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Search indexed bioRxiv preprints in genomics, neuroscience, cell biology and bioinformatics. Read source abstracts and check manuscript versions; preprints are not peer reviewed.

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bioRxiv2018

A Whole-Genome Association Approach for Large-scaled Inter-species Trait

Genome wide association studies (GWAS) have provided an avenue for the association between common genetic variants and complex traits. However, using SNP as a genetic marker, GWAS has been confined to detect genetic basis traits only for within species but not for the large-scale inter-species traits. Here, we propose a practical statistical approach that is using kmer frequencies as the genetic markers to associate genetic variants with large scale inter-species traits. We applied this new approach to the trait of chromosome number in 96 mammalian proteomes, and we prioritized 130 genes including TP53 and BAD, of which 6 were candidate genes. These genes were proved to be associated with cellular reaction of DNA double-strand breaks caused by chromosome fission/fusion. Our study provides a new effective genomic strategy to perform association studies for large-scaled inter-species traits, using the chromosome number as a case. We hope this approach could provide exploration for broadly widely traits.

genomics↗

bioRxiv2018

Neural dynamics at rest associated with patterns of ongoing thought

Conscious experience is dynamic, and its fluidity is particularly marked when attention is not occupied by events in the external world and our minds are free to wander. Our study used measures of neural function, and advanced analyses techniques to examine how unconstrained neural state transitions relate to patterns of ongoing experience. Neural activity was recorded during wakeful rest using functional magnetic resonance imaging and Hidden Markov modelling identified recurrent patterns of brain activity constituting functional dynamic brain states. Individuals making more frequent transitions between states subsequently described experiences highlighting problem solving and lacking unpleasant intrusive features. Frequent switching between states also predicted better health and well-being as assessed by questionnaire. These data provide evidence that the fluidity with which individuals shift through dynamic neural states has an impact on the nature of ongoing thought, and suggest that greater flexibility at rest is an important indicator of a healthy mind.

neuroscience↗

bioRxiv2018

In vitro model of inflammatory, hypoxia, and cancer stem cell signaling in pancreatic cancer using heterocellular 3-dimensional spheroids

IntroductionAs one of the most aggressive cancers worldwide, pancreatic cancer is associated with an extremely poor prognosis. The pancreatic tumor microenvironment consists of cancer cells and other tumor associated cells. Cross-talk between these different cell types through various signaling molecules results in the development of a more aggressive and malignant phenotype. Additionally, due to the highly dysregulated vasculature of tumors, the inner tumor core becomes hypoxic and eventually necrotic. Therefore, there is a need for the development of a physiologically relevant in vitro model that recapitulates these dynamic cell-cell interactions and the 3-dimensional (3D) structure of pancreatic tumors.\n\nMethodsFour different 3D co-culture spheroid models using different combinations of Panc-1 tumor cells, J774.A1 macrophages, and NIH-3T3 fibroblast cell lines were reproducibly developed using the hanging drop technique in order to mimic the tumor microenvironment and to evaluate the differences in expression of various inflammatory, hypoxia, and cancer stem cell markers, including IL-8, TNF-, TGF-{beta}, HIF-1 HIF-2, SCF, and LDH-A. Additionally, immunofluorescence studies were employed to investigate whether these spheroids tested positive for a cancer stem cell population.\n\nResultsPronounced differences in morphology as well as expression of signalling markers were observed using qPCR, indicative of strong influences of co-culturing different cell lines. These models also tested positive for cancer stem cell (CSCs) markers based on immunofluorescence and qPCR analysis.\n\nConclusionOur results demonstrate the potential of 3D co-culture spheroid models to capture the inflammatory and hypoxic markers of pancreatic tumor microenvironment. We further demonstrate the presence of cancer cells with stem cell markers, similar to actual pancreatic cancer tumor. These spheroids present excellent in vitro system to study tumor-immune-stromal cell interactions as well as test deliverability of potential therapeutics in the tumor microenvironment with accurate physical and physiological barriers.

cancer biology↗

bioRxiv2018

Effects of the Salinity under Soilless Culture Systems on Gamma Linolenic Acid Levels in Borage Seed Oil

Borage is a well-known plant of great importance in human nutrition and health. Expanding knowledge of particular plants that have anti-cancer products is a global concern. There is substantial information regarding the benefits, presence and extraction of gamma linolenic acid (GLA) in different plants around the world, especially in borage seeds. However, there is little information concerning the effects of the salinity of the nutrient solution on the growth and presence of GLA in borage seeds. The objective of this work was to determine the optimal salinity of the nutrient solution for obtaining GLA in soilless cultivation systems. Borage plants were grown in coconut fibre and provided three treatments of nutrient solution of 2.20, 3.35 and 4.50 dS m-1, increasing solution salinity with the standard nutrient solution of concentrated macronutrients as a reference. Vegetative growth, seed production and GLA ratio were measured. The results of vegetative development and GLA production doubled and tripled with the increase in salinity of the nutrient solution, respectively.

plant biology↗

bioRxiv2018

Validation of a low-cost, carbon dioxide-based cryoablation system for percutaneous tumor ablation

Breast cancer rates are rising in low- and middle-income countries (LMICs), yet there is a lack of accessible and cost-effective treatment. As a result, the cancer burden and death rates are highest in LMICs. In an effort to meet this need, our work presents the design and feasibility of a low-cost cryoablation system using widely-available carbon dioxide as the only consumable. This system uses an 8-gauge outer-diameter needle and Joule-Thomson expansion to percutaneously necrose tissue with cryoablation. Bench top experiments characterized temperature dynamics in ultrasound gel demonstrated that isotherms greater than 2 cm were formed. Further, this system was applied to mammary tumors in an in vivo rat model and necrosis was verified by histopathology. Finally, freezing capacity under a large heat load was assessed with an in vivo porcine study, where volumes of necrosis greater than 1.5 cm in diameter confirmed by histopathology were induced in a highly perfused liver after two 7-minute freeze cycles. These results demonstrate the feasibility of a carbon-dioxide based cryoablation system for improving solid tumor treatment options in resource-constrained environments.

bioengineering↗

bioRxiv2018

Cell-autonomous transcriptional mechanism for enhancement of translation capacity in secretory cells

Translation is a basic cellular process and its capacity is adapted to cell function. In particular, secretory cells achieve high protein synthesis levels without triggering the protein stress response. It is unknown how and when translation capacity is increased during differentiation. Here, we show that the transcription factor Creb3l2 is a scaling factor for translation capacity in secretory cells and that it directly binds ~75% of regulatory and effector genes for translation. In parallel with this cell-autonomous mechanism, implementation of the physiological UPR pathway prevents triggering the protein stress response. The pituitary differentiation factor Tpit activates Creb3l2 expression, the Creb3l2-dependent regulatory network as well as the physiological UPR pathway. Thus, Creb3l2 implements high basal translation levels through direct targeting of translation effector genes acting downstream of signaling pathways that otherwise regulate protein synthesis. Expression of Creb3l2 may be a useful means to enhance production of therapeutic proteins.

cell biology↗

bioRxiv2018

Evolutionary exploitation of PD-L1 expression in hormone receptor positive breast cancer

Based on clinical data from hormone positive breast cancer patients, we determined that there is a potential tradeoff between reducing tumor burden and altering metastatic potential when administering combination therapy of aromatase inhibitors and immune checkpoint inhibitors. While hormone-deprivation therapies serve to reduce tumor size in the neoadjuvant setting pre-surgery, they may induce tumors to change expression patterns towards a metastatic phenotype. We used mathematical modeling to explore how the timing of the therapies affects tumor burden and metastatic potential with an eye toward developing a dynamic prognostic score and reducing both tumor size and risk of metastasis.

cancer biology↗

bioRxiv2018

Climate drives spatial variation in Zika epidemics in Latin America

Between 2015 and 2017, Zika virus spread rapidly through populations in the Americas with no prior exposure to the disease. Although climate is a known determinant of many Aedes-transmitted diseases, it is currently unclear whether climate was a major driver the of Zika epidemic and how climate might have differentially impacted outbreak intensity across locations within Latin America. Here, we estimated force of infection for Zika over time and across provinces in Latin America using a time-varying Susceptible Infectious Recovered model. Climate factors explained less than 5% of the variation in weekly transmission intensity in a spatiotemporal model of force of infection by province over time, suggesting that week to week transmission within provinces may be too stochastic to predict. By contrast, climate and population factors were highly predictive of spatial variation in the presence and intensity of Zika transmission among provinces, with pseudo R2 values between 0.33 and 0.60. Temperature, temperature range, rainfall, and population size were the most important predictors of where Zika transmission occurred, while rainfall, relative humidity, and a nonlinear effect of temperature were the best predictors of Zika intensity and burden. Surprisingly, force of infection was greatest in locations with temperatures near 24{degrees}C, much lower than previous estimates from mechanistic models, potentially suggesting that existing vector control programs and/or prior exposure to other mosquito-borne diseases may have limited transmission in locations most suitable for Aedes aegypti, the main vector of Zika, dengue, and chikungunya viruses in Latin America.

ecology↗

bioRxiv2018

Atlas of Subcellular RNA Localization Revealed by APEX-seq

We introduce APEX-seq, a method for RNA sequencing based on spatial proximity to the peroxidase enzyme APEX2. APEX-seq in nine distinct subcellular locales produced a nanometer-resolution spatial map of the human transcriptome, revealing extensive and exquisite patterns of localization for diverse RNA classes and transcript isoforms. We uncover a radial organization of the nuclear transcriptome, which is gated at the inner surface of the nuclear pore for cytoplasmic export of processed transcripts. We identify two distinct pathways of messenger RNA localization to mitochondria, each associated with specific sets of transcripts for building complementary macromolecular machines within the organelle. APEX-seq should be widely applicable to many systems, enabling comprehensive investigations of the spatial transcriptome.

cell biology↗

bioRxiv2018

Microbiota-metabolites interactions in non-human primate gastrointestinal tract

BackgroundThe microbiota has been recognised as an important part for maintaining human health. Perturbation to its structure has been implicated in many diseases, such as obesity and cancers. The microbiota is highly metabolically active and fills in many niche metabolic pathways absent from the human host. Diseases such as obesity, cardiovascular disease and colorectal cancer has been linked to altered microbiota metabolism. However, there is a gap in the current knowledge on how mucosal-associated microbiota and colon mucosa interact. Here we performed an integrated analysis between the mucosal-associated microbiota and the mucosal tissue metabolites in healthy non-human primates.\n\nResultsWe found that the overall microbiota composition is influenced by both the tissue location as well as the host. We also identified bacteria signatures for different intestinal locations. The distal colon bacterial signature includes Ruminococcaceae, Bacteroidales, Christensenellaceae, Clostridiales, Sphaerochaeta, Victivallaceae, GMD14H09, CF231, ML615J-28, RF39 and R4-45B taxa. In the cecum, the signatures include Prevotella, Anaerovibrio, Roseburia, and Anaerostipes. Desulfovibrionaceae family is the only taxon that may be a signature for the duodenum. We also found an intricate global relationship between the microbiota and the host tissue metabolome that is mainly driven by the distal colon. Most importantly, we found microbial-centric tissue metabolites clusters that may have potential implications to studying host-microbiota metabolic interactions.

genomics↗

bioRxiv2018

PS membrane asymmetry influences the folding and insertion of a transmembrane helix

The plasma membrane (PM) contains an asymmetric distribution of lipids between the inner and outer leaflets of its bilayer. A lipid of special interest in eukaryotic cells is the negatively charged phosphatidylserine (PS). In healthy cells, PS is actively sequestered to the inner leaflet of the PM but can redistribute to the outer leaflet when the cell is damaged or at the onset of apoptosis. The influence of PS asymmetry and its loss on membrane protein structure and organization have not been widely addressed. Marginally hydrophobic membrane proteins contain acidic residues in their transmembrane sequence, which can enable topological transitions after membrane association. The pH low insertion peptide (pHLIP), which undergoes a topological reorientation and inserts into the membrane at acidic pH - as its name implies, is a useful and well-characterized model for studying these transitions. Although it is known that the inclusion of PS in symmetric vesicles affects the membrane insertion process of pHLIP by lowering the pH midpoint of insertion, it is unclear how PS asymmetry influences these topological transitions. Here, we studied pHLIPs topology using freely-floating asymmetric phosphatidylcholine (PC)/PS vesicles with PS enriched in the inner leaflet. We developed a modified protocol to create asymmetric vesicles containing PS and employed Annexin V labeled with an Alexa 568 fluorophore as a new probe to quantifying PS asymmetry. For pHLIP, membrane insertion was affected by the surface charge difference between bilayer leaflets caused by the asymmetric distribution of charged lipids between the leaflets. We thus conclude that lipid asymmetry can have consequences for the behavior of membrane-associated proteins. A corollary is that model studies using symmetric bilayers to mimic the PM may fail to capture important aspects of protein-membrane interactions.

biophysics↗

bioRxiv2018

Sex allocation conflict and sexual selection throughout the lifespan of eusocial colonies

Models of sex allocation conflict are central to evolutionary biology but have mostly assumed static decisions, where resource allocation strategies are constant over colony lifespan. Here, we develop a model to study how the evolution of dynamic resource allocation strategies is affected by the queen-worker conflict in annual eusocial insects. We demonstrate that the time of dispersal of sexuals affects the sex allocation ratio through sexual selection on males. Furthermore, our model provides three predictions that depart from established results of classic static allocation models. First, we find that the queen wins the sex allocation conflict, while the workers determine the maximum colony size and colony productivity. Second, male-biased sex allocation and protandry evolve if sexuals disperse directly after eclosion. Third, when workers are more related to new queens, then the proportional investment into queens is expected to be lower, which results from the interacting effect of sexual selection (selecting for protandry) and sex allocation conflict (selecting for earlier switch to producing sexuals). Overall, we find that colony ontogeny crucially affects the outcome of sex-allocation conflict because of the evolution of distinct colony growth phases, which decouples how queens and workers affect allocation decisions and can result in asymmetric control.

evolutionary biology↗

bioRxiv2018

Causally investigating cortical dynamics and signal processing by targeting natural system attractors with precisely timed stimulation.

1Electrical stimulation is a promising tool for interacting with neuronal dynamics to identify neural mechanisms that underlie cognitive function. Since effects of a single short stimulation pulse typically vary greatly and depend on the current network state, many experimental paradigms have rather resorted to continuous or periodic stimulation in order to establish and maintain a desired effect. However, such an approach explicitly leads to forced and unnatural brain activity. Further, continuous stimulation can make it hard to parse the recorded activity and separate neural signal from stimulation artifacts. In this study we propose an alternate strategy: by monitoring a system in realtime, we use the existing preferred states or attractors of the network and to apply short and precise pulses in order to switch between its preferred states. When pushed into one of its attractors, one can use the natural tendency of the system to remain in such a state to prolong the effect of a stimulation pulse, opening a larger window of opportunity to observe the consequences on cognitive processing. To elaborate on this idea, we consider flexible information routing in the visual cortex as a prototypical example. When processing a stimulus, neural populations in the visual cortex have been found to engage in synchronized gamma activity. In this context, selective signal routing is achieved by changing the relative phase between oscillatory activity in sending and receiving populations (communication through coherence, CTC). In order to explore how perturbations interact with CTC, we investigate a biophysically realistic network exhibiting similar synchronization and signal routing phenomena. We develop a closed-loop stimulation paradigm based on the phase-response characteristics of the network and demonstrate its ability to establish desired synchronization states. By measuring information content throughout the model, we evaluate the effect of signal contamination caused by the stimulation in relation to the magnitude of the injected pulses and intrinsic noise in the system. Finally, we demonstrate that, up to a critical noise level, precisely timed perturbations can be used to artificially induce the effect of attention by selectively routing visual signals to higher cortical areas.

neuroscience↗

bioRxiv2018

fruitless functions downstream of doublesex to promote sexual dimorphism of the gonad stem cell niche

Backgrounddoublesex (dsx) and fruitless (fru) are the two downstream transcription factors that actuate Drosophila sex determination. While dsx assists fru to regulate sex-specific behavior, whether fru collaborates with dsx in regulating other aspects of sexual dimorphism remains unknown. One important aspect of sexual dimorphism is found in the gonad stem cell (GSC) niches, where male and female GSCs are regulated to create large numbers of sperm and eggs.\n\nResultsHere we report that Fru is expressed male-specifically in the GSC niche and plays important roles in the development and maintenance of these cells. Unlike previously studied regulation of sex-specific Fru expression, which is regulated by alternative splicing by Transformer (Tra), we show that male-specific expression of fru is regulated downstream of dsx, and is independent of Tra. Regulation of fru by dsx also occurs in the nervous system. fru genetically interacts with dsx to support maintenance of the hub throughout development. Ectopic expression of fru inhibited female niche formation and partially masculinized the ovary. fru is also required autonomously for cyst stem cell maintenance and cyst cell survival. Finally, we identified a conserved Dsx binding site upstream of fru promoter P4 that regulates fru expression in the hub, indicating that fru is likely a direct target for transcriptional regulation by Dsx.\n\nConclusionsThese findings demonstrate that fru acts outside the nervous system to influence sexual dimorphism and reveal a new mechanism for regulating sex-specific expression of fru that is regulated at the transcriptional level by Dsx, rather than by alternative splicing by Tra.

developmental biology↗

bioRxiv2018

Genome-wide association analysis of excessive daytime sleepiness identifies 42 loci that suggest phenotypic subgroups

Excessive daytime sleepiness (EDS) affects 10-20% of the population and is associated with substantial functional deficits. We identified 42 loci for self-reported EDS in GWAS of 452,071 individuals from the UK Biobank, with enrichment for genes expressed in brain tissues and in neuronal transmission pathways. We confirmed the aggregate effect of a genetic risk score of 42 SNPs on EDS in independent Scandinavian cohorts and on other sleep disorders (restless leg syndrome, insomnia) and sleep traits (duration, chronotype, accelerometer-derived sleep efficiency and daytime naps or inactivity). Strong genetic correlations were also seen with obesity, coronary heart disease, psychiatric diseases, cognitive traits and reproductive ageing. EDS variants clustered into two predominant composite phenotypes - sleep propensity and sleep fragmentation - with the former showing stronger evidence for enriched expression in central nervous system tissues, suggesting two unique mechanistic pathways. Mendelian randomization analysis indicated that higher BMI is causally associated with EDS risk, but EDS does not appear to causally influence BMI.

genomics↗

bioRxiv2018

Bacteriophages dynamically modulate the gut microbiota and metabolome

The human gut microbiome is comprised of densely colonizing micro-organisms in dynamic interaction with each other and the host. While the bacterial component of the microbiome is under intense investigation, far less is known about how bacteriophages impact bacterial communities in the gut. We investigated the dynamic effects of phages on a model microbiome using gnotobiotic mice colonized by commensal bacteria that colonize the human infant gut, and found that phage predation not only directly impacts susceptible bacteria but also leads to cascading effects on other bacterial species via inter-bacterial interactions. Using metabolomic profiling, we also found that the shifts in the microbiome caused by phage predation have a direct consequence on the gut metabolome. Our work provides insight into the ecological importance of phages as modulators of bacterial colonization, and additionally suggests the potential impact of gut phages on the host with implications for the use of phages as therapeutic tools to rationally and precisely modulate the microbiome.

microbiology↗

bioRxiv2018

Rapid Tilt-Series Acquisition for Electron Cryotomography

Using a new Titan Krios stage equipped with a single-axis holder, we developed two methods to accelerate the collection of tilt-series. We demonstrate a continuous-tilting method that can record a tilt-series in seconds (about 100x faster than current methods), but with loss of details finer than [~]4 nm. We also demonstrate a fast-incremental method that can record a tilt-series about 10x faster than current methods and with similar resolution. We characterize the utility of both methods in real biological electron cryotomography workflows. We identify opportunities for further improvements in hardware and software and speculate on the impact such advances could have on structural biology.

biophysics↗

bioRxiv2018

Enumeration, Antagonism and Enzymatic Activities of Microorganisms Isolated from Railway Station Soil

Soil is the well-known hotspot for microbial diversity. Therefore, for our investigation, we isolated, characterized, and identified microorganisms from railway station soil. Sampling was done subsequently after every 15 days interval, and from two different soil depths i.e. 0-15 cm and below during March to May of 2013. Further, soil isolates were examined for their antagonistic activity, against four soil born plant pathogens namely, Rhizoctonia solani, Aspergillus niger, Fusarium f sp pisi, and Sclerotinia sclerotiorum. Subsequently, isolates were screened for the presence of amylases, proteases, lipases and cellulases. For each interval of soil sampling, a gradual reduction in the microbial count was noticed from month March to May. Mucor species was observed only in the rainy days. The most promising enzymes producers were Bacillus sp., Aspergillus and Penicillium sp. Overall, the fungal isolates were better producers of enzymes as compared to bacterial isolates.

microbiology↗