bluuebunny/crossref_metadata_2025 huggingface dataset:
Long-read error correction: a survey and qualitative comparison
Authors: Morisse Pierre , Lecroq Thierry , Lefebvre Arnaud
Published: March 2020

Third generation sequencing technologies Pacific Biosciences and Oxford Nanopore Technologies were respectively made available in 2011 and 2014. In contrast with second generation sequencing technologies such as Illumina, these new technologies allow the sequencing of long reads of tens to hundreds of kbp. These so called long reads are particularly promising, and are especially expected to solve various problems such as contig and haplotype assembly or scaffolding, for instance. However, these reads are also much more error prone than second generation reads, and display error rates reaching 10 to 30%, according to the sequencing technology and to the version of the chemistry. Moreover, these errors are mainly composed of insertions and deletions, whereas most errors are substitutions in Illumina reads. As a result, long reads require efficient error correction, and a plethora of error correction tools, directly targeted at these reads, were developed in the past ten years. These methods can adopt a hybrid approach, using complementary short reads to perform correction, or a self-correction approach, only making use of the information contained in the long reads sequences. Both these approaches make use of various strategies such as multiple sequence alignment, de Bruijn graphs, Hidden Markov Models, or even combine different strategies. In this paper, we describe a complete survey of long-read error correction, reviewing all the different methodologies and tools existing up to date, for both hybrid and self-correction. Moreover, the long reads characteristics, such as sequencing depth, length, error rate, or even sequencing technology, have huge impacts on how well a given tool or strategy performs, and can thus drastically reduce the correction quality. We thus also present an in-depth benchmark of available long-read error correction tools, on a wide variety of datasets, composed of both simulated and real data, with various error rates, coverages, and read lengths, ranging from small bacterial to large mammal genomes.
Long-term T cell fitness and proliferation is driven by AMPK-dependent regulation of oxygen reactive species
Authors: Lepez Anouk , Pirnay Tiphène , Denanglaire Sébastien , Perez-Morga David , Vermeersch Marjorie , Leo Oberdan , Andris Fabienne
Published: March 2020

The AMP-activated kinase (AMPK) is a major energy sensor metabolic enzyme that is activated early during T cell immune responses but its role in the generation of effector T cells is still controversial.

Using bothin vitroandin vivomodels of T cell proliferation, we show herein that AMPK is dispensable for early TCR signaling and short-term proliferation but required for sustained long-term T cell proliferation and effector / memory T cell survival. In particular, AMPK promoted accumulation of effector / memory T cells in competitive homeostatic proliferation settings. Transplantation of AMPK-deficient hematopoïetic cells into allogeneic host recipients led to a reduced graft-versus-host disease, further bolstering a role for AMPK in the expansion and pathogenicity of effector T cells.

Mechanistically, AMPK expression enhances the mitochondrial membrane potential of T cells, limits reactive oxygen species (ROS) production, and resolves ROS-mediated toxicity. Moreover, dampening ROS production alleviates the proliferative defect of AMPK-deficient T cells, therefore indicating a role for an AMPK-mediated ROS control of T cell fitness.
Repeatable differences in exploratory behaviour predict tick infestation probability in wild great tits
Authors: Rollins Robert E. , Mouchet Alexia , Margos Gabriele , Fingerle Volker , Becker Noémie S. , Dingemanse Niels J.
Published: March 2020

Ticks are parasites that feed on the blood of various vertebrate hosts, including many species of bird. Birds can disperse ticks over short and long distances, therefore impacting tick population dynamics. The likelihood that birds attract ticks should depend on their behaviour and the environment. We studied various key ecological variables (breeding density, human disturbance) and phenotypic traits (exploratory behaviour; body condition) proposed to predict tick burden in great tits (Parus major). Our study spanned over three years and 12 human-recreated plots, equipped with nest-boxes in southern Germany. Adult breeders were assessed for exploratory behaviour, tick burden, and body condition. For each plot, human disturbance was quantified as a human recreational pressure index during biweekly nest box inspections by scoring the number of recreants using the plots. Infestation probability but not tick burden increased with exploratory behaviour. We also found moderate support for a positive effect of recreational pressure on infestation probability. Further, body condition negatively predicted tick burden. Individuals were repeatable in tick burden across years. Our study implies that infestation probability and tick burden are governed by distinct ecological and phenotypic drivers. Our findings also highlight the importance of incorporating ecological and individual variation in host phenotypes to predict spatiotemporal distributions of ticks in nature. (207/250-word limit)

Lay Summary

Ticks use many birds as hosts, but why do some individuals have more or fewer ticks? Using a data collected over three years on great tit adults inhabiting 12 different nest-box plots, we showed that more explorative birds and those in highly recreated habitats were more likely to be infested with ticks. Exploratory behaviour and human disturbance could modify great tit habitat choice and, therefore, impact how often a birds and ticks encounter each other.
Dynamics of protein binding to sites of nascent unscheduled DNA repair synthesis in non-proliferating cells
Authors: Scalera Claudia , Dutto Ilaria , Barbazza Francesca , Abou Khouzam Raefa , Ticli Giulio , Cazzalini Ornella , Stivala Lucia A. , Prosperi Ennio
Published: March 2020

The analysis of DNA repair mechanisms is of fundamental importance to understand how cells remove DNA damage and maintain their genome stability. Investigating the dynamic association of proteins at sites of active DNA synthesis has been successfully performed at DNA replication forks, providing important information on the process, and allowing the identification of new players acting at these sites. However, the applicability of these studies to DNA repair events at sites of nascent unscheduled DNA synthesis (UDS) in non-proliferating cells has been never tested. Here, we describe the analysis of dynamics association of protein participating in nucleotide excision repair (NER), and in other DNA repair processes, at sites of nascent UDS in non-proliferating cells, to avoid interference by DNA replication. Labeling with 5-ethynyl-2’-deoxyuridine (EdU) after DNA damage, followed by click reaction to biotinylate these sites, permits the analysis of dynamic association of proteins, such as DNA polymerases δ and κ, as well as PCNA, to active DNA repair synthesis sites. The suitability of this technique to identify new factors present at active UDS sites is illustrated by two examples of proteins previously unknown to participate in the UV-induced DNA repair process.
Homologous organization of cerebellar pathways to sensory, motor, and associative forebrain
Authors: Pisano Thomas J. , Dhanerawala Zahra M. , Kislin Mikhail , Bakshinskaya Dariya , Engel Esteban A. , Hansen Ethan J. , Hoag Austin T. , Lee Junuk , de Oude Nina L. , Venkataraju Kannan Umadevi , Verpeut Jessica L. , Hoebeek Freek E. , Richardson Ben D. , Boele Henk-Jan , Wang Samuel S.-H.
Published: March 2020

Cerebellar outputs take polysynaptic routes to reach the rest of the brain, impeding conventional tracing. Here we quantify pathways between cerebellum and forebrain using transsynaptic tracing viruses and a whole-brain quantitative analysis pipeline. Retrograde tracing found a majority of descending paths originating from somatomotor cortex. Anterograde tracing of ascending paths encompassed most thalamic nuclei, especially ventral posteromedial, lateral posterior, mediodorsal, and reticular nuclei; in neocortex, sensorimotor regions contained the most labeled neurons, but higher densities were found in associative areas, including orbital, anterior cingulate, prelimbic, and infralimbic cortex. Patterns of ascending expression correlated with c-Fos expression after optogenetic inhibition of Purkinje cells. Our results reveal homologous networks linking single areas of cerebellar cortex to diverse forebrain targets. We conclude that shared areas of cerebellum are positioned to provide sensory-motor information to regions implicated in both movement and nonmotor function.

Graphical Abstract
Mechanosensing through direct binding of tensed F-actin by LIM domains
Authors: Sun Xiaoyu , Phua Donovan Y. Z. , Axiotakis Lucas , Smith Mark A. , Blankman Elizabeth , Gong Rui , Cail Robert C. , Espinosa de Los Reyes Santiago , Beckerle Mary C. , Waterman Clare M. , Alushin Gregory M.
Published: March 2020

Mechanical signals transmitted through the cytoplasmic actin cytoskeleton must be relayed to the nucleus to control gene expression. LIM domains are protein-protein interaction modules found in cytoskeletal proteins and transcriptional regulators; however, it is unclear if there is a direct link between these two functions. Here we identify three LIM protein families (zyxin, paxillin, and FHL) whose members preferentially localize to the actin cytoskeleton in mechanically-stimulated cells through their tandem LIM domains. A minimal actin-myosin reconstitution system reveals that representatives of all three families directly bind F-actin only in the presence of mechanical force. Point mutations at a site conserved in each LIM domain of these proteins selectively disrupt tensed F-actin bindingin vitroand cytoskeletal localization in cells, demonstrating a common, avidity-based mechanism. Finally, we find that binding to tensed F-actin in the cytoplasm excludes the cancer-associated transcriptional co-activator FHL2 from the nucleus in stiff microenvironments. This establishes direct force-activated F-actin binding by FHL2 as a mechanosensing mechanism. Our studies suggest that force-dependent sequestration of LIM proteins on the actin cytoskeleton could be a general mechanism for controlling nuclear localization to effect mechanical signaling.
A method for large scale implantation of 3D microdevice ensembles into brain and soft tissue
Authors: Sigurdsson Stefan A. , Yu Zeyang , Lee Joonhee , Nurmikko Arto
Published: March 2020

Wireless networks of implantable electronic sensors and actuators on the microscale (sub-mm) are being explored for monitoring and modulation of physiological activity for medical diagnostics and therapeutic purposes. Beyond the requirement of integrating multiple electronic or chemical functions within small device volumes, a key challenge is the development of high-throughput methods for implantation of large numbers of microdevices into soft tissues with minimal damage. To that end, we have developed a method for high-throughput implantation of ∼100-200 μm size devices which are here simulated by proxy microparticle ensembles. While generally applicable to subdermal tissue, our main focus and experimental testbed is the implantation of microparticles into the brain. The method deploys a scalable delivery tool composed of a 2-dimensional array of polyethylene glycol tipped microneedles which confine the microparticle payloads. Upon dissolution of the bioresorbable polyethylene glycol, the supporting array structure is retrieved and the microparticles remain embedded in the tissue, distributed spatially and geometrically according to the design of the microfabricated delivery tool. We first evaluated the method in an agarose testbed in terms of spatial precision and throughput for up to 1000 passive spherical and planar microparticles acting as proxy devices. We then performed the same evaluations of particles implanted into the rat cortex under acute conditions and assessed the tissue injury produced by our method of implantation under chronic conditions.
Frequency-dependent interactions determine outcome of competition between two breast cancer cell lines
Authors: Freischel Audrey R. , Damaghi Mehdi , Cunningham Jessica J. , Ibrahim-Hashim Arig , Gillies Robert J. , Gatenby Robert A. , Brown Joel S.
Published: March 2020

Tumors are highly dynamic ecosystems in which diverse cancer cell subpopulations compete for space and resources. These complex, often non-linear interactions govern continuous spatial and temporal changes in the size and phenotypic properties of these subpopulations. Because intra-tumoral blood flow is often chaotic, competition for resources may be a critical selection factor in progression and prognosis. Here, we quantify resource competition using 3D spheroid cultures with MDA-MB-231 and MCF-7 breast cancer cells. We hypothesized that MCF-7 cells, which primarily rely on efficient aerobic glucose metabolism, would dominate the population under normal pH and low glucose conditions; and MDA-MB-231 cells, which exhibit high levels of glycolytic metabolism, would dominate under low pH and high glucose conditions. In spheroids with single populations, MCF-7 cells exhibited equal or superior intrinsic growth rates (density-independent measure of success) and carrying capacities (density-dependent measure of success) when compared to MDA-MB-231 cells under all pH and nutrient conditions. Despite these advantages, when grown together, MCF-7 cells do not always outcompete MDA-MB-231 cells. MDA-MB-231 cells outcompete MCF-7 cells in low glucose conditions and coexistence is achieved in low pH conditions. Under all conditions, MDA-MB-231 has a stronger competitive effect (frequency-dependent interaction) on MCF-7 cells than vice-versa. This, and the inability of growth rate or carrying capacity when grown individually to predict the outcome of competition, suggests a reliance on frequency-dependent interactions and the need for competition assays. We frame these results in a game-theoretic (frequency-dependent) model of cancer cell interactions and conclude that competition assays can demonstrate critical density-independent, density-dependent and frequency-dependent interactions that likely contribute toin vivooutcomes.

Highlights

Demonstrate how mixed-culture spheroids must be used to characterize competition between two cancer cell lines.

Competition alters growth dynamics of cancer cells.

Competition growth models can be used to quantify density-independent, density-dependent and frequency-dependent effects on competition.

Competition affects tumor progression and structure, making it key to understanding tumor development and evolution.
HumanMETTL7BEncodes an Alkyl Thiol Methyltransferase that Methylates Hydrogen Sulfide
Authors: Maldonato Benjamin J. , Totah Rheem A.
Published: March 2020

Summary Paragraph/Abstract

Methyltransferase-like protein 7B (METTL7B) is implicated in tumor growth and progression while gene expression is upregulated in several different disease states such as rheumatoid arthritis and breast cancer. Yet, the catalytic function of METTL7B has not been characterized. Here we demonstrate thatMETTL7Bencodes a protein that catalyzes the transfer of a methyl group from S-adenosyl-L-methionine (SAM) to hydrogen sulfide (H2S) to form methanethiol (CH3SH). Several exogenous aliphatic thiols were also identified as substrates. Modulation ofMETTL7Bgene expression in HepG2 and HeLa cell culture directly alters the methylation of captopril, a marker reaction of alkyl thiol methyltransferase (TMT) activity(1, 2). Furthermore, cloned and recombinantly expressed and purified METTL7B full length protein methylates several thiol compounds, including hydrogen sulfide, 7α-thiospironolactone, captopril, and L-penicillamine in a concentration dependent manner. Endogenous thiols such as glutathione and cysteine or classic probe substrates of other known small moleculeS-,N-, andO- methyltransferases were not substrates for METTL7B. Our results unequivocally demonstrate, and for the first time, that METTL7B, a protein implicated in several disease states, is an alkyl thiol methyltransferase(3–5). Identifying the catalytic function of METTL7B will enable future pharmacological research in disease pathophysiology whereMETTL7Bexpression and H2S levels can potentially alter the redox state and growth cycle of cells.
Adhesion-mediated mechanosignaling forces mitohormesis
Authors: Tharp Kevin M. , Higuchi-Sanabria Ryo , Timblin Greg A. , Ford Breanna , Garzon-Coral Carlos , Schneider Catherine , Muncie Jonathon M. , Stashko Connor , Daniele Joseph R. , Moore Andrew S. , Frankino Phillip A. , Manoli Sagar S. , Shao Hao , Richards Alicia L. , Chen Kuei-Ho , Ku Gregory M. , Hellerstein Marc , Nomura Daniel K. , Saijo Karou , Gestwicki Jason , Dunn Alexander R. , Krogan Nevan J. , Swaney Danielle L. , Dillin Andrew , Weaver Valerie M.
Published: March 2020

Mitochondria control eukaryotic cell fate by producing the energy needed to support life and the signals required to execute programmed cell death. The biochemical milieu is known to affect mitochondrial function and contribute to the dysfunctional mitochondrial phenotypes implicated in cancer and the morbidities of ageing. However, the physical characteristics of the extracellular matrix are also altered in cancer and in aging tissues. We demonstrate that cells sense the physical properties of the extracellular matrix and activate a mitochondrial stress response that adaptively tunes mitochondrial functionviaSLC9A1-dependent ion exchange and HSF1-dependent transcription. Overall, our data indicate that adhesion-mediated mechanosignaling may play an unappreciated role in the altered mitochondrial functions observed in aging and cancer.

Graphical Abstract
A validated quantitative method for the assessment of neuroprotective barrier impairment in neurodegenerative disease models
Authors: Kumar Vinod , Lee John D. , Coulson Elizabeth J. , Woodruff Trent M.
Published: March 2020

The blood brain barrier (BBB) and blood spinal cord barrier (BSCB) are highly specialised structures that limit molecule entry from the blood and maintain homeostasis within the central nervous system (CNS). BBB and BSCB breakdown are associated with multiple neurodegenerative diseases. Given the key role of neuroprotective barrier impairment in neurodegeneration, it is important to identify an effective quantitative method to assess barrier integrity in animal models. In the present study, we developed and validated a quantitative method for assessing BBB and BSCB integrity using sodium fluorescein, a compound that outperformed other fluorescent dyes. We demonstrated using this method that multiple CNS regions progressively increase in permeability in models of Huntington’s disease and amyotrophic lateral sclerosis, while biphasic disruption occurred in a mouse model of Alzheimer’s disease with disease progression. Collectively, we report a quantitative fluorometric marker with validated reproducible experimental methods, that allows the effective assessment of BBB and BSCB integrity in animal models. This method could be useful to further the understanding of the contribution of these neuroprotective barriers to neurodegeneration processes.
Monoclonal antibodies for the S2 subunit of spike of SARS-CoV cross-react with the newly-emerged SARS-CoV-2
Authors: Zheng Zhiqiang , Monteil Vanessa M. , Maurer-Stroh Sebastian , Yew Chow Wenn , Leong Carol , Mohd-Ismail Nur Khairiah , Arularasu Suganya Cheyyatraivendran , Chow Vincent Tak Kwong , Pin Raymond Lin Tzer , Mirazimi Ali , Hong Wanjin , Tan Yee-Joo
Published: March 2020

The emergence of a novel coronavirus, SARS-CoV-2, at the end of 2019 has resulted in widespread human infections across the globe. While genetically distinct from SARS-CoV, the etiological agent that caused an outbreak of severe acute respiratory syndrome (SARS) in 2003, both coronaviruses exhibit receptor binding domain (RBD) conservation and utilize the same host cell receptor, angiotensin-converting enzyme 2 (ACE2), for virus entry. Therefore, it will be important to test the cross-reactivity of antibodies that have been previously generated against the surface spike (S) glycoprotein of SARS-CoV in order to aid research on the newly emerged SARS-CoV-2. Here, we show that an immunogenic domain in the S2 subunit of SARS-CoV S is highly conserved in multiple strains of SARS-CoV-2. Consistently, four murine monoclonal antibodies (mAbs) raised against this immunogenic SARS-CoV fragment were able to recognise the S protein of SARS-CoV-2 expressed in a mammalian cell line. Importantly, one of them (mAb 1A9) was demonstrated to detect S in SARS-CoV-2-infected cells. To our knowledge, this is the first study showing that mAbs targeting the S2 domain of SARS-CoV can cross-react with SARS-CoV-2 and this observation is consistent with the high sequence conservation in the S2 subunit. These cross-reactive mAbs may serve as tools useful for SARS-CoV-2 research as well as for the development of diagnostic assays for its associated coronavirus disease COVID-19.
Transcriptome analysis of the NematodeCaenorhabditis elegansin acidic stress environments
Authors: Cong Yanyi , Yang Hanwen , Zhang Pengchi , Xie Yusu , Cao Xuwen , Zhang Liusuo
Published: March 2020

Ocean acidification and acid rain, caused by modern industrial fossil fuels burning, lead to decrease of living environmental pH, which results in a series of negative effects on many organisms. However, the underlying mechanisms of animals’response to acidic pH stress are largely unknown. In this study, we used the nematodeCaenorhabditis elegansas an animal model to explore the regulatory mechanisms of organisms’response to pH decline. Two major stress-responsive pathways were found through transcriptome analysis in acidic stress environments. Firstly, when the pH dropped from 6.33 to 4.33, the worms responded to the pH stress by up-regulation of thecol,nasanddpygenes, which are required for cuticle synthesis and structure integrity. Secondly, when the pH continued to decrease from 4.33, the metabolism of xenobiotics by cytochrome P450 pathway genes (cyp, gst, ugt,and ABC transporters) played a major role in protecting the nematodes from the toxic substances probably produced by the more acidic environment. At the same time, cuticle synthesis slowed down might due to its insufficient protective ability. Moreover, the systematic regulation pattern we found in nematodes, might also be applied to other invertebrate and vertebrate animals to survive in the changing pH environments. Thus, our data might lay the foundation to identify the master gene(s) responding and adaptation to acidic pH stress in further studies, and might also provide new solutions to improve assessment and monitoring of ecological restoration outcomes, or generate novel genotypes via genome editing for restoring in challenging environments especially in the context of acidic stress through global climate change.
Rcirc: an R package for circRNA analyses and visualization
Authors: Sun Peisen , Wang Haoming , Li Guanglin
Published: March 2020

Circular RNA (circRNA), which has a closed-loop structure, is a kind of special endogenous RNA and plays important roles in many biological processes. With the improvement of next-generation sequencing technology and bioinformatics methods, some tools have been published for circRNA detection based on RNA-seq. However, only a few tools focus on downstream analyses, and they have poor visualization ability. Here, we developed the R package ‘Rcirc’ for further analyses of circRNA after its detection. Rcirc identifies the coding ability of circRNA and visualize various aspects of this feature. It also provides general visualization for both single circRNAs and meta-features of thousands of circRNAs. Rcirc was designed as a user-friendly tool that covers many highly automatic functions without running many complicated processes by users. It is available on GitHub (https://github.com/PSSUN/Rcirc) under the license GPL 3.0.
Deep learning-based adaptive detection of fetal nucleated red blood cells
Authors: Sun Chao , Wang Ruijie , Zhao Lanbo , Han Lu , Ma Sijia , Liang Dongxin , Wang Lei , Tuo Xiaoqian , Zhong Dexing , Li Qiling
Published: March 2020

Aim

this study, we established an artificial intelligence system for rapid identification of fetal nucleated red blood cells (fNRBCs).

Method

Density gradient centrifugation and magnetic-activated cell sorting were used for the separation of fNRBCs from umbilical cord blood. The cell block technique was used for fixation. We proposed a novel preprocessing method based on imaging characteristics of fNRBCs for region of interest (ROI) extraction, which automatically segmented individual cells in peripheral blood cell smears. The discriminant information from ROIs was encoded into a feature vector and pathological diagnosis were provided by the prediction network.

Results

Four umbilical cord blood samples were collected and validated based on a large dataset containing 260 samples. Finally, the dataset was classified into 3,720 and 1,040 slides for training and testing, respectively. In the test set, classifier obtained 98.5% accuracy and 96.5% sensitivity.

Conclusion

Therefore, this study offers an effective and accurate method for fNRBCs preservation and identification.
Unsupervised cell interaction profiling reveals major architectural differences between small intestinal and colonic epithelial crypts
Authors: Serviss Jason T. , Andrews Nathanael , Andersson Agneta B. , Dzwonkowska Ewa , Heijboer Rosan , Geyer Natalie , Gerling Marco , Enge Martin
Published: March 2020

Cellular identity in complex multicellular organisms is strictly maintained over the course of life. This control is achieved in part by the organ structure itself, such that neighboring cells influence each other’s identity. However, large-scale investigation of the cellular interactome has been technically challenging. Here, we develop CIM-seq, an unsupervised and high-throughput method to analyze direct physical cell-cell interactions between every cell type in a given tissue. CIM-seq is based on RNA sequencing of incompletely dissociated cells, followed by computational deconvolution of these into their constituent cell types using machine learning. We use CIM-seq to define the cell interaction landscape of the mouse small intestinal and colonic epithelium, uncovering both known and novel interactions. Specifically, we find that the general architecture of the stem cell niche is radically different between the two tissues. In small intestine, the stem-Paneth cell interaction forms an exceptionally strong and exclusive niche, in which Paneth cells provide Wnt ligands1. In colonic epithelium, no similar compartment exists to support stem cells, and Wnt signaling is provided by a mesenchymal cell layer2,3. However, colonic stem cells are supported by an adjacent, previously unrecognized goblet cell subtype expressing the wound-healing marker Plet1, which is also highly upregulated during regeneration of colon epithelium. These results identify novel cellular interactions specific for the colonic stem cell niche and suggest an additional level of structural control in the colon. CIM-seq is broadly applicable to studies that aim to simultaneously investigate the constituent cell types and the global interaction profile in a specific tissue.
Metabolic labeling of RNA using multiple ribonucleoside analogs enables simultaneous evaluation of transcription and degradation rates
Authors: Kawata Kentaro , Wakida Hiroyasu , Yamada Toshimichi , Taniue Kenzui , Han Han , Seki Masahide , Suzuki Yutaka , Akimitsu Nobuyoshi
Published: March 2020

Gene expression is one of the factors determining cellular conditions, and its level is determined by the balance between transcription and RNA degradation. However, it has been not well elucidated how transcription and degradation are related to each other. To elucidate the relationship of them, methods enabling simultaneous measurement of transcription and degradation are required. Here, we report the development of “Dyrec-seq” to evaluate transcription and RNA degradation rates simultaneously, by using 4-thiouridine and 5-bromouridine. Using Dyrec-seq, we quantified the transcription and degradation rates of 4,702 genes in HeLa cells. Functional enrichment analysis showed that the transcription and degradation rates of genes are actually determined by the genes’ biological functions. Comparison of theoretical and experimental analysis results revealed that the amount of RNA was determined by the ratio of transcription to degradation rates, while the rapidity of responses to external stimuli was determined only by the degradation rate. This study emphasizes that degradation as well as transcription is important in determining the behavior of RNA.
Photo-excited Toluidine Blue disaggregates the Repeat Tau and modulates cytoskeletal structure in neuronal cells
Authors: Dubey Tushar , Gorantla Nalini Vijay , Chinnathambi Subashchandrabose
Published: March 2020

Alzheimer’s disease is a progressive neurological disorder characterized by the intracellular accumulation of Tau protein aggregates. Inhibition of protein aggregation by photo-excited dyes is emerging as novel strategy for the treatment of certain diseases. Toluidine Blue is a basic phenothiazine dye having potency of photo-excitation by irradiation with red light at 630±20 nm. In present work, we studied the effect of Toluidine Blue and photo-excited TB on aggregation of repeat Tau in-vitrousing Thioflavin S fluorescence assay, SDS-PAGE and electron microscopy. Results show that TB efficiently inhabited the formation of higher order aggregates. Moreover, the photo-excited TB led to disaggregation of the mature repeat Tau fibrils. Further, studies on the effect of Toluidine blue on cell viability and cytoskeleton network of Neuro2acells show that TB was not toxic to neuronal cells at lower concentrations but at high concentrations (> 5 μM) both TB and photo-excited TB induced significant toxicity. Immunofluorescence studies on the cytoskeleton of Neuro2a cells show that Toluidine Blue and photo-excited Toluidine Blue treatment at non-toxic concentration of 0.5 μM stimulated formation of actin rich lamellipodia and filopodia structures. Tubulin networks were also differentially modulated after the treatment of Toluidine Blue and photo-excited Toluidine Blue. End Binding protein 1 (EB1) levels were observed to increase after Toluidine Blue and photo-excited Toluidine Blue treatment indicating the accelerated microtubule polymerization. The overall study suggested that Toluidine Blue inhibited the aggregation of soluble Tau and photo-excited Toluidine Blue disaggregated the pre-formed Tau filaments.
Unprecedentedly efficient CUG initiation of an overlapping reading frame inPOLGmRNA yields novel protein POLGARF
Authors: Loughran G , Zhdanov AV , Mikhaylova MS , Rozov FN , Datskevich PN , Kovalchuk SI , Serebryakova MV , Kiniry S , Michel AM , O’Connor PBF , Papkovsky DB , Atkins JF , Baranov PV , Shatsky IN , Andreev DE
Published: March 2020

While near cognate codons are frequently used for translation initiation in eukaryotes, their efficiencies are usually low (<10% compared to an AUG in optimal context). Here we describe a rare case of highly efficient near cognate initiation. A CUG triplet located in the 5’ leader ofPOLGmRNA initiates almost as efficiently (~60-70%) as an AUG in optimal context. This CUG directs translation of a conserved 260 triplet-long overlapping ORF, which we callPOLGARF(POLGAlternativeReadingFrame). Translation of a short upstream ORF 5’ of this CUG governs the ratio between DNA polymerase and POLGARF produced from a singlePOLGmRNA. Functional investigation of POLGARF points to extracellular signalling. While unprocessed POLGARF resides in the nucleoli together with its interacting partner C1QBP, serum stimulation results in rapid secretion of POLGARF C-terminal fragment. Phylogenetic analysis shows thatPOLGARFevolved ~160 million years ago due to an MIR transposition into the 5’ leader sequence of the mammalianPOLGgene which became fixed in placental mammals. The discovery ofPOLGARFunveils a previously undescribed mechanism ofde novoprotein-coding gene evolution.

Significance Statement

In this study, we describe previously unknown mechanism ofde novoprotein-coding gene evolution. We show that thePOLGgene, which encodes the catalytic subunit of mitochondrial DNA polymerase, is in fact a dual coding gene. Ribosome profiling, phylogenetic conservation, and reporter construct analyses all demonstrate thatPOLGmRNA possesses a conserved CUG codon which serves as a start of translation for an exceptionally long overlapping open reading frame (260 codons in human) present in all placental mammals. We called the protein encoded in this alternative reading frame POLGARF. We provide evidence that the evolution ofPOLGARFwas incepted upon insertion of an MIR transposable element of the SINE family.
Irgm2 and Gate-16 cooperatively dampen targeting of caspase-11 to Gram-negative bacterial products
Authors: Eren Elif , Planès Rémi , Bagayoko Salimata , Bordignon Pierre-Jean , Chaoui Karima , Hessel Audrey , Santoni Karin , Pinilla Miriam , Burlet-Schiltz Odile , Howard Jonathan C. , Yamamoto Masahiro , Meunier Etienne
Published: March 2020

Inflammatory caspase-11 (rodent) and caspases-4 and -5 (human) detect gram-negative bacterial component LPS in the host cell cytosol, which promotes activation of the non-canonical inflammasome. Although non-canonical inflammasome-induced pyroptosis and IL-1 related cytokine release is of importance to mount an efficient immune response against various bacteria, its unrestrained activation drives sepsis. This suggests that cellular components might tightly control the threshold level of the non-canonical inflammasome in order to ensure efficient but not deleterious inflammatory response. Here we show that the IFN-inducible protein Irgm2 and the ATG8 family member Gate-16 cooperatively slow down non-canonical inflammasome activation both in macrophages andin vivo. Specifically, the Irgm2/Gate-16 axis dampens caspase-11 targeting to intracellular bacteria, which lower caspase-11-mediated pyroptosis and cytokine release. Specifically, deficiency inIrgm2orGate16opens an alternative road for caspase-11 targeting to intracellular bacteria, independently of the classical pathway driven by the Guanylate Binding Proteins (GBPs). Thus, our findings provide new molecular effectors involved at fine-tuning the optimal non-canonical inflammasome response and add novel insights in the understanding of the immune pathways they control.
DMLDA-LocLIFT: Identification of multi-label protein subcellular localization using DMLDA dimensionality reduction and LIFT classifier
Authors: Zhang Qi , Li Shan , Yu Bin , Zhang Qingmei , Zhang Yan , Ma Qin
Published: March 2020

Background

Multi-label proteins occur in two or more subcellular locations, which play a vital part in cell development and metabolism. Prediction and analysis of multi-label subcellular localization (SCL) can present new angle with drug target identification and new drug design. However, the prediction of multi-label protein SCL using biological experiments is expensive and labor-intensive. Therefore, predicting large-scale SCL with machine learning methods has turned into a hot study topic in bioinformatics.

Methods

In this study, a novel multi-label learning means for protein SCL prediction, called DMLDA-LocLIFT, is proposed. Firstly, the dipeptide composition, encoding based on grouped weight, pseudo amino acid composition, gene ontology and pseudo position specific scoring matrix are employed to encode subcellular protein sequences. Then, direct multi-label linear discriminant analysis (DMLDA) is used to reduce the dimension of the fused feature vector. Lastly, the optimal feature vectors are input into the multi-label learning with Label-specIfic FeaTures (LIFT) classifier to predict the location of multi-label proteins.

Results

The jackknife test showed that the overall actual accuracy on Gram-negative bacteria, Gram-positive bacteria, and plant datasets are 98.60%, 99.60%, and 97.90% respectively, which are obviously better than other state-of-the-art prediction methods.

Conclusion

The proposed model can effectively predict SCL of multi-label proteins and provide references for experimental identification of SCL. The source codes and data are publicly available athttps://github.com/QUST-AIBBDRC/DMLDA-LocLIFT/.
Conjugative dissemination of plasmids in rapid sand filters: a trojan horse strategy to enhance pesticide degradation in groundwater treatment
Authors: Pinilla-Redondo Rafael , Olesen Asmus Kalckar , Russel Jakob , de Vries Lisbeth Elvira , Christensen Lisbeth Damkjær , Musovic Sanin , Nesme Joseph , Sørensen Søren Johannes
Published: March 2020

The supply of clean water for human consumption is being challenged by the appearance of pesticide pollutants in groundwater ecosystems. Biological rapid sand filtration is a commonly employed method for the removal of organic and inorganic impurities in water which relies on the degradative properties of microorganisms for the removal of diverse contaminants, including pesticides. Although sustainable and relatively inexpensive, the bioremediation capabilities of rapid sand filters vary greatly across waterworks. Bioaugmentation efforts with degradation-proficient bacteria have proven difficult due to the inability of the exogenous microbes to stably colonize the sand filters. Pesticide degrading genes, however, are often encoded naturally by plasmids—extrachromosomal DNA elements that can transfer between bacteria—yet their ability to spread within rapid sand filters have remained unknown. To evaluate the potential use of plasmids for the dissemination of pesticide degrading genes, we examined the permissiveness of rapid sand filter communities towards four environmental transmissible plasmids; RP4, RSF1010, pKJK5 and TOL (pWWO), using a dual-fluorescent bioreporter platform combined with FACS and 16S rRNA gene amplicon sequencing. Our results reveal that plasmids can transfer at high frequencies and across distantly related taxa from rapid sand filter communities, emphasizing their suitability for introducing pesticide degrading determinants in the microbiomes of underperforming water purification plants.
Altered Sensorimotor-to-Transmodal Hierarchical Organization in Schizophrenia
Authors: Dong Debo , Yao Dezhong , Wang Yulin , Hong Seok-Jun , Genon Sarah , Xin Fei , Jung Kyesam , He Hui , Chang Xuebin , Duan Mingjun , Bernhardt Boris , Margulies Daniel S. , Sepulcre Jorge , Eickhoff Simon B. , Luo Cheng
Published: March 2020

For decades, schizophrenia has been primarily conceptualized as a disorder of high-order cognitive functions with deficits in executive brain regions. Yet due to the increasing reports of early sensory processing deficit, recent models focus more on the developmental effects of impaired sensory process on high-order functions. The present study examined whether this pathological interaction relates to an overarching system-level imbalance, specifically a disruption in macroscale hierarchy affecting integration and segregation of unimodal and transmodal networks. We applied a novel combination of connectome gradient and stepwise connectivity analysis to resting-state functional magnetic resonance imaging (rsfMRI) to characterize the sensorimotor-to-transmodal cortical hierarchy organization (96 patients vs. 122 controls). Using these techniques, we demonstrated compression of the cortical hierarchy organization in schizophrenia, with a prominent compression from the sensorimotor region and a less prominent compression from the frontal-parietal region, resulting in a diminished separation between sensory and fronto-parietal cognitive systems. Further analyses suggested reduced differentiation related to atypical functional connectome transition from unimodal to transmodal brain areas. Specifically, we found hypo-connectivity within unimodal regions and hyper-connectivity between unimodal regions and frontoparietal and ventral attention regions along the classical sensation-to-cognition continuum established in prior neuroanatomical work. The compression of cortical hierarchy organization represents a novel and integrative system-level substrate underlying the pathological interaction of early sensory and cognitive function in schizophrenia. This abnormal cortical hierarchy organization suggests cascaded impairments stemming from the disrupted somatosensory-motor system and inefficient integration of bottom-up sensory information with attentional demands and executive control processes partially account for high-level cognitive deficits characteristic of schizophrenia.
Rapid mechanoenzymatic saccharification of lignocellulosic biomass without bulk water or chemical pre-treatment
Authors: Hammerer Fabien , Ostadjoo Shaghayegh , Dietrich Karolin , Dumont Marie-Josée , Del Rio Luis F. , Friščić Tomislav , Auclair Karine
Published: March 2020

Lignocellulosic material is an abundant renewable resource with the potential to replace petroleum as a feedstock for the production of fuels and chemicals. The large scale deployment of biomass saccharification is, however, hampered by the necessity to use aggressive reagents and conditions, formation of side-products, and the difficulty to reach elevated monosaccharide concentrations in the crude product. Herein we report the high efficacy of Reactive Aging (or Raging, a technique where enzymatic reaction mixtures, without any bulk aqueous or organic solvent, are treated to multiple cycles of milling and aging) for gram-scale saccharification of raw lignocellulosic biomass samples from different agricultural sources (corn stover, wheat straw, and sugarcane bagasse). The solvent-free enzymatic conversion of lignocellulosic biomass was found to proceed in excellent yields (ca. 90%) at protein loadings as low as 2% w/w, without the need for any prior chemical pre-treatment or high temperatures, to produce highly concentrated (molar) monosaccharides. This crude product of mechanoenzymatic depolymerization is non-toxic to bacteria and can be used as a carbon source for bacterial growth.
Evolutionarily diverse LIM domain-containing proteins bind stressed actin filaments through a conserved mechanism
Authors: Winkelman Jonathan D. , Anderson Caitlin A. , Suarez Cristian , Kovar David R. , Gardel Margaret L.
Published: March 2020

The actin cytoskeleton assembles into diverse load-bearing networks including stress fibers, muscle sarcomeres, and the cytokinetic ring to both generate and sense mechanical forces. The LIM (Lin11, Isl-1 & Mec-3) domain family is functionally diverse, but most members can associate with the actin cytoskeleton with apparent force-sensitivity. Zyxin rapidly localizes via its LIM domains to failing stress fibers in cells, known as strain sites, to initiate stress fiber repair and maintain mechanical homeostasis. The mechanism by which these LIM domains associate with stress fiber strain sites is not known. Additionally, it is unknown how widespread strain sensing is within the LIM protein family. We observe that many, but not all, LIM domains from functionally diverse proteins localize to spontaneous or induced stress fiber strain sites in mammalian cells. Additionally, the LIM domain region from the fission yeast protein paxillin like 1 (Pxl1) also localizes to stress fiber strain sites in mammalian cells, suggesting that the strain sensing mechanism is ancient and highly conserved. Sequence analysis and mutagenesis of the LIM domain region of zyxin indicate a requirement of tandem LIM domains, which contribute additively, for sensing stress fiber strain sites.In vitro, purified LIM domains from mammalian zyxin and fission yeast Pxl1 bind to mechanically stressed F-actin networks but do not associate with relaxed actin filaments. We propose that tandem LIM domains recognize an F-actin conformation that is rare in the relaxed state but is enriched in the presence of mechanical stress.
Understanding the adaptive evolution of mitochondrial genomes in intertidal chitons
Authors: Dhar Dipanjana , Dey Debayan , Basu Soumalee , Fortunato Helena
Published: March 2020

Mitochondria are the centre of energy metabolism in eukaryotic cells and its genes are thus key to the evolution of molecular mechanisms that metabolize cellular energy. Intertidal zone is one of the most stressful environments with extreme shifts in temperature, salinity, pH and oxygen concentrations. Marine molluscs, particularly chitons belong to the ecologically dominant organisms in this extreme environment, symbolizing an ideal model to understand mitochondrial stress adaptation. Here, we used concatenated mitochondrial genetic components separately from seven chitons of the intertidal zone to reconstruct phylogenetic relationships among these species. We performed selection analyses considering sites and branches of individual protein-coding genes to identify potentially adaptive residues and localize them in the protein structures of mt subunits. Our results exhibited significant amino acid changes in sites under diversifying selection of all the protein-coding genes, indicative of the adaptive evolution of mitochondrial genome in chitons. Furthermore, we obtained sites in the transmembrane helices lining the proton translocation channel as well as in surrounding loop regions, providing implication towards functional modification of the OXPHOS proteins essential for survival in dynamic environment of the intertidal zone.