bluuebunny/crossref_metadata_2025 huggingface dataset:
Warning coloration, body size and the evolution of gregarious behavior in butterfly larvae
Authors: McLellan Callum F , Montgomery Stephen H , Cuthill Innes C
Published: July 2022

Many species gain anti-predator benefits by combining gregarious behavior with warning coloration, yet there is debate over which trait evolves first, and which is the secondary adaptive enhancement. Body size can also influence how predators receive aposematic signals, and potentially constrain the evolution of gregarious behavior. To our knowledge, the causative links between the evolution of gregariousness, aposematism and larger body sizes have not been fully resolved. Here, using the most recently resolved butterfly phylogeny and an extensive new dataset of larval traits, we reveal the evolutionary interactions between important traits linked to larval gregariousness. We show that larval gregariousness has arisen many times across the butterflies, and aposematism is a likely prerequisite for gregariousness to evolve. We also find that body size may be an important factor for determining the coloration of solitary, but not gregarious larvae. Additionally, by exposing artificial ‘larvae’ to wild avian predation, we show that undefended, cryptic ‘larvae’ are heavily predated when aggregated but benefit from solitariness, whereas the reverse is true for aposematic prey. Our data reinforce the importance of aposematism for gregarious larval survival, whilst identifying new questions about the roles of body size and toxicity in the evolution of grouping behavior.
Invasion and secondary site colonization as a function of in vitro primary tumor matrix stiffness
Authors: Shah Lekha , Latif Ayşe , Williams Kaye J. , Mancuso Elena , Tirella Annalisa
Published: July 2022

Increased breast tissue stiffness is correlated with breast cancer risk and invasive cancer progression. However, its role in promoting bone metastasis, which shares a large burden of breast cancer deaths, has not yet been understood. To better understand the cause-effect relationship of tissue stiffness on breast cancer’s metastatic potential, we fabricated three-dimensional (3D) models to mimic breast and bone tissue in vitro. Based on our previous work, we used alginate-based hydrogels allowing precise control over stiffness and composition of extracellular breast tissue matrix; and 3D printed poly-caprolactone (PCL)-composite scaffolds to mimic the bone. The latter were further modified by promoting bone-ECM deposition using Saos-2 cells. After a decellularization step, PCL scaffolds were assembled with alginate-gelatin hydrogels and a novel breast-to-bone in vitro model was established. It was observed that increased stiffness of hydrogel resulted in higher migration and invasion capacity of MDA-MB 231 cells. Additionally, PTHrP and IL-6 expression, both of which are implicated in bone metastasis, were higher when cells from stiff hydrogels were cultured in bone/PCL scaffolds. These breast-to-bone in vitro models pose as a novel non-animal technology to pave the way for incorporating important tissue microenvironmental factors of the disease physiology (e.g. tissue stiffness) and emerge as promising future platforms for monitoring metastatic disease phenotypes and therapeutic efficacy.
Mining the human gut microbiome identifies mycobacterial d-arabinan degrading enzymes
Authors: Al-Jourani Omar , Benedict Samuel , Ross Jennifer , Layton Abigail , van der Peet Phillip , Marando Victoria M. , Bailey Nicholas P. , Heunis Tiaan , Manion Joseph , Mensitieri Francesca , Franklin Aaron , Abellon-Ruiz Javier , Oram Sophia L. , Parsons Lauren , Cartmell Alan , Wright Gareth S. A. , Baslé Arnaud , Trost Matthias , Henrissat Bernard , Munoz-Munoz Jose , Hirt Robert P. , Kiessling Laura L. , Lovering Andrew , Williams Spencer J. , Lowe Elisabeth C. , Moynihan Patrick J.
Published: July 2022

Division and degradation of bacterial cell walls requires coordinated action of a myriad of enzymes. This particularly applies to the elaborate cell walls of acid-fast organisms such asMycobacterium tuberculosis, which consist of a multi-layered cell wall that contains an unusual glycan called arabinogalactan. Enzymes that cleave thed-arabinan core of this structure have not previously been identified in any organism. We have interrogated the diverse carbohydrate degrading enzymes expressed by the human gut microbiota and uncovered four families of glycoside hydrolases with the capability to degrade thed-arabinan ord-galactan components of arabinogalactan. Using novel exo-d-galactofuranosidases from gut bacteria we generated enrichedd-arabinan and used it to identifyD. gadeias a D-arabinan degrader. This enabled the discovery of endo- and exo-acting enzymes that cleave D-arabinan. We have identified new members of the DUF2961 family (GH172), and a novel family of glycoside hydrolases (DUF4185) that display endo-d-arabinofuranase activity. The DUF4185 enzymes are conserved in mycobacteria and found in many microbes, suggesting that the ability to degrade mycobacterial glycans plays an important role in the biology of diverse organisms. All mycobacteria encode two conserved endo-d-arabinanases that display different preferences for thed-arabinan-containing cell wall components arabinogalactan and lipoarabinomannan, suggesting they are important for cell wall modification and/or degradation. The discovery of these enzymes will support future studies into the structure and function of the mycobacterial cell wall.
Remodeling of Il4-Il13-Il5 locus underlies selective gene expression
Authors: Nagashima Hiroyuki , Petermann Franziska , Pękowska Aleksandra , Chaitankar Vijender , Kanno Yuka , O’Shea John J.
Published: July 2022

The type 2 cytokines, interleukin (IL)-4, IL-5 and IL-13 reside within a tandem multi-gene cluster in mammals. These cytokines represent the hallmark of type 2 immune responses controlling parasites, promoting tissue repair as well as causing allergic diseases. Both innate and adaptive lymphocytes secrete type 2 cytokines with discordant production spectra. We took a holistic structural and functional view of the type 2 cytokine locus before and after activation, comparing innate (ILC2) and adaptive (Th2) lymphocytes to understand mechanisms underlying their distinctive programs. Rapid induction of IL-5 dominates in ILC2, whereas IL-4 does so in Th2 cells. Using high-resolution chromatin conformation capture we found that global cellular chromatin architecture remained constant, whereas the type 2 cytokine locus rapidly remodeled. In ILC2, Il13 and Il5 loci were aligned in proximity whereas Il4 locus was insulated. In Th2 cells, Il4 and Il13 positioned in proximity while the Il5 locus remained distal. Select REs were separately deleted in mice to confirm cell-type specific and activation-dependent roles in type 2 responses in vivo. Thus, contrary to the premise that chromatin architecture plays a minimal role in steady-state gene induction, signal-dependent remodeling of 3D configuration underlies the discordant cytokine outputs in ILC2s versus Th2 cells.
Large-scale in vivo CRISPR screens identify SAGA complex members as a key regulators of HSC lineage commitment and aging
Authors: Haney Michael S. , Shankar Archana , Hsu Ian , Miyauchi Masashi , Pálovics Róbert , Khoo Hwei Minn , Igarashi Kyomi J. , Bhadury Joydeep , Munson Christy , Mack Paul K. , Tan Tze-Kai , Wyss-Coray Tony , Nakauchi Hiromitsu , Wilkinson Adam C.
Published: July 2022

The biological mechanisms that sustain the vast blood production required for healthy life remain incompletely understood. To address this knowledge gap, we developed an in vivo hematopoietic stem cell (HSC)-based large-scale CRISPR knockout screening platform to enable the genetic interrogation of hematopoiesis and broad aspects of immune cell function in vivo. Targeting ∼7000 genes with this methodology, we discovered SAGA complex members Tada2b and Taf5l as key regulators of HSC lineage commitment. Loss of Tada2b or Taf5l inhibited hematopoiesis in vivo and was associated with upregulation of interferon response gene expression. SAGA complex member expression is significantly reduced in aged HSCs and upregulated with heterochronic parabiosis, suggesting a novel mechanism of age-associated hematopoietic decline and rejuvenation. Our study provides a rich functional genetics resource of hematopoiesis regulators accessible through a public interactive database (www.hematopoiesiscrisprscreens.com), a novel mechanism regulating age-related decline of hematopoiesis, and a new methodology with broad applications to systematically probe the development and functions of the lymphohematopoietic system.
Laboratory evolution and polyploid SCRaMbLE reveal genomic plasticity to synthetic chromosome defects and rearrangements
Authors: Williams Thomas C. , Kroukamp Heinrich , Xu Xin , Wightman Elizabeth L. I. , Llorente Briardo , Borneman Anthony R. , Carpenter Alexander C. , Van Wyk Niel , Espinosa Monica I. , Daniel Elizabeth L. , Walker Roy S. K. , Cai Yizhi , Nevalainen Helena K. M. , Curach Natalie C. , Deveson Ira W. , Mercer Timothy R. , Johnson Daniel L. , Mitchell Leslie A. , Bader Joel S. , Stracquadanio Giovanni , Boeke Jef D. , Goold Hugh D. , Pretorius Isak S. , Paulsen Ian T.
Published: July 2022

We have designed, constructed, and debugged a synthetic 753,096 bp version of Saccharomyces cerevisiae chromosome XIV as part of the international Sc2.0 project. We showed that certain synthetic loxPsym recombination sites can interfere with mitochondrial protein localization, that the deletion of one intron (NOG2) reduced fitness, and that a reassigned stop codon can lead to a growth defect. In parallel to these rational debugging modifications, we used Adaptive Laboratory Evolution to generate a general growth defect suppressor rearrangement in the form of increased TAR1 copy number. We also extended the utility of the Synthetic Chromosome Recombination and Modification by LoxP-mediated Evolution (SCRaMbLE) system by engineering synthetic-wild-type tetraploid hybrid strains that buffer against essential gene loss. The presence of wild-type chromosomes in the hybrid tetraploids increased post-SCRaMbLE viability and heterologous DNA integration, highlighting the plasticity of the S. cerevisiae genome in the presence of rational and non-rational modifications.
FT-GO: a multiplex fluorescent tyramide signal amplification system for histochemical analysis
Authors: Yamauchi Kenta , Okamoto Shinichiro , Ishida Yoko , Konno Kohtarou , Hoshino Kisara , Furuta Takahiro , Takahashi Megumu , Koike Masato , Isa Kaoru , Watanabe Masahiko , Isa Tadashi , Hioki Hiroyuki
Published: July 2022

Tyramide signal amplification (TSA) is a highly sensitive method for histochemical analysis. Previously, we reported a TSA system, BT-GO, for bright-filed imaging. Here, we develop FT-GO (Fluorochromized Tyramide-Glucose Oxidase) as a multiplex fluorescent TSA system. FT-GO involves peroxidase-catalyzed deposition of FT with hydrogen peroxide produced in enzymatic reaction between glucose and glucose oxidase. We showed that FT-GO enhanced immunofluorescence signals while maintaining low background signals. Compared with indirect immunofluorescence detections, FT-GO demonstrated a more widespread distribution of monoaminergic projection systems in mouse and marmoset brains. For multiplex labeling with FT-GO, we quenched Ab-conjugated peroxidase using sodium azide. We applied FT-GO to multiplex fluorescent in situ hybridization, and succeeded in labeling neocortical interneuron subtypes by coupling with immunofluorescence. FT-GO immunofluorescence further increased the detectability of an adeno-associated virus tracer. Given its simplicity and a staining with a high signal-to-noise ratio, FT-GO would provide a versatile platform for histochemical analysis.
M2M-InvNet: Human Motor Cortex Mapping from Multi-Muscle Response Using TMS and Generative 3D Convolutional Network
Authors: Akbar Md Navid , Yarossi Mathew , Rampersad Sumientra , Lockwood Kyle , Masoomi Aria , Tunik Eugene , Brooks Dana , Erdoğmuş Deniz
Published: July 2022

Transcranial magnetic stimulation (TMS) is often applied to the motor cortex to stimulate a collection of motor evoked potentials (MEPs) in groups of peripheral muscles. The causal interface between TMS and MEP is the selective activation of neurons in the motor cortex; moving around the TMS ‘spot’ over the motor cortex causes different MEP responses. A question of interest is whether a collection of MEP responses can be used to identify the stimulated locations on the cortex, which could potentially be used to then place the TMS coil to produce chosen sets of MEPs. In this work we leverage our previous report on a 3D convolutional neural network (CNN) architecture that predicted MEPs from the induced electric field, to tackle an inverse imaging task in which we start with the MEPs and estimate the stimulated regions on the motor cortex. We present and evaluate five different inverse imaging CNN architectures, both conventional and generative, in terms of several measures of reconstruction accuracy. We found that one architecture, which we propose as M2M-InvNet, consistently achieved the best performance.
Integrative mapping of the dog epigenome: reference annotation for comparative inter-tissue and cross-species studies
Authors: Son Keun Hong , Aldonza Mark Borris D. , Nam A-Reum , Lee Kang-Hoon , Lee Jeong-Woon , Shin Kyung-Ju , Kang Keunsoo , Cho Je-Yoel
Published: July 2022

The domestic dog has become a valuable model in exploring multifaceted diseases and biology important for human health. Large-scale dog genome projects produced high-quality draft references but still lack comprehensive annotation of encoded functional elements. Through the integrative next generation sequencing of transcriptomes paired with histone marks and DNA methylome profiling of 11 adult tissue types, implemented in a cross-species approach, we generated a reference epigenome of a domesticated dog. Using genome orthologues and synthenies, we deciphered the dog’s epigenetic code by defining distinct chromatin states, allowing for genome-wide, integratable data production. We then characterized somatic super-enhancer landscapes and showed that genes mapped on these regions are associated with a broad range of biological and disease traits and are traceable to their tissue-of-origin. Ultimately, we delineated conserved epigenomic changes at the tissue- and species-specific resolutions. Our study provides an epigenomic blueprint of the dog for comparative biology and medical research.
Benchmarking long-read RNA-sequencing analysis tools usingin silicomixtures
Authors: Dong Xueyi , Du Mei R. M. , Gouil Quentin , Tian Luyi , Jabbari Jafar S. , Bowden Rory , Baldoni Pedro L. , Chen Yunshun , Smyth Gordon K. , Amarasinghe Shanika L. , Law Charity W. , Ritchie Matthew E.
Published: July 2022

The current lack of benchmark datasets with inbuilt ground-truth makes it challenging to compare the performance of existing long-read isoform detection and differential expression analysis workflows. Here, we present a benchmark experiment using two human lung adenocarcinoma cell lines that were each profiled in triplicate together with synthetic, spliced, spike-in RNAs (“sequins”). Samples were deeply sequenced on both Illumina short-read and Oxford Nanopore Technologies long-read platforms. Alongside the ground-truth available via the sequins, we createdin silicomixture samples to allow performance assessment in the absence of true positives or true negatives. Our results show that,StringTie2andbambuoutperformed other tools from the 6 isoform detection tools tested,DESeq2, edgeRandlimma-voomwere best amongst the 5 differential transcript expression tools tested and there was no clear front-runner for performing differential transcript usage analysis between the 5 tools compared, which suggests further methods development is needed for this application.
Cytoflow: A Python Toolbox for Flow Cytometry
Authors: Teague Brian
Published: July 2022

Cytoflow is a free, open-source flow cytometry toolbox that enables quantitative and reproducible analyses of flow cytometry experiments. Comprised of a set of well-documented Python modules wrapped by a graphical user interface, Cytoflow allows both programmers and bench scientists to apply modern data analysis methods (including machine learning) to high-dimensional flow data sets. Modern analyses may also lead to new insight about the biological systems that are studied with this powerful technique.
Bioinformatics analysis of immune-related prognostic genes and immunotherapy in renal clear cell carcinoma
Authors: Pan Ziwen , Chang Sheng , Chen Song , Zhao Daqiang , Zou Zhiyu , Dai Linrui , Hou Yibo , Zhang Qianqian , Yang Yuanyuan , Chen Zhishui , Zhang Weijie , Zhao Yuanyuan
Published: July 2022

Clear cell renal cell carcinoma (ccRCC) is an immunogenic tumor and investigating the immunorelated genes is of great significance. To investigate the immunoprognostic genes of ccRCC, we analyzed the data assimilated from a public database (The Cancer Genome Atlas (TCGA) database and the gene expression omnibus (GEO) database) using bioinformatics. Then, a immunoprognosis model was constructed to identify 4 hub genes with moderate predictive values for the prognosis of ccRCC patients. Interestingly, these 4 genes were associated with the prognosis of ccRCC patients based on Oncomine and Gena Expression Profiling Interactive Analysis (GEPIA) databases. The correlation analysis between the immune infiltrate, immune checkpoints, and immunotherapy and this immunoprognosis model showed that immune infiltrate and could predict the immunotherapy effects. We also conducted a quantitative real-time polymerase chain reaction analysis and found that the expressions of 3 hub genes were associated with tumor progression (P<0.1). In conclusion, 4 genes that may serve as potential biomarkers in ccRCC were identified with respect to prognosis.
Utilizing a Cell-free Protein Synthesis Platform for Natural Product Synthesis
Authors: Ditzel Alex , Zhao Fanglong , Gao Xue , Phillips George N.
Published: July 2022

Natural products are a great source of pharmaceuticals, providing a majority of all small molecule drugs that exist today. However, creating natural products through organic synthesis or in heterologous hosts can be difficult and time-consuming. Therefore, to allow for easier screening and production of natural products, we demonstrated the use of a cell-free protein synthesis (CFPS) system to partially assemble natural products in vitro using coupled enzyme reactions. The tea caffeine synthase TCS1 was utilized to synthesize caffeine within a CFPS system. Cell-free systems also provide the benefit of allowing the use of substrates that would normally be toxic in a cellular environment to synthesize novel products. The automation and reduced metabolic engineering requirements of CFPS systems combined with other synthesis methods can allow for the efficient generation of new compounds.
Drug repositioning with gender perspective focused on Adverse Drug Reactions
Authors: Otero Carrasco Belén , Pérez Pérez Aurora , Ruiz Ernestina Menasalvas , Caraça-Valente Hernández Juan Pedro , Prieto Santamaría Lucía , Rodríguez-González Alejandro
Published: July 2022

Drug repositioning is a novel, useful, and crucial technique to find new uses for existing drugs. In this field of study, when the clinical trials necessary to obtain successful drug repositioning have been carried out, the female gender has not been given much consideration. Thus far, the participation of women in clinical trials has been very limited. There were several argued reasons to exclude them from trials, like the likelihood of pregnancy or sudden hormonal changes. This has meant that for a long time the adverse effects of a drug on women were unknown. Scientifically, it was known that due to the biological processes of pharmacokinetics and pharmacodynamics, the response to drugs was not the same in both genders, but despite this evidence, there is still no difference in the dosage or form of using a drug between men and women. In this study, we made a preliminary analysis where the main goal is to investigate gender differences within the drug repositioning field through the adverse effects produced by such treatments. A special section on specific cases of drug repositioning in rare diseases will also be considered to carry out the same verification previously mentioned in the text.
Cortical grey matter mediates increases in model-based control and learning from positive feedback from adolescence to adulthood
Authors: Scholz Vanessa , Waltmann Maria , Herzog Nadine , Reiter Andrea , Horstmann Annette , Deserno Lorenz
Published: July 2022

Adolescents undergo maturation in cognition and brain structure. Model-based (MB) control is known to increase from childhood to young adulthood, which is mediated by cognitive abilities. Here, we asked two questions unaddressed in previous developmental studies: Firstly, what are the brain structural correlates of age-related increases in MB control? Secondly, how are age-related increases in MB control from adolescence to adulthood influenced by motivational context? A developmental sample (n=103, age: 12-42) completed structural MRI and an established task to capture MB control. The task was modified with respect to outcome valence by including (1) reward and punishment blocks to manipulate the motivational context and (2) an additional choice test to assess learning from positive vs. negative feedback. After replicating that an age-dependent increase in MB control is mediated by cognitive abilities, we demonstrate first-time evidence that grey matter density (GMD) in the parietal cortex mediates the increase of MB control with age. While motivational context did not relate to age-related changes in MB control, learning from positive feedback improved with age. Meanwhile, negative feedback learning showed no age effects. We present a first report that an age-related increase in learning from positive feedback was mediated by reduced GMD in the parietal, medial and dorsolateral prefrontal cortex. Our findings indicate that efficient brain maturation, as putatively reflected in lower GMD, in distinct and partially overlapping brain regions is a key developmental step towards age-related increases in planning and value-based choice.

Significance Statement

Adolescents undergo extensive maturation in cognition and brain structure. Interestingly, model-based decision-making is also known to increase from childhood to adulthood. Here, we demonstrate for the first time that grey matter density in the parietal cortex mediates an age-dependent increase in model-based control. An age-related increase in positive feedback learning was mediated by reduced grey matter density in the parietal, medial and dorsolateral prefrontal cortex. Interestingly, a manipulation of motivational context (gain reward vs. avoid punishment) did not impact age-related changes in model-based control. These findings highlight that efficient brain maturation in distinct and overlapping cortical brain regions constitutes a key developmental step towards increases in model-based planning and value-based choice.
Engineering of Pseudomonas putida for accelerated co-utilization of glucose and cellobiose yields aerobic overproduction of pyruvate explained by an upgraded metabolic model
Authors: Bujdoš Dalimil , Popelářová Barbora , Volke Daniel C. , Nikel Pablo. I. , Sonnenschein Nikolaus , Dvořák Pavel
Published: July 2022

Pseudomonas putida KT2440 is an attractive bacterial host for biotechnological production of valuable chemicals from renewable lignocellulosic feedstocks as it can valorize lignin-derived aromatics or cellulosic glucose. P. putida EM42, a genome-reduced variant of P. putida KT2440 endowed with advantageous physiological properties, was recently engineered for growth on cellobiose, a major cellooligosaccharide product of enzymatic cellulose hydrolysis. Co-utilization of cellobiose with glucose was achieved in a mutant lacking periplasmic glucose dehydrogenase Gcd (PP_1444). However, the cause of the observed co-utilization was not understood and the Δgcd strain suffered from a significant growth defect. In this study, we aimed to investigate the basis of the simultaneous uptake of the two sugars and accelerate the growth of P. putida EM42 Δgcd mutant for the bioproduction of valuable compounds from glucose and cellobiose. We show that the gcd deletion abolished the inhibition of the exogenous β-glucosidase BglC from Thermobifida fusca by the intermediates of the periplasmic glucose oxidation pathway. The additional deletion of the hexR gene, which encodes a repressor of the upper glycolysis genes, failed to restore the rapid growth on glucose. The reduced growth rate of the Δgcd mutant was partially compensated by the implantation of heterologous glucose (Glf from Zymomonas mobilis) and cellobiose (LacY from Escherichia coli) transporters. Remarkably, this intervention resulted in the accumulation of pyruvate in aerobic P. putida cultures. We demonstrated that the excess of this key metabolic intermediate can be redirected to the enhanced biosynthesis of ethanol and lactate. The overproduction of pyruvate was then unveiled by an upgraded genome-scale metabolic model constrained with proteomic and kinetic data. The model pointed to the saturation of glucose catabolism enzymes due to unregulated substrate uptake and it predicted improved bioproduction of pyruvate-derived chemicals by the engineered strain. This work sheds light on the co-metabolism of cellulosic sugars in an attractive biotechnological host and introduces a novel strategy for pyruvate overproduction in bacterial cultures under aerobic conditions.

Highlights

Co-utilization of glucose and cellobiose achieved in P. putida EM42 Δgcd mutant.

Growth defect of the mutant compensated by implanting exogenous sugar transporters.

Enhanced influx of carbon caused aerobic overproduction of pyruvate and acetate.

Carbon from excess pyruvate streamed into ethanol or L-lactate.

Pyruvate overproduction unveiled by a mathematical model of P. putida metabolism.
Evaluation of the nemabiome approach for the study of equine strongylid communities
Authors: Courtot Élise , Boisseau Michel , Dhorne-Pollet Sophie , Serreau Delphine , Gesbert Amandine , Reigner Fabrice , Basiaga Marta , Kuzmina Tetiana , Lluch Jérôme , Annonay Gwenolah , Kuchly Claire , Diekmann Irina , Krücken Jürgen , Samson-Himmelstjerna Georg von , Mach Nuria , Sallé Guillaume
Published: July 2022

Basic knowledge on the biology and epidemiology of equine strongylid species remains insufficient although it would contribute to the design of better parasite control strategies. Nemabiome is a convenient tool to quantify and to identify species in bulk samples that could overcome the hurdle that cyathostomin morphological identification represents. To date, this approach has relied on the internal transcribed spacer 2 (ITS-2) of the ribosomal RNA cistron and its predictive performance and associated biases both remain unaddressed.

This study aimed to bridge this knowledge gap using cyathostomin mock communities and comparing performances of the ITS-2 and acytochrome c oxidase subunit I(COI) barcode newly developed in this study. The effects of bioinformatic parameters were investigated to determine the best analytical pipelines. Subsequently, barcode predictive abilities were compared across various mock community compositions. The replicability of the approach and the amplification biases of each barcode were estimated. Results were also compared between various types of biological samples, i.e. eggs, infective larvae or adults.

Overall, the proposed COI barcode was suboptimal relative to the ITS-2 rDNA region, because of PCR amplification biases, a reduced sensitivity and higher divergence from the expected community composition. Metabarcoding yielded consistent community composition across the three sample types, although infective larvae may remain the most tractable in the field. Additional strategies to improve the COI barcode performances are discussed. These results underscore the critical need of mock communities for metabarcoding purposes.
Combined Scattering, Interferometric and Fluorescence Oblique Illumination for Live Cell Nanoscale Imaging
Authors: Zheng Yujie , Lim Yean Jin , Lin Hanqi , Xu Tienan , Longbottom Carmen , Delghingaro-Augusto Viviane , Thong Yee Lin , Parish Christopher R. , Gardiner Elizabeth E. , Lee Woei Ming
Published: July 2022

To determine the molecular and/or mechanical basis of cell migration using live cell imaging tools, it is necessary to correlate multiple 3D spatiotemporal events simultaneously. Fluorescence nanoscopy and label free nanoscale imaging can complement each other by providing both molecular specificity and structural dynamics of sub-cellular structure. In doing so, a combined imaging system would permit quantitative 3D spatial temporal detail of individual cellular components. In this paper, we empirically determined a series of optimal azimuthal scanning angles and rotating beam to achieve simultaneous and label-free nanoscale and fluorescence imaging. Label-free nanoscale imaging here refers to interferometric, brightfield (BF) and darkfield (DF) rotating coherence scattering (ROCS) microscopy, while fluorescence refers to high inclined Laminated Oblique (HiLO) and total internal reflection fluorescence (TIRF) imaging. The combined capabilities of interferometric, scattering and fluorescence imaging enables (1) the identification of molecular targets (substrate or organelle), (2) quantification of 3D cell morphodynamics, and (3) tracking of intracellular organelles in 3D. This combined imaging tool was then used to characterize migrating platelets and adherent endothelial cells, both critical to the process of infection and wound healing. The combined imaging results of over ∼1000 platelets, suggested that serum albumin (bovine) was necessary for platelets to migrate and scavenge fibrin/fibrinogen. Furthermore, we determine new asynchronous membrane fluctuations between the leading and rear edge of a migrating platelet. We further demonstrated that interferometric imaging permitted the quantification of mitochondria dynamics on lung microvascular cells (HMVEC). Our data suggests that axial displacement of mitochondria is minimized when it is closer to the nucleus or the leading edge of a cell membrane that exhibits retrograde motion. Taken together, this combined imaging platform has proven to quantify multiple spatial temporal events of a migrating cell, that will undoubtedly open ways to new quantitative correlative nanoscale live cell imaging.
An immunoresponsive three-dimensional urine-tolerant human urothelial (3D-UHU) model to study urinary tract infection
Authors: Jafari Nazila V. , Rohn Jennifer L.
Published: July 2022

Murine models of urinary tract infection (UTI) have significantly improved our understanding of host-pathogen interactions. However, given some differences between the rodent and human bladder which may modulate bacterial response, including certain biomarkers, urothelial thickness and the concentration of urine, the development of new human-based models is important to complement mouse studies and to provide a more complete picture of UTI in patients. We originally developed a human urothelial three-dimensional (3D) model which was urine tolerant and demonstrated several biomarkers of the urothelium, but it only achieved human thickness in heterogenous, multi-layered zones and did not demonstrate the comprehensive differentiation status needed to achieve barrier function. Here, we report an improved 3D urine-tolerant human urothelial (3D-UHU) model, which after 18-20 days of growth, stratifies uniformly to 7 layers. We confirmed by flow-cytometric analysis that the model is comprised of the three expected, distinct human cell types. The apical surface differentiated into large, CD227+ umbrella-like cells expressing uroplakin-1A, II, III, and cytokeratin 20, all of which are important terminal differentiation markers, and a glycosaminoglycan layer. Below this layer, several layers of intermediate cells were present, with a single underlying layer of CD271+ basal cells. The apical surface also expressed E-cadherin, ZO-1, claudin-1 and -3, necessary for barrier formation; barrier integrity was confirmed by transepithelial electrical resistance and FITC-dextran permeability assay. Infection with both Gram-negative and Gram-positive bacterial classes elicited elevated levels of pro-inflammatory cytokines and chemokines characteristic of urinary tract infection in humans, and caused a decrease in barrier function, suggesting that the 3D-UHU model holds promise for studying host-pathogen interactions and host innate immune response.
Evolutionary responses to acquiring a multidrug resistance plasmid are dominated by metabolic functions across diverse Escherichia coli lineages
Authors: Carrilero Laura , Dunn Steven , McNally Alan , Brockhurst Michael
Published: July 2022

Multidrug resistance (MDR) plasmids drive the spread of antibiotic resistance between bacterial lineages. The immediate impact of MDR plasmid acquisition on fitness and cellular processes varies among bacterial lineages, but how the evolutionary processes enabling the genomic integration of MDR plasmids vary is less well understood, particularly in clinical pathogens. Using diverse Escherichia coli lineages experimentally evolved for ∼700 generations, we show that the evolutionary response to gaining the MDR plasmid pLL35 was dominated by chromosomal mutations affecting metabolic and regulatory functions, with both strain-specific and shared mutational targets. The expression of several of these functions, such as anaerobic metabolism, is known to be altered upon acquisition of pLL35. Interactions with resident mobile genetic elements, notably several IS-elements, potentiated parallel mutations, including insertions upstream of hns that were associated with its upregulation and the downregulation of the plasmid-encoded extended-spectrum beta-lactamase gene. Plasmid parallel mutations targeted conjugation-related genes, whose expression was also commonly downregulated in evolved clones. Beyond their role in horizontal gene transfer, plasmids can be an important selective force shaping the evolution of bacterial chromosomes and core cellular functions.
A large-scale brain network of species-specific dynamic human body perception
Authors: Li Baichen , Solanas Marta Poyo , Marrazzo Giuseppe , Raman Rajani , Taubert Nick , Giese Martin , Vogels Rufin , de Gelder Beatrice
Published: July 2022

This ultrahigh field 7T fMRI study addressed the question of whether there exists a core network of brain areas at the service of different aspects of body perception. Participants viewed naturalistic videos of monkey and human faces, bodies, and objects along with mosaic-scrambled videos for control of low-level features. ICA-based network analysis was conducted to find body and species modulations at both the voxel and the network levels. Among the body areas, the highest species selectivity was found in the middle frontal gyrus and amygdala. Two large-scale networks were highly selective to bodies, dominated by the lateral occipital cortex and right superior temporal sulcus (STS) respectively. The right STS network showed high species selectivity, and its significant human body-induced node connectivity was focused around the extrastriate body area (EBA), STS, temporoparietal junction (TPJ), premotor cortex, and inferior frontal gyrus (IFG). The human body-specific network discovered here may serve as a brain-wide internal model of the human body serving as an entry point for a variety of processes relying on body descriptions as part of their more specific categorization, action, or expression recognition functions.
Spontaneous binding of single-stranded RNAs to RRM proteins visualised by unbiased atomistic simulations with rescaled RNA force field
Authors: Krepl Miroslav , Pokorna Pavlina , Mlynsky Vojtech , Stadlbauer Petr , Sponer Jiri
Published: July 2022

Recognition of single-stranded RNA (ssRNA) by RNA recognition motif (RRM) domains is an important class of protein-RNA interactions. Many such complexes were characterized using NMR and/or X-ray crystallography techniques, revealing ensemble-averaged pictures of the bound states. However, it is becoming widely accepted that better understanding of protein-RNA interactions would be obtained from ensemble descriptions. Indeed, earlier molecular dynamics (MD) simulations of bound states indicated visible dynamics at the RNA-RRM interfaces. Here, we report the first atomistic simulation study of spontaneous binding of short RNA sequences to RRM domains of HuR and SRSF1 proteins. Using millisecond-scale aggregate ensemble of unbiased simulations we were able to observe a few dozens of binding events. The HuR RRM3 utilizes a pre-binding state to navigate the RNA sequence to its partially disordered bound state and then to dynamically scan its different binding registers. The SRFS1 RRM2 binding is more straightforward but still multiple-pathway. The present study necessitated development of a goal-specific force-field modification scaling down the intramolecular vdW interactions of the RNA which also improves description of the RNA-RRM bound state. Our study opens a new avenue for large-scale atomistic investigations of binding landscapes of protein-RNA complexes and future perspectives of such research are discussed.
THINGS-data: A multimodal collection of large-scale datasets for investigating object representations in human brain and behavior
Authors: Hebart M.N. , Contier O. , Teichmann L. , Rockter A.H. , Zheng C.Y. , Kidder A. , Corriveau A. , Vaziri-Pashkam M. , Baker C.I.
Published: July 2022

Understanding object representations requires a broad, comprehensive sampling of the objects in our visual world with dense measurements of brain activity and behavior. Here we present THINGS-data, a multimodal collection of large-scale neuroimaging and behavioral datasets in humans, comprising densely-sampled functional MRI and magnetoencephalographic recordings, as well as 4.70 million similarity judgments in response to thousands of photographic images for up to 1,854 object concepts. THINGS-data is unique in its breadth of richly-annotated objects, allowing for testing countless hypotheses at scale while assessing the reproducibility of previous findings. Beyond the unique insights promised by each individual dataset, the multimodality of THINGS-data allows combining datasets for a much broader view into object processing than previously possible. Our analyses demonstrate the high quality of the datasets and provide five examples of hypothesis-driven and data-driven applications. THINGS-data constitutes the core public release of the THINGS initiative (https://things-initiative.org) for bridging the gap between disciplines and the advancement of cognitive neuroscience.
MS2Query: Reliable and Scalable MS2 Mass Spectral-based Analogue Search
Authors: de Jonge Niek F. , Louwen Joris R. , Chekmeneva Elena , Camuzeaux Stephane , Vermeir Femke J. , Jansen Robert S. , Huber Florian , van der Hooft Justin J.J.
Published: July 2022

Metabolomics-driven discoveries of biological samples remain hampered by the grand challenge of metabolite annotation and identification. Only few metabolites have an annotated spectrum in spectral libraries; hence, searching only for exact library matches generally returns a few hits. An attractive alternative is searching for so-called analogues as a starting point for structural annotations; analogues are library molecules which are not exact matches, but display a high chemical similarity. However, current analogue search implementations are not yet very reliable and relatively slow. Here, we present MS2Query, a machine learning-based tool that integrates mass spectral embedding-based chemical similarity predictors (Spec2Vec and MS2Deepscore) as well as detected precursor masses to rank potential analogues and exact matches. Benchmarking MS2Query on reference mass spectra and experimental case studies demonstrates an improved reliability and scalability. Thereby, MS2Query offers exciting opportunities for further increasing the annotation rate of complex metabolite mixtures and for discovering new biology.
Paralog Explorer: a resource for mining information about paralogs in common research organisms
Authors: Hu Yanhui , Ewen-Campen Ben , Comjean Aram , Rodiger Jonathan , Mohr Stephanie E. , Perrimon Norbert
Published: July 2022

Paralogs are genes which arose via gene duplication, and when such paralogs retain overlapping or redundant function, this poses a challenge to functional genetics research. Recent technological advancements have made it possible to systematically probe gene function for redundant genes using dual or multiplex gene perturbation, and there is a need for a simple bioinformatic tool to identify putative paralogs of a gene(s) of interest. We have developed Paralog Explorer (https://www.flyrnai.org/tools/paralogs/), an online resource that allows researchers to quickly and accurately identify candidate paralogous genes in the genomes of the model organisms D. melanogaster, C. elegans, D. rerio, M. musculus, and H. sapiens. Paralog Explorer deploys an effective between-species ortholog prediction software, DIOPT, to analyze within-species paralogs. Paralog Explorer allows users to identify candidate paralogs, and to navigate relevant databases regarding gene co-expression, protein-protein and genetic interaction, as well as gene ontology and phenotype annotations. Altogether, this tool extends the value of current ortholog prediction resources by providing sophisticated features useful for identification and study of paralogous genes.
Adiponectin Reverses β-Cell Damage and Impaired Insulin Secretion Induced by Obesity
Authors: Munhoz Ana Cláudia , Serna Julian D. C. , Vilas-Boas Eloisa Aparecida , da Silva Camille C. Caldeira , dos Santos Tiago Goss , Mosele Francielle C. , Felisbino Sergio L. , Martins Vilma Regina , Kowaltowski Alicia J.
Published: July 2022

Obesity significantly decreases life expectancy and increases the incidence of age-related dysfunctions, including β-cell dysregulation leading to inadequate insulin secretion. Here, we show that diluted plasma from obese human donors acutely impairs β-cell integrity and insulin secretion relative to plasma from lean subjects. Similar results were observed with diluted sera from obese rats fedad libitum, when compared to sera from lean, calorically-restricted, animals. The damaging effects of obese circulating factors on β-cells occurs in the absence of nutrient overload, and mechanistically involves mitochondrial dysfunction, limiting glucose-supported oxidative phosphorylation and ATP production. We demonstrate that increased levels of adiponectin, as found in lean plasma, are the protective characteristic preserving β-cell function; indeed, sera from adiponectin knockout mice limits β-cell metabolic fluxes relative to controls. Furthermore, oxidative phosphorylation and glucose-sensitive insulin secretion, which are completely abrogated in the absence of this hormone, are restored by the presence of adiponectin alone, surprisingly even in the absence of other serological components, for both the insulin-secreting INS1 cell line and primary islets. The addition of adiponectin to cells treated with plasma from obese donors completely restored β-cell functional integrity, indicating the lack of this hormone was causative of the dysfunction. Overall, our results demonstrate that low circulating adiponectin is a key damaging element for β-cells, and suggest strong therapeutic potential for the modulation of the adiponectin signaling pathway in the prevention of age-related β-cell dysfunction.

Abstract Figure

Graphical Abstract:

Incubation of β-cells with sera or plasma from obese rats and humans hampers mitochondrial oxidative phosphorylation and glucose-stimulated insulin secretion (GSIS) relative to sera and plasma from lean rats and humans. Adiponectin, found at elevated levels in lean subjects, supports β-cell function on its own, in the absence of sera, and also reverses the effects of obese plasma. Prepared using Biorender.com.
GLUT1 is redundant in hypoxic and glycolytic nucleus pulposus cells of the intervertebral disc
Authors: Johnston Shira N. , Silagi Elizabeth S. , Madhu Vedavathi , Nguyen Duc H. , Shapiro Irving M. , Risbud Makarand V.
Published: July 2022

Glycolysis is central to homeostasis of nucleus pulposus (NP) cells in the avascular intervertebral disc. Since the glucose importer, GLUT1, is a highly enriched phenotypic marker of NP cells, we hypothesized that it is vital for the development and post-natal maintenance of the disc. Surprisingly, primary NP cells treated with two well-characterized GLUT1 inhibitors maintained normal rates of glycolysis and ATP production, indicating intrinsic compensatory mechanisms. We show in vitro that NP cells mitigate GLUT1 loss by rewiring glucose import through GLUT3. Noteworthy, we demonstrate that substrates, such as glutamine and palmitate, do not compensate for glucose restriction resulting from dual inhibition of GLUT1/3 and inhibition compromises long-term cell viability. To investigate the redundancy of GLUT1 function in NP, we generated two NP-specific knockout mice: Krt19CreERT; Glut1f/fand Foxa2Cre; Glut1f/f. Noteworthy, there were no apparent defects in post-natal disc health or development and maturation in mutant mice. Microarray analysis confirmed that GLUT1 loss did not cause transcriptomic alterations in the NP, supporting that cells are refractory to GLUT1 loss. These observations provide the first evidence of functional redundancy in GLUT transporters in the physiologically hypoxic intervertebral disc and underscore the importance of glucose as the indispensable substrate for NP cells.
Systematic integration of protein affecting mutations, gene fusions, and copy number alterations into a comprehensive somatic mutational profile
Authors: Striker Shawn S , Wilferd Sierra F , Lewis Erika M , O’Connor Samantha A , Plaisier Christopher L
Published: July 2022

Somatic mutations occur as random genetic changes in genes through protein-affecting mutations (PAMs), gene fusions, or copy number alterations (CNAs). Mutations of different types can have a similar phenotypic effect (i.e., allelic heterogeneity) and should be integrated into a unified gene mutation profile. We developed OncoMerge to fill this niche of integrating somatic mutations to capture allelic heterogeneity, assign a function to mutations, and overcome known obstacles in cancer genetics. Application of OncoMerge to the TCGA Pan-Cancer Atlas increased the number and frequency of somatically mutated genes and improved the prediction of the somatic mutation role as either activating or loss of function. Using integrated somatic mutation matrices increased the power to infer gene regulatory networks and uncovered the enrichment of switch-like feedback motifs and delay-inducing feed-forward loops. These studies demonstrate that OncoMerge efficiently integrates PAMs, fusions, and CNAs and strengthens downstream analyses linking somatic mutations to cancer phenotypes.

Motivation

Genes are mutated in tumors through either PAMs, CNAs, or gene fusions, thereby splitting the signal of the somatic mutation effect across these three mutation types. We developed OncoMerge to systematically integrate the three mutation types into a single mutation profile that better captures the impact of somatic mutations on cancer phenotypes. As a tool OncoMerge fills the gap between the sophisticated variant calling pipelines and downstream analyses.