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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 Read source abstracts and check manuscript versions; preprints are not peer reviewed.

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Prokaryotic community shifts during soil formation on sands in the tundra zone

A chronosequence approach, i.e., a comparison of spatially distinct plots with different stages of succession, is commonly used for studying microbial community dynamics during paedogenesis. The successional traits of prokaryotic communities following sand fixation processes have previously been characterized for arid and semi-arid regions, but they have not been considered for the tundra zone, where the environmental conditions are unfavourable for the establishment of complicated biocoenoses. In this research, we characterized the prokaryotic diversity and abundance of microbial genes found in a typical tundra and wooded tundra along a gradient of increasing vegetation - unfixed aeolian sand, semi-fixed surfaces with mosses and lichens, and mature soil under fully developed plant cover. Microbial communities from typical tundra and wooded tundra plots at three stages of sand fixation were compared using quantitative polymerase chain reaction (qPCR) and high-throughput sequencing of 16S rRNA gene libraries. The abundances of ribosomal genes increased gradually in both chronosequences, and a similar trend was observed for the functional genes related to the nitrogen cycle (nifH, bacterial amoA, nirK and nirS). The relative abundance of Planctomycetes increased, while those of Thaumarchaeota, Cyanobacteria and Chloroflexi decreased from unfixed sands to mature soils. According to {beta}-diversity analysis, prokaryotic communities of unfixed sands were more heterogeneous compared to those of mature soils. Despite the differences in the plant cover of the two mature soils, the structural compositions of the prokaryotic communities were shaped in the same way.

microbiology

Taking a deeper look: Quantifying the differences in fish assemblages between shallow and mesophotic temperate rocky reefs

The spatial distribution of a species assemblage is often determined by habitat and climate. In the marine environment, depth can become an important factor as degrading light leads to changes in the biological habitat structure. To date, much of the focus of ecological fish research has been based on reefs in less than 40 m with little research on the ecological role of mesophotic reefs. We deployed baited remote underwater stereo video systems (stereo-BRUVS) on temperate reefs in two depth categories: shallow (20-40m) and mesophotic (80-120m), off Port Stephens, Australia. Sites were selected using data collected by swath acoustic sounder to ensure stereo-BRUVS were deployed on reef. The sounder also provided rugosity, slope and relief data for each stereo-BRUVS deployment. Multivariate analysis indicates that there are significant differences in the fish assemblages between shallow and mesophotic reefs, primarily driven by Ophthalmolepis lineolatus and Notolabrus gymnogenis only occurring on shallow reefs and schooling species of fish that were unique to each depth category: Atypichthys strigatus on shallow reefs and Centroberyx affinis on mesophotic reefs. While shallow reefs had a greater species richness and abundance of fish when compared to mesophotic reefs, mesophotic reefs hosted the same species richness of fishery targeted species. Chrysophrys auratus (pink snapper) and Nemodactylus douglassii (grey morwong) are two highly targeted species in this region. While C. auratus was numerically more abundant on shallow reefs, mesophotic reefs provide habitat for larger fish. In comparison, N. douglassii were evenly distributed across all sites sampled. Generalized linear models revealed that depth and habitat type provided the most parsimonious model for predicting the distribution of C. auratus, while habitat type alone best predicted the distribution of N. douglassii. These results demonstrate the importance of mesophotic reefs to fishery targeted species and therefore have implications for informing the management of these fishery resources on shelf rocky reefs.

ecology

Cytologic, Genetic, and Proteomic Analysis of a Yellow Leaf Mutant of Sesame (Sesamum indicum L.), Siyl-1

Leaf color mutation in sesame always affects the growth and development of plantlets, and their yield. To clarify the mechanisms underlying leaf color regulation in sesame, we analyzed a yellow-green leaf mutant. Genetic analysis of the mutant selfing revealed 3 phenotypes--YY, light-yellow (lethal); Yy, yellow-green; and yy, normal green--controlled by an incompletely dominant nuclear gene, Siyl-1. In YY and Yy, the number and morphological structure of the chloroplast changed evidently, with disordered inner matter, and significantly decreased chlorophyll content. To explore the regulation mechanism of leaf color mutation, the proteins expressed among YY, Yy, and yy were analyzed. All 98 differentially expressed proteins (DEPs) were classified into 5 functional groups, in which photosynthesis and energy metabolism (82.7%) occupied a dominant position. Our findings provide the basis for further molecular mechanism and biochemical effect analysis of yellow leaf mutants in plants.

genetics

Disrupted reinforcement learning during post-error slowing in ADHD

ADHD is associated with altered dopamine regulated reinforcement learning on prediction errors. Despite evidence of categorically altered error processing in ADHD, neuroimaging advances have largely investigated models of normal reinforcement learning in greater detail. Further, although reinforcement leaning critically relies on ventral striatum exerting error magnitude related thresholding influences on substantia nigra (SN) and dorsal striatum, these thresholding influences have never been identified with neuroimaging. To identify such thresholding influences, we propose that error magnitude related activities must first be separated from opposite activities in overlapping neural regions during error detection. Here we separate error detection from magnitude related adjustment (post-error slowing) during inhibition errors in the stop signal task in typically developing (TD) and ADHD adolescents using fMRI. In TD, we predicted that: 1) deactivation of dorsal striatum on error detection interrupts ongoing processing, and should be proportional to right frontoparietal response phase activity that has been observed in the SST; 2) deactivation of ventral striatum on post-error slowing exerts thresholding influences on, and should be proportional to activity in dorsal striatum. In ADHD, we predicted that ventral striatum would instead correlate with heightened amygdala responses to errors. We found deactivation of dorsal striatum on error detection correlated with response-phase activity in both groups. In TD, post-error slowing deactivation of ventral striatum correlated with activation of dorsal striatum. In ADHD, ventral striatum correlated with heightened amygdala activity. Further, heightened activities in locus coeruleus (norepinephrine), raphe nucleus (serotonin) and medial septal nuclei (acetylcholine), which all compete for control of DA, and are altered in ADHD, exhibited altered correlations with SN. All correlations in TD were replicated in healthy adults. Results in TD are consistent with dopamine regulated reinforcement learning on post-error slowing. In ADHD, results are consistent with heightened activities in the amygdala and non-dopaminergic neurotransmitter nuclei preventing reinforcement learning.

neuroscience

Designer Sinorhizobium meliloti strains and multi-functional vectors for direct inter-kingdom transfer of high G+C content DNA

Storage and manipulation of large DNA fragments is crucial for synthetic biology applications, yet DNA with high G+C content can be unstable in many host organisms. Here, we report the development of Sinorhizobium meliloti as a new universal host that can store DNA, including high G+C content, and mobilize DNA to Escherichia coli, Saccharomyces cerevisiae, and the eukaryotic microalgae Phaeodactylum tricornutum. We deleted the S. meliloti hsdR restriction-system to enable DNA transformation with up to 1.4 x 105 efficiency. Multi-host and multi-functional shuttle vectors (MHS) were constructed and shown to stably replicate in S. meliloti, E. coli, S. cerevisiae, and P. tricornutum, with a copy-number inducible E. coli origin for isolating plasmid DNA. Crucially, we demonstrated that S. meliloti can act as a universal conjugative donor for MHS plasmids with a cargo of at least 62 kb of G+C rich DNA derived from Deinococcus radiodurans.

synthetic biology

Assessment of Menstrual Hygiene Management and Its Determinants among Adolescent Girls: A Cross-Sectional Study in School adolescent girls in Addis Ababa, Ethiopia.

IntroductionManaging menstruation is essentially dealing with menstrual flow and also in continuing regular activities like going to school, working etc. However, menstruation can place significant obstacles in girls access to health, education and future prospects if they are not equipped for effective menstrual hygiene management.\n\nObjectiveTo assess the menstrual hygiene management and its determinant among school girls in Addis Ababa, Ethiopia.\n\nMethodsCross-sectional study design with quantitative method was carried out among 770 systematically selected adolescent school girls of Addis Ababa from April 1 to May 5, 2017. A self-administered pre-test close ended Amharic questionnaire at school setting was used for data collection. The coding was done using the original English version and entered to EPI-7 software. The quantitative file exported to statistical package for social science (SPSS) version 25.0 software for analysis. Total mean score was used to categorize individuals as good and poor while AOR; 95% CI with p < 0.05 was used to determine factors of menstrual hygiene management practice.\n\nResultThis study had 98% response rate. 530 (70.1%) and 388(51.3%) respondents had good knowledge and practice of menstrual hygiene respectively. The findings also showed a significant positive association between good knowledge of menstruation and girls from mothers whose education were secondary (AOR = 10.012, 95 % CI = 3.628-27.629). Wealth index quantile five (AOR = 9.038, 95 % CI = 3.728-21.909) revealed significant positive association with good practice of menstrual hygiene.\n\nConclusion and recommendationMajority of participants had good knowledge and practice of menstrual hygiene and majority of them were from private school. Although knowledge was better than practice, girls should be educated about the process, use of proper pads or absorbents and its proper disposal.

epidemiology

Are working memory training effects paradigm-specific?

A randomized controlled trial compared complex span and n-back training regimes to investigate the generality of training benefits across materials and paradigms. The memory items and training intensities were equated across programs, providing the first like-with-like comparison of transfer in these two widely-used training paradigms. The stimuli in transfer tests of verbal and visuo-spatial n-back and complex span differed from the trained tasks, but were matched across the untrained paradigms. Pre-to-post changes were observed for untrained n-back tasks following n-back training. Following complex span training there was equivocal evidence for improvements on a verbal complex span task, but no evidence for changes on an untrained visuo-spatial complex span activity. Relative to a no intervention group, the evidence supported no change on an untrained verbal complex span task following either n-back or complex span training. Equivocal evidence was found for improvements on visuo-spatial complex span and verbal and visuo-spatial n-back tasks following both training regimes. Evidence for selective transfer (comparing the two active training groups) was only found for an untrained visuo-spatial n-back task following n-back training. There was no evidence for cross-paradigm transfer. Thus transfer is constrained by working memory paradigm and the nature of individual processes executed within complex span tasks. However, within-paradigm transfer can occur when the change is limited to stimulus category, at least for n-back.

neuroscience

Timing and causes of the distribution pattern of Oncomelania hupensis estimated by molecular and geologic data

AbstractAs the only intermediate host of Schistosoma japonicum, Oncomelania hupensis plays an irreplaceable role in the prevalence of schistosomiasis japonica. Several living subspecies of Oncomelania hupensis are found in Asia, especially in China, Japan,the Philippines, and Sulawesi of Indonesia. The existing geographical distribution pattern of O. hupensis has been influenced by geological events. This study used existing mitochondrial gene data for O. hupensis in the GenBank database and the molecular clock method to estimate the divergence time of each subspecies of O. hupensis. For the first time, the timing and causes of the distribution pattern of the different O. hupensis subspecies were studied by combining molecular data with data on geologic events. The results showed that the uplift and isolation of the Qinghai-Tibet Plateau caused Oncomelania hupensis robertsoni to differentiate 4.76 Ma(Million anniversary), while Oncomelania hupensis guangxiensis was affected by the third Himalayan orogenic movement, differentiating 1.10 Ma. Oncomelania hupensis nosophora was influenced by the formation of the Yonaguni Strait and diverged 1.43 Ma. Influenced by ice ages and interglacial periods, Oncomelania hupensis tangi and Oncomelania hupensis formosana diverged 0.57 Ma. The link of the ancient Yangtze River promoted the spread of O. hupensis to the middle and lower reaches of the Yangtze River, and the developed water network facilitated gene exchange among Oncomelania hupensis hupensis in the area. Eventually, 0.62 Ma, O. h. hupensis differentiated.\n\nAuthor summaryPhylogenetic analysis of Pomatiopsidae species showed that Oncomelania was isolated from other genera and clustered independently in phylogenetic trees. Further analysis of the species Oncomelania hupensis and its subspecies was performed. The snail species O. hupensis has multiple subspecies that exhibit certain differences. These subspecies are distributed across Asia, from Chinas Yunnan Province in the west to Japan in the east and south to the Philippines and Indonesia. In addition, the subspecies are widespread in the middle and lower reaches of the Yangtze River in China, and the distribution ranges of the different subspecies do not overlap. The formation of this distribution pattern of each subspecies of O. hupensis has a profound impact on the prevalence of Schistosoma japonicum. Therefore, the authors analyzed molecular data and geological historical events to investigate the timing and causes of the distribution pattern of each subspecies of O. hupensis.

evolutionary biology

Axl-mediated activation of TBK1 drives epithelial plasticity in pancreatic cancer

Pancreatic ductal adenocarcinoma (PDA) is characterized by an activating mutation in KRAS, which is critical for the biology of PDA progression. Direct inhibition of KRAS through pharmacological means remains a challenge; however, targeting key KRAS effectors has therapeutic potential. We investigated the contribution of TANK-binding kinase 1 (TBK1), a critical downstream effector of mutant active KRAS, to PDA progression. We report that higher levels of TBK1 mRNA are associated with poorer overall survival in human PDA patients and that TBK1 supports the growth and metastasis of KRAS-mutant PDA by driving an epithelial plasticity program in tumor cells that enhances invasive and metastatic capacity. Further, we identify that the receptor tyrosine kinase Axl induces TBK1 activity in a Ras-RalB-dependent manner. These findings demonstrate that TBK1 is central to an Axl-driven epithelial-mesenchymal transition in KRAS-mutant PDA and suggest that interruption of the Axl-TBK1 signaling cascade above or below KRAS has potential therapeutic efficacy in this recalcitrant disease.

cancer biology

Oral microbial dysbiosis linked to worsened periodontal condition in rheumatoid arthritis patients

Rheumatoid arthritis (RA) is an autoimmune disorder associated with increased periodontal destruction. It is thought that RA increases the risk of periodontal disease; it is not known how it influences the oral microbiota. Our aim was to analyze the impact of RA on subgingival microbiota and its association with periodontal inflammation and RA activity. Forty-two patients with RA were compared to 47 control subjects without RA. Patients were screened for probing depth, clinical attachment level, bleeding on probing and classified as with or without periodontitis. Subgingival plaque was examined by Illumina MiSeq Sequencing of 16S rRNA gene V4 region and inflammatory cytokines were measured in saliva. RA was associated to severe periodontal disease. In addition, the severity of RA, reflected by the number of tender and swollen joints, was significantly correlated with the presence of pathogenic oral bacteria (i.e. Fusobacterium nucleatum and Treponema socransky). Non-periodontitis RA patients compared to healthy controls had increased microbial diversity and bacterial load, higher levels of pathogenic species (Prevotella, Selenomonas, Anaeroglobus geminatus, Parvimonas micra, Aggregatibacter actinomycetemcomitans) and reduction of health-related species (Streptococcus, Rothia aeria, Kingela oralis). Genes involved with bacterial virulence (i.e. lipopolysaccharide biosynthesis, peptidases) were more prevalent in the subgingival metagenome of subjects with RA. In addition, the degree of oral inflammation reflected by IL-2, IL-6, TNF-, IFN-{gamma} salivary levels was increased in non-periodontitis RA patients in comparison with controls. Our findings support the hypothesis that RA triggers dysbiosis of subgingival microbiota, which may contribute to worsening periodontal status.\n\nAuthor SummaryRheumatoid arthritis (RA) is an autoimmune disease characterized by joints inflammation, swelling, pain and stiffness. Exactly what starts this disease is still unclear. Some recent studies have suggested mucosal surfaces in the body, like those in the gums, could affect the disease process. It has been observed that people with RA have higher risk of periodontitis (a bacterial inflammatory disease of the gums), compared with the general population, and this may be the start of the autoimmune process. Also, periodontitis increases the severity of RA while interventions by treating periodontitis can improve the symptoms of RA. One of the possible mechanisms that link the higher prevalence of periodontitis in RA patients is the dysbiosis of the oral microbiota triggered by the chronic inflammation in RA. Increased levels of molecules of inflammation may affect the oral environment and change the type of bacteria that live there. Here, we examined RA patients and healthy subjects, screening their oral health and inflammatory markers. We collected their saliva and the dental plaque from the space between the teeth and the gum. We found that RA patients exhibited severe periodontitis, increased levels of inflammatory mediators on their saliva and distinct bacterial communities, with higher proportions of bacteria species linked to periodontal disease, even in patients without periodontitis. We also found that the presence of these bacteria species was linked to worse RA conditions. Our study provides new insights to understand the bi-directional mechanisms linking periodontal disease to the development of RA, showing that we need to pay attention to the oral cavity in patients with RA and refer people for dental evaluation. This practice might have a positive impact in the course of RA.

microbiology

Bayesian phylodynamics of avian influenza virus H9N2 in Asia with time-dependent predictors of migration

Model-based phylodynamic approaches recently employed generalized linear models (GLMs) to uncover potential predictors of viral spread. Very recently some of these models have allowed both the predictors and their coefficients to be time-dependent. However, these studies mainly focused on predictors that are assumed to be constant through time. Here we inferred the phylodynamics of H9N2 viruses isolated in 12 Asian countries and regions under both discrete trait analysis (DTA) and structured coalescent (MASCOT) approaches. Using MASCOT we applied a new time-dependent GLM to uncover the underlying factors behind H9N2 spread. We curated a rich set of time-series predictors including annual international live poultry trade and national poultry production figures. This time-dependent phylodynamic prediction model was compared to commonly employed time-independent alternatives. Additionally the time-dependent MASCOT model allowed for the estimation of viral effective sub-population sizes and their changes through time and these effective population dynamics within each country were predicted by a GLM. International annual poultry trade is a strongly supported predictor of virus migration rates. There was also strong support for geographic proximity as a predictor of migration rate in all GLMs investigated. In time-dependent MASCOT models, national poultry production was also identified as a predictor of virus genetic diversity through time and this signal was obvious in mainland China and Bangladesh. Our application of a recently introduced time-dependent GLM predictors integrated rich time-series data in Bayesian phylodynamic prediction. We demonstrated the contribution of poultry trade and geographic proximity (potentially unheralded wild bird movements) to avian influenza spread in Asia. To gain a better understanding of the drivers of H9N2 spread, we suggest increased surveillance of the H9N2 virus in countries that are currently under-sampled as well as in wild bird populations in the most affected countries.\n\nAuthor summaryWhat drives the geographic dispersal and genetic diversity of H9N2 avian influenza virus in Asia? We used two model-based approaches, DTA and MASCOT, to reconstruct the phylogeographic dynamics of the virus. Further, multiple potential predictors were used to inform the virus spread and population dynamics by GLMs. Here, we maximised the power of time-series predictors in Bayesian phylodynamic prediction. For the first time, we were able to quantify the contribution of both time-series and constant predictors to both migration rates and effective population sizes in a structured population. We identified a positive association of international poultry trade and national poultry production time-series with virus migration rates and effective population sizes respectively. We also identify geographic proximity as a strongly supported driver to virus migration rates and this points to the potential role of wild bird populations in virus dispersal across countries. Our study is a practical exemplar of the use of temporal information in predictors to model heterogeneous spatial diffusion and population dynamic processes and provides direction to H9N2 control efforts in Asia.

epidemiology

Aging Boosts Antiviral CD8+T Cell Memory Through Improved Engagement Of Diversified Recall Response Determinants

The determinants of protective CD8+ memory T cell (CD8+TM) immunity remain incompletely defined and may in fact constitute an evolving agency as aging CD8+TM progressively acquire enhanced rather than impaired recall capacities. Here, we show that old as compared to young antiviral CD8+TM more effectively harness disparate molecular processes (cytokine signaling, trafficking, effector functions, and co-stimulation/inhibition) that in concert confer greater secondary reactivity. The relative reliance on these pathways is contingent on the nature of the secondary challenge (greater for chronic than acute viral infections) and over time, aging CD8+TM re-establish a dependence on the same accessory signals required for effective priming of naive CD8+T cells in the first place. Thus, our findings are consistent with the recently proposed \"rebound model\" that stipulates a gradual alignment of naive and CD8+TM properties, and identify a diversified collection of potential targets that may be exploited for the therapeutic modulation of CD8+TM immunity.

immunology

Apicomplexan motility depends on the operation of an endocytic-secretory cycle

Apicomplexan parasites invade host cells in an active process, involving their ability to move by gliding motility and invasion. While the acto-myosin-system of the parasite plays a crucial role in the formation and release of attachment sites during this process, there are still open questions, such as how the force powering motility is generated. In many eukaryotes a secretory-endocytic cycle leads to recycling of receptors (integrins), necessary to form attachment sites, regulation of surface area during motility and generation of retrograde membrane flow. Here we demonstrate that endocytosis operates during gliding motility in Toxoplasma gondii and appears to be crucial for the establishment of retrograde membrane flow, since inhibition of endocytosis blocks retrograde flow and motility. We identified lysophosphatidic acid (LPA) as a potent stimulator of endocytosis and demonstrate that extracellular parasites can efficiently incorporate exogenous material, such as nanogold particles. Furthermore, we show that surface proteins of the parasite are recycled during this process. Interestingly, the endocytic and secretory pathways of the parasite converge, and endocytosed material is subsequently secreted, demonstrating the operation of an endocytic-secretory cycle. Together our data consolidate previous findings and we propose a novel model that reconciles parasite motility with observations in other eukaryotes: the fountain-flow-model for apicomplexan parasite motility.

molecular biology

Adding function to the genome of African Salmonella ST313

Salmonella Typhimurium ST313 causes invasive nontyphoidal Salmonella (iNTS) disease in sub-Saharan Africa, targeting susceptible HIV+, malarial or malnourished individuals. An in-depth genomic comparison between the ST313 isolate D23580, and the well-characterized ST19 isolate 4/74 that causes gastroenteritis across the globe, revealed extensive synteny. To understand how the 856 nucleotide variations generated phenotypic differences, we devised a large-scale experimental approach that involved the global gene expression analysis of strains D23580 and 4/74 grown in sixteen infection-relevant growth conditions. Comparison of transcriptional patterns identified virulence and metabolic genes that were differentially expressed between D23580 versus 4/74, many of which were validated by proteomics. We also uncovered the S. Typhimurium D23580 and 4/74 genes that showed expression differences during infection of murine macrophages. Our comparative transcriptomic data are presented in a new enhanced version of the Salmonella expression compendium SalComD23580: bioinf.gen.tcd.ie/cgi-bin/salcom_v2.pl. We discovered that the ablation of melibiose utilization was caused by 3 independent SNP mutations in D23580 that are shared across ST313 lineage 2, suggesting that the ability to catabolise this carbon source has been negatively selected during ST313 evolution. The data revealed a novel plasmid maintenance system involving a plasmid-encoded CysS cysteinyl-tRNA synthetase, highlighting the power of large-scale comparative multi-condition analyses to pinpoint key phenotypic differences between bacterial pathovariants.

microbiology

Parallel comparison of pre-conditioning and post-conditioning effects in human cancers and keratinocytes upon acute gamma irradiation

PURPOSETo determine and compare the effects of pre-conditioning and post-conditioning towards gamma radiation responses in human cancer cells and keratinocytes\n\nMATERIALS AND METHODSThe clonogenic survival of glioblastoma cells (T98G), keratinocytes (HaCaT), and colorectal carcinoma cells (HCT116 p53+/+ and p53-/-) was assessed following gamma ray exposure from a Cs-137 source. The priming dose preceded the challenge dose in pre-conditioning whereas the priming dose followed the challenge dose in post-conditioning. The priming dose was either 5 mGy or 0.1 Gy. The challenge dose was 0.5 - 5 Gy.\n\nRESULTSIn both pre- and post-conditioning where the priming dose was 0.1 Gy and the challenge dose was 4 Gy, RAR developed in T98G but not in HaCaT cells. In HCT116 p53+/+, pre-conditioning had either no effect or a radiosensitizing effect and whereas post-conditioning induced either radiosensitizing or radioadaptive effect. The different observed outcomes were dependent on dose, the time interval between the priming and challenge dose, and the time before the first irradiation. Post-conditioning effects could occur with a priming dose as low as 5 mGy in HCT116 p53+/+ cells. When HCT116 cells had no p53 protein expression, the radiosensitizing or radioadaptive response by the conditioning effect was abolished.\n\nCONCLUSIONSThe results suggest that radiation conditioning responses are complex and depend on at least the following factors: the magnitude of priming/challenge dose, the time interval between priming and challenge dose, p53 status, cell seeding time prior to the first radiation treatment. This work is the first parallel comparison demonstrating the potential outcomes of pre- and post-conditioning in different human cell types using environmentally and medically relevant radiation doses.

cancer biology

Efficient Proximal Gradient Algorithm for Inference of Differential Gene Networks

BackgroundGene networks in living cells can change depending on various conditions such as caused by different environments, tissue types, disease states, and development stages. Identifying the differential changes in gene networks is very important to understand molecular basis of various biological process. While existing algorithms can be used to infer two gene networks separately from gene expression data under two different conditions, and then to identify network changes, such an approach does not exploit the data jointly, and it is thus suboptimal. A desirable approach would be clearly to infer two gene networks jointly, which can yield improved estimates of network changes.\n\nResultsIn this paper, we developed a proximal gradient algorithm for differential network (ProGAdNet) inference, that jointly infers two gene networks under different conditions and then identifies changes in the network structure. Computer simulations demonstrated that our ProGAdNet outperformed existing algorithms in terms of inference accuracy, and was much faster than a similar approach for joint inference of gene networks. Gene expression data of breast tumors and normal tissues in the TCGA database were analyzed with our ProGAdNet, and revealed that 268 genes were involved in the changed network edges. Gene set enrichment analysis of this set of 268 genes identified a number of gene sets related to breast cancer or other types of cancer, which corroborated the gene set identified by ProGAdNet was very informative about the cancer disease status. A software package implementing the ProGAdNet and computer simulations is available upon request.\n\nConclusionWith its superior performance over existing algorithms, ProGAdNet provides a valuable tool for finding changes in gene networks, which may aid the discovery of gene-gene interactions changed under different conditions.

bioinformatics

Rapid embryonic cell cycles defer the establishment of heterochromatin by Eggless/SetDB1 in Drosophila

Acquisition of chromatin modifications during embryogenesis distinguishes different regions of an initially naive genome. In many organisms, repetitive DNA is packaged into constitutive heterochromatin that is marked by di/tri methylation of histone H3K9 and the associated protein HP1a. These modifications enforce the unique epigenetic properties of heterochromatin. However, in the early Drosophila melanogaster embryo the heterochromatin lacks these modifications which only appear later when rapid embryonic cell cycles slow down at the Mid-Blastula Transition or MBT. Here we focus on the initial steps restoring heterochromatic modifications in the embryo. We describe the JabbaTrap, a technique for inactivating maternally provided proteins in embryos. Using the JabbaTrap we reveal a major requirement for the methyltransferase Eggless/SetDB1 in the establishment of heterochromatin. In contrast, other methyltransferases contribute minimally. Live-imaging reveals that endogenous Eggless gradually accumulates on chromatin in interphase, but then dissociates in mitosis and its accumulation must restart in the next cell cycle. Cell cycle slowing as the embryo approaches the MBT permits increasing accumulation and action of Eggless at its targets. Experimental manipulation of interphase duration shows that cell cycle speed regulates Eggless. We propose that developmental slowing of the cell cycle times embryonic heterochromatin formation.

developmental biology

Bayesian inference of metabolic kinetics from genome-scale multiomics data

Modern biological tools generate a wealth of data on metabolite and protein concentrations that can be used to help inform new strain designs. However, integrating these data sources to generate predictions of steady-state metabolism typically requires a kinetic description of the enzymatic reactions that occur within a cell. Parameterizing these kinetic models from biological data can be computationally difficult, especially as the amount of data increases. Robust methods must also be able to quantify the uncertainty in model parameters as a function of the available data, which can be particularly computationally intensive. The field of Bayesian inference offers a wide range of methods for estimating distributions in parameter uncertainty. However, these techniques are poorly suited to kinetic metabolic modeling due to the complex kinetic rate laws typically employed and the resulting dynamic system that must be solved. In this paper, we employ linear-logarithmic kinetics to simplify the calculation of steady-state flux distributions and enable efficient sampling and variational inference methods. We demonstrate that detailed information on the posterior distribution of kinetic model parameters can be obtained efficiently at a variety of different problem scales, including large-scale kinetic models trained on multiomics datasets. These results allow modern Bayesian machine learning tools to be leveraged in understanding biological data and developing new, efficient strain designs.

systems biology