title: Investigating Carboxysome Morphology Dynamics with a Rotationally Invariant Variational Autoencoder

abstract: Carboxysomes are a class of bacterial microcompartments that form proteinaceous organelles within the cytoplasm of cyanobacteria and play a central role in photosynthetic metabolism by defining a cellular microenvironment permissive to CO2 fixation. Critical aspects of the assembly of the carboxysomes remain relatively unknown, especially with regard to the dynamics of this microcompartment. We have recently expressed an exogenous protease as a way of gaining control over endogenous protein levels, including carboxysomal components, in the model cyanobacterium Synechococcous elongatus PCC 7942. By utilizing this system, proteins that compose the carboxysome can be tuned in real-time as a method to examine carboxysome dynamics. Yet, analysis of subtle changes in carboxysome morphology with microscopy remains a low-throughput and subjective process. Here we use deep learning techniques, specifically a Rotationally Invariant Variational Autoencoder (rVAE), to analyze the fluorescence microscopy images and quantitatively evaluate how carboxysome shell remodelling impacts trends in the morphology of the microcompartment over time. We find that rVAEs are able to assist in the quantitative evaluation of changes in carboxysome location, shape, and size over time. We propose that rVAEs may be a useful tool to accelerate the analysis of carboxysome assembly and dynamics in response to genetic or environmental perturbation, and may be more generally useful to probe regulatory processes involving a broader array of bacterial microcompartments.


title: Mobilome-driven segregation of the resistome in biological wastewater treatment

abstract: Biological wastewater treatment plants (BWWTP) are considered to be hotspots of evolution and subsequent spread of antimicrobial resistance (AMR). Mobile genetic elements (MGEs) promote the mobilization and dissemination of antimicrobial resistance genes (ARGs) and are thereby critical mediators of AMR within the BWWTP microbial community. At present, it is unclear whether specific AMR categories are differentially disseminated via bacteriophages (phages) or plasmids. To understand the segregation of AMR in relation to MGEs, we analyzed meta-omic (metagenomic, metatranscriptomic and metaproteomic) data systematically collected over 1.5 years from a BWWTP. Our results showed a core group of fifteen AMR categories which were found across all timepoints. Some of these AMR categories were disseminated exclusively (bacitracin) or primarily (aminoglycoside, MLS, sulfonamide) via plasmids or phages (fosfomycin and peptide), whereas others were disseminated equally by both MGEs. Subsequent expression- and protein-level analyses further demonstrated that aminoglycoside, bacitracin and sulfonamide resistance genes were expressed more by plasmids, in contrast to fosfomycin and peptide AMR expression by phages, thereby validating our genomic findings. Longitudinal assessment further underlined these findings whereby the log2-fold changes of aminoglycoside, bacitracin and sulfonamide resistance genes were increased in plasmids, while fosfomycin and peptide resistance showed similar trends in phages. In the analyzed communities, the dominant taxon Candidatus Microthrix parvicella was a major contributor to several AMR categories whereby its plasmids primarily mediated aminoglycoside resistance. Importantly, we also found AMR associated with ESKAPEE pathogens within the BWWTP, for which MGEs also contributed differentially to the dissemination of ARGs. Collectively our findings pave the way towards understanding the segmentation of AMR within MGEs, thereby shedding new light on resistome populations and their mediators, essential elements that are of immediate relevance to human health.

category: microbiology


title: Wolbachia endosymbionts in two Anopheles species indicates independent acquisitions and lack of prophage elements

abstract:
Wolbachia is a genus of obligate bacterial endosymbionts that infect a diverse range of arthropod species as well as filarial nematodes, with its single described species, Wolbachia pipientis, divided into several  supergroups based on multilocus sequence typing. Wolbachia strains in mosquitoes have been shown to inhibit the transmission of human pathogens including Plasmodium malaria parasites and arboviruses. Despite their large host range, Wolbachia strains within the major malaria vectors of the Anopheles (A.) gambiae and A. funestus complexes appear at low density based solely on PCR-based methods. Questions have been raised as to whether this represents a true endosymbiotic relationship. However, recent definitive evidence for two distinct, high-density strains of supergroup B Wolbachia within A. demeilloni and A. moucheti has opened exciting possibilities to explore naturally occurring Wolbachia endosymbionts in Anopheles for biocontrol strategies to block Plasmodium transmission. Here we utilise genomic analyses to demonstrate that both Wolbachia strains have retained all key metabolic and transport pathways despite their smaller genome size. We further confirm the presence of cytoplasmic incompatibility factor genes, despite noticeably few prophage regions. Additionally, phylogenetic analysis indicates that these Wolbachia strains may have been introduced into these two Anopheles species via horizontal transmission events, and unlikely to be by ancestral acquisition and subsequent loss events in the Anopheles gambiae species complex. These are the first Wolbachia genomes that enable us to study the relationship between natural strains Plasmodium malaria parasites and their Anopheline hosts.

Impact statementWolbachia naturally infects a wide range of arthropod species, including insect vectors of human pathogens, where they may play a role in inhibiting their replication. These bacteria have been commonly found within Aedes (Ae.) albopictus and Culex pipiens mosquitoes but have been noticeably absent in the Anopheles mosquito genera, which includes all species responsible for malaria transmission. Recent PCR-based methods have suggested the potential for natural Wolbachia strains within the A. gambiae species complex, which includes major malaria vector species including A. gambiae s.s., A. coluzzii and A. arabiensis. We recently reported the presence of stable Wolbachia strains naturally occurring within two different Anopheles species (A. demeilloni and A. moucheti). In this study, we perform comparative genomic analysis of these two Wolbachia genomes against each other and published Wolbachia strains. The current assemblies are some of the smallest sequenced Wolbachia strains of insects, although their metabolic pathway repertoire is comparable to other strains. Interestingly, prophage fragments were identified within only one of the two strains. The findings of this study will be of significant interest to researchers investigating Wolbachia as a potential malaria biocontrol strategy, giving greater insight into the evolution and diversity of this obligate intracellular endosymbiont.

Data summarySequence data generated and used for this analysis are available in the National Centre for Biotechnology Information Sequence Read Archive (NCBI SRA bioproject number PRJNA642000). The two assembled Wolbachia genomes are available with genome accession numbers GCA_018491735.2 and GCA_018491625.2. Additional Wolbachia genomes used for comparative analysis are described in the supplementary material.

The authors confirm all supporting data, code and protocols have been provided within the article or through supplementary data files. Additional supplementary data files used to generate several figures can be found at: https://figshare.com/projects/Wolbachia_endosymbionts_in_two_Anopheles_species_indicates_independent_acquisitions_and_lack_of_prophage_elements/126533

category: cell biology


title: Efficient inhibition of cell proliferation and promotion of apoptosis requires continuous treatment with abemaciclib.

abstract: Abemaciclib is an oral, selective cyclin-dependent kinase 4 & 6 inhibitor (CDK4 & 6i), approved for hormone receptor-positive (HR+), human epidermal growth factor receptor 2-negative (HER2-) advanced breast cancer (ABC) as monotherapy for endocrine refractory disease, and with endocrine therapy (ET) for initial treatment and after progression on ET. Abemaciclib has also shown clinical activity in combination with ET in patients with high risk early BC (EBC). Here, we examined the preclinical attributes of abemaciclib and other CDK4 & 6i using biochemical and cell-based assays. In vitro, abemaciclib preferentially inhibited CDK4 kinase activity versus CDK6, resulting in inhibition of cell proliferation in a panel of BC cell lines with higher average potency than palbociclib or ribociclib. Abemaciclib showed activity regardless of HER2 amplification and phosphatidylinositol 3-kinase (PI3KCA) gene mutation status. In human bone marrow progenitor cells, abemaciclib showed lower impact on myeloid maturation than other CDK4 & 6i when tested at unbound concentrations similar to those observed in clinical trials. Continuous abemaciclib treatment provided profound inhibition of cell proliferation, and triggered senescence and apoptosis. These preclinical results support the unique efficacy and safety profile of abemaciclib observed in clinical trials.


title: Genetic coordination of sperm morphology and seminal fluid proteins promotes male reproductive success in Drosophila melanogaster

abstract:
Spermatozoal morphology is highly variable both among and within species and in ways that can significantly impact fertilization success. In Drosophila melanogaster, paternity success depends on sperm length of both competing males and length of the females primary sperm storage organ. We found that genes upregulated in long sperm testes are enriched for lncRNAs and seminal fluid proteins (Sfps). Transferred in seminal fluid to the female during mating, Sfps are secreted by the male accessory glands (AG) and affect female remating rate, physiology, and behavior with concomitant advantages for male reproductive success. Despite being upregulated in long sperm testes, they have no known function in testis tissue. We found that Sex Peptide and ovulin (Acp26Aa) knockouts resulted in shorter sperm, suggesting that Sfps may regulate sperm length during spermatogenesis. However, knockout of AG function did not affect sperm length, suggesting that AG expression has no influence on spermatogenic processes. We also found that long sperm males are better able to delay female remating, suggesting higher Sfp expression in AG. These results might suggest that long sperm males have a double advantage in sperm competition by both delaying female remating, likely through transfer of more Sfps, and by resisting sperm displacement. However, we also found that this extra advantage does not necessarily translate to more progeny or higher paternity success. Thus, we found that multiple components of the ejaculate coordinate to promote male reproductive success at different stages of reproduction, but the realized fitness advantages in sperm competition are uncertain.

Significance StatementThe ejaculate is comprised of sperm produced in the testis and seminal fluid primarily produced in the male accessory glands (AG). These complementary components are both critical for male reproductive success, but they are largely considered to be functionally, genetically, and developmentally independent. In a quest to understand genetic mechanisms of sperm length variation, we found that genes upregulated in long sperm testes are enriched for lncRNAs and seminal fluid proteins (Sfps). Knockout of two Sfps, Sex Peptide and ovulin, results in shorter sperm, though knockout of AG function has no effect. Moreover, long sperm males delay female remating longer. These results suggest sophisticated testis-AG coordination that amplifies male reproductive success, with implications for evolutionary integration of sexually selected traits.

category: genetics


title: A cell wall-associated gene network shapes leaf boundary domains

abstract:
Boundary domains delimit and organize organ growth throughout plant development almost relentlessly building plant architecture and morphogenesis. Boundary domains display reduced growth and orchestrate development of adjacent tissues in a non-cell autonomous manner. How these two functions are achieved remains elusive despite the identification of several boundary-specific genes. Here, we show using morphometrics at the organ and cellular levels that leaf boundary domain development requires SPINDLY (SPY), an O-fucosyltransferase, to act as cell growth repressor. Further we show that SPY acts redundantly with the CUP-SHAPED COTYLEDON transcription factors (CUC2 and CUC3), which are major determinants of boundaries development. Accordingly at the molecular level, CUC2 and SPY repress a common set of genes involved in cell wall loosening providing a molecular framework for the growth repression associated with boundary domains. Atomic force microscopy (AFM) confirmed that young leaf boundary domain cells have stiffer cell walls than marginal outgrowth. This differential cell wall stiffness was reduced in spy mutant. Taken together our data reveal a concealed CUC2 cell wall associated gene network linking tissue patterning with cell growth and mechanics.

Summary statementDecreased cell-wall loosening gene expression contributes to the coordination of cell growth and mechanics with tissue patterning thus driving boundary development.

category: plant biology


title: Effector loss drives adaptation of Pseudomonas syringae pv. actinidiae to Actinidia arguta

abstract: A pandemic isolate of Pseudomonas syringae pv. actinidiae biovar 3 (Psa3) has devastated kiwifruit orchards growing cultivars of Actinidia chinensis. In contrast, A. arguta (kiwiberry) is resistant to Psa3. This resistance is mediated via effector-triggered immunity, as demonstrated by induction of the hypersensitive response in infected A. arguta leaves, observed by microscopy and quantified by ion-leakage assays. Isolates of Psa3 that cause disease in A. arguta have been isolated and analyzed, revealing a 49 kb deletion in the exchangeable effector locus (EEL). This natural EEL-mutant isolate and strains with synthetic knockouts of the EEL were more virulent in A. arguta plantlets than wild-type Psa3. Screening of a complete library of Psa3 effector knockout strains identified increased growth in planta for knockouts of four effectors - AvrRpm1a, HopF1c, HopZ5a, and the EEL effector HopAW1a - suggesting a resistance response in A. arguta. Hypersensitive response (HR) assays indicate that three of these effectors trigger a host species-specific HR. A Psa3 strain with all four effectors knocked out escaped host recognition, but a cumulative increase in bacterial pathogenicity and virulence was not observed. These avirulence effectors can be used in turn to identify the first cognate resistance genes in Actinidia for breeding durable resistance into future kiwifruit cultivars.


title: An atypical NLR protein modulates the NRC immune receptor network

abstract: The NRC immune receptor network has evolved in asterid plants from a pair of linked genes into a genetically dispersed and phylogenetically structured network of sensor and helper NLR (nucleotide-binding domain and leucine-rich repeat-containing) proteins. In some species, such as the model plant Nicotiana benthamiana and other Solanaceae, the NRC network forms up to half of the NLRome, and NRCs are scattered throughout the genome in gene clusters of varying complexities. Here, we describe NRCX, an atypical, but essential member of the NRC family that lacks canonical features of these NLR helper proteins, such as a functional N-terminal MADA motif and the capacity to trigger autoimmunity. In contrast to other NRCs, systemic gene silencing of NRCX markedly impairs plant growth resulting in a dwarf phenotype. Remarkably, dwarfism of NRCX silenced plants is partially dependent on NRCX paralogs NRC2 and NRC3, but not NRC4. Despite its negative impact on plant growth when silenced systemically, transient RNA interference of NRCX in mature N. benthamiana leaves doesnt result in visible cell death phenotypes. However, alteration of NRCX expression modulates the hypersensitive response mediated by NRC2 and NRC3 in a manner consistent with a negative role for NRCX in the NRC network. We conclude that NRCX is an atypical member of the NRC network that has evolved to contribute to the homeostasis of this genetically unlinked NLR network.


title: Protein Engineering with A Glycosylation Circuit Enables Improved Enzyme Characteristics

abstract: Protein glycosylation is one of the most crucial and common post-translational modifications. It plays a fate-determining role and can alter many properties of proteins, making it an interesting for many biotechnology applications. The discovery of bacterial glycosylation mechanisms, opened a new perspective and transfer of C.jejuni N-linked glycosylation into laboratory work-horse E. coli increased research pace in the field exponentially. It has been previously showed that utilizing N-Linked Glycosylation, certain recombinant proteins have been furnished with improved features, such as stability and solubility. In this study, we utilized N-linked Glycosylation to glycosylate alkaline phosphatase (ALP) enzyme in E. coli and investigate the effects of glycosylation on an enzyme. Considering the glycosylation mechanism is highly dependent on the acceptor protein, ALP constructs carrying glycosylation tag at different locations of the gene has been created and glycosylation rates have been calculated. The most glycosylated construct has been selected for comparison with the native enzyme. We investigated the performance of glycosylated ALP in terms of its thermostability, proteolytic stability, tolerance to suboptimal pH and under denaturing conditions. Studies showed that glycosylated ALP performed remarkably better at optimal and harsh conditions Therefore, N-linked Glycosylation mechanism can be employed for enzyme engineering purposes and is a useful tool for industrial applications that require enzymatic activity.

category: synthetic biology


title: Min waves without MinC can pattern FtsA-FtsZ filaments on model membranes

abstract: Although the essential proteins that drive bacterial cytokinesis have been identified and reconstituted in vitro, the precise mechanisms by which they dynamically interact to enable symmetrical division are largely unknown. In Escherichia coli, cell division begins with the formation of a proto-ring composed of FtsZ and its membrane-tethering proteins FtsA and ZipA. In the broadly proposed molecular scenario for ring positioning, Min waves composed of MinD and MinE distribute the FtsZ-polymerization inhibitor MinC away from mid-cell, where the Z-ring can form. Therefore, MinC is believed to be an essential element connecting the Min and FtsZ systems. Here, by using cell-free gene expression on planar lipid membranes, we demonstrate that MinDE drive the formation of dynamic, antiphase patterns of FtsZ-FtsA co-filaments even in the absence of MinC. This behavior is also observed when the proteins are compartmentalized inside microdroplets. These results suggest that Z-ring positioning may be achieved with a more minimal set of proteins than previously envisaged, providing a fresh perspective about the role of MinC. Moreover, we propose that MinDE oscillations may constitute the minimal localization mechanism of an FtsA-FtsZ constricting ring in a prospective synthetic cell.


title: Essential functions of MLL1 and MLL2 in retinal development and cone cell maintenance

abstract: MLL1 (KMT2A) and MLL2 (KMT2B) are homologous members of the mixed-lineage leukemia (MLL) family of histone methyltransferases involved in epigenomic transcriptional regulation. Their sequence variants have been associated with neurological and psychological disorders, but little is known about their roles and mechanism of action in CNS development. Using mouse retina as a model, we previously reported MLL1s role in retinal neurogenesis and horizontal cell maintenance. Here we determine roles of MLL2 and MLL1/MLL2 together in retinal development using conditional knockout (CKO) mice. Deleting Mll2 from Chx10+ retinal progenitors resulted in a similar phenotype as Mll1 CKO, but removal of both alleles produced much more severe deficits than each single CKO: 1-month double CKO mutants displayed null light responses in electroretinogram; thin retinal layers, including shorter photoreceptor outer segments with impaired phototransduction gene expression; and reduced numbers of M-cones, horizontal and amacrine neurons, followed by fast retinal degeneration. Despite moderately reduced progenitor cell proliferation at P0, the neurogenic capacity was largely maintained in double CKO mutants. However, upregulated apoptosis and reactive gliosis were detected during postnatal retinal development. Finally, the removal of both MLLs in fated rods produced a normal phenotype, but the CKO in M-cones impaired M-cone function and survival, indicating both cell non-autonomous and autonomous mechanisms. Altogether, our results suggest that MLL1/MLL2 play redundant roles in maintaining specific retinal neurons after cell fate specification and are essential for establishing functional neural networks.

category: neuroscience


title: Molecular dynamics simulations reveal the selectivity mechanism of structurally similar agonists to TLR7 and TLR8

abstract: TLR7 and TLR8 are key members of the Toll-like receptor family, playing crucial roles in the signaling pathways of innate immunity, and thus become attractive therapeutic targets of many diseases including infections and cancer. Although TLR7 and TLR8 show a highly degree of sequence homology, their biological response to small molecule binding is very different. Aiming to understand the mechanism of selective profiles of small molecule modulators against TLR7 and TLR8, we carried out molecular dynamic simulations on three imidazoquinoline derivatives bound to the receptors separately. They are Resiquimod (R), Hybrid-2 (H), and Gardiquimod (G), selective agonists of TLR7 and TLR8. Our MD trajectories indicated that in the complex of TLR7-R and TLR7-G, the two chains forming the TLR7 dimer tended to remain "open" conformation, while the rest systems maintained in the closed format. The agonists R, H, and G developed conformational deviation mainly on the aliphatic tail. Furthermore, we attempted to quantify the selectivity between TLR7 and TLR8 by binding free energies via MM-GBSA method. It showed that the three selected modulators were more favorable for TLR7 than TLR8, and the ranking from the strongest to the weakest was H, R and G, aligning well with experiment data. In the TLR7, the flexible and hydrophobic aliphatic side chain of H has stronger van der Waals interactions with Val381 and Phe351 but only pick up interaction with one amino acid residue i.e. Tyr353 of TLR8. Unsurprisingly, the positively charged side chain of G has less favor interaction with Ile585 of TLR7 and Val573 of TLR8 explaining G is weak agonist in both TLR7 and TLR8. All three imidazoquinolines can form stable hydrogen bonds with Asp555 of TLR7 and the corresponding Asp543 of TLR8. In brief, the set of total 400ns MD studies sheds light on the potential selective mechanisms of agonists towards TLR7 and TLR8, indicating the van der Waals interaction as the driving force for the agonists binding, thus provides us insights for more potent and selective modulators to cooperate with the hydrophobic nature of the binding pocket.

category: immunology


title: A Marmoset Model for Mycobacterium avium Complex Pulmonary Disease

abstract:
RationaleMycobacterium avium complex, is the most common nontuberculous mycobacterial respiratory pathogen in humans. Disease mechanisms are poorly understood due to the absence of a reliable animal model for M. avium complex pulmonary disease.

ObjectiveAssess the susceptibility, immunologic and histopathologic responses of the common marmoset (Callithrix jacchus) to M. avium complex pulmonary infection.

Methods7 adult female marmosets underwent endobronchial inoculation with 108 colony-forming units of M. intracellulare and were monitored for 30 or 60 days. Prior to infection, chest radiograph and serum cytokines were assessed; serum cytokines were also monitored weekly for 30 days. At sacrifice 30 days (3 animals) or 60 days (4 animals) after infection, chest radiograph, serum and bronchoalveolar lavage cytokines, histopathology, and cultures of the bronchoalveolar lavage, lungs, liver, and kidney were analyzed.

Measurements and Main ResultsFive of seven animals (two at 30 days and three at 60 days of infection) had positive lung cultures for M. intracellulare. Extra-pulmonary cultures were positive in three animals. All animals appeared healthy throughout the study. All five animals with positive lung cultures had radiographic changes consistent with pneumonitis. At 30 days, those with M. intracellulare lung infection showed granulomatous inflammation while at 60 days there was less inflammatory change, but bronchiectasis was noted. The cytokine response in the bronchoalveolar lavage fluid was uniformly greater in the animals with positive M. intracellulare cultures than those without a productive infection with greater levels at 30-days compared to 60-days. Similarly, serum cytokines were more elevated in the animals that had positive M. intracellulare cultures compared to those without a productive infection, peaking 14-21 days after inoculation.

ConclusionEndobronchial instillation of M. intracellulare resulted in pulmonary mycobacterial infection in marmosets with a differential immune response, radiographic and histopathologic abnormalities, and an indolent course consistent with M. avium complex lung infection in humans.


title: Estimating the Mosquito Density in Guangzhou city, China

abstract: Mosquito is a vector of many diseases. Predicting the trend of mosquito density is important for early warning and control of mosquito diseases. In this paper, we fit a discrete time mosquito model developed by Gong et al. in 2011, which considers the immature and adult stages, and weather dependent model parameters, to the Breteau Index and Bite Index data for Aedes aegypti in Guangzhou city, China in 2014, as well as the weather data for average temperature, precipitation, evaporation and daylight for the same period. We estimated the model parameters using the Markov Chain Monte-Carlo (MCMC) method. We find that many parameters are not identifiable. We revise and simplify the model so that the parameters of our new model are identifiable. Our results indicate that the model predicted mosquito prevalence agrees well with data. We then use the fitted parameter values against the Breteau Index and Bite Index data for Guangzhou city in 2017 and 2018, and show that the estimated parameter values are applicable for other seasons.

category: ecology


title: Distinct properties in ventral pallidum projection neuron subtypes

abstract: The ventral pallidum (VP), a major component of the basal ganglia, plays a critical role in motivational disorders. It sends projections to many different brain regions but it is not yet known whether and how these projections differ in their cellular properties, gene expression patterns, connectivity and role in reward seeking. In this study, we focus on four major outputs of the VP - to the lateral hypothalamus (LH), ventral tegmental area (VTA), mediodorsal thalamus (MDT), and lateral habenula (LHb) - and examine the differences between them in 1) baseline gene expression profiles using projection-specific RNA-sequencing; 2) physiological parameters using whole-cell patch clamp; and 3) their influence on cocaine reward using chemogenetic tools. We show that these four VP efferents differ in all three aspects and highlight specifically differences between the projections to the LH and the VTA. These two projections originate largely from separate populations of neurons, express distinct sets of genes related to neurobiological functions, and show opposite physiological and behavioral properties. Collectively, our data demonstrates for the first time that VP neurons exhibit distinct molecular and cellular profiles in a projection-specific manner, suggesting that they represent different cell types.


title: Cortex-independent open-loop control of a voluntary orofacial motor action

abstract: Whether using our eyes or our hands, we interact with our environment through mobile sensors. The efficient use of these sensory organs implies the ability to track their position; otherwise, perceptual stability and prehension would be profoundly impeded1,2. The nervous system may be informed about the position of a sensory organ via two complementary feedback mechanisms: peripheral reafference (external, sensory feedback) and efference copy (internal feedback)3-6. Yet, the potential contributions of these mechanisms remain largely unexplored. By training rats to place their vibrissae within a predetermined angular range without contact, a task that depends on knowledge of vibrissa position relative to their face, we found that peripheral reafference is not required. The presence of motor cortex is not required either, even in the absence of peripheral reafference. On the other hand, the red nucleus, which receives descending inputs from motor cortex and the cerebellum and projects to facial motoneurons7-10, is critical for the execution of the vibrissa task. All told, our results demonstrate the existence of an open-loop control by an internal model that is sufficient to drive voluntary motion. The internal model is independent of motor cortex and likely contains the cerebellum and associated nuclei.


title: Schema support for forming inferences in the human brain

abstract:
Associative inference, the process of drawing novel links between existing knowledge to rapidly integrate associated information, is supported by the hippocampus and neocortex. Within the neocortex, the medial prefrontal cortex (mPFC) has been implicated in the rapid cortical learning of new information that is congruent with an existing framework of knowledge, or schema. How the brain integrates associations to form inferences, specifically how inferences are represented, is not well understood. In this study, we investigate how the brain uses schemas to facilitate memory integration in an associative inference paradigm (A-B-C-D). We conducted two event-related fMRI experiments in which participants retrieved previously learned direct (AB, BC, CD) and inferred (AC, AD) associations between word pairs for items that are schema congruent or incongruent. Additionally, we investigated how two factors known to affect memory, a delay with sleep, and reward, modulate the neural integration of associations within, and between, schema. Schema congruency was found to benefit the integration of associates, but only when retrieval immediately follows learning. RSA revealed that neural patterns of inferred pairs (AC) in the PHc, mPFC, and posHPC were more similar to their constituents (AB and BC) when the items were schema congruent, suggesting that schema facilitates the assimilation of paired items into a single inferred unit containing all associated elements. Furthermore, a delay with sleep, but not reward, impacted the assimilation of inferred pairs. Our findings reveal that the neural representations of overlapping associations are integrated into novel representations through the support of memory schema.

Significance StatementOur ability to draw novel links between pieces of existing knowledge allows us to understand how information in memory is related. Existing knowledge (memory  schema) can facilitate learning, and then integration, of new related information. We ask how the human brain uses schema to form links between related pieces of information, and how sleep and reward affect this process. Our results suggest that memory schema helps pieces of knowledge become a single inferred unit in the brains memory systems. A delay with sleep between learning and retrieval, though not reward, is important for how schema achieve this.


title: River network rearrangements promote speciation in lowland Amazonian birds

abstract: Large Amazonian rivers impede dispersal for many species, but lowland river networks frequently rearrange, thereby altering the location and effectiveness of river-barriers through time. These rearrangements may promote biotic diversification by facilitating episodic allopatry and secondary contact among populations. We sequenced genome-wide markers to evaluate histories of divergence and introgression in six Amazonian avian species-complexes. We first tested the assumption that rivers are barriers for these taxa and found that even relatively small rivers facilitate divergence. We then tested whether species diverged with gene flow and recovered reticulate histories for all species, including one potential case of hybrid speciation. Our results support the hypothesis that river dynamics promote speciation and reveal that many rainforest taxa are micro-endemic, unrecognized and thus threatened with imminent extinction. We propose that Amazonian hyper-diversity originates in part from fine-scale barrier displacement processes -including river dynamics- which allow small populations to differentiate and disperse into secondary contact.

category: evolutionary biology


title: Activation of NLRP3 Inflammasome by Virus-like Particles of Human Polyomaviruses in Macrophages

abstract: Viral antigens can activate phagocytes inducing inflammation but the mechanisms are barely explored. This study aimed to investigate the capability of viral oligomeric proteins of different structure to induce inflammatory response in macrophages. Human THP-1 cell line was used to prepare macrophages which were treated with filamentous nucleocapsid-like particles (NLPs) of paramyxoviruses and spherical virus-like particles (VLPs) of human polyomaviruses. The effects of viral proteins on cell viability, pro-inflammatory cytokines production and formation of NLRP3 inflammasome components, ASC specks, were investigated. Filamentous NLPs did not induce inflammation markers while spherical VLPs mediated inflammatory response followed by NLRP3 inflammasome activation. Inhibitors of cathepsins and K+ efflux decreased IL-1{beta} levels and cell death indicating a complex inflammasome activation process. Similar activation pattern was observed in primary human macrophages treated with VLPs. Single cell RNAseq analysis of THP-1 cells revealed several cell activation states characterized by high expression of inflammation-related genes. This study provides new insights into interaction of viral proteins with innate immune cells and suggests that structural properties of oligomeric proteins may define cell activation pathways.


title: Clostridioides difficile phosphoproteomics shows an expansion of phosphorylated proteins in stationary growth phase

abstract:
Phosphorylation is a post-translational modification that can affect both house-keeping functions and virulence characteristics in bacterial pathogens. In the Gram-positive enteropathogen Clostridioides difficile the extent and nature of phosphorylation events is poorly characterized, though a protein-kinase mutant strain demonstrates pleiotropic phenotypes. Here, we used an immobilized metal affinity chromatography strategy to characterize serine, threonine and tyrosine phosphorylation in C. difficile. We find limited protein phosphorylation in the exponential growth phase but a sharp increase in the number of phosphopeptides after the onset of stationary growth phase. Among the overall more than 1500 phosphosites, our approach identifies expected targets and phosphorylation sites, including the protein kinase PrkC, the anti-sigma-F factor antagonist (SpoIIAA), the anti-sigma-B factor antagonist (RsbV) and HPr kinase/phosphorylase (HprK). Analysis of high-confidence phosphosites shows that phosphorylation on serine residues is most common, followed by threonine and tyrosine phosphorylation. This work forms the basis for a further investigation into the contributions of individual kinases to the overall phosphoproteome of C. difficile and the role of phosphorylation in C. difficile physiology and pathogenesis.

ImportanceIn this manuscript, we present a comprehensive analysis of protein phosphorylation in the Gram-positive enteropathogen Clostridioides difficile. To date, only limited evidence on the role of phosphorylation in regulation in this organism has been published; the current study is expected to form the basis for research on this post-translational modification in C. difficile.


title: Putative novel avian paramyxoviruses identified from wild bird surveillance (United States, 2016?2018) and retrospective analysis of APMV-2s and APMV-6s in GenBank

abstract:
Avian paramyxoviruses (APMVs) (subfamily Avulavirinae) have been isolated from over 200 species of wild and domestic birds from around the world. The International Committee on Taxonomy of Viruses (ICTV) currently defines 22 different APMV species, with Avian orthoavulavirus 1 (whose viruses are designated as APMV-1) being the most frequently studied due to its economic burden to the poultry industry. Less is known about other APMV species, including limited knowledge on the genetic diversity in wild birds and there is a paucity of public whole genome sequences for APMV-2 to -22. The goal of this study was to use MinION sequencing to genetically characterize APMVs isolated from wild bird swab samples collected during 2016-2018 in the United States. Multiplexed MinION libraries were prepared using a random strand-switching approach using 37 egg-cultured, influenza-negative, hemagglutination-positive samples. Thirty-five APMV isolates that had complete polymerase coding sequences were speciated using ICTVs current Paramyxoviridae phylogenetic methodology. Viruses from APMV-1, -4, -6, -8 were classified, one putative novel species (Avian orthoavulavirus 23) was identified from viruses isolated in this study, two putative new APMV species (Avian metaavulavirus 24 and 27) were identified from viruses isolated in this study and from retrospective GenBank sequences, and two putative new APMV species (Avian metaavulavirus 25 and 26) were identified solely from retrospective GenBank sequences. Furthermore, co-infections of APMVs were identified in a subset of the samples. The potential limitations of the branch length being the only speciation criterion and the potential benefit of a group pairwise distance analysis are discussed.

ImportanceMost species of APMVs are understudied and/or underreported and many species were incidentally identified from asymptomatic wild birds; however, the disease significance of APMVs in wild birds is not fully determined. The rapid rise in high-throughput sequencing coupled with avian influenza surveillance programs have identified 12 different APMV species in the last decade and have challenged the resolution of classical serological methods to identify new viral species. Currently, ICTVs only criterion for Paramyxoviridae species classification is the requirement of a branch length >0.03 using a phylogenetic tree constructed from polymerase (L) amino acid sequences. The results from this study identify one new APMV species, propose four additional new APMV species, and highlight that the criterion may have insufficient resolution for APMV species demarcation and that refinement or expansion of this criterion may need to be established for Paramyxoviridae speciation.


title: MiR-144 regulates adipogenesis by mediating formation of C/EBPα-FoxO1 protein complex

abstract: Excessive adipogenesis caused obesity, which was a serious risk of health and led to a series of diseases, including type II diabetes (T2D) for example. Adipocyte as the basic unit of adipose tissue has emerged as one of significant target of the treatment of obesity-related metabolic syndromes by revealed its adipogenic molecular mechanism. MicroRNAs (miRNAs) have been demonstrated involving adipogenesis, and played a crucial role in the competitive endogenous RNA (ceRNA) effect. Besides that, C/EBP as a crucial adipogenic regulator still lacked epigenetic explanation during pre-adipocyte adipogenesis. In this study, we first verified FoxO1 was one of the ceRNA of C/EBP. They co-regulated adipogenesis through formed a protein complex that directly bound to its promoter to activate AdipoQ, and AdipoQ (Adiponectin) was a negative adipocytokines that suppressed adipogenesis, which played an important role in retaining adipogensis balance. Moreover, an adipose tissue specific enriched miRNA, miR-144 was the key regulator of the ceRNA effect between C/EBP and FoxO1, which mediated the C/EBP-FoxO1 complex formation, thus altered AdipoQ, furthermore regulated pre-adipocyte adipogenesis. This research will provide a new supplementary idea of the C/EBP epigenetic role in pre-adipocyte adipogenesis.


title: Polo-like kinase 4 homodimerization is not required for catalytic activation, autodestruction, or centriole assembly

abstract: Polo-like kinase 4 (Plk4) is the master-regulator of centriole assembly and cell cycle-dependent regulation of its activity maintains proper centrosome number. During most of the cell cycle, Plk4 levels are nearly undetectable due to its ability to autophosphorylate and trigger its own ubiquitin-mediated degradation. However, during mitotic exit, Plk4 forms a single aggregate on the centriole surface to stimulate centriole duplication. Whereas most Polo-like kinase family members are monomeric, Plk4 is unique because it forms homodimers. Notably, Plk4 trans-autophosphorylates a degron near its kinase domain, a critical step in autodestruction. While it is thought that the purpose of homodimerization is to promote trans-autophosphorylation, this has not been tested. Here, we generate separation-of-function Plk4 mutants that fail to dimerize, and we show that homodimerization is required to create a binding site for the Plk4 activator, Asterless. Surprisingly, Plk4 dimer mutants are catalytically active in cells, promote centriole assembly, and can trans-autophosphorylate by a process based its on concentration-dependent aggregation. Our findings implicate a concentration-dependent pathway of Plk4 activation that does not require Asterless binding or homodimerization. Lastly, we propose a model of Plk4 cell cycle regulation that utilizes both activation pathways - Asterless-dependent and aggregation-driven - to restrict centriole assembly to mother centrioles.


title: Cell cycle difference creates cortical tension difference that separates germ layer fates.

abstract: The segregation of germ layer fates is a fundamental step for embryogenesis, but the underlying molecular mechanism is unclear. In ascidians, mRNA localization coupled to nuclear migration and subsequent asymmetrical partitioning of the mRNA separates mesodermal and endodermal fates. The lack of quantitative characterization of nuclear and mRNA localization has hindered our understanding of the molecular basis of fate separation. Here, we quantitatively examined the movement of the nucleus and changes in cell shape and found that the nucleus moves to the mesodermal cell side across the region of the future cleavage furrow. However, this migration was not decisive for the asymmetric distribution of Not mRNA. Asymmetry of surface tension, caused by cell cycle difference between animal and vegetal hemisphere cells, deformed the mesendoderm cell and determined the position of the cleavage furrow, thereby ensuring the asymmetric partitioning of Not mRNA and segregation of fates. This study demonstrates how cell cycle control and the physical force relationships between cells are involved in the segregation of developmental fates.

category: developmental biology


title: Telomerase and Alternative Lengthening of Telomeres coexist in the regenerating zebrafish caudal fins

abstract: Telomeres are essential for chromosome protection and genomic stability, and telomerase function is critical to organ homeostasis. Zebrafish has become a useful vertebrate model for understanding the cellular and molecular mechanisms of regeneration. The regeneration capacity of the caudal fin of wild-type zebrafish is not affected by repetitive amputation, but the behavior of telomeres during this process has not yet been studied. In this study, the regeneration process was characterized in a telomerase deficient zebrafish model. Moreover, the regenerative capacity after repetitive amputations and at different ages was studied. Regenerative efficiency decreases with aging in all genotypes and surprisingly, telomere length is maintained even in telomerase deficient genotypes. Our results suggest that telomere length can be maintained by the regenerating cells through the recombination-mediated Alternative Lengthening of Telomeres (ALT) pathway, which is likely to support high rates of cell proliferation during the tailfin regeneration process. As far as we know, this is the first animal model to study ALT mechanism in regeneration, which opens a wealth of possibilities to study new treatments of ALT dependent processes.


title: Oligogenic heterozygous inheritance of sperm abnormalities in mouse

abstract: Male infertility is an important health concern that is expected to have a major genetic etiology. Although high-throughput sequencing has linked gene defects to more than 50% of rare and severe sperm anomalies, less than 20% of common and moderate forms are explained. We hypothesized that this low success rate could at least be partly due to oligogenic defects - the accumulation of several rare heterozygous variants in distinct, but functionally connected, genes. Here, we compared fertility and sperm parameters in male mice harboring one to four heterozygous truncating mutations of genes linked to multiple morphological anomalies of the flagellum (MMAF) syndrome. Results indicated progressively deteriorating sperm morphology and motility with increasing numbers of heterozygous mutations. This first evidence of oligogenic inheritance in failed spermatogenesis strongly suggests that oligogenic heterozygosity could explain a significant proportion of asthenoteratozoospermia cases. The findings presented pave the way to further studies in mice and man.


title: The evolution of widespread recombination suppression on the Dwarf Hamster (Phodopus) X chromosome

abstract:
The mammalian X chromosome shows strong conservation among distantly related species, limiting insights into the distinct selective processes that have shaped sex chromosome evolution. We constructed a chromosome-scale de novo genome assembly for the Siberian dwarf hamster (Phodopus sungorus), a species reported to show extensive recombination suppression across an entire arm of the X chromosome. Combining a physical genome assembly based on shotgun and long-range proximity ligation sequencing with a dense genetic map, we detected widespread suppression of female recombination across [~]65% of the Phodopus X chromosome. This region of suppressed recombination likely corresponds to the Xp arm, which has previously been shown to be highly heterochromatic. Using additional sequencing data from two closely-related species (P. campbelli and P. roborovskii), we show that recombination suppression on Xp appears to be independent of major structural rearrangements. The suppressed Xp arm was enriched for several transposable element families and de-enriched for genes primarily expressed in the placenta, but otherwise showed similar gene densities, expression patterns, and rates of molecular evolution when compared to the recombinant Xq arm. Phodopus Xp gene content and order was also broadly conserved relative to the more distantly related rat X chromosome. Collectively, these data suggest that widespread suppression of recombination has likely evolved through the transient induction of facultative heterochromatin on the Phodopus Xp arm without major changes in chromosome structure or genetic content. Thus, dramatic changes in the recombination landscape have so far had relatively subtle influences on overall patterns of X-linked molecular evolution.

Significance StatementSex chromosome evolution represents a dynamic process of genomic specialization that is thought to be dependent on evolution of recombination. Here we use genome sequencing and genetic mapping to show that one arm comprising the majority of the X chromosome in a species of dwarf hamster has largely lost the ability to recombine in males and females. Although these dramatic shifts in recombination frequencies might eventually lead to sex chromosome degeneration, loss of recombination on this arm is associated with relatively minor changes in chromosome structure and gene contents in this species. These results underscore the conservation of the X chromosome across mammals, and allow us to test predictions about how genetic recombination influences sex chromosome evolution.

category: genomics


title: Rewiring glucose metabolism improves 5-FU efficacy in glycolytic p53-deficient colorectal tumors

abstract: 5-fluorouracil (5-FU) is the backbone for chemotherapy in colorectal cancer (CRC). Response rates in patients are, however, limited to 50%. Despite the importance of 5-FU, the molecular mechanisms by which it induces toxicity remain unclear, limiting the development of strategies to improve efficacy. How fundamental aspects of cancer, such as driver mutations and phenotypic intra-tumor heterogeneity, relate to the 5-FU response is also ill-defined. This is largely due to the shortage of mechanistic studies executed in pre-clinical models that can faithfully recapitulate key CRC features. Here, we analyzed the 5-FU response in human organoids genetically engineered to reproduce the different stages of CRC progression. We find that 5-FU induces pyrimidine imbalance, which leads to DNA damage and cell death. Actively proliferating cancer (stem) cells are accordingly efficiently targeted by 5-FU. Importantly, p53 behaves as a discriminating factor for 5-FU sensitivity, whereas p53-deficiency leads to DNA damage-induced cell death, active p53 protects from these effects through inducing cell cycle arrest. Moreover, we find that targeting the Warburg effect, by rewiring glucose metabolism, enhances 5-FU toxicity by further altering the nucleotide pool and without increasing toxicity in healthy-non-transformed cells. Thus, targeting cancer metabolism in combination with replication stress-inducing chemotherapies emerges as a promising strategy for CRC treatment.

category: cancer biology


title: MKK6 deficiency promotes cardiac dysfunction through MKK3-p38γ/δ-mTOR hyperactivation

abstract:
Stress-activated p38 kinases control a plethora of functions and their dysregulation has been linked to development of steatosis, obesity, immune disorders and cancer. Therefore, they have been identified as potential targets for novel therapeutic strategies. There are four p38 family members (p38, p38{beta}, p38{gamma}, and p38{delta}) that are activated by MKK3 and MKK6. Here we demonstrate that lack of MKK6 reduces the life span in mice. Longitudinal study of cardiac function in Mkk6-/- mice showed that young mice have cardiac hypertrophy which progresses to cardiac dilatation and fibrosis with age. Mechanistically, lack of MKK6 blunts p38 activation while causing MKK3-p38{gamma}/{delta} hyperphosphorylation and increased mTOR signaling, resulting in cardiac hypertrophy. Cardiac hypertrophy in Mkk6-/- mice is reverted by knocking out either p38{gamma} or p38{delta}, or by inhibiting mTOR pathway with rapamycin. In conclusion, we have identified a key role for the MKK3/6-p38{gamma}/{delta} pathway in the development of cardiac hypertrophy, which has important implications for the clinical use of p38 inhibitors in the long-term treatment since they might result in cardiotoxicity.

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category: molecular biology


title: Predicting human decision making in psychological tasks with recurrent neural networks

abstract:
Unlike traditional time series, the action sequences of human decision making usually involve many cognitive processes such as beliefs, desires, intentions and theory of mind, i.e. what others are thinking. This makes predicting human decision making challenging to be treated agnostically to the underlying psychological mechanisms. We propose to use a recurrent neural network architecture based on long short-term memory networks (LSTM) to predict the time series of the actions taken by the human subjects at each step of their decision making, the first application of such methods in this research domain. In this study, we collate the human data from 8 published literature of the Iterated Prisoners Dilemma comprising 168,386 individual decisions and postprocess them into 8,257 behavioral trajectories of 9 actions each for both players. Similarly, we collate 617 trajectories of 95 actions from 10 different published studies of Iowa Gambling Task experiments with healthy human subjects. We train our prediction networks on the behavioral data from these published psychological experiments of human decision making, and demonstrate a clear advantage over the state-of-the-art methods in predicting human decision making trajectories in both single-agent scenarios such as the Iowa Gambling Task and multi-agent scenarios such as the Iterated Prisoners Dilemma. In the prediction, we observe that the weights of the top performers tends to have a wider distribution, and a bigger bias in the LSTM networks, which suggests possible interpretations for the distribution of strategies adopted by each group.

Author summaryThe challenge of predicting human decision is important for many application domains like economy, marketing and artificial intelligence. But the domain where the human behavior modeling is especially crucial is psychology, where the goal is to describe, explain and predict these behaviors. Within this domain, creating agents that effectively mimic human decision making is particularly important. However, despite the many behavioral tasks and analytical methods developed to simulate the process of human decision making in real situations, there have not been a predictive model that can well predict the human decision making trajectories in these psychological tasks. In this predictive modeling problem, we propose to use the long short-term memory networks (LSTM), a popular recurrent neural network architecture and effectively predict the time series of the actions taken by the human subjects at each step of their decision making in both the Iowa Gambling Task, a single-agent game with monetary reward, and the Iterated Prisoners Dilemma, a complex multi-agent social game with non-monetary capital at stake. To the best of our knowledge, this is the first application of such methods in this research domain.


title: Function of FMRP domains in regulating distinct roles of neuronal protein synthesis

abstract: The Fragile X Mental Retardation Protein (FMRP) is an RNA Binding Protein that regulates translation of mRNAs, essential for synaptic development and plasticity. FMRP interacts with a specific set of mRNAs and aids in their microtubule dependent transport and regulates their translation through its association with ribosomes. However, the biochemical role of individual domains of FMRP in forming neuronal granules and associating with microtubules and ribosomes is currently undefined. Here, we report that the C-terminus domain of FMRP is sufficient to bind to ribosomes as well as polysomes akin to the full-length protein. Furthermore, the C-terminus domain alone is essential and responsible for FMRP-mediated translation repression in neurons. However, FMRP-mediated puncta formation and microtubule association is favored by the synergistic combination of FMRP domains and not by individual domains. Interestingly, we show that the phosphorylation of hFMRP at Serine-500 is important in modulating the dynamics of translation by controlling ribosome/polysome association. This is a fundamental mechanism governing the size and number of FMRP puncta, which appear to contain actively translating ribosomes. Finally through the use of pathogenic mutations, we emphasize the hierarchy of the domains of FMRP in their contribution to translation regulation.


title: Atypical relationships between neurofunctional features of print-sound integration and reading abilities in Chinese children with dyslexia

abstract:
Conquering print-sound mappings (e.g., grapheme-phoneme correspondence rules) is vital for developing fluent reading skills. In neuroimaging research, this ability can be indexed by activation differences between audiovisual congruent against incongruent conditions in brain areas such as the left superior temporal cortex. In line with it, individuals with dyslexia have difficulty in tasks requiring print-sound processing, accompanied by a reduced neural integration. However, existing evidence is almost restricted to alphabetic languages. Whether and how multisensory processing of print and sound is impaired in Chinese dyslexia remains underexplored. In this study, we applied a passive audiovisual integration paradigm with functional magnetic resonance imaging to investigate the possible dysfunctions in processing character-sound (opaque; semantics can be automatically accessed) and pinyin-sound associations (transparent; no particular meaning can be confirmed) in Chinese dyslexic children. Unexpectedly, the dyslexic group did not show reduced neural integration compared with typically developing readers in either character or pinyin experiment. However, the results revealed atypical correlations between neural integration and different reading abilities in dyslexia. Specifically, while the neural integration in the left inferior frontal cortex in processing character-sound pairs correlated with silent reading comprehension in both children with and without dyslexia, it was associated with morphological awareness (semantic-related) in controls but with rapid naming (phonological-related) in dyslexics. This result indicates Chinese dyslexic children may not use the same grapho-semantic processing strategy as their typical peers do. As for pinyin-sound processing, while a stronger neural integration in the direction of "congruent > incongruent" in the left occipito-temporal cortex and bilateral superior temporal cortices was associated with better oral reading fluency in the control group, an opposite pattern was found in dyslexia. This finding may reflect dyslexias dysfunctional recruitment of the regions in grapho-phonological processing, which further impedes character learning.

HighlightsO_LINeurofunctional correlates of print-sound integration in Chinese children with and without dyslexia are investigated.
C_LIO_LIDyslexic children show atypical relationships between neural audiovisual integration and reading abilities.
C_LIO_LIChinese children with dyslexia are likely to use inefficient strategies to process characters and pinyin.
C_LI


title: Neural decoding dissociates perceptual grouping between proximity and similarity in visual perception

abstract:
Previous research on perceptual grouping primarily focused on the dynamics of single grouping principle in light of the Gestalt psychology. Yet, there has been comparatively little emphasis on the dissociation across two or more grouping principles. To tackle this issue, the current study aims at investigating how, when, and where the processing of two grouping principles (proximity and similarity) are established in the human brain by using a dimotif lattice paradigm and adjusting the strength of one grouping principle. Specifically, we measured the modulated strength of the other grouping principle, thus forming six visual stimuli. The current psychophysical results showed that similarity grouping effect was enhanced with reduced proximity effect when the grouping cues of proximity and similarity were presented simultaneously. Meanwhile, electrophysiological (EEG) response patterns were able to decode the specific pattern out of the six visual stimuli involving both principles in each trail by using time-resolved multivariate pattern analysis (MVPA). The onsets of the dissociation between the two grouping principles coincided within three time windows: the earliest proximity-defined local visual element arrangement in the middle occipital cortex, the middle-stage processing for feature selection modulating low-level visual cortex in the inferior occipital cortex and fusiform cortex, and the higher-level cognitive integration to make decisions for specific grouping preference in the parietal areas. In addition, brain responses were highly correlated with behavioral grouping. The results therefore provide direct evidence for a link between human perceptual space of grouping decision-making and neural space of these brain response patterns.

Significance statementHow does our brain aggregate meaningless local elements to meaningful global patterns? Here, we used visual stimuli that can be perceived as a whole orientation from one of the two grouping cues (proximity and similarity) when they were presented simultaneously. Behavioral responses showed a trade-off between proximity and similarity. Further, time-resolved MVPA and source estimation results showed three stages for the processing of two grouping cues, involving an early stage in the low-level visual cortex, then the middle stage in the lateral visual cortex, and finally the late stage in the parietal areas. This was among the first attempt employing multivariate analysis to decode the dissociative processing of both proximity and similarity principles within one single study.


title: Postnatal development of centrifugal inputs to the olfactory bulb

abstract: Processing in primary sensory areas is influenced by centrifugal inputs from higher brain areas, providing information about behavioral state, attention, or context. Activity in the olfactory bulb, the first central processing stage of olfactory information, is dynamically modulated by direct projections from a variety of areas in adult mice. Despite the early onset of olfactory sensation compared to other senses, the development of centrifugal inputs to the olfactory bulb remains largely unknown. Using retrograde tracing across development, we show that centrifugal projections to the olfactory bulb are established during the postnatal period in an area-specific manner. While feedback projections from the piriform cortex are already present shortly after birth, they strongly increase in number during postnatal development with an anterior-posterior gradient. Contralateral projections from the anterior olfactory nucleus are present at birth but only appeared postnatally for the nucleus of the lateral olfactory tract. Numbers of olfactory bulb projecting neurons from the lateral entorhinal cortex, ventral hippocampus, and cortical amygdala show a sudden increase at the beginning of the second postnatal week and a delayed development compared to more anterior areas. These anatomical data suggest that limited top-down influence on odor processing in the olfactory bulb may be present at birth, but strongly increases during postnatal development and is only fully established later in life.


title: Role of cation-chloride cotransporters, Na/K-pump, and channels in cell water/ionic balance regulation under hyperosmolar conditions: in silico and experimental studies of opposite RVI and AVD responses of U937 cells to hyperosmolar media

abstract: The work provides a modern mathematical description of animal cell electrochemical system under a balanced state and during the transition caused by an increase in external osmolarity, considering all the main ionic pathways in the cell membrane: the sodium pump, K+, Na+, Cl- electroconductive channels and cotransporters NC, KC, and NKCC. The description is applied to experimental data obtained on U937 cells cultured in suspension, which allows the required assays to be performed, including determination of cell water content using buoyant density, cell ion content using flame photometry, and optical methods using flow cytometry. The study of these cells can serve as a useful model for understanding the general mechanisms of regulation of cellular water and ionic balance, which cannot be properly analyzed in many important practical cases, such as ischemic disturbance of cellular ionic and water balance, when cells cannot be isolated. An essential part of the results is the developed software supplied with an executable file, which allows researchers with no programming experience to calculate unidirectional fluxes of monovalent ions through separate pathways and ion-electrochemical gradients that move ions through them, which is important for studying the functional expression of channels and transporters. It is shown how the developed approach is used to reveal changes in channels and transporters underlying the RVI and AVD responses to the hyperosmolar medium in the studied living U937 cells.


title: Nascent adhesions differentially regulate lamellipodium velocity and persistence

abstract: Cell migration is essential to physiological and pathological biology. Migration is driven by the motion of a leading edge, in which actin polymerization pushes against the edge and adhesions transmit traction to the substrate while membrane tension increases. How the actin and adhesions synergistically control edge protrusion remains elusive. We addressed this question by developing a computational model in which the Brownian ratchet mechanism governs actin filament polymerization against the membrane and the molecular clutch mechanism governs adhesion to the substrate (BR-MC model). Our model predicted that actin polymerization is the most significant driver of protrusion, as actin had a greater effect on protrusion than adhesion assembly. Increasing the lifetime of nascent adhesions also enhanced velocity, but decreased the protrusions motional persistence, because filaments maintained against the cell edge ceased polymerizing as membrane tension increased. We confirmed the model predictions with measurement of adhesion lifetime and edge motion in migrating cells. Adhesions with longer lifetime were associated with faster protrusion velocity and shorter persistence. Experimentally increasing adhesion lifetime increased velocity but decreased persistence. We propose a mechanism for actin polymerization-driven, adhesion-dependent protrusion in which balanced nascent adhesion assembly and lifetime generates protrusions with the power and persistence to drive migration.


title: Artificial selection for predatory behavior results in dietary niche differentiation in an omnivorous mammal

abstract: The diet of an individual is a result of the availability of dietary items and the individuals foraging skills and preferences. Behavioral differences may thus influence diet variation, but the evolvability of diet choice through behavioral evolution has not been studied. We used experimental evolution combined with a field enclosure experiment to test whether behavioral selection leads to dietary divergence. We analysed the individual dietary niche via stable isotope ratios of nitrogen ({delta}15N) and carbon ({delta}13C) in the hair of an omnivorous mammal, bank vole, from 4 lines selected for predatory behavior and 4 unselected control lines. Predatory voles had higher hair {delta}15N values than control voles, supporting our hypothesis that predatory voles would consume a higher trophic level diet (more animal vs. plant foods). This difference was significant in the early but not the late summer season. The {delta}13C values also indicated a seasonal change in the consumed plant matter and a difference in food sources among selection lines in the early summer. These results imply that environmental factors interact with evolved behavioral tendencies to determine dietary niche heterogeneity. Behavioral selection thus has potential to contribute to the evolution of diet choice and ultimately the species ecological niche breadth.


title: A computational study on the optimization of transcranial temporal interfering stimulation with high-definition electrode using unsupervised neural network

abstract: Transcranial temporal interfering stimulation (tTIS) can focally stimulate deep parts of the brain, which are related to specific functions, by using beats at two high AC frequencies that do not affect the human brain. However, it has limitations in terms of calculation time and precision for optimization because of its complexity and non-linearity. We aimed to propose a method using an unsupervised neural network (USNN) for tTIS to optimize quickly the interfering current value of high-definition electrodes, which can finely stimulate the deep part of the brain, and analyze the performance and characteristics of tTIS. A computational study was conducted using 16 realistic head models. This method generated the strongest stimulation on the target, even when targeting deep areas or multi-target stimulation. The tTIS was robust with target depth compared with transcranial alternating current stimulation, and mis-stimulation could be reduced compared with the case of using two-pair inferential stimulation. Optimization of a target could be performed in 3 min. By proposing the USNN for tTIS, we showed that the electrode currents of tTIS can be optimized quickly and accurately, and the possibility of stimulating the deep part of the brain precisely with transcranial electrical stimulation was confirmed.

category: bioengineering


title: The assessment of similarity vectors of fingerprint and UMLS in adverse drug reaction prediction

abstract: Identifying and controlling adverse drug reactions is a complex problem in the pharmacological field. Despite the studies done in different laboratory stages, some adverse drug reactions are recognized after being released, such as Rosiglitazone. Due to such experiences, pharmacists are now more interested in using computational methods to predict adverse drug reactions. In computational methods, finding and representing appropriate drug and adverse reaction features are one of the most critical challenges. Here, we assess fingerprint and target as drug features; and phenotype and unified medical language system as adverse reaction features to predict adverse drug reaction. Meanwhile, we show that drug and adverse reaction features represented by similarity vectors can improve adverse drug prediction. In this regard, we propose four frameworks. Two frameworks are based on random forest classification and neural networks as machine learning methods called F_RF and F_NN, respectively. The rest of them improve two state-of-art matrix factorization models, CS and TMF, by considering target as a drug feature and phenotype as an adverse reaction feature. However, machine learning frameworks with fewer drug and adverse reaction features are more accurate than matrix factorization frameworks. In addition, the F_RF framework performs significantly better than F_NN with ACC = %89.15, AUC = %96.14 and AUPRC = %92.9. Next, we contrast F_RF with some well-known models designed based on similarity vectors of drug and adverse reaction features. Unlike other methods, we do not remove rare reactions from the data set in our frameworks. The data and implementation of proposed frameworks are available at http://bioinformatics.aut.ac.ir/ADRP-ML-NMF/.

category: bioinformatics


title: Deep-BGCpred: A unified deep learning genome-mining framework for biosynthetic gene cluster prediction

abstract: Natural products produced by microorganisms constitute an important source of essential pharmaceuticals, including antimicrobial and anti-tumor drugs. These bioactive molecules are microbial secondary metabolites synthesized by co-localized genes termed Biosynthetic Gene Clusters (BGCs). The rapid increase of microbial genomics resources, due to the availability of high-throughput sequencing technologies, has spurred the development of computational methods for microbial genome mining for BGC discovery. Current machine learning methods, however, have limited successes in uncovering novel BGCs due to an excessive number of false positives in their predictions. To this end, we propose Deep-BGCpred, a framework that effectively addresses the aforementioned issue by improving a deep learning model termed DeepBGC. The new model embeds multi-source protein family domains and employs a stacked Bidirectional Long Short-Term Memory model to boost accuracy for BGC identifications. In particular, it integrates two customized strategies, sliding window strategy and dual-model serial screening, to improve the models performance stability and reduce the number of false positive in BGC predictions. We compare the proposed model against other well-established methods on common benchmarks and achieve new state-of-the-art results with convincing evidences. We expect that researchers working on genome mining for natural products may be greatly benefited from our newly proposed method, Deep-BGCpred.


title: PPAR-delta acts as a metabolic master checkpoint for metastasis in pancreatic cancer

abstract: SO_SCPLOWUMMARYC_SCPLOWIn pancreatic cancer, emerging evidence suggests that PPAR-{delta} overexpression is associated with tumor progression and metastasis, but a mechanistic link is still missing. Here we now show that PPAR-{delta} acts as the integrating upstream regulator for the metabolic rewiring, which is preceding the subsequent initiation of an invasive/metastatic program. Specifically, paracrine and metabolic cues regularly found in the metastasis-promoting tumor stroma consistently enhance, via induction of PPAR-{delta} activity, the glycolytic capacity and reserve of pancreatic cancer cells, respectively, accompanied by decreased mitochondrial oxygen consumption. Consequently, genetic or pharmacological inhibition of PPAR-{delta} results in reduced invasiveness and metastasis. Mechanistically, PPAR-{delta} acts by shifting the MYC/PGC1A balance towards MYC, enhancing metabolic plasticity. Targeting MYC similarly prevents the metabolic switch and subsequent initiation of invasiveness. Therefore, our data demonstrate that PPAR-{delta} is a key initiator for the metabolic reprogramming in pancreatic cancer, thereby acting as a checkpoint for the phenotypic change towards invasiveness. These findings provide compelling evidence for a novel treatment strategy to combat pancreatic cancer progression.


title: Improved two-photon imaging of GPCR-based optogenetic neurotransmitter sensors using orthogonally polarized excitation

abstract: Fluorescent proteins such as GFP are best excited by light that is polarized parallel to the dipole axis of the fluorophore. In most cases, fluorescent proteins are randomly oriented, resulting in unbiased images even when polarized light is used for excitation, e.g. in two-photon microcopy. Here we reveal a surprisingly strong polarization sensitivity in a class of GPCR-based neurotransmitter sensors where the fluorophore is anchored on both ends. In tubular structures such as dendrites, this effect led to a complete loss of membrane signal in dendrites running parallel to the polarization direction of the excitation beam. Our data reveal a major problem for two-photon measurements of neurotransmitter concentration that has not been recognized by the neuroscience community. To remedy the sensitivity to dendritic orientation, we designed an optical device that generates interleaved pulse trains of orthogonal polarization, removing the orientation bias from images. The passive device, which we inserted in the beam path of an existing two-photon microscope, also removed the strong direction bias in second harmonic generation (SHG) images. We conclude that for optical measurements of transmitter concentration with GPCR-based sensors, orthogonally polarized excitation is essential.


title: Relating spinal injury-induced neuropathic pain and spontaneous afferent activity to sleep and respiratory dysfunction

abstract: Spinal cord injury (SCI) can induce dysfunction in a multitude of neural circuits including those that lead to impaired sleep, respiratory dysfunction and neuropathic pain. We used a lower thoracic rodent contusion SCI model - known to develop mechanosensory stimulus hypersensitivity, and spontaneous activity in primary afferents that associates neuropathic pain - and paired this with new approaches that enabled chronic capture of three state sleep and respiration to characterize dysfunction and assess possible interrelations. Noncontact electric field sensors were embedded into home cages for noninvasive capture in naturally behaving mice of the temporal evolution of sleep and respiration changes for 6 weeks after SCI. Hindlimb mechanosensitivity was assessed weekly, and terminal experiments measured primary afferent spontaneous activity in situ from intact lumbar dorsal root ganglia (DRG). We observed that SCI led to increased spontaneous primary afferent activity (both firing rate and the number of spontaneously active DRGs) that correlated with reduced hindpaw mechanical sensitivity, increased respiratory rate variability, and increased sleep fragmentation. This is the first study to measure and link sleep dysfunction and variability in respiratory rate in a SCI model of neuropathic pain, and thereby provide broader insight into the magnitude of overall stress burden initiated by neural circuit dysfunction after SCI.


title: Defining the Transcriptional and Epigenetic Basis of Organotypic Endothelial Diversity in the Developing and Adult Mouse

abstract: Significant phenotypic differences exist between the vascular endothelium of different organs, including cell-cell junctions, paracellular fluid transport, shape, and mural cell coverage. These organ-specific morphological features ultimately manifest as different functional capacities, as demonstrated by the dramatic differences in capillary permeability between the leaky vessels of the liver compared to the almost impermeable vasculature found in the brain. While these morphological and functional differences have been long appreciated, the molecular basis of endothelial organ specialization remains unclear. To determine the epigenetic and transcriptional mechanisms driving this functional heterogeneity, we profiled accessible chromatin, as well as gene expression, in six different organs, across three distinct time points, during murine development and in adulthood. After identifying both common, and organ-specific DNA motif usage and transcriptional signatures, we then focused our studies on the endothelium of the central nervous system. Using single cell RNA-seq, we identified key gene regulatory networks governing brain blood vessel maturation, including TCF/LEF and FOX transcription factors. Critically, these unique regulatory regions and gene expression signatures are evolutionarily conserved in humans. Collectively, this work provides a valuable resource for identifying the transcriptional regulators controlling organ-specific endothelial specialization and provides novel insight into the gene regulatory networks governing the maturation and maintenance of the cerebrovasculature.


title: Detection of insect health with deep learning on near-infrared sensor data

abstract:
Conventional monitoring methods for disease vectors, pollinators or agricultural pests require time-consuming trapping and identification of individual insects. Automated optical sensors that detect backscattered near-infrared modulations created by flying insects are increasingly used to identify and count live insects, but do not inform about the health status of individual insects. Here we show that deep learning in trained convolutional neural networks in conjunction with sensors is a promising emerging method to detect infected insects. Health status was correctly determined in 85.6% of cases as early as two days post infection with a fungal pathogen. The ability to monitor insect health in real-time potentially has wide-reaching implications for preserving pollinator biodiversity and the rapid assessment of disease carrying individuals in vector populations.

One sentence summaryAutomated optical sensors distinguish between fungus-infected and healthy insects.


title: Multivalent peptide ligands to probe the chromocenter microenvironment in living cells

abstract: Chromatin is spatially organized into functional states that are defined by both the presence of specific histone post-translational modifications (PTMs) and a defined set of chromatin-associated  reader proteins. Different models for the underlying mechanism of such compartmentalization have been proposed, including liquid-liquid phase separation (LLPS) of chromatin-associated proteins to drive spatial organization. Heterochromatin, characterized by lysine 9 methylation on histone H3 (H3K9me3) and the presence of heterochromatin protein 1 (HP1) as a multivalent reader, represents a prime example of a spatially defined chromatin state. Heterochromatin foci exhibit features of protein condensates driven by LLPS; however, the exact nature of the physicochemical environment within heterochromatin in different cell types is not completely understood. Here, we present tools to interrogate the environment of chromatin sub-compartments in the form of modular, cell-permeable, multivalent and fluorescent peptide probes. These probes can be tuned to target specific chromatin states by providing binding sites to reader proteins and can thereby integrate into the PTM-reader interaction network. As a target, here we generate probes specific to HP1, directing them to heterochromatin at chromocenters in mouse fibroblasts. Moreover, we use a polarity-sensing photoactivatable probe that photoconverts to a fluorescent state in phase-separated protein droplets and thereby reports on the local microenvironment. Equipped with this dye, our probes indeed turn fluorescent in murine chromocenters. However, image analysis and single-molecule tracking experiments reveal that the compartments are less dense and more dynamic than HP1 condensates obtained in vitro. Our results thus demonstrate that the local organization of heterochromatin in chromocenters is internally more complex than an HP1 condensate.


title: A trans-acting long non-coding RNA represses flowering in Arabidopsis

abstract: Eukaryotic genomes give rise to thousands of long non-coding RNAs (lncRNAs), yet the purpose of lncRNAs remains largely enigmatic. Functional characterization of lncRNAs is challenging due to multiple orthogonal hypothesis for molecular activities of lncRNA loci. Here, we identified a flowering associated intergenic lncRNA (FLAIL) that represses flowering in Arabidopsis. An allelic series of flail loss-of-function mutants generated by CRISPR/Cas9 and T-DNA mutagenesis showed an early flowering phenotype. Gene expression analyses in flail mutants revealed differentially expressed genes linked to the regulation of flowering. A genomic rescue fragment of FLAIL introduced in flail mutants complemented gene expression defects and early flowering, consistent with trans-acting effects of the FLAIL RNA. Knock-down of FLAIL RNA levels using the artificial microRNA approach revealed an early flowering phenotype shared with genomic mutations, indicating a trans-acting role of FLAIL RNA in the repression of flowering time. Genome-wide detection of FLAIL-DNA interactions by ChIRP-seq suggested that FLAIL may directly bind genomic regions. FLAIL bound to genes involved in regulation of flowering that were differentially expressed in flail, consistent with the interpretation of FLAIL as a trans-acting lncRNA directly shaping gene expression. Our findings highlight FLAIL as a trans-acting lncRNA that affects flowering in Arabidopsis, likely through mediating transcriptional regulation of genes directly bound by FLAIL.


title: Extensive gene duplication in Arabidopsis revealed by pseudo-heterozygosity

abstract:
BackgroundIt is apparent that genomes harbor massive amounts of structural variation, and that this variation has largely gone undetected for technical reasons. In addition to being inherently interesting, structural variation can cause artifacts when short-read sequencing data are mapped to a reference genome. In particular, spurious SNPs (that do not show Mendelian segregation) may result from mapping of reads to duplicated regions. Calling SNP using the raw reads of the 1001 Arabidopsis Genomes Project we identified 3.3 million heterozygous SNPs (44% of total). Given that Arabidopsis thaliana (A. thaliana) is highly selfing, we hypothesized that these SNPs reflected cryptic copy number variation, and investigated them further.

ResultsThe heterozygosity we observed consisted of particular SNPs being heterozygous across individuals in a manner that strongly suggests it reflects shared segregating duplications rather than random tracts of residual heterozygosity due to occasional outcrossing. Focusing on such pseudo-heterozygosity in annotated genes, we used GWAS to map the position of the duplicates, identifying 2500 putatively duplicated genes. The results were validated using de novo genome assemblies from six lines. Specific examples included an annotated gene and nearby transposon that, in fact, transpose together. Finally, we use existing bisulfite sequencing data to demonstrate that cryptic structural variation can produce highly inaccurate estimates of DNA methylation polymorphism.

ConclusionsOur study confirms that most heterozygous SNPs calls in A. thaliana are artifacts, and suggest that great caution is needed when analyzing SNP data from short-read sequencing. The finding that 10% of annotated genes exhibit copy-number variation, and the realization that neither gene- nor transposon-annotation necessarily tells us what is actually mobile in the genome suggest that future analyses based on independently assembled genomes will be very informative.


title: Prey speed up, predators slow down: non-consumptive effects on movement behavior of a ciliate predator-prey pair

abstract:
Non-consumptive effects (NCEs) of predators on prey, such as induced defensive strategies, are frequently neglected in the analysis of predator-prey interactions. Yet these effects can have demographic impacts as strong as consumption. As a counterpart to NCEs, resource-availability effects (RAEs) can prompt changes in predators as well, e.g., in their foraging behavior. We studied NCEs and RAEs in the ciliate predator-prey pair Didinium nasutum and Paramecium caudatum. We examined the dependence of prey/predator swimming speed and body size on predator/prey presence. We also investigated prey spatial grouping behavior and the dependence of predator movement on local prey abundance. We collected individual movement and morphology data through videography of laboratory-based populations. We compared swimming speeds and body sizes based on their distributions. We used linear models to respectively quantify the effects of local prey abundance on predator displacements and of predator presence on prey grouping behavior. In the presence of prey, predator individuals swam more slowly, were bigger and made smaller displacements. Further, their displacements decreased with increasing local prey abundance. In contrast, in the presence of predators, proportionally more prey individuals showed a fast-swimming behavior and there was weak evidence for increased prey grouping. Trait changes entail energy expenditure shifts, which likely affect interspecific interactions and populations, as has been shown for NCEs. Less is known about the link between RAEs and demography, but it seems likely that the observed effects scale up to influence community and ecosystem stability, yet this remains largely unexplored.

Significance StatementTo maximize their fitness, organisms balance investment in foraging and avoiding being eaten. The behaviors of prey and predators are thus expected to depend on the presence and absence of each other and serve either to boost the chances of predation evasion or to increase predation success. Here we provide an example of the co-dependence of behaviors in the predator-prey pair Didinium nasutum and Paramecium caudatum. We show that the predator slows down and searches in smaller areas when prey are present, while the prey speeds up and possibly groups more as a response to the presence of predators. Such behavioral changes are likely to have a demographic and community impact that is not accounted for with common measures of predators-prey interactions.

category: animal behavior and cognition


title: Generating weighted and thresholded gene coexpression networks using signed distance correlation

abstract:
Even within well-studied organisms, many genes lack useful functional annotations. One way to generate such functional information is to infer biological relationships between genes or proteins, using a network of gene coexpression data that includes functional annotations. Signed distance correlation has proved useful for the construction of unweighted gene coexpression networks. However, transforming correlation values into unweighted networks may lead to a loss of important biological information related to the intensity of the correlation. Here introduce a principled method to construct weighted gene coexpression networks using signed distance correlation. These networks contain weighted edges only between those pairs of genes whose correlation value is higher than a given threshold. We analyse data from different organisms and find that networks generated with our method based on signed distance correlation are more stable and capture more biological information compared to networks obtained from Pearson correlation. Moreover, we show that signed distance correlation networks capture more biological information than unweighted networks based on the same metric. While we use biological data sets to illustrate the method, the approach is general and can be used to construct networks in other domains.

Data and code availabilityhttps://github.com/javier-pardodiaz/sdcorGCN


title: Explainability methods for differential gene analysis of single cell RNA-seq clustering models

abstract:
Single-cell RNA sequencing (scRNA-seq) produces transcriptomic profiling for individual cells. Due to the lack of cell-class annotations, scRNA-seq is routinely analyzed with unsupervised clustering methods. Because these methods are typically limited to producing clustering predictions (that is, assignment of cells to clusters of similar cells), numerous model agnostic differential expression (DE) libraries have been proposed to identify the genes expressed differently in the detected clusters, as needed in the downstream analysis. In parallel, the advancements in neural networks (NN) brought several model-specific explainability methods to identify salient features based on gradients, eliminating the need for external models.

We propose a comprehensive study to compare the performance of dedicated DE methods, with that of explainability methods typically used in machine learning, both model agnostic (such as SHAP, permutation importance) and model-specific (such as NN gradient-based methods). The DE analysis is performed on the results of 3 state-of-the-art clustering methods based on NNs. Our results on 36 simulated datasets indicate that all analyzed DE methods have limited agreement between them and with ground-truth genes. The gradients method outperforms the traditional DE methods, which en-courages the development of NN-based clustering methods to provide an out-of-the-box DE capability. Employing DE methods on the input data preprocessed by clustering method outperforms the traditional approach of using the original count data, albeit still performing worse than gradient-based methods.


title: NucleoMap: a computational tool for identifying nucleosomes in ultra-high resolution contact maps

abstract: 1Although poorly positioned nucleosomes are ubiquitous in the prokaryote genome, they are difficult to identify with existing nucleosome identification methods. Recently available enhanced high-throughput chromatin conformation capture techniques such as Micro-C, DNase Hi-C, and Hi-CO characterize nucleosome-level chromatin proximity, probing the positions of mono-nucleosomes and the spacing between nucleosome pairs at the same time, enabling profiling of nucleosomes in poorly positioned regions. Here we develop a novel computational approach, NucleoMap, to identify nucleosome positioning from ultra-high resolution chromatin contact maps. By integrating nucleosome binding preferences, read density, and pairing information, NucleoMap precisely locates nucleosomes in both eukaryotic and prokaryotic genomes and outperforms existing nucleosome identification methods in precision and recall. We rigorously characterize genome-wide association in eukaryotes between the spatial organization of mono-nucleosomes and their corresponding histone modifications, protein binding activities, and higher-order chromatin functions. We also predict two tetra-nucleosome folding structures in human embryonic stem cells using machine learning methods and analysis their distribution at different structural and functional regions. Based on the identified nucleosomes, nucleosome contact maps are constructed, reflecting the inter-nucleosome distances and preserving the original datas contact distance profile.


title: The influence of the extracellular domains on the dynamic behavior of membrane proteins

abstract: The dynamic behavior of the plasma membrane proteins mediates various cellular processes, such as cell-cell interactions, transmembrane transport and signaling. It is widely accepted that the dynamics of the membrane proteins is determined either by the interactions of the transmembrane domain with the surrounding lipids or by the interaction of the intracellular domain with cytosolic components such as cortical actin. However, the impact of the extracellular domains (ECDs) on the dynamics of membrane proteins is rather unexplored. Here, we investigate how the ECD size influences protein dynamics in lipid bilayer. We reconstitute ECDs of different molecular weights and heights in model membrane systems and analyze ECD-driven protein sorting in lipid domains as well as protein mobility. We observe that increasing the ECD size leads to a decrease in ordered domain partitioning as well as diffusivity. Our data suggests a critical role of the ECDs on membrane protein behavior in the plasma membrane and paves the way to a more complete understanding of membrane protein dynamics that includes interaction with the extracellular matrix and glycocalyx in health and disease.

category: biophysics


title: Niche difference determines coexistence and similar underlying processes in four ecological groups

abstract: Understanding the drivers of species coexistence is an important objective in ecology. Yet, the multitude of methods to study coexistence hampers cross-community comparisons. Here, we standardized niche and fitness differences (i.e how species limit themselves compared to others and their competitive ability, respectively) across 1018 species pairs to investigate species coexistence across ecological groups and methodological settings (experimental setup, natural co-occurrence, population model used, and growth method). We find that, first, coexistence is driven by large niche differences, not by small fitness differences. Second, species group into clear clusters of coexisting and non-coexisting species along the niche axis. Finally, these clusters are not driven by ecological or methodological settings. This suggests differences between coexisting and non-coexisting communities transcending those measured in our empirical systems. Overall, our results show that species coexistence is mainly influenced by mechanisms acting on niche differences.


title: Niche differences, not fitness differences, explain coexistence across ecological groups