlier and greater magnitude of CD4+T cell activation. The results provide evidence that strain-specific differences in interactions with lung leukocytes can shape adaptive immune responsesin vivo.

IMPORTANCE

Tuberculosis is a leading infectious disease killer world-wide and is caused byMycobacterium tuberculosis. After exposure toM. tuberculosis,outcomes range from apparent elimination to active disease. Early innate immune responses may contribute to differences in outcomes, yet it is not known how bacterial strains alter the early dynamics of innate immune and T cell responses. We infected mice with distinct strains ofM. tuberculosisand discovered striking differences in innate cellular recruitment, cell- to-cell spread of bacteria in the lungs, and kinetics of initiation of antigen-specific CD4 T cell responses. We also found thatM. tuberculosiscan spread beyond alveolar macrophages even before a large influx of inflammatory cells. These results provide evidence that distinct strains ofM. tuberculosiscan exhibit differential kinetics in cell-to- cell spread which is not directly linked to early recruitment of phagocytes but is subsequently linked to adaptive immune responses.
Fermented foods restructure gut microbiota and promote immune regulation via microbial metabolites
Authors: Spencer Sean Paul , Silva Evelyn Giselle Lemus , Caffery Elisa Benedetti , Carter Matthew Merrill , Culver Rebecca Neal , Wang Min , Gellman Rebecca Hope , Wastyk Hannah Constance , Higginbottom Steven Kyle , Sonnenburg Justin Laine
Published: May 2022

Fermented foods are ancient and ubiquitous, thought to be consumed in nearly every culture over the last 10,000 years and as part of the hominin diet for millions of years. A growing body of evidence supports their potential health benefits, but the mechanistic basis of their effects on the gut microbiome and host immunity remain to be elucidated. Fermented foods are diverse, each representing a complex mixture of food, microbes, and metabolites creating a significant challenge to disentangle the effects of individual components. Herein, we further define the chemical signature of individual fermented foods to categorize them based on the primary metabolic end-products of fermentation. Using mouse models, we find that fermented foods have both microbiome directed as well as differential host directed effects that correspond to their metabolite composition. Fermented food brine drink shows site-specific restructuring of the gut microbiome and promotion of tolerogenic barrier immunity; fractionation of the brine to examine the effects of the microbe-free, metabolite rich supernatant shows similar activity. Lactate, the main metabolite of lactic acid fermentation and the major metabolite within the brine drink, when administered in water, fuels a trans-kingdom metabolic network to selectively promote the growth of Akkermansia muciniphila. in the small intestine, while promoting immune tolerance via an increase in microbiota-dependent Regulatory T-cells. These findings suggest that the beneficial effects of fermented food consumption can be mediated by microbial metabolites within fermented foods, independent of microbial content, and highlight the importance of further defining the diverse chemical landscape of fermented foods to inform their potential health benefits and therapeutic use.
Recombinant Origin and Interspecies Transmission of a HERV-K(HML-2)-related Primate Retrovirus With a Novel RNA Transport Element
Authors: Williams Zachary H. , Gaucherand Lea , Lee Derek C. , Mostafa Salwa Mohd , Phelan James , Coffin John M. , Johnson Welkin E.
Published: May 2022

HERV-K(HML-2), the youngest clade of human endogenous retroviruses (HERVs), includes many intact or nearly intact proviruses, but no replication competent HML-2 proviruses have been identified in humans. HML-2-related proviruses are present in other primates, including rhesus macaques, but the extent and timing of HML-2 activity in macaques remains unclear. We have identified 145 HML-2-like proviruses in rhesus macaques, including a clade of young, rhesus-specific insertions. Age estimates, intact ORFs, and insertional polymorphism of these insertions are consistent with recent or ongoing infectious activity in macaques. 108 of the proviruses form a clade characterized by an ~750 bp sequence between env and the 3’ LTR, derived from an ancient recombination with a HERV-K(HML-8)-related virus. This clade is found in Old World monkeys (OWM), but not great apes, suggesting it originated after the ape/OWM split. We identified similar proviruses in white-cheeked gibbons; the gibbon insertions cluster within the OWM recombinant clade, suggesting interspecies transmission from OWM to gibbons. The LTRs of the youngest proviruses have deletions in U3, which disrupt the Rec Response Element (RcRE), required for nuclear export of unspliced viral RNA. We show that the HML-8 derived region functions as a Rec-independent constitutive transport element (CTE), indicating the ancestral Rec-RcRE export system was replaced by a CTE mechanism.
Gene mapping methodology powered by induced genome rearrangements
Authors: Yone Hideyuki , Kono Hiromitsu , Hirai Hayato , Ohta Kunihiro
Published: May 2022

Phenotypic variation occurs through genome rearrangements and mutations in certain responsible genes; however, systematic gene identification methodologies based on genome rearrangements have not been fully established. Here, we explored the loci responsible for the given phenotype using the TAQing system and compared it with a conventional mutagenesis-based method. Two yeast strains with different genetic backgrounds and flocculation phenotypes were fused and genomic rearrangements were induced by transient DNA breaks. Then, selection pressure was applied and multiple mutants were generated, showing different flocculation abilities. We also raised mutants with altered cohesiveness due to spontaneous mutations during long-term recursive passages of haploid strains without TAQing treatment. Comparative genomic analysis of the TAQed mutants revealed three chromosomal regions harboring pivotal flocculation genes, whereas conventional mutagenesis generated a more diverse list of candidate loci after prolonged selection. The combined use of these approaches will accelerate the identification of genes involved in complex phenotypes.
Near Infrared Diffuse In Vivo Flow Cytometry
Authors: Pace Joshua , Ivich Fernando , Marple Eric , Niedre Mark
Published: May 2022

Significance

Diffuse in vivo Flow Cytometry (DiFC) is an emerging technique for enumerating rare fluorescently labeled circulating cells non-invasively in the bloodstream. Thus far we have reported red and blue-green versions of DiFC. Use of near-infrared (NIR) fluorescent light would in principle allow use of DiFC in deeper tissues and would be compatible with emerging NIR fluorescence molecular contrast agents.

Aim

In this work, we describe the design of a NIR-DiFC instrument and demonstrate its use in optical flow phantoms in vitro and in mice in vivo.

Approach

We developed an improved optical fiber probe design for efficient collection of fluorescence from individual circulating cells, and efficient rejection of instrument autofluorescence. We built a NIR-DiFC instrument. We tested this with NIR fluorescent microspheres and cell lines labeled with OTL38 fluorescence contrast agent in a flow phantom model. We also tested NIR-DiFC in nude mice injected intravenously with OTL38-labeled L1210A cells.

Results

NIR-DiFC allowed detection of CTCs in flow phantoms with mean signal to noise ratios (SNRs) of 19 to 32 dB. In mice, fluorescently-labeled CTCs were detectable with mean SNR of 26 dB. NIR-DiFC also exhibited orders significantly lower autofluorescence and false-alarm rates than blue-green DiFC.

Conclusions

NIR-DiFC allows use of emerging NIR contrast agents. This work could pave the way for future use of NIR-DiFC in humans.
A User-Friendly Guide to Using Distance Measures to Compare Time Series in Ecology
Authors: Dove Shawn , Böhm Monika , Freeman Robin , Jellesmark Sean , Murrell David
Published: May 2022

Time series are a critical component of ecological analysis, used to track changes in biotic and abiotic variables. Information can be extracted from the properties of time series for tasks such as classification, clustering, prediction, and anomaly detection. These common tasks in ecological research rely on the notion of (dis-) similarity which can be determined by using distance measures. A plethora of distance measures have been described in the scientific literature, but many of them have not been introduced to ecologists. Furthermore, little is known about how to select appropriate distance measures and the properties they focus on for time-series related tasks.

Here we describe 16 potentially desirable properties of distance measures, test 42 distance measures for each property, and present an objective method to select appropriate distance measures for any task and ecological dataset. We then demonstrate our selection method by applying it to a set of real-world data on breeding bird populations in the UK. We also discuss ways to overcome some of the difficulties involved in using distance measures to compare time series.

Our real-world population trends exhibit a common challenge for time series comparison: a high level of stochasticity. We demonstrate two different ways of overcoming this challenge, first by selecting distance measures with properties that make them well-suited to comparing noisy time series, and second by applying a smoothing algorithm before selecting appropriate distance measures. In both cases, the distance measures chosen through our selection method are not only fit-for-purpose but are consistent in their rankings of the population trends.

The results of our study should lead to an improved understanding of, and greater scope for, the use of distance measures for comparing time series within ecology, and allow for the answering of new ecological questions.
Rapid modeling of experimental molecular kinetics with simple electronic circuits instead of with complex differential equations
Authors: Deng Yijie , Beahm Douglas Raymond , Ran Xinping , Riley Tanner G , Sarpeshkar Rahul
Published: May 2022

Kinetic modeling has relied on using a tedious number of mathematical equations to describe molecular kinetics in interacting reactions. The long list of differential equations with associated abstract variables and parameters inevitably hinders readers’ easy understanding of the models. However, the mathematical equations describing the kinetics of biochemical reactions can be exactly mapped to the dynamics of voltages and currents in simple electronic circuits wherein voltages represent molecular concentrations and currents represent molecular fluxes. For example, we theoretically derive and experimentally verify accurate circuit models for Michaelis-Menten kinetics. Then, we show that such circuit models can be scaled via simple wiring among circuit motifs to represent more and arbitrarily complex reactions. Hence, we can directly map reaction networks to equivalent circuit schematics in a rapid, quantitatively accurate, and intuitive fashion without needing mathematical equations. We verify experimentally that these circuit models are quantitatively accurate. Examples include i) different mechanisms of competitive, noncompetitive, uncompetitive, and mixed enzyme inhibition, important for understanding pharmacokinetics; ii) product-feedback inhibition, common in biochemistry; iii) reversible reactions, important in many metabolic pathways; and iv) translation and transcription dynamics in a cell-free system, which brings insight into the functioning of all gene-protein networks. We envision that circuit modeling and simulation could become a powerful scientific communication language and tool for quantitative studies of kinetics in biology.
A synthetic communication system uncovers extracellular immunity that self-limits bacteriophage transmission
Authors: Pathania Amit , Hopper Corbin , Pandi Amir , Függer Matthias , Nowak Thomas , Kushwaha Manish
Published: May 2022

Understanding how delivery and exchange of genetic information by bacteriophages shapes bacterial populations is important for designing applications for phage therapy, biocontrol, and microbiome engineering. Here, we present a synthetic intercellular communication system that repurposes phage M13 for genetic exchange between Escherichia coli cells and build mathematical models of the communication behaviour. Our models, based on Chemical Reaction Networks, capture the growth burden, cell density, and growth phase dependence of phage secretion and infection kinetics and predict the stochasticity characterising phage-bacterial interactions at low numbers. In co-cultures of phage sender and receiver cells, resource sharing and selection pressure determine the choice of horizontal versus vertical phage transmission. Surprisingly, we discover that a phage-encoded immunity factor confers extracellular protection to uninfected bacteria, reducing infection rates by 70%. In a simulated gut environment, this novel “self-jamming” mechanism enables the phage to farm uninfected bacteria for future infections, increasing the overall success of both M13 and E. coli. The synthetic system developed here lays the groundwork for implementing population level controls in engineered bacterial communities, using phage signals for communication.
An expanding arsenal of immune systems that protect bacteria from phages
Authors: Millman Adi , Melamed Sarah , Leavitt Azita , Doron Shany , Bernheim Aude , Hör Jens , Lopatina Anna , Ofir Gal , Hochhauser Dina , Stokar-Avihail Avigail , Tal Nitzan , Sharir Saar , Voichek Maya , Erez Zohar , Ferrer Jose Lorenzo M. , Dar Daniel , Kacen Assaf , Amitai Gil , Sorek Rotem
Published: May 2022

Bacterial anti-phage defense systems are frequently clustered in microbial genomes, forming defense islands. This genomic property enabled the recent discovery of multiple defense systems based on their genomic co-localization with known systems, but the full arsenal of anti-phage mechanisms in bacteria is still unknown. In this study we report the discovery of 21 new defense systems that protect bacteria from phages, based on computational genomic analyses and phage infection experiments. We find multiple systems with protein domains known to be involved in eukaryotic anti-viral immunity, including ISG15-like proteins, dynamin-like proteins, and SEFIR domains, and show that these domains participate in bacterial defense against phages. Additional systems include protein domains predicted to manipulate DNA and RNA molecules, as well as multiple toxin-antitoxin systems shown here to function in anti-phage defense. The systems we discovered are widely distributed in bacterial and archaeal genomes, and in some bacteria form a considerable fraction of the immune arsenal. Our data substantially expand the known inventory of defense systems utilized by bacteria to counteract phage infection.
Intermittent fasting mitigates cognitive deficits in Alzheimer’s disease via the gut-brain axis
Authors: Jia Mengzhen , Shi Lin , Zhao Yihang , Hu Xinyu , Zhao Junhe , Ding Chen , Shang Yiqiu , Li Xin , Jin Xin , Dai Xiaoshuang , Liu Xuebo , Liu Zhigang
Published: May 2022

Intermittent fasting (IF) is suggested to mitigate cognitive impairment in Alzheimer’s disease (AD). We detailed the effects of IF in AD development and assessed the contribution of the gut microbiota-metabolite-brain axis in promoting the effects of fasting. A 16-week IF regimen significantly improved spatial memory and cognitive function in AD transgenic mice; this improvement was accompanied by decreased Aβ accumulation and suppression of neuroinflammation. IF reshaped the microbiota and beneficially altered the microbial metabolites related to cognitive function. Multi-OMICs integration demonstrated a strong connection between IF induced changes in hippocampus gene expression, the composition of the gut microbes, and the serum metabolites beneficial for cognitive function. Removal of gut microbes with antibiotics abolished the neuroprotective effects of IF. These findings suggest new avenues for therapy and nutritional intervention to prevent the development of AD and other neurodegenerative diseases.
Global early replication disrupts gene expression and chromatin conformation in a single cell cycle
Authors: Santos Miguel M. , Johnson Mark C. , Fiedler Lukáš , Zegerman Philip
Published: May 2022

The early embryonic divisions of many organisms, including fish, flies and frogs are characterised by a very rapid S-phase caused by high rates of replication initiation. In somatic cells, S-phase is much longer due to both a reduction in the total number of initiation events and the imposition of a temporal order of origin activation. The physiological importance of changes in the rate and timing of replication initiation in S-phase remains unclear. Here we assess the importance of the temporal control of replication initiation using a conditional system in budding yeast to drive the early replication of all origins in a single cell cycle. We show that global early replication disrupts the expression of over a quarter of all genes. By deleting individual origins, we show that delaying replication is sufficient to restore normal gene expression, directly establishing replication timing control in this regulation. Global early replication disrupts nucleosome positioning and transcription factor binding during S-phase, suggesting that the rate of S-phase is important to regulate the chromatin landscape. Together these data provide new insight into the role of a temporal order of origin firing for coordinating replication, gene expression and chromatin establishment as occurs in the early embryo.
Long-term ecological and evolutionary dynamics in the gut microbiomes of carbapenemase-producing Enterobacteriaceae colonized subjects
Authors: Kang Jonathan T. L. , Teo Jonathan , Bertrand Denis , Ng Amanda , Ravikrishnan Aarthi , Yong Melvin , Tek Ng Oon , Marimuthu Kalisvar , Chen Swaine , Rei Chng Kern , Yunn-Hwen Gan , Nagarajan Niranjan
Published: May 2022

Long-term colonization of the gut microbiome by carbapenemase-producing Enterobacteriaceae (CPE) is a growing area of public health concern as it can lead to community transmission and rapid increase in cases of life-threatening CPE infections. Leveraging the observation that many subjects are decolonized without interventions within a year, we used longitudinal shotgun metagenomics (up to 12 timepoints) for detailed characterization of ecological and evolutionary dynamics in the gut microbiome of a cohort of CPE-colonized subjects and family members (n=46; 361 samples). Subjects who underwent decolonization exhibited a distinct ecological shift marked by recovery of microbial diversity, key commensals and anti-inflammatory pathways. In addition, colonization was marked by elevated but unstable Enterobacteriaceae abundances, which exhibited distinct strain-level dynamics for different species (Escherichia coli and Klebsiella pneumoniae). Finally, comparative analysis with whole genome sequencing data from CPE isolates (n=159) helped identify sub-strain variation in key functional genes and the presence of highly similar E. coli and K. pneumoniae strains with variable resistance profiles and plasmid sharing. These results provide an enhanced view into how colonization by multi-drug resistant bacteria associates with altered gut ecology and can enable transfer of resistance genes, even in the absence of overt infection and antibiotic usage.
Gateway Identity and Spatial Remapping in a Combined Grid and Place Cell Attractor
Authors: Baumann Tristan , Mallot Hanspeter A.
Published: May 2022

The spatial specificities of hippocampal place cells, i.e., their firing fields, are subject to change if the rat enters a new compartment in the experimental maze. This effect is known as remapping. It cannot be explained from path integration (grid cell activity) and local sensory cues alone but requires additional knowledge of the different compartments in the form of context recognition at the gateways between them. Here we present a model for the hippocampalentorhinal interplay in which the activity of place and grid cells follows a joint attractor dynamic. Place cells depend on the current grid cell activity but can also reset the grid cell activity in the remapping process. Remapping is triggered by the passage through a gateway. When this happens, a previously stored pattern of place cell activity associated with the gateway is reactivated from a “gateway database”. The joint attractor will then reinstate the grid cell pattern that was active when the gateway had first been learned and path integration can proceed from there. The model is tested with various mazes used in the experimental literature and reproduces the published results, and we make predictions for remapping in a new maze type. We propose the involvement of memory in the form of “gate cells” that drive the place cells and with them the joint hippocampal-entorhinal loop into the corresponding attractor whenever a compartment is entered.
A label-free method to track individuals and lineages of budding cells
Authors: Pietsch Julian M. J. , Muñoz Alán F. , Adjavon Diane-Yayra A. , Farquhar Iseabail , Clark Ivan B. N. , Swain Peter S.
Published: May 2022

Much of biochemical regulation ultimately controls growth rate, particularly in microbes. Although time-lapse microscopy visualises cells, determining their growth rates is challenging because cells often overlap in images, particularly for those that divide asymmetrically, like Saccharomyces cerevisiae. Here we present the Birth Annotator for Budding Yeast (BABY), an algorithm to determine single-cell growth rates from label-free images. Using a convolutional neural network, BABY resolves overlaps through separating cells by size and assigns buds to mothers by identifying bud necks. BABY uses machine learning to track cells and determine lineages, estimates growth rates as the rate of change of volumes, and identifies cytokinesis by how growth varies. Using BABY and a microfluidic device, we show that bud growth is first sizer- then timer-controlled, that the nuclear concentration of Sfp1, a regulator of ribosome biogenesis, varies before the growth rate does, and that growth rate can be used for real-time control. Growth rate and fitness are strongly correlated, and BABY should therefore generate much biological insight.
Activation of TnSmu1, an integrative and conjugative element, by an ImmR-like transcriptional regulator in Streptococcus mutans
Authors: King Shawn , Quick Allison , King Kalee , Walker Alejandro R. , Shields Robert C.
Published: May 2022

Integrative and conjugative elements (ICEs) are chromosomally encoded mobile genetic elements that can transfer DNA between bacterial strains. Recently, as part of efforts to determine hypothetical gene functions, we have discovered an important regulatory module encoded on an ICE known as TnSmu1 on the Streptococcus mutans chromosome. The regulatory module consists of a cI-like repressor with a helix-turn-helix DNA binding domain immRSmu (immunity repressor) and a metalloprotease immASmu (anti-repressor). It is not possible to create an in-frame deletion mutant of immRSmu and repression of immRSmu with CRISPRi causes substantial cell defects. We used a bypass of essentiality (BoE) screen to discover genes that allow deletion of the regulatory module. This revealed that conjugation genes, located within TnSmu1, can restore the viability of an immRSmu mutant. Deletion of immRSmu also leads to production of a circular intermediate form of TnSmu1, that is also inducible by the genotoxic agent mitomycin C. To gain further insights into potential regulation of TnSmu1 by ImmRSmu and broader effects on S. mutans UA159 physiology we used CRISPRi and RNA-seq. Strongly induced genes included all the TnSmu1 mobile element, genes involved in amino acid metabolism, transport systems, and a Type I-C CRISPR-Cas system. Lastly, bioinformatic analysis shows that the TnSmu1 mobile element and its associated genes are well distributed across S. mutans isolates. Taken together, our results show that activation of TnSmu1 is controlled by the immRASmu module, and that activation is deleterious to S. mutans, highlighting the complex interplay between mobile elements and their host.