Urease-Powered Micromotors with Spatially Selective Distribution of Enzymes for Capturing and Sensing Exosomes

Enzyme-catalyzed micro/nanomotors (MNMs) exhibit tremendous potential for biological isolation and sensing, because of their biocompatibility, versatility, and ready access to biofuel. However, flow field generated by enzyme-catalyzed reactions might significantly hinder performance of surface-linked functional moieties, e.g., the binding interaction between MNMs and target cargos. Herein, we develop enzymatic micromotors with spatially selective distribution of urease to enable the independent operation of various modules and facilitate the capture and sensing of exosomes. When urease is modified into the motors' cavity, the flow field from enzyme catalysis has little effect on the exterior surface of the motors. The active motion and encapsulating urease internally result in enhancement of ∼35% and 18% in binding efficiency of target cargos, e.g., exosomes as an example here, compared to their static counterparts and moving micromotors with urease modified externally, respectively. Once exosomes are trapped, they can be transferred to a clean environment by the motors for Raman signal detection and/or identification using the surface Raman enhancement scattering (SERS) effect of coated gold nanoshell. The biocatalytic micromotors, achieving spatial separation between driving module and function module, offer considerable promise for future design of multifunctional MNMs in biomedicine and diagnostics.

Functional Modules in the Meristems: "Tinkering" in Action

BACKGROUND

A feature of higher plants is the modular principle of body organisation. One of these conservative morphological modules that regulate plant growth, histogenesis and organogenesis is meristems-structures that contain pools of stem cells and are generally organised according to a common principle. Basic content: The development of meristems is under the regulation of molecular modules that contain conservative interacting components and modulate the expression of target genes depending on the developmental context. In this review, we focus on two molecular modules that act in different types of meristems. The WOX-CLAVATA module, which includes the peptide ligand, its receptor and the target transcription factor, is responsible for the formation and control of the activity of all meristem types studied, but it has its own peculiarities in different meristems. Another regulatory module is the so-called florigen-activated complex, which is responsible for the phase transition in the shoot vegetative meristem (e.g., from the vegetative shoot apical meristem to the inflorescence meristem).

CONCLUSIONS

The review considers the composition and functions of these two functional modules in different developmental programmes, as well as their appearance, evolution and use in plant breeding.

Metagenomic study of the gut microbiota associated with cow milk consumption in Chinese peri-/postmenopausal women

Cow milk consumption (CMC) and alterations of gut bacterial composition are proposed to be closely related to human health and disease. Our research aims to investigate the changes in human gut microbial composition in Chinese peri-/postmenopausal women with different CMC habits. A total of 517 subjects were recruited and questionnaires about their CMC status were collected; 394 subjects were included in the final analyses. Fecal samples were used for studying gut bacterial composition. All the subjects were divided into a control group (n = 248) and a CMC group (n = 146) according to their CMC status. Non-parametric tests and LEfSe at different taxonomic levels were used to reveal differentially abundant taxa and functional categories across different CMC groups. Relative abundance (RA) of one phylum (p_Actinobacteria), three genera (g_Bifidobacterium, g_Anaerostipes, and g_Bacteroides), and 28 species diversified significantly across groups. Specifically, taxa g_Anaerostipes (p < 0.01), g_Bacteroides (p < 0.05), s_Anaerostipes_hadrus (p < 0.01), and s_Bifidobacterium_pseudocatenulatum (p < 0.01) were positively correlated with CMC levels, but p_Actinobacteria (p < 0.01) and g_Bifidobacterium (p < 0.01) were negatively associated with CMC levels. KEGG module analysis revealed 48 gut microbiome functional modules significantly (p < 0.05) associated with CMC, including Vibrio cholerae pathogenicity signature, cholera toxins (p = 9.52e-04), and cephamycin C biosynthesis module (p = 0.0057), among others. In conclusion, CMC was associated with changes in gut microbiome patterns including beta diversity and richness of some gut microbiota. The alterations of certain bacteria including g_Anaerostipes and s_Bifidobacterium_pseudocatenulatum in the CMC group should be important for human health. This study further supports the biological value of habitual cow milk consumption.

Large-Scale Integrative Analysis of Soybean Transcriptome Using an Unsupervised Autoencoder Model

Plant tissues are distinguished by their gene expression patterns, which can help identify tissue-specific highly expressed genes and their differential functional modules. For this purpose, large-scale soybean transcriptome samples were collected and processed starting from raw sequencing reads in a uniform analysis pipeline. To address the gene expression heterogeneity in different tissues, we utilized an adversarial deconfounding autoencoder (AD-AE) model to map gene expressions into a latent space and adapted a standard unsupervised autoencoder (AE) model to help effectively extract meaningful biological signals from the noisy data. As a result, four groups of 1,743, 914, 2,107, and 1,451 genes were found highly expressed specifically in leaf, root, seed and nodule tissues, respectively. To obtain key transcription factors (TFs), hub genes and their functional modules in each tissue, we constructed tissue-specific gene regulatory networks (GRNs), and differential correlation networks by using corrected and compressed gene expression data. We validated our results from the literature and gene enrichment analysis, which confirmed many identified tissue-specific genes. Our study represents the largest gene expression analysis in soybean tissues to date. It provides valuable targets for tissue-specific research and helps uncover broader biological patterns. Code is publicly available with open source at https://github.com/LingtaoSu/SoyMeta.

Genomic Characterization of Two Novel RCA Phages Reveals New Insights into the Diversity and Evolution of Marine Viruses

Viruses are the most abundant living entities in marine ecosystems, playing critical roles in altering the structure and function of microbial communities and driving ocean biogeochemistry. Phages that infect Roseobacter clade-affiliated (RCA) cluster strains are an important component of marine viral communities. Here, we characterize the genome sequences of two new RCA phages, CRP-9 and CRP-13, which infect RCA strain FZCC0023. Genomic analysis reveals that CRP-9 and CRP-13 represent a novel evolutionary lineage of marine phages. They both have a DNA replication module most similar to those in Cobavirus group phages. In contrast, their morphogenesis and packaging modules are distinct from those in cobaviruses but homologous to those in HMO-2011-type phages. The genomic architecture of CRP-9 and CRP-13 suggests a genomic recombination event between distinct phage groups. Metagenomic data sets were examined for metagenome-assembled viral genomes (MAVGs) with similar recombinant genome architectures. Fifteen CRP-9-type MAVGs were identified from marine viromes. Additionally, 158 MAVGs were identified containing HMO-2011-type morphogenesis and packaging modules with other types of DNA replication genes, providing more evidence that recombination between different phage groups is a major driver of phage evolution. Altogether, this study significantly expands the understanding of diversity and evolution of marine roseophages. Meanwhile, the analysis of these novel RCA phages and MAVGs highlights the critical role of recombination in shaping phage diversity. These phage sequences are valuable resources for inferring the evolutionary connection of distinct phage groups. IMPORTANCE Diversity and evolution of phages that infect the relatively slow-growing but dominant Roseobacter lineages are largely unknown. In this study, RCA phages CRP-9 and CRP-13 have been isolated on a Roseobacter RCA strain and shown to have a unique genomic architecture, which appears to be the result of a recombination event. CRP-9 and CRP-13 have a DNA replication module most similar to those in Cobavirus group phages and morphogenesis and packaging modules most similar to those in HMO-2011-type phages. HMO-2011-type morphogenesis and packaging modules are found in combination with distinct types of DNA replication genes, suggesting compatibility with various DNA replication modules. Altogether, this study contributes toward a better understanding of marine viral diversity and evolution.

Nitrospina-like Bacteria Are Dominant Potential Mercury Methylators in Both the Oyashio and Kuroshio Regions of the Western North Pacific

Highly neurotoxic methylmercury (MeHg) accumulates in marine organisms, thereby negatively affecting human and environmental health. Recent studies have revealed that oceanic prokaryotes harboring the hgcAB gene pair are involved in Hg methylation. Presently, little is known about the distribution and phylogeny of these genes in distinct oceanic regions of the western North Pacific. In this study, we used metagenomics to survey the distribution of hgcAB genes in the seawater columns of the subarctic Oyashio region and the subtropical Kuroshio region. The hgcAB genes were detected in the MeHg-rich offshore mesopelagic layers of both the Oyashio region, which is a highly productive area in the western North Pacific, and the Kuroshio region, which has low productivity. Comparative analysis revealed that hgcAB genes belonging to the Nitrospina-like lineage were dominant in the MeHg-rich mesopelagic layers of both regions. These results indicate that Nitrospina-like bacteria are the dominant Hg methylators in the mesopelagic layers throughout the western North Pacific. IMPORTANCE MeHg is highly neurotoxic and accumulates in marine organisms. Thus, understanding MeHg production in seawater is critical for environmental and human health. Recent studies have shown that microorganisms harboring mercury-methylating genes (hgcA and hgcB) are involved in MeHg production in several marine environments. Knowing the distribution and phylogeny of hgcAB genes in seawater columns can facilitate assessment of microbial MeHg production in the ocean. We report that hgcAB genes affiliated with the microaerophilic Nitrospina lineage were detected in the MeHg-rich mesopelagic layers of two hydrologically distinct oceanic regions of the western North Pacific. This finding facilitates understanding of the microbial Hg methylation and accumulation in seawater columns of the western North Pacific.

Fluorine-Driven Enhancement of Birefringence in the Fluorooxosulfate: A Deep Evaluation from a Joint Experimental and Computational Study

Understanding and exploring the functional modules (FMs) consisting of local atomic groups can promote the development of the materials with functional performances. Oxygen-containing tetrahedral modules are popular in deep-ultraviolet (DUV) optical materials, but their weak optical anisotropy is adverse to birefringence. Here, the fluorooxosulfate group is proved as a new birefringence-enhanced FM for the first time. The birefringence of fluorooxosulfates can be 4.8-15.5 times that of sulfates with the same metal cations while maintaining a DUV band gap. The polarizing microscope measurement confirms the birefringence enhancement by using the millimeter crystals experimentally. The theoretical studies from micro and macro levels further reveal a novel universal strategy that the fluorine induced anisotropic electronic distribution in fluorooxo-tetrahedral group is responsible for the enhancement of birefringence. This study will guide the future discovery of DUV optical materials with enlarged birefringence.

Systematic prediction of autophagy-related proteins using Arabidopsis thaliana interactome data

Autophagy is a self-degradative process that is crucial for maintaining cellular homeostasis by removing damaged cytoplasmic components and recycling nutrients. Such an evolutionary conserved proteolysis process is regulated by the autophagy-related (Atg) proteins. The incomplete understanding of plant autophagy proteome and the importance of a proteome-wide understanding of the autophagy pathway prompted us to predict Atg proteins and regulators in Arabidopsis. Here, we developed a systems-level algorithm to identify autophagy-related modules (ARMs) based on protein subcellular localization, protein-protein interactions, and known Atg proteins. This generates a detailed landscape of the autophagic modules in Arabidopsis. We found that the newly identified genes in each ARM tend to be upregulated and coexpressed during the senescence stage of Arabidopsis. We also demonstrated that the Golgi apparatus ARM, ARM13, functions in the autophagy process by module clustering and functional analysis. To verify the in silico analysis, the Atg candidates in ARM13 that are functionally similar to the core Atg proteins were selected for experimental validation. Interestingly, two of the previously uncharacterized proteins identified from the ARM analysis, AGD1 and Sec14, exhibited bona fide association with the autophagy protein complex in plant cells, which provides evidence for a cross-talk between intracellular pathways and autophagy. Thus, the computational framework has facilitated the identification and characterization of plant-specific autophagy-related proteins and novel autophagy proteins/regulators in higher eukaryotes.

GelFAP: Gene Functional Analysis Platform for Gastrodia elata

Gastrodia elata, also named Tianma, is a valuable traditional Chinese herbal medicine. It has numerous important pharmacological roles such as in sedation and lowering blood pressure and as anticonvulsant and anti-aging, and it also has effects on the immune and cardiovascular systems. The whole genome sequencing of G. elata has been completed in recent years, which provides a strong support for the construction of the G. elata gene functional analysis platform. Therefore, in our research, we collected and processed 39 transcriptome data of G. elata and constructed the G. elata gene co-expression networks, then we identified functional modules by the weighted correlation network analysis (WGCNA) package. Furthermore, gene families of G. elata were identified by tools including HMMER, iTAK, PfamScan, and InParanoid. Finally, we constructed a gene functional analysis platform for G. elata . In our platform, we introduced functional analysis tools such as BLAST, gene set enrichment analysis (GSEA), and cis-elements (motif) enrichment analysis tool. In addition, we analyzed the co-expression relationship of genes which might participate in the biosynthesis of gastrodin and predicted 19 mannose-binding lectin antifungal proteins of G. elata. We also introduced the usage of the G. elata gene function analysis platform (GelFAP) by analyzing CYP51G1 and GFAP4 genes. Our platform GelFAP may help researchers to explore the gene function of G. elata and make novel discoveries about key genes involved in the biological processes of gastrodin.

Nitrospina-Like Bacteria Are Potential Mercury Methylators in the Mesopelagic Zone in the East China Sea

In natural environments, the production of neurotoxic and bioaccumulative methylmercury (MeHg) is mediated by microorganisms carrying the genes hgcA and hgcB. However, the contribution of these microorganisms to mercury (Hg) methylation or MeHg accumulation in the ocean is poorly understood. Here we determined the total Hg (THg) and MeHg concentrations in seawater samples and conducted a metagenomic survey of the hgcAB genes and functional modules involved in metabolic pathways in the East China Sea (ECS). In the metagenomic analyses, we used paired-end reads and assembled contigs for hgcAB enumeration and phylogenetic analyses in the seawater column. To evaluate the relative abundance of hgcAB in the metagenomic data, we estimated the abundance of recA (single-copy gene of bacteria) as well and then compared them. Moreover, the profiles of prokaryotic community composition were analyzed by 16S rRNA gene (V4 region) deep-sequencing. In the mesopelagic layers, the hgcA sequences were detected, and there was a positive correlation between hgcA abundance relative to the recA and MeHg concentrations. Thus, the quantification of the hgcA sequences could provide valuable information to evaluate the potential environments of microbial MeHg accumulation in the seawater column. A phylogenetic analysis using the assembled contigs revealed that all of the hgcA sequences in the mesopelagic layers were affiliated with Nitrospina-like sequences. The 16S rRNA gene analysis revealed that Nitrospinae were abundant in the mesopelagic layers. Although the lineages of Deltaproteobacteria, Firmicutes, and Spirochaetes were detected in the seawater column, their hgcAB sequences were not detected in our metagenomes, despite the fact that they are closely related to previously identified Hg methylators. The metabolic pathway analysis revealed that the modules related to sulfur and methane metabolism were prominent in the mesopelagic layers. However, no hgcA sequences affiliated with sulfate-reducing bacteria (SRB) or methanogens were detected in these layers, suggesting that these bacteria could not be strongly involved in the Hg accumulation in the seawater column. Our results indicate that Nitrospina-like bacteria with hgcAB genes could play a critical role in microbial Hg accumulation in the oxygenated mesopelagic layers of the ECS.

Dual regulation of xylem formation by an auxin-mediated PaC3H17-PaMYB199 module in Populus

Wood (secondary xylem) formation in tree species is dependent on auxin-mediated vascular cambium activity in stems. However, the complex regulatory networks underlying xylem formation remain elusive. Xylem development in Populus was characterized based on microscopic observations of stem sections in transgenic plants. Transcriptomic, quantitative real-time PCR, chromatin immunoprecipitation PCR, and electrophoretic mobility shift assay analyses were conducted to identify target genes involved in xylem development. Yeast two-hybrid, pull-down, bimolecular fluorescence complementation, and co-immunoprecipitation assays were used to validate protein-protein interactions. PaC3H17 and its target PaMYB199 were found to be predominantly expressed in the vascular cambium and developing secondary xylem in Populus stems and play opposite roles in controlling cambial cell proliferation and secondary cell wall thickening through an overlapping pathway. Further, PaC3H17 interacts with PaMYB199 to form a complex, attenuating PaMYB199-driven suppression of its xylem targets. Exogenous auxin application enhances the dual control of the PaC3H17-PaMYB199 module during cambium division, thereby promoting secondary cell wall deposition. Dual regulation of xylem formation by an auxin-mediated PaC3H17-PaMYB199 module represents a novel regulatory mechanism in Populus, increasing our understanding of the regulatory networks involved in wood formation.

A network-based algorithm for the identification of moonlighting noncoding RNAs and its application in sepsis

Moonlighting proteins provide more options for cells to execute multiple functions without increasing the genome and transcriptome complexity. Although there have long been calls for computational methods for the prediction of moonlighting proteins, no method has been designed for determining moonlighting long noncoding ribonucleicacidz (RNAs) (mlncRNAs). Previously, we developed an algorithm MoonFinder for the identification of mlncRNAs at the genome level based on the functional annotation and interactome data of lncRNAs and proteins. Here, we update MoonFinder to MoonFinder v2.0 by providing an extensive framework for the detection of protein modules and the establishment of RNA-module associations in human. A novel measure, moonlighting coefficient, was also proposed to assess the confidence of an ncRNA acting in a moonlighting manner. Moreover, we explored the expression characteristics of mlncRNAs in sepsis, in which we found that mlncRNAs tend to be upregulated and differentially expressed. Interestingly, the mlncRNAs are mutually exclusive in terms of coexpression when compared to the other lncRNAs. Overall, MoonFinder v2.0 is dedicated to the prediction of human mlncRNAs and thus bears great promise to serve as a valuable R package for worldwide research communities (https://cran.r-project.org/web/packages/MoonFinder/index.html). Also, our analyses provide the first attempt to characterize mlncRNA expression and coexpression properties in adult sepsis patients, which will facilitate the understanding of the interaction and expression patterns of mlncRNAs.

[Nature-effect relationship research of cold and warm medicinal properties of traditional Chinese medicine for promoting blood circulation and removing blood stasis based on nature combination]

Traditional Chinese medicine for promoting blood circulation and removing blood stasis is a kind of drug with cold or warm medicinal properties which is commonly used in clinical practice. It is an excellent carrier for studying the nature-effect relationship of traditional Chinese medicine. Therefore,this study will acquire the main active components and targets based on the drug-based research method. The Cytoscape 3. 5. 1 platform was used to construct the protein interaction network,and the Bin GO plug-in was used to perform functional annotation and statistical analysis on the identified functional modules. The results showed that the bitter-liver protein interaction network mainly participates in cell cycle process,lipid catabolic process,blood circulation to exert the effect of promoting blood circulation and removing blood stasis; the cold protein interaction network mainly participates in vasoconstriction through targets such as EDNRA,regulates blood coagulation through targets such as PLAU,and thus exerts the effect of cooling blood and eliminating phlegm; warm protein interaction network mainly participates in the regulation of platelet activation through targets such as P2 RY12,thereby exerting the effect of promoting blood circulation,relieving pain and relieving pain. This study explains the common characteristics of the bitter-liver combination and the specific characteristics of cold or warm medicinal properties from the molecular network level,which provides a new idea for the intrinsic relationship between the medicinal properties and efficacy of traditional Chinese medicine.

croFGD: Catharanthus roseus Functional Genomics Database

Catharanthus roseus is a medicinal plant, which can produce monoterpene indole alkaloid (MIA) metabolites with biological activity and is rich in vinblastine and vincristine. With release of the scaffolded genome sequence of C. roseus, it is necessary to annotate gene functions on the whole-genome level. Recently, 53 RNA-seq datasets are available in public with different tissues (flower, root, leaf, seedling, and shoot) and different treatments (MeJA, PnWB infection and yeast elicitor). We used in-house data process pipeline with the combination of PCC and MR algorithms to construct a co-expression network exploring multi-dimensional gene expression (global, tissue preferential, and treat response) through multi-layered approaches. In the meanwhile, we added miRNA-target pairs, predicted PPI pairs into the network and provided several tools such as gene set enrichment analysis, functional module enrichment analysis, and motif analysis for functional prediction of the co-expression genes. Finally, we have constructed an online croFGD database (http://bioinformatics.cau.edu.cn/croFGD/). We hope croFGD can help the communities to study the C. roseus functional genomics and make novel discoveries about key genes involved in some important biological processes.

AppleMDO: A Multi-Dimensional Omics Database for Apple Co-Expression Networks and Chromatin States

As an economically important crop, apple is one of the most cultivated fruit trees in temperate regions worldwide. Recently, a large number of high-quality transcriptomic and epigenomic datasets for apple were made available to the public, which could be helpful in inferring gene regulatory relationships and thus predicting gene function at the genome level. Through integration of the available apple genomic, transcriptomic, and epigenomic datasets, we constructed co-expression networks, identified functional modules, and predicted chromatin states. A total of 112 RNA-seq datasets were integrated to construct a global network and a conditional network (tissue-preferential network). Furthermore, a total of 1,076 functional modules with closely related gene sets were identified to assess the modularity of biological networks and further subjected to functional enrichment analysis. The results showed that the function of many modules was related to development, secondary metabolism, hormone response, and transcriptional regulation. Transcriptional regulation is closely related to epigenetic marks on chromatin. A total of 20 epigenomic datasets, which included ChIP-seq, DNase-seq, and DNA methylation analysis datasets, were integrated and used to classify chromatin states. Based on the ChromHMM algorithm, the genome was divided into 620,122 fragments, which were classified into 24 states according to the combination of epigenetic marks and enriched-feature regions. Finally, through the collaborative analysis of different omics datasets, the online database AppleMDO (http://bioinformatics.cau.edu.cn/AppleMDO/) was established for cross-referencing and the exploration of possible novel functions of apple genes. In addition, gene annotation information and functional support toolkits were also provided. Our database might be convenient for researchers to develop insights into the function of genes related to important agronomic traits and might serve as a reference for other fruit trees.

Spatial dynamics within and between brain functional domains: A hierarchical approach to study time-varying brain function

The analysis of time-varying activity and connectivity patterns (i.e., the chronnectome) using resting-state magnetic resonance imaging has become an important part of ongoing neuroscience discussions. The majority of previous work has focused on variations of temporal coupling among fixed spatial nodes or transition of the dominant activity/connectivity pattern over time. Here, we introduce an approach to capture spatial dynamics within functional domains (FDs), as well as temporal dynamics within and between FDs. The approach models the brain as a hierarchical functional architecture with different levels of granularity, where lower levels have higher functional homogeneity and less dynamic behavior and higher levels have less homogeneity and more dynamic behavior. First, a high-order spatial independent component analysis is used to approximate functional units. A functional unit is a pattern of regions with very similar functional activity over time. Next, functional units are used to construct FDs. Finally, functional modules (FMs) are calculated from FDs, providing an overall view of brain dynamics. Results highlight the spatial fluidity within FDs, including a broad spectrum of changes in regional associations, from strong coupling to complete decoupling. Moreover, FMs capture the dynamic interplay between FDs. Patients with schizophrenia show transient reductions in functional activity and state connectivity across several FDs, particularly the subcortical domain. Activity and connectivity differences convey unique information in many cases (e.g., the default mode) highlighting their complementarity information. The proposed hierarchical model to capture FD spatiotemporal variations provides new insight into the macroscale chronnectome and identifies changes hidden from existing approaches.

Co-expression Gene Network Analysis and Functional Module Identification in Bamboo Growth and Development

Bamboo is one of the fastest-growing non-timber forest plants. Moso bamboo (Phyllostachys edulis) is the most economically valuable bamboo in Asia, especially in China. With the release of the whole-genome sequence of moso bamboo, there are increasing demands for refined annotation of bamboo genes. Recently, large amounts of bamboo transcriptome data have become available, including data on the multiple growth stages of tissues. It is now feasible for us to construct co-expression networks to improve bamboo gene annotation and reveal the relationships between gene expression and growth traits. We integrated the genome sequence of moso bamboo and 78 transcriptome data sets to build genome-wide global and conditional co-expression networks. We overlaid the gene expression results onto the network with multiple dimensions (different development stages). Through combining the co-expression network, module classification and function enrichment tools, we identified 1,896 functional modules related to bamboo development, which covered functions such as photosynthesis, hormone biosynthesis, signal transduction, and secondary cell wall biosynthesis. Furthermore, an online database (http://bioinformatics.cau.edu.cn/bamboo) was built for searching the moso bamboo co-expression network and module enrichment analysis. Our database also includes cis-element analysis, gene set enrichment analysis, and other tools. In summary, we integrated public and in-house bamboo transcriptome data sets and carried out co-expression network analysis and functional module identification. Through data mining, we have yielded some novel insights into the regulation of growth and development. Our established online database might be convenient for the bamboo research community to identify functional genes or modules with important traits.

Nitrogen deposition increases root production and turnover but slows root decomposition in Pinus elliottii plantations

Fine roots of woody plants comprise multiple root orders, which can be functionally partitioned into two pools: absorptive fine roots (AFRs, orders 1, 2) and transport fine roots (TFRs, orders 3-5). However, the function-based fine-root dynamics and especially their responses to increased nitrogen (N) availability remain unclear. We explored dynamic responses of both AFRs and TFRs of Pinus elliottii to N addition in subtropical China based on a 4-yr minirhizotron experiment and a two-stage - early (0.5 yr) vs late (4 yr) - decomposition experiment. N addition increased the production, mortality, and turnover of AFRs but not TFRs. High rates of N persistently inhibited AFR decomposition but affected TFR decomposition differentially at the early (no effect) and late (negative effect) stages. The increased production of AFRs was driven by N-induced decrease in foliar and soil phosphorus (P) concentrations. The decreased decomposition of AFRs might be due to the increased acid-unhydrolyzable residues in decomposing roots. AFRs are the resource-acquiring module, the increased carbon allocation to AFRs may represent a P-acquiring strategy when N no longer limits growth of P. elliottii. Our results suggest that AFRs and TFRs respond differently to N deposition, both in terms of production, mortality, and turnover and in terms of decomposition.

Structure versus time in the evolutionary diversification of avian carotenoid metabolic networks

Historical associations of genes and proteins are thought to delineate pathways available to subsequent evolution; however, the effects of past functional involvements on contemporary evolution are rarely quantified. Here, we examined the extent to which the structure of a carotenoid enzymatic network persists in avian evolution. Specifically, we tested whether the evolution of carotenoid networks was most concordant with phylogenetically structured expansion from core reactions of common ancestors or with subsampling of biochemical pathway modules from an ancestral network. We compared structural and historical associations in 467 carotenoid networks of extant and ancestral species and uncovered the overwhelming effect of pre-existing metabolic network structure on carotenoid diversification over the last 50 million years of avian evolution. Over evolutionary time, birds repeatedly subsampled and recombined conserved biochemical modules, which likely maintained the overall structure of the carotenoid metabolic network during avian evolution. These findings explain the recurrent convergence of evolutionary distant species in carotenoid metabolism and weak phylogenetic signal in avian carotenoid evolution. Remarkable retention of an ancient metabolic structure throughout extensive and prolonged ecological diversification in avian carotenoid metabolism illustrates a fundamental requirement of organismal evolution - historical continuity of a deterministic network that links past and present functional associations of its components.

Sharing the SAGA

Transcription initiation is a major regulatory step in eukaryotic gene expression. Co-activators establish transcriptionally competent promoter architectures and chromatin signatures to allow the formation of the pre-initiation complex (PIC), comprising RNA polymerase II (Pol II) and general transcription factors (GTFs). Many GTFs and co-activators are multisubunit complexes, in which individual components are organized into functional modules carrying specific activities. Recent advances in affinity purification and mass spectrometry analyses have revealed that these complexes often share functional modules, rather than containing unique components. This observation appears remarkably prevalent for chromatin-modifying and remodeling complexes. Here, we use the modular organization of the evolutionary conserved Spt-Ada-Gcn5 acetyltransferase (SAGA) complex as a paradigm to illustrate how co-activators share and combine a relatively limited set of functional tools.

Identification of genes associated with tongue cancer in patients with a history of tobacco and/or alcohol use

The present study aimed to identify genes associated with tongue cancer in patients with a history of tobacco and/or alcohol use. Microarray dataset GSE42023, including 10 tissue samples of tongue cancer from patients with a history of tobacco and/or alcohol use (habit group) and 11 tissue samples of non-habit-associated tongue cancer (non-habit group), were downloaded from the Gene Expression Omnibus database. Differentially-expressed genes (DEGs) between the habit and non-habit groups were identified using the Linear Models for Microarray Data software package. The enrichment functions and pathways of these genes were subsequently predicted using Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analysis. Transcription factors (TFs) and tumor-associated genes (TAGs) were selected from the DEGs using the Encyclopedia of DNA Elements database and the TAG database, respectively. Protein-protein interaction (PPI) networks for DEGs were constructed using Cytoscape. In addition, functional module analysis was performed using BioNet. This analysis identified 642 DEGs between the habit and non-habit groups, including 200 upregulated and 442 downregulated genes. The majority of upregulated DEGs were functionally enriched in the regulation of apoptosis and the calcium signaling pathway. The majority of downregulated DEGs were functionally enriched in fat cell differentiation and the adipocytokine signaling pathway. In addition, 31 TFs and 42 TAGs were identified from the DEGs. Furthermore, this analysis demonstrated that certain DEGs, including AKT serine/threonine kinase 1 (AKT1), E1A binding protein p300 (EP300), erb-b2 receptor tyrosine kinase 2 (ERBB2) and epiregulin (EREG), had high connectivity degrees in the PPI networks and/or functional modules. Overall, DEGs in a functional module, such as AKT1, EP300, ERBB2 and EREG, may serve important roles in the development of tongue cancer in patients with a history of tobacco and/or alcohol use. These DEGs are potential therapeutic targets for the treatment of tongue cancer in these groups.

The Effects of the X Chromosome on Intrinsic Functional Connectivity in the Human Brain: Evidence from Turner Syndrome Patients

Turner syndrome (TS), a disorder caused by the congenital absence of one of the 2 X chromosomes in female humans, provides a valuable human "knockout model" for studying the functions of the X chromosome. At present, it remains unknown whether and how the loss of the X chromosome influences intrinsic functional connectivity (FC), a fundamental phenotype of the human brain. To address this, we performed resting-state functional magnetic resonance imaging and specific cognitive assessments on 22 TS patients and 17 age-matched control girls. A novel data-driven approach was applied to identify the disrupted patterns of intrinsic FC in TS. The TS girls exhibited significantly reduced whole-brain FC strength within the bilateral postcentral gyrus/intraparietal sulcus, angular gyrus, and cuneus and the right cerebellum. Furthermore, a specific functional subnetwork was identified in which the intrinsic FC between nodes was mostly reduced in TS patients. Particularly, this subnetwork is composed of 3 functional modules, and the disruption of intrinsic FC within one of these modules was associated with the deficits of TS patients in math-related cognition. Taken together, these findings provide novel insight into how the X chromosome affects the human brain and cognition, and emphasize an important role of X-linked genes in intrinsic neural coupling.

Mining Functional Modules in Heterogeneous Biological Networks Using Multiplex PageRank Approach

Identification of functional modules/sub-networks in large-scale biological networks is one of the important research challenges in current bioinformatics and systems biology. Approaches have been developed to identify functional modules in single-class biological networks; however, methods for systematically and interactively mining multiple classes of heterogeneous biological networks are lacking. In this paper, we present a novel algorithm (called mPageRank) that utilizes the Multiplex PageRank approach to mine functional modules from two classes of biological networks. We demonstrate the capabilities of our approach by successfully mining functional biological modules through integrating expression-based gene-gene association networks and protein-protein interaction networks. We first compared the performance of our method with that of other methods using simulated data. We then applied our method to identify the cell division cycle related functional module and plant signaling defense-related functional module in the model plant Arabidopsis thaliana. Our results demonstrated that the mPageRank method is effective for mining sub-networks in both expression-based gene-gene association networks and protein-protein interaction networks, and has the potential to be adapted for the discovery of functional modules/sub-networks in other heterogeneous biological networks. The mPageRank executable program, source code, the datasets and results of the presented two case studies are publicly and freely available at http://plantgrn.noble.org/MPageRank/.

A link partition approach for finding overlapping functional modules in the transcriptional regulatory network

The transcriptional regulation of cellular functions is carried out by the overlapping functional modules of a complex network. In this paper, a statistical approach for detecting functional modules in the transcriptional regulatory networks (TRNs) is studied. The proposed method defines modules as groups of links rather than nodes since nodes naturally belong to more than one module. Furthermore, the proposed algorithm is evaluated on the Escherichia coli TRN. The experimental results demonstrate that it detected a suitable number of overlapping modules that were biologically meaningful without any prior knowledge about the modules.

The neurobiology of imagination: possible role of interaction-dominant dynamics and default mode network

This work aims at presenting some hypotheses about the potential neurobiological substrate of imagery and imagination. For the present purposes, we will define imagery as the production of mental images associated with previous percepts, and imagination as the faculty of forming mental images of a novel character relating to something that has never been actually experienced by the subject but at a great extent emerges from his inner world. The two processes appear intimately related and imagery can arguably be considered as one of the main components of imagination. In this proposal, we argue that exaptation and redeployment, two basic concepts capturing important aspects of the evolution of biological structures and functions (Anderson, 2007), could also be useful in explaining imagery and imagination. As far as imagery is concerned it is proposed that neural structures originally implicated in performing certain functions, e.g., motor actions, can be reused for the imagery of the virtual execution of that function. As far as imagination is concerned we speculate that it can be the result of a “tinkering” that combines and modifies stored perceptual information and concepts leading to the creation of novel “mental objects” that are shaped by the subject peculiar inner world. Hence it is related to his self-awareness. The neurobiological substrate of the tinkering process could be found in a hierarchical model of the brain characterized by a multiplicity of functional modules (FMs) that can be assembled according to different spatial and temporal scales. Thus, it is surmised that a possible mechanism for the emergence of imagination could be represented by modulatory mechanisms controlling the perviousness of “modifiers” along the communication channels within and between FMs leading to their dynamically reassembling into novel configurations.

Flower power: its association with bee power and floral functional morphology in papilionate legumes

BACKGROUND AND AIMS

A test was made of the hypothesis that papilionate legume flowers filter pollinators according to their ability to exert strength to open flowers to access rewards. In addition, interactions with pollen vectors were expected to explain the structural complexity of the architecture of these flowers since operative flower strength may be determined by a combination of morphological traits which form part of an intrafloral functional module.

METHODS

Six papilionate species were studied: Collaea argentina, Desmodium uncinatum, Galactia latisiliqua, Lathyrus odoratus, Spartium junceum and Tipuana tipu. Measurements were made of the strength needed to open keels and the strength that pollinators were capable of exerting. Morphological traits of all petals were also measured to determine which of them could be either mutually correlated or correlated with operative strength and moment of strength and participated in a functional module.

KEY RESULTS

It was observed that pollinators were capable in all cases of exerting forces higher and often several times higher than that needed to access floral rewards, and no association could be detected between floral operative strength and strength exerted by the corresponding pollinators. On the other hand, strong and significant correlations were found among morphometric traits and, of these, with operative strength and moment. This was particularly evident among traits of the keel and the wings, presumably involved in the functioning of the floral moveable mechanism.

CONCLUSIONS

Though visitors are often many times stronger than the operative strength of the flowers they pollinate, exceptionally weak bees such as Apis mellifera cannot open the strongest flowers. On the other hand, strong correlations among certain petal morphometric traits (particularly between the keel and wings) give support to the idea that an intrafloral module is associated with the functioning of the mechanism of these legume flowers. In addition, the highly significant correlations found across petals support the view of functional phenotypic integration transcending the ontogenetic organization of flower structure.

Pigmentation pathway evolution after whole-genome duplication in fish

Whole-genome duplications (WGDs) have occurred repeatedly in the vertebrate lineage, but their evolutionary significance for phenotypic evolution remains elusive. Here, we have investigated the impact of the fish-specific genome duplication (FSGD) on the evolution of pigmentation pathways in teleost fishes. Pigmentation and color patterning are among the most diverse traits in teleosts, and their pigmentary system is the most complex of all vertebrate groups.

Using a comparative genomic approach including phylogenetic and synteny analyses, the evolution of 128 vertebrate pigmentation genes in five teleost genomes following the FSGD has been reconstructed. We show that pigmentation genes have been preferentially retained in duplicate after the FSGD, so that teleosts have 30% more pigmentation genes compared with tetrapods. This is significantly higher than genome-wide estimates of FSGD gene duplicate retention in teleosts. Large parts of the melanocyte regulatory network have been retained in two copies after the FSGD. Duplicated pigmentation genes follow general evolutionary patterns such as the preservation of protein complex stoichiometries and the overrepresentation of developmental genes among retained duplicates. These results suggest that the FSGD has made an important contribution to the evolution of teleost-specific features of pigmentation, which include novel pigment cell types or the division of existing pigment cell types into distinct subtypes. Furthermore, we have observed species-specific differences in duplicate retention and evolution that might contribute to pigmentary diversity among teleosts.

Our study therefore strongly supports the hypothesis that WGDs have promoted the increase of complexity and diversity during vertebrate phenotypic evolution.