Extracting Functional Modules from Biological Pathways

It has been proposed that functional modules are the fundamental units of cellular function. Methods to identify these modules have thus far relied on gene expression data or protein-protein interaction (PPI) data, but have a few limitations. We propose a new method, using biological pathway data to identify functional modules, that can potentially overcome these limitations. We also construct a network of these modules using functionally relevant PPI data. This network displays the flow and integration of information between modules and can be used to map cellular function

Cross‐species systems analysis of evolutionary toolkits of neurogenomic response to social challenge

Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/147855/1/gbb12502.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/147855/2/gbb12502-sup-0002-TableS1.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/147855/3/gbb12502_am.pd

Studies on metal-organic frameworks of Cu(II) with isophthalate linkers for hydrogen storage

Hydrogen (H2) is a promising alternative energy carrier due to its environmental benefits, high energy density and its abundance. However, development of a practical storage system to enable the “Hydrogen Economy” remains a huge challenge. Metal-organic frameworks (MOFs) are an important class of crystalline coordination polymers constructed by bridging metal centers with organic linkers, and show promise for H2 storage due to their high surface area and tuneable properties. We summarize our research on novel porous materials with enhanced H2 storage properties, and describe frameworks derived from 3,5-substituted dicarboxylates (isophthalates) that serve as versatile molecular building blocks for the construction of a range of interesting coordination polymers with Cu(II) ions. A series of materials has been synthesised by connecting linear tetracarboxylate linkers to {Cu(II)2} paddlewheel moieties. These (4,4)-connected frameworks adopt the fof-topology in which the Kagomé lattice layers formed by {Cu(II)2} paddlewheels and isophthalates are pillared by the bridging ligands. These materials exhibit high structural stability and permanent porosity, and the pore size, geometry and functionality can be modulated by variation of the organic linker to control the overall H2 adsorption properties. NOTT-103 shows the highest H2 storage capacity of 77.8 mg g−1 at 77 K, 60 bar among the fof-type frameworks. H2 adsorption at low, medium and high pressures correlates with the isosteric heat of adsorption, surface area and pore volume, respectively. Tri-branched C3-symmetric hexacarboxylate ligands with Cu(II) give highly porous (3,24)-connected frameworks incorporating {Cu(II)2} paddlewheels. These ubt-type frameworks comprise three types of polyhedral cage: a cuboctahedron, truncated tetrahedron and a truncated octahedron which are fused in the solid state in the ratio 1:2:1, respectively. Increasing the length of the hexacarboxylate struts directly tunes the porosity of the resultant material from micro- to mesoporosity. These materials show exceptionally high H2 uptakes owing to their high surface area and pore volume. NOTT-112, the first reported member of this family reported, adsorbs 111 mg g−1 of H2 at 77 K , 77 bar. More recently, enhanced H2 adsorption in these ubt-type frameworks has been achieved using combinations of polyphenyl groups linked by alkynes to give an overall gravimetric gas capacity for NU-100 of 164 mg g−1 at 77 K, 70 bar. However, due to its very low density NU-100 shows a lower volumetric capacity of 45.7 g L-1 compared with 55.9 g L-1 for NOTT-112, which adsorbs 2.3 wt% H2 at 1 bar, 77K. This significant adsorption of H2 at low pressures is attributed to the arrangement of the {Cu24(isophthalate)24} cuboctahedral cages within the polyhedral structure. Free metal coordination positions are the first binding sites for D2, and in these ubt-type frameworks there are two types of Cu(II) centres, one with its vacant site pointing into the cuboctahedral cage and another pointing externally. D2 molecules bind first at the former position, and then at the external open metal sites. However, other adsorption sites between the cusp of three phenyl groups and a Type I pore window in the framework are also occupied. Ligand and complex design feature strongly in enhancing and maximising H2 storage, and, although current materials operate at 77 K, research continues to explore routes to high capacity H2 storage materials that can function at higher temperatures

A robust binary supramolecular organic framework (SOF) with high CO2 adsorption and selectivity

A robust binary hydrogen-bonded supramolecular organic framework (SOF-7) has been synthesized by solvothermal reaction of 1,4-bis-(4-(3,5-dicyano-2,6 dipyridyl)dihydropyridyl)benzene (1) and 5,5’-bis-(azanediyl)-oxalyl-diisophthalic acid (2). Single crystal X-ray diffraction analysis shows that SOF-7 comprises 2 and 1,4-bis-(4-(3,5-dicyano-2,6-dipyridyl)pyridyl)benzene (3), the latter formed in situ from the oxidative dehydrogenation of 1. SOF-7 shows a three-dimensional four-fold interpenetrat-ed structure with complementary O−H···N hydrogen bonds to form channels that are decorated with cyano- and amide-groups. SOF-7 exhibits excellent thermal stability and sol-vent and moisture durability, as well as permanent porosity. The activated desolvated material SOF-7a shows high CO2 sorption capacity and selectivity compared with other po-rous organic materials assembled solely through hydrogen bonding

Meta-analysis of shared genetic architecture across ten pediatric autoimmune diseases

Genome-wide association studies (GWASs) have identified hundreds of susceptibility genes, including shared associations across clinically distinct autoimmune diseases. We performed an inverse χ(2) meta-analysis across ten pediatric-age-of-onset autoimmune diseases (pAIDs) in a case-control study including more than 6,035 cases and 10,718 shared population-based controls. We identified 27 genome-wide significant loci associated with one or more pAIDs, mapping to in silico-replicated autoimmune-associated genes (including IL2RA) and new candidate loci with established immunoregulatory functions such as ADGRL2, TENM3, ANKRD30A, ADCY7 and CD40LG. The pAID-associated single-nucleotide polymorphisms (SNPs) were functionally enriched for deoxyribonuclease (DNase)-hypersensitivity sites, expression quantitative trait loci (eQTLs), microRNA (miRNA)-binding sites and coding variants. We also identified biologically correlated, pAID-associated candidate gene sets on the basis of immune cell expression profiling and found evidence of genetic sharing. Network and protein-interaction analyses demonstrated converging roles for the signaling pathways of type 1, 2 and 17 helper T cells (TH1, TH2 and TH17), JAK-STAT, interferon and interleukin in multiple autoimmune diseases

The architecture of intra-organism mutation rate variation in plants.

Given the disposability of somatic tissue, selection can favor a higher mutation rate in the early segregating soma than in germline, as seen in some animals. Although in plants intra-organismic mutation rate heterogeneity is poorly resolved, the same selectionist logic can predict a lower rate in shoot than in root and in longer-lived terminal tissues (e.g., leaves) than in ontogenetically similar short-lived ones (e.g., petals), and that mutation rate heterogeneity should be deterministic with no significant differences between biological replicates. To address these expectations, we sequenced 754 genomes from various tissues of eight plant species. Consistent with a selectionist model, the rate of mutation accumulation per unit time in shoot apical meristem is lower than that in root apical tissues in perennials, in which a high proportion of mutations in shoots are themselves transmissible, but not in annuals, in which somatic mutations tend not to be transmissible. Similarly, the number of mutations accumulated in leaves is commonly lower than that within a petal of the same plant, and there is no more heterogeneity in accumulation rates between replicate branches than expected by chance. High mutation accumulation in runners of strawberry is, we argue, the exception that proves the rule, as mutation transmission patterns indicate that runner has a restricted germline. However, we also find that in vitro callus tissue has a higher mutation rate (per unit time) than the wild-grown comparator, suggesting nonadaptive mutational "fragility". As mutational fragility does not obviously explain why the shoot-root difference varies with plant longevity, we conclude that some mutation rate variation between tissues is consistent with selectionist theory but that a mechanistic null of mutational fragility should be considered

Integrated Analysis of Genetic Ancestry and Genomic Alterations across Cancers

Disparities in cancer care have been a long-standing challenge. We estimated the genetic ancestry of The Cancer Genome Atlas patients, and performed a pan-cancer analysis on the influence of genetic ancestry on genomic alterations. Compared with European Americans, African Americans (AA) with breast, head and neck, and endometrial cancers exhibit a higher level of chromosomal instability, while a lower level of chromosomal instability was observed in AAs with kidney cancers. The frequencies of TP53 mutations and amplification of CCNE1 were increased in AAs in the cancer types showing higher levels of chromosomal instability. We observed lower frequencies of genomic alterations affecting genes in the PI3K pathway in AA patients across cancers. Our result provides insight into genomic contribution to cancer disparities. [Display omitted] •The genetic ancestry of TCGA patients was estimated at global and local levels•The Cancer Genetic Ancestry Atlas, a publicly accessible resource, was developed•The frequencies of TP53 mutations and CCNE1 amplification were higher among AAs•The frequencies of the alterations in the PI3K pathway were lower among AAs By analyzing TCGA cohorts, Yuan et al. show that breast, head and neck, and endometrial cancers of African Americans (AA) have higher levels of chromosomal instability than those of European Americans whereas the frequency of genetic alternations in the PI3K pathway in AA patients is lower across cancers