bluuebunny/crossref_metadata_2025 huggingface dataset:
Anthropogenic disturbance impacts gut microbiome homeostasis in a Malagasy primate
Authors: Wasimuddin  , Malik Hina , Ratovonamana Yedidya R , Rakotondranary S Jacques , Ganzhorn Jörg U. , Sommer Simone
Published: April 2022

Increasing anthropogenic disturbances in Madagascar are exerting constrains on endemic Malagasy lemurs and their habitats, with possible effects on their health and survival. An important component of health is the gut microbiome, which might be disrupted by various stressors associated with environmental change. We have studied the gut microbiome of grey-brown mouse lemurs (Microcebus griseorufus), one of the smallest Malagasy primates and an important model of the convergent evolution of diseases. We sampled two sites: one situated in a national park and the other consisting of a more disturbed site around human settlement. We found that more intense anthropogenic disturbances indeed disrupted the gut microbiome of this lemur species with a marked reduction in its diversity and led to a shift in microbial community composition. Interestingly, we noted a decrease in beneficial bacteria together with a slight increase in disease-associated bacteria and alterations in microbial metabolic functions. Because of the crucial services provided by the microbiome to host health and in disease, such negative alterations in the gut microbiome of the lemur from anthropogenically disturbed habitat might impact the health of mouse lemurs, rendering them susceptible to diseases and ultimately affecting their survival in the shrinking biodiversity seen in Madagascar. Gut microbiome analyses might thus serve as an early warning signal for pending threats to lemur populations.
Sloppiness: fundamental study, new formalism and its application in model assessment
Authors: Jagadeesan Prem , Raman Karthik , Tangirala Arun K
Published: April 2022

Computational modelling of biological processes poses multiple challenges in each stage of the modelling exercise. Some significant challenges include identifiability, precisely estimating parameters from limited data, informative experiments and anisotropic sensitivity in the parameter space. One of these challenges’ crucial but inconspicuous sources is the possible presence of large regions in the parameter space over which model predictions are nearly identical. This property, known as sloppiness, has been reasonably well-addressed in the past decade, studying its possible impacts and remedies. However, certain critical unanswered questions concerning sloppiness, particularly related to its quantification and practical implications in various stages of system identification, still prevail. In this work, we systematically examine sloppiness at a fundamental level and formalise two new theoretical definitions of sloppiness. Using the proposed definitions, we establish a mathematical relationship between the parameter estimates’ precision and sloppiness in linear predictors. Further, we develop a novel computational method and a visual tool to assess the goodness of a model around a point in parameter space by identifying local structural identifiability and sloppiness and finding the most sensitive and least sensitive parameters for non-infinitesimal perturbations. We demonstrate the working of our method in benchmark systems biology models of various complexities. The pharmacokinetic HIV infection model analysis identified a new set of biologically relevant parameters that can be used to control the free virus in an active HIV infection.

Author summary
Persistent pervasive transcription in RNA exosome depleted oocytes results in loss of female fertility
Authors: Wu Di , Dean Jurrien
Published: April 2022

Maturing mammalian oocytes are transcriptionally inactive and attendant RNA degradation determines the maternal transcriptome for embryonic development1. Perturbing oocyte RNA degradation can result in failure of meiosis, fertilization, or zygotic gene activation1-5. We recently reported that conditional depletion of EXOSC10, an RNA exosome associated RNase, blocks oocyte growth-to-maturation transition by interfering with ribosomal RNA processing and meiotic checkpoint genes3. Here we have established oocyte-specific knockout mice of a second RNA exosome associated RNase, Dis3. Mutant females (Dis3cKO) exhibit significantly reduced fertility because oocytes arrest at early maturation. DIS3 depletion allows persistent pervasive transcription, which blocks transcription termination and sequesters RNA polymerase II in intergenic regions. In addition, Dis3cKO oocytes gain H3K27me3 at pre-defined loci6 due to insufficient demethylases KDM6A/B. Oocyte double knockout of Dis3 and Exosc10 causes much earlier growth defects for similar persistence of pervasive transcription, suggesting the RNA exosome complex plays a critical role to ensure transcriptome integrity during oocyte development.
Neuroendocrine control of the proteostatic network by HPK-1 delays aging
Authors: Lazaro-Pena Maria I. , Diaz-Balzac Carlos A. , Das Ritika , Samuelson Andrew V.
Published: April 2022

The nervous system systemically coordinates proteostasis to delay organismal aging. However, the neuronal regulatory mechanisms that coordinate cellular anti-aging programs across tissue and cell-types are relatively unknown. In this work, we identify the homeodomain-interacting protein kinase (HPK-1), a transcriptional cofactor, as a novel neuronal component of the proteostatic network: its overexpression produces a paracrine signal to hyper-induce molecular chaperones and a neuroendocrine signal to induce autophagy in peripheral tissues. Neuronal HPK-1 signaling improves proteostasis in distal tissues through neurotransmitters. These pro-longevity modalities are independently regulated within serotonergic and GABAergic neurons, respectively, through distinct adaptive responses, either of which improve proteostasis in a cell non-autonomous manner. Serotonergic HPK-1 activity amplifies the heat shock response and protects the proteome from acute stress, without altering longevity. Conversely, increased GABAergic HPK-1 activity is sufficient to induce autophagy and extend longevity, without altering acute stress survival. Consistently, GABAergic neurons, but not serotonin, is essential for the cell non-autonomous induction of autophagy by neuronal HPK-1. These findings provide novel insight into how the nervous system partitions and coordinates unique adaptive response pathways to delay organismal aging, and reveals a key role for neuronal HPK-1 in regulating the proteostatic network throughout an intact metazoan animal.

Significance Statement

Aging and the age-associated decline of the proteome is determined in part through neuronal control of evolutionarily conserved transcriptional effectors, which safeguard homeostasis under fluctuating metabolic and stress conditions by regulating an expansive proteostatic network in peripheral tissues. How neuronal signaling mechanisms are primed, relayed through an organism, and specific responses are initiated in receiving cell types remain poorly understood. We have discovered that the Caenorhabditis elegans homeodomain-interacting protein kinase (HPK-1) is a novel transcriptional effector that functions within two distinct neuronal cell-types to non-autonomously regulate divergent components of the proteostatic network to enhance stress resistance, improve proteostasis and delay aging.
Nuclear inhibitor of protein phosphatase 1 (NIPP1) regulates CNS tau phosphorylation and myelination during development
Authors: McKee Cody , Shrager Peter , Mazumder Arindam , Ganguly Archan , Mayer Abigail , Foley Karl , Ward Nancy , Youngman Margaret , Hou Hailong , Xia Houhui
Published: April 2022

Nuclear inhibitor of protein phosphatase 1 (NIPP1) is a known regulator of gene expression and has been shown to play roles in many physiological or pathological processes such as stem cell proliferation and skin inflammation. While NIPP1 has many regulatory roles in proliferating cells, its function in the central nervous system (CNS) has not been directly investigated. In the present study, we examined NIPP1 CNS function using a conditional knockout (cKO) mouse model, in which the nipp1 gene is excised from neural precursor cells. These mice demonstrate severe developmental impairments that lead to premature lethality within the first few postnatal weeks. To delineate some of the neurological changes occurring in these animals, we first assessed microtubule associated protein tau, a known target of NIPP1 activity. Furthermore, observed tremors prompted exploration of myelin integrity, an integral structure for CNS function, whose disruption is associated with various neurological disorders and neurodegenerative diseases. First, immunoblotting demonstrated increased phospho-tau and altered AKT and PP1 activity in NIPP1 cKO mice, suggesting increased tau phosphorylation likely results from a shift in kinase/phosphatase activity. Second, immunoblots, electron microscopy, and electrophysiology demonstrated a myelin deficit within the brain and optic nerve. Our study suggests that NIPP1 in neural precursors regulates phosphorylation of tau and CNS myelination and may represent a novel therapeutic target for neurodegenerative diseases.
Retinal aging transcriptome and cellular landscape in association with the progression of age-related macular degeneration
Authors: Wang Jiang-Hui , Wong Raymond C.B. , Liu Guei-Sheung
Published: April 2022

Age is the main risk factor for age-related macular degeneration (AMD), a leading cause of blindness in the elderly, with limited therapeutic options. Here we systematically analyzed the transcriptomic characteristics and cellular landscape of the aging retina from controls and patients with AMD. We identify the aging genes in the retina that are associated with innate immune response and inflammation. Deconvolution analysis reveals that the estimated proportion of M2 and M0 macrophages is increased and decreased, respectively with both age and AMD severity. Moreover, we find that Müller glia are increased with age but not with disease severity. Several genes associated with both age and disease severity in AMD, particularly C1s and MR1, are strong positively correlated with the proportions of Müller glia. Our studies expand the genetic and cellular landscape of AMD and provide avenues for further studies on the relationship between age and AMD.
DeepVelo: Deep Learning extends RNA velocity to multi-lineage systems with cell-specific kinetics
Authors: Cui Haotian , Maan Hassaan , Taylor Michael D. , Wang Bo
Published: April 2022

1

The introduction of RNA velocity in single-cell studies has opened new ways of examining cell differentiation and tissue development. Existing RNA velocity estimation methods rely on strong assumptions of predefined dynamics and cell-agnostic constant transcriptional kinetic rates, which are often violated in complex and heterogeneous single-cell RNA sequencing (scRNA-seq) data. To overcome these limitations, we propose DeepVelo, a novel method that estimates thecell-specificdynamics of splicing kinetics using Graph Convolution Networks (GCNs). DeepVelo generalizes RNA velocity to cell populations containing time-dependent kinetics and multiple lineages, which are common in developmental and pathological systems. We applied DeepVelo to disentangle multifaceted kinetics in the processes of dentate gyrus neurogenesis, pancreatic endocrinogenesis, and hindbrain development. The method infers time-varying cellular rates of transcription, splicing and degradation, recovers each cell’s stage in the underlying differentiation process, and detects functionally relevant driver genes regulating these processes. DeepVelo relaxes the constraints of previous techniques, facilitates the study of more complex differentiation and lineage decision events in heterogeneous scRNA-seq data, and is more computationally efficient than previous techniques.
Illuminating kinase inhibitors biology by cell signaling profiling
Authors: Medvedev Alexander V. , Makarov Sergei , Medvedeva Lyubov A. , Martsen Elena , Gorman Kristen L. , Lin Benjamin , Makarov Sergei S.
Published: April 2022

Protein kinase inhibitors (PKI) are promising drug candidates for many diseases. However, even selective PKIs interact with multiple kinases and non-kinase targets. Existing technologies detect these interactions but not the resultant biological effects. Here, we describe an orthogonal PKI evaluation approach that entails fingerprinting of cell signaling responses. As the readout, we profiled the activity of 45 transcription factors linking signaling pathways to genes. We found that inhibitors of the same kinase family exhibited a consensus TF activity profile (TFAP) invariant to PKI chemistry and mode of action (allosteric, ATP-competitive, or genetic). Specific PKI consensus signatures were found for multiple kinase families (Akt, CDK, Aurora, RAF, MEK, and ERK) with high-similarity consensus signatures of signaling cascade kinases. Thus, the PKI consensus signatures provide bona fide markers of cell response to on-target PKI activity. However, the consensus signatures appeared only at certain inhibitor concentrations (‘on-target windows’). Using concentration-response signature analysis, we identified PKI interactions dominating cell response at other concentrations. Finally, we illustrate this approach by selecting putative chemical probes for evaluated kinases. Therefore, the effect-based TFAP approach illuminates PKI biology invisible to target-based technologies and provides clear quantitative metrics to aid the selection of polypharmacological PKIs as chemical probes and drug leads.
Behavioral dysregulation and monoaminergic deficits precede memory impairments in human tau-overexpressing (htau) mice
Authors: Khan Kanza M. , Selvakumar Govindhasamy Pushpavathi , Balasubramanian Nagalakshmi , Wang Ruixiang , Pierson Samantha , Hefti Marco , Marcinkiewcz Catherine A
Published: April 2022

Alzheimer’s disease (AD) poses an ever-increasing public health concern as the population ages, affecting more than 6 million Americans. AD patients present with mood and sleep changes in the prodromal stages that may be partly driven by loss of monoaminergic neurons in brainstem, but a causal relationship has not been firmly established. The goal of the present study was to evaluate depressive and anxiety-like behaviors in a mouse model of human tauopathy (htau mice) at 4 and 6 months of age prior to the onset of cognitive impairments and correlate these behavior changes with tau pathology, neuroinflammation, and monoaminergic dysregulation in the DRN and LC. We observed depressive-like behaviors at 4 months of age in male and female htau mice and hyperlocomotion in male htau mice. At 6 months, male htau mice developed anxiety-like behavior in the EZM, whereas hyperlocomotion had resolved by this time point. Depressive-like behaviors in the social interaction test persisted at 6 months but were resolved in the sucrose preference test. There was also a significant reduction in number and density of 5-HT-immunoreactive neurons in the rostral DRN in htau mice at 4 months and 5-HT neuronal density was negatively correlated with the intensity of phosphorylated tau staining in this subregion. Additionally, we found evidence of microglial activation in the mid and caudal DRN and astrocytic activation in the rostral DRN. 5-HT neuronal activity was reduced in the DRN and accompanied by downregulation of Tph2 and Sert, whereas genes that promote neuroinflammation and tau phosphorylation were upregulated. Finally, there was enhanced ptau202/205 staining and microglial activity in the LC of htau mice and reduced TH optical density, although the number and density of TH+ neurons were not altered. In total, these results suggest that tau pathology in the DRN and the resulting loss of serotonergic neurotransmission may drive depressive-like behaviors in the early stages of AD, whereas anxiety-like behaviors develop later and may result from neurodegeneration in other regions.
Gut Enterochromaffin Cells are Critical Drivers of Visceral Pain and Anxiety
Authors: Bayrer James R. , Castro Joel , Venkataraman Archana , Touhara Kouki K. , Rossen Nathan D. , Morrie Ryan D. , Hendry Aenea , Madden Jessica , Braverman Kristina N. , Schober Gudrun , Brizuela Mariana , Silva Carla Bueno , Ingraham Holly A. , Brierley Stuart M. , Julius David
Published: April 2022

Gastrointestinal (GI) discomfort is a hallmark of most gut disorders and represents a significant component of chronic visceral pain 1. For the growing population afflicted by irritable bowel syndrome (IBS), GI hypersensitivity and pain persist long after signs of tissue injury have resolved 2. IBS also exhibits a strong sex bias afflicting women three-fold more than men 1. Identifying the molecules, cells, and circuits that mediate both the acute and persistent phases of visceral pain is a critical first step in understanding how environmental and endogenous factors produce long-term changes in the nervous system or associated tissues to engender chronic pain syndromes 3,4. Enterochromaffin (EC) cells within the gut epithelium are exceedingly rare sensory neuroendocrine cells that detect and transduce noxious stimuli to nearby nerve endings via serotonin. Here, we manipulate murine EC cell activity using genetic strategies to ascertain their contributions to visceral pain. We show that acute EC cell activation is sufficient to elicit hypersensitivity to gut distension and necessary for the sensitizing actions of isovalerate, a bacterially derived short-chain fatty acid irritant associated with inflammatory GI disorders. Remarkably, prolonged EC cell activation by itself is sufficient to produce persistent visceral hypersensitivity, even in the absence of an instigating inflammatory episode. Perturbing the activity of these rare EC cells led to a marked increase in anxiety-like behaviors that normalized after blocking serotonergic signaling. Sex differences were also observed accross a range of assays indicating that females have a higher baseline visceral sensitivity. Our findings validate a critical role for EC cell-mucosal afferent signaling in acute and persistent GI pain while highlighting mechanistically defined genetic models for studying visceral hypersensitivity, sex differences, and associated behaviors.
Information theory characteristics improve the prediction of lithium response in bipolar disorder patients using an SVM classifier
Authors: Tripathi Utkarsh , Mizrahi Liron , Alda Martin , Falkovich Gregory , Stern Shani
Published: April 2022

Bipolar disorder (BD) is a mood disorder with a high morbidity and death rate. Lithium (Li), a prominent mood stabilizer, is fully effective in roughly 30% of BD patients. The remaining patients respond partially or do not respond at all. Another drug used to treat BD patients is valproate (VPA). Plenty of efforts has been made to understand how these drugs affect the patients’ neurons. We have performed electrophysiological recordings in patient-derived dentate gyrus (DG) granule neurons for three groups: control individuals, BD patients who respond to Li treatment (LR), and BD patients who do not respond to Li treatment (NR). The recordings were analyzed by the statistical tools of modern information theory, which enabled us to recognize new relationships between the electrophysiological features. These added features included the entropy of several electrophysiological measurements and the mutual information between different types of electrophysiological measurements. Information theory features provided further knowledge about the distribution of the electrophysiological entities, which improved basic classification schemes. These newly added features enabled a significant improvement in our ability to distinguish the BD patients from the control individuals (an improvement from 60% accuracy to 74% accuracy) and the Li responders from the non-responders in the BD population using Support Vector Machine (SVM) classification algorithms (an improvement from 81% accuracy to 99% accuracy). These new tools showed that LR neurons are less distinguishable from control neurons after Li treatment but not after VPA treatment, whereas NR neurons become more distinguishable from control neurons after Li treatment.
Single-cell multimodal modeling with deep parametric inference
Authors: Hu Huan
Published: April 2022

The paired measurement of multiple modalities, known as the multimodal analysis, is an exciting frontier for connecting single-cell genomics with epitopes and functions. Mapping of transcriptomes in single-cells and the integration with cell phenotypes enable a better understanding of cellular states. However, assembling these paired omics into a unified representation of the cellular state remains challenging with the unique technical characteristics of each measurement. In this study, we built a deep parameter inference model (DPI) based on the properties of single-cell multimodal data. DPI is a complete single-cell multimodal omics analysis framework, which has built in multimodal data preprocessing, multimodal data integration, multimodal data reconstruction, reference and query, disturbance prediction and other analysis functions.
Multistate structures of the MLL1-WRAD complex bound to H2B-ubiquitinated nucleosome
Authors: Hoffmann Niklas A. , Rahman Sanim , Worden Evan J. , Smith Marissa L. , Namitz Kevin E.W. , Knutson Bruce A. , Cosgrove Michael S. , Wolberger Cynthia
Published: April 2022

The human Mixed Lineage Leukemia-1 (MLL1) complex orchestrates methylation of histone H3K4 to promote transcription and is stimulated by monoubiquitination of histone H2B. Recent structures of the MLL1-WRAD core complex, which comprises the MLL1 methyltransferase, WDR5, RbBp5, Ash2L, and DPY-30, have revealed variation in the docking of MLL1-WRAD on nucleosomes and left ambiguous portions of Ash2L and the position of DPY30. We used an integrated approach combining cryo-electron microscopy and mass spectrometry-crosslinking to determine structures of the MLL1-WRAD complex bound to ubiquitinated nucleosomes containing the Ash2L intrinsically disordered region (IDR), SPRY insertion region, Sdc1-DPY30 interacting region (SDI-motif), and the DPY30 dimer. We resolved three additional states of MLL1-WRAD lacking one or more subunits, which may reflect different steps in the assembly of MLL1-WRAD. The subunits in all four states are positioned on the nucleosome in manner that is similar to a previous structure of MLL1-WRAD bound to ubiquitinated nucleosome, but that differs from structures with unmodified nucleosomes, suggesting that H2B-ubiquitin favors assembly of the active complex. Our results provide a more complete picture of MLL1-WRAD and the role of ubiquitin in promoting formation of the active methyltransferase complex.

Significance

The Mixed Lineage Leukemia-1 (MLL1) complex plays a role in activating transcription by methylating lysine 4 in histone H3, a reaction that is stimulated by the presence of ubiquitin conjugated to histone H2B. Recent structures of the core MLL1 complex, termed MLL1-WRAD, have revealed the existence of multiple docking states and have also left ambiguous portions of the structure. Here we combine mass spectrometry-cross linking with cryo-EM to model additional regions of the MLL1-WRAD complex and identify a series of states that light on complex assembly and the role that ubiquitin plays in orienting MLL1-WRAD on nucleosomes.
Bird community structure in a mixed forest-production landscape in the northern Western Ghats, India
Authors: Munje Avishkar , Kumar Ajith
Published: April 2022

Production landscapes outside protected areas are important for the conservation of wildlife, especially in countries like India with high biodiversity and human densities. Production landscapes like plantations often occur in close proximity to biodiversity-rich areas. Rubber and cashew are lucrative plantation crops in India, which although grown under similar environmental conditions, vary in their management and productivity. These plantation crops are often found along the edges of forests, thereby creating a buffer between forested and urban landscapes. While these areas have the potential to be a refuge for species otherwise restricted to natural forests, they are poorly-studied. To address this knowledge gap, we studied how habitat type (cashew, rubber or forest) and habitat characteristics affect bird diversity and guild structure in the Tillari landscape of Western Ghats, Maharashtra. Additionally, we examined how these effects are mediated by distance of plantations to nearest forest edge. In each habitat type, in 2018, we sampled birds six times each in 30 locations using fixed radius point counts. We found that bird diversity in cashew plantations (14 species) was comparable to that of adjoining forests (15 species). Rubber plantations, on the other hand, had lower bird diversity (9 species) than that in cashew or forests. When bird diversity was analysed based on dietary guilds, rubber plantations had fewer bird species in all guilds and cashew plantations had higher abundance of nectivores and lower richness of insectivores than in forest. Distance from the forest did not affect bird diversity in rubber plantations, whereas cashew plantations had fewer nectivorous birds and higher insectivorous birds away from the forest edge. Our results show that cashew plantations can serve as an important surrogate habitat for forest birds in the northern Western Ghats. The findings indicate the unsuitability of rubber plantations for sustaining bird diversity. While there are many studies available on bird diversity in rubber plantations, this is among the first studies of bird community structure in cashew plantations. At a time when forests are rapidly being cleared for plantations, our findings provide valuable data to examine the differential impacts of plantation type on biodiversity.
Circular RNA’s competing endogenous gene pair as motif in serous ovarian cancer
Authors: Li Haili , Zheng Xubin , Zhang Ning , Gao Jing , Leung Kwong-Sak , Wong Man-Hon , Yang Shu , Liu Yakun , Dong Ming , Bai Huimin , Ye Xiufeng , Cheng Lixin
Published: April 2022

The non-coding RNA (ncRNA) regulation apprears to be associated to the diagnosis and targeted therapy of complex diseases. Motifs of non-coding RNAs and genes in the competing endogenous RNA (ceRNA) network would probably contribute to the accurate prediction of serous ovarian carcinoma (SOC). Hence, we profiled a whole transcriptome of eight human SOCs and eight controls and constructed a ceRNA network including mRNAs, long ncRNAs, and circular RNAs (circRNAs). We identified the mRNA–ncRNA–mRNA motifs in the ceRNA network named the non-coding RNA’s competing endogenous gene pairs (ceGPs), through the denoised individualized pair analysis of gene expression (deiPAGE) proposed in this study. 18 cricRNA’s ceGPs (cceGPs) were identified from multiple cohorts and were fused as an indicator (SOC index) for SOC discrimination, which carried a high predictive capacity in independent cohorts. It was found that the index was negatively correlated with the CD8+/CD4+ ratio in tumour-infiltration, reflecting the migration and growth of tumour cells in ovarian cancer progression.
One-trial social learning of vervet monkey alarm calling
Authors: Deshpande Adwait , Van Boekholt Bas , Zuberbuhler Klaus
Published: April 2022

How do non-human primates learn to use their alarm calls? Social learning is a promising candidate, but its role in the acquisition of meaning and call usage has not been studied systematically, neither during ontogeny nor in adulthood. To investigate the role of social learning in alarm call comprehension and use, we exposed groups of wild vervet monkeys to two unfamiliar animal models in the presence or absence of conspecific alarm calls. To assess the learning outcome of these experiences, we then presented the models for a second time to the same monkeys, but now without additional alarm call information. In subjects previously exposed in conjunction with alarm calls, we found heightened predator inspection compared to control subjects exposed without alarm calls, indicating one-trial social learning of ‘meaning’. Moreover, some juveniles (but not adults) produced the same alarm calls they heard during the initial exposure whereas the authenticity of the models had an additional effect. We concluded that, in non-human primates, call meaning can be acquired by one-trail social learning but that subject age and core knowledge about predators additionally moderate the acquisition of novel call-referent associations.
Two functionally distinct heme/iron transport systems are virulence determinants of the fish pathogen Flavobacterium psychrophilum
Authors: Zhu Yueying , Lechardeur Delphine , Bernardet Jean-François , Kerouault Brigitte , Guérin Cyprien , Rigaudeau Dimitri , Nicolas Pierre , Duchaud Eric , Rochat Tatiana
Published: April 2022

Bacterial pathogens have a critical impact on aquaculture, a sector that accounts for half of the human fish consumption. Flavobacterium psychrophilum (phylum Bacteroidetes) is responsible for bacterial cold-water disease in salmonids worldwide. The molecular factors involved in host invasion, colonization and hemorrhagic septicaemia are mostly unknown. In this study, we identified two new TonB-dependent receptors, HfpR and BfpR, that are required for adaptation to iron conditions encountered during infection and for virulence in rainbow trout. Transcriptional analyses revealed that their expression is tightly controlled and upregulated under specific iron sources and concentrations. Characterization of deletion mutants showed that they act without redundancy: BfpR is required for optimal growth in the presence of high hemoglobin level, while HfpR confers the capacity to acquire nutrient iron from heme or hemoglobin under iron scarcity. The gene hfpY, co-transcribed with hfpR, encodes a protein related to the HmuY family. We demonstrated that HfpY binds heme and contributes significantly to host colonization and disease severity. Overall, these results are consistent with a model in which both BfpR and Hfp systems promote heme uptake and respond to distinct signals to adapt iron acquisition to the different stages of pathogenesis. Our findings give insight into the molecular basis of pathogenicity of a serious pathogen belonging to the understudied family Flavobacteriaceae and point to the newly identified heme receptors as promising targets for antibacterial development.
Tumor spheroids accelerate persistently invading cancer cells
Authors: Audoin Melanie , Søgaard Maria Tangen , Jauffred Liselotte
Published: April 2022

Glioblastoma brain tumors form in brains’ white matter and remains one of the most lethal cancers despite intensive therapy and surgery. The complex morphology of these tumors includes infiltrative growth and gain of cell motility. Therefore, various brain-mimetic model systems have been developed to investigate invasion dynamics. Despite this, exactly how gradients of cell density, chemical signals and metabolites influence individual cells’ migratory behavior remains elusive. Here we show that the gradient field – induced by the spheroid – accelerates cells’ invasion of the extracellular matrix. We show that cells are pushed away from the spheroid along a radial gradient, as predicted by a biased persistent random walk (BPRW). Thus, our results grasp in a simple model the complex behavior of metastasizing cells. We anticipate that this well-defined and quantitative assay could be instrumental in the development of new anti-cancer strategies.
Application of light-sheet mesoscopy to image host-pathogen interactions in intact organs
Authors: Battistella Eliana , Quintana Juan F. , McConnell Gail
Published: April 2022

Human African Trypanosomiasis (HAT) is a disease caused by the extracellular parasite Trypanosoma brucei that affects the central nervous system (CNS) during the chronic stage of the infection, inducing neuroinflammation, coma, and death if left untreated. However, little is known about the structural change happening in the brain as result of the infection. So far, infection-induced neuroinflammation has been observed with conventional methods, such as immunohistochemistry, electron microscopy, and 2-photon microscopy only in small portions of the brain, which may not be representative of the disease. In this paper, we have used a newly-developed light-sheet illuminator to image the level of neuroinflammation in chronically infected mice and we use analyse these data to compare the infection in naïve controls. This system was developed for imaging in combination with the Mesolens objective lens, providing sub-cellular resolution for imaging volumes exceeding 39 mm3 in an acquisition time of only 8 hours. The mouse brain specimens were cleared using CUBIC+, followed by antibody staining to locate Glial Fibrillary Acid Protein (GFAP) expressing cells, primarily astrocytes and ependymocytes, used here as a proxy for cell reactivity and gliosis. The large capture volume allowed us to detect GFAP+ cells and spatially resolve the innate responses to T. brucei infection. Based on morphometric analyses and spatial distribution of GFAP+ cells, our data demonstrates a significant increase in cell dendrite branching around the lateral ventricle, as well as dorsal and ventral third ventricles, that are negatively correlated with the branch extension in distal sites from the circumventricular spaces. To our knowledge, this is the first report highlighting the potential of light-sheet mesoscopy to characterise the inflammatory responses of the mouse brain to parasitic infection at the cellular level in intact cleared organs, opening new avenues for the development of new mesoscale imaging techniques for the study of host-pathogen interactions.
Talin-drug interaction reveals a key molecular determinant for biphasic mechanical effect: studied under single-molecule resolution
Authors: Chakraborty Soham , Bhatt Madhu , Chowdhury Debojyoti , Chaudhuri Deep , Haldar Shubhasis
Published: April 2022

Talin as an adhesion protein, exhibits a strong force-dependent structure-function dynamics. Being a mechanosensitive focal adhesion (FA) protein, talin might interact to several FA targeting drugs; however, the molecular mechanism of talin-drug interactions remains elusive. Here we combined magnetic tweezers and molecular dynamics (MD) simulation to explore mechanical stability of talin with three drugs based on their talin specificity. Interestingly, our study revealed that talin displays a bimodal force distribution with a low and high unfolding force population. We observed that talin nonspecific drugs (tamoxifen and letrozole) display biphasic effect: increase talin mechanical stability upto optimum concentration, followed by a decrease in stability with further concentration increase. By contrast, talin-specific cyanidin 3-O-glucoside promotes a steady increase to talin mechanical stability with its concentration. We reconciled our observation from the simulation study: tamoxifen enters into talin hydrophobic core, eventually destabilizing the protein; whereas cyanidin 3-O-glucoside stabilizes the protein core by maintaining the inter-helix distance. Finally, we observed a strong correlation among hydrophobicity and cavity analysis, illustrating a detailed mechanistic analysis of drug effect on the mechanosensitive protein. Overall this study presents a novel perspective for drug designing against mechanosensitive proteins and studying off-target effects of already known drugs.
mRNAid, an Open-Source Platform for Therapeutic mRNA Design and Optimization Strategies
Authors: Vostrosablin Nikita , Lim Shuhui , Gopal Pooja , Brazdilova Kveta , Parajuli Sushmita , Wei Xiaona , Gromek Anna , Spale Martin , Muzdalo Anja , Yeo Constance , Wardyn Joanna , Mejzlik Petr , Henry Brian , Partridge Anthony W. , Bitton Danny A.
Published: April 2022

Recent COVID-19 vaccines unleashed the potential of mRNA-based therapeutics. mRNA optimization is indispensable for reducing immunogenicity, ensuring stability, and maximizing protein output. We present mRNAid, an experimentally validated software for mRNA optimization and visualization that generates mRNA sequences with comparable if not superior characteristics to commercially optimized sequences. To encompass all aspects of mRNA design, we also interrogated the impact of uridine content, nucleoside analogs and UTRs on expression and immunogenicity.
Protein evidence of unannotated ORFs inDrosophilareveals unappreciated diversity in the evolution of young proteins
Authors: Zheng Eric B , Zhao Li
Published: April 2022

De novogene origination, where a previously non-genic genomic sequence becomes genic through evolution, has been increasingly recognized as an important source of evolutionary novelty across diverse taxa. Manyde novogenes have been proposed to be protein-coding, and in several cases have been experimentally shown to yield protein products. However, the systematic study ofde novoproteins has been hampered by doubts regarding the translation of their transcripts without the experimental observation of protein products. Using a systematic, ORF-focused mass-spectrometry-first computational approach, we identify almost 1000 unannotated open reading frames with evidence of translation (utORFs) in the model organismDrosophila melanogaster, 371 of which have canonical start codons. To quantify the comparative genomic similarity of these utORFs acrossDrosophilaand to infer phylostratigraphic age, we further develop a synteny-based protein similarity approach. Combining these results with reference datasets on tissue- and life-stage-specific transcription and conservation, we identify different properties amongst these utORFs. Contrary to expectations, the fastest-evolving utORFs are not the youngest evolutionarily. We observed more utORFs in the brain than in the testis. Most of the identified utORFs may be ofde novoorigin, even accounting for the possibility of false-negative similarity detection. Finally, sequence divergence after an inferredde novoorigin event remains substantial, raising the possibility thatde novoproteins turn over frequently. Our results suggest that there is substantial unappreciated diversity inde novoprotein evolution: many more may exist than have been previously appreciated; there may be divergent evolutionary trajectories; andde novoproteins may be gained and lost frequently. All in all, there may not exist a single characteristic model ofde novoprotein evolution, but rather complex origins and evolutionary trajectories forde novoproteins.

Impact statement

The analysis of mass-spectrometry data for all possible open reading frames reveals protein evidence for evolutionarily young, unannotated proteins with distinct characters.
Downregulation of dystrophin expression occurs across diverse tumors, correlates with the age of onset, staging and reduced survival of patients
Authors: Alnassar Nancy , Borczyk Malgorzata , Tsagkogeorga Georgia , Korostynski Michal , Han Namshik , Górecki Dariusz C
Published: April 2022

Mutations of theDMDgene, encoding dystrophins, cause Duchenne muscular dystrophy (DMD). Some tumors also display altered dystrophin expression and recent studies identified a developmental onset of DMD. Given that embryogenesis and carcinogenesis share many mechanisms, we analyzed a broad spectrum of tumors to establish whether dystrophin loss evokes related outcomes. Transcriptomic, proteomic, and mutation datasets from fifty tumor tissues and matching controls (10,894 samples) and 140 corresponding tumor cell lines were analyzed. Interestingly,DMDexpression was widespread across healthy tissues at levels comparable to housekeeping genes. In 80% of tumors,DMDexpression was reduced due to transcriptional downregulation and not somatic mutations. The full-length transcript encoding Dp427 was decreased in 68% of tumors, while Dp71 variants showed variability of expression. Hierarchical clustering analysis ofDMDtranscripts distinguished malignant from control tissues. Transcriptomes of primary tumors and tumor cell lines with lowDMDexpression showed enrichment of specific pathways in the differentially expressed genes. Pathways consistently identified: ECM-receptor interaction, calcium signaling and PI3K-Akt, are also altered in DMD muscle. Notably, lowDMDexpression was associated with a more advanced stage, older age of onset, and reduced survival across different tumors. Thus,DMDtranscription occurs throughout a spectrum of normal tissues. The molecular signature associated with its frequent downregulation in malignancies is concordant with changes found in Duchenne muscles, even though these malignancies originate from tissues never previously associated with dystrophin expression or function. Therefore, the importance of this largest known gene extends beyond its roles identified in DMD, certainly into oncology.
Centriolar satellites expedite mother centriole remodeling to promote ciliogenesis
Authors: Hall Emma A. , Kumar Dhivya , Prosser Suzanna L. , Yeyati Patricia L. , Pérez Vicente Herranz , García Verdugo Jose Manuel , Rose Lorraine , McKie Lisa , Dodd Daniel O. , Tennant Peter A. , Megaw Roly , Murphy Laura C. , Ferreira Marissa , Grimes Graeme , Williams Lucy , Quidwai Tooba , Pelletier Laurence , Reiter Jeremy F. , Mill Pleasantine
Published: April 2022

Centrosomes are orbited by centriolar satellites, dynamic multiprotein assemblies nucleated by PCM1. To study the requirement for centriolar satellites, we generated mice lacking PCM1. Pcm1−/− mice display partially penetrant perinatal lethality with survivors exhibiting hydrocephalus, oligospermia and cerebellar hypoplasia, as well as variable expressivity of other ciliopathy features including cystic kidneys. Pcm1−/− multiciliated ependymal cells and PCM1−/− retinal pigmented epithelial 1 (RPE1) cells showed reduced ciliogenesis. PCM1−/− RPE1 cells displayed reduced docking of the mother centriole to the ciliary vesicle and removal of CP110 and CEP97 from the distal mother centriole, indicating compromized early ciliogenesis. We show these molecular cascades are maintained in vivo, and we suggest that the cellular threshold to trigger ciliogenesis varies between cell types. We propose that PCM1 and centriolar satellites facilitate efficient trafficking of proteins to and from centrioles, inducing the departure of CP110 and CEP97 to initiate ciliogenesis.
A Deep Learning Method for MiRNA/IsomiR Target Detection
Authors: Talukder Amlan , Zhang Wencai , Li Xiaoman , Hu Haiyan
Published: April 2022

Motivation

Accurate identification of microRNA (miRNA) targets at base-pair resolution has been an open problem for over a decade. The recent discovery of miRNA isoforms (isomiRs) adds more complexity to this problem. Despite the existence of many methods, none considers isomiRs, and their performance is still suboptimal. We hypothesize that by taking the isomiR-mRNA interaction into account and applying a deep learning model to study miRNA-mRNA interaction features, we may improve the accuracy of miRNA target predictions.

Results

We developed a deep learning tool called DMISO to capture the intricate features of miRNA/isomiR-mRNA interactions. Based on 10-fold cross-validation, DMISO showed high precision (95%) and recall (90%). Evaluated on three independent datasets, DMISO had superior performance to five tools, including three popular conventional tools and two recently developed deep learning-based tools. By applying two popular feature interpretation strategies, we demonstrated the importance of the miRNA regions other than their seeds and the potential contribution of the RNA-binding motifs within miRNAs/isomiRs and mRNAs to the miRNA/isomiR-mRNA interactions.

Availability

The source code and tool are available athttp://hulab.ucf.edu/research/projects/DMISO.

Contact

haihu@cs.ucf.edu,xiaoman@mail.ucf.edu

Supplementary information

Supplementary data are available online.
Tissue-wide Genetic and Cellular Landscape Shapes the Execution of Sequential PRC2 Functions in Neural Stem Cell Lineage Progression
Authors: Amberg Nicole , Pauler Florian M. , Streicher Carmen , Hippenmeyer Simon
Published: April 2022

The generation of a correctly-sized cerebral cortex with all-embracing neuronal and glial cell-type diversity critically depends on faithful radial glial progenitor (RGP) cell proliferation/differentiation programs. Temporal RGP lineage progression is regulated by Polycomb Repressive Complex 2 (PRC2) and loss of PRC2 activity results in severe neurogenesis defects and microcephaly. How PRC2-dependent gene expression instructs RGP lineage progression is unknown. Here we utilize Mosaic Analysis with Double Markers (MADM)-based single cell technology and demonstrate that PRC2 is not cell-autonomously required in neurogenic RGPs but rather acts at the global tissue-wide level. Conversely, cortical astrocyte production and maturation is cell-autonomously controlled by PRC2-dependent transcriptional regulation. We thus reveal highly distinct and sequential PRC2 functions in RGP lineage progression that are dependent on complex interplays between intrinsic and tissue-wide properties. In a broader context our results imply a critical role for the genetic and cellular niche environment in neural stem cell behavior.
Screening candidate genes related to psoas muscle traits in Debao and Landrace pigs based on transcriptome analysis
Authors: Chen Chang-yi , Zeng Su-xian , Ma Yuan-ding , Zheng Jun-wen , Li Xin , Xiong Chen-yong , Zhou Hong-jin , Wei Chun-tao , Li Zong-qiang
Published: April 2022

To identify the important genes that affect the phenotypic differences between the Landrace and Debao pigs, especially the differences in metabolism and muscle growth. Differentially expressed genes of psoas major were detected by mRNA transcriptome sequencing in Landrace and Debao pigs. By extracting the total RNA of the psoas major muscle of the Landrace pig and the Debao pig, purifying the mRNA, constructing the cDNA library, conducting transcriptome sequencing, and then through the sequencing quality evaluation, we know that the sequencing quality of this study is relatively high. A total of 17,943 genes were detected in all samples, including 17,870 known genes and 73 new genes. Defined genes with |log2FC| greater than 2 and Q-value less than 0.001, and screened them as significantly differentially expressed genes. A total of 1661 differentially expressed genes were screened from the samples of Landrace pigs and Debao pigs, among which 1255 genes were differentially up-regulated and 406 genes were differentially down-regulated. Through differential gene analysis, it is concluded that these genes are mainly involved in metabolic regulation, muscle and fat development and other processes, especially some important functional genes such as MAPK14, FOS, SIRT1, KRAS, EGR1, CDNNB1, etc. To sum up, this study used transcriptome sequencing method, and then selected differentially expressed genes between Landrace pigs and Debao pigs through data analysis, and finally screened out important genes affecting phenotypic differences, which provided genetic support for breeding better breeds in the future.