Complexity, Networks, and Non-Uniqueness

The aim of the paper is to introduce some of the history and key concepts of network science to a philosophical audience, and to highlight a crucial—and often problematic—presumption that underlies the network approach to complex systems. Network scientists often talk of “the structure” of a given complex system or phenomenon, which encourages the view that there is a unique and privileged structure inherent to the system, and that the aim of a network model is to delineate this structure. I argue that this sort of naïve realism about structure is not a coherent or plausible position, especially given the multiplicity of types of entities and relations that can feature as nodes and links in complex networks.     

Spruce beetle ( Dendroctonus rufipennis ) outbreak in Engelmann spruce ( Picea Engelmannii ) in central Utah, 1986-1998

Extensive Engelmann spruce ( Picea engelmannii Parry ex Engelm.) mortality caused by the spruce beetle ( Dendroctonus rufipennis Kirby) has been occurring at the southern end of the Wasatch Plateau in central Utah. This spruce beetle outbreak is the largest recorded in Utah history. An extensive ground survey was conducted in 1996 on the Manti-LaSal National Forest, Sanpete and Ferron Ranger Districts, to document mortality and impact of a major spruce beetle outbreak on post-outbreak forest composition. In 1998 the same sites were resurveyed. Survey results indicate Engelmann spruce basal area (BA) loss averaged 78% in trees ≥5 inches diameter breast height (DBH) in 1996. Ninety percent of BA ≥5 inches DBH was lost within the same sites by 1998. Tree mortality of spruce ≥5 inches DBH expressed in trees per acre (TPA) averaged 53% in 1996. In 1998 TPA ≥5 inches DBH mortality averaged 73%. Before the outbreak live Engelmann spruce BA ≥5 inches DBH averaged 99 square feet, and TPA ≥5 inches DBH averaged 97. In the sites surveyed in 1996 and resurveyed in 1998, Engelmann spruce BA ≥5 inches DBH averaged 21 and 9 square feet, and TPA ≥5 inches DBH averaged 43 and 25, respectively. Overstory tree species composition changed from stands dominated by spruce to subalpine fir. Stand ratings for potential spruce beetle outbreaks were high to mostly medium hazard pre-outbreak and medium to primarily low hazard by 1998, as a result of reduction in average spruce diameter, total basal area, and overstory spruce.     

Meta-analysis of three genome-wide association studies identifies susceptibility loci for colorectal cancer at 1q41, 3q26.2, 12q13.13 and 20q13.33

Genome-wide association studies (GWAS) have identified ten loci harboring common variants that influence risk of developing colorectal cancer (CRC). To enhance the power to identify additional CRC risk loci, we conducted a meta-analysis of three GWAS from the UK which included a total of 3,334 affected individuals (cases) and 4,628 controls followed by multiple validation analyses including a total of 18,095 cases and 20,197 controls. We identified associations at four new CRC risk loci: 1q41 (rs6691170, odds ratio (OR) = 1.06, P = 9.55 × 10?1? and rs6687758, OR = 1.09, P = 2.27 × 10??, 3q26.2 (rs10936599, OR = 0.93, P = 3.39 × 10??), 12q13.13 (rs11169552, OR = 0.92, P = 1.89 × 10?1? and rs7136702, OR = 1.06, P = 4.02 × 10??) and 20q13.33 (rs4925386, OR = 0.93, P = 1.89 × 10?1?). In addition to identifying new CRC risk loci, this analysis provides evidence that additional CRC-associated variants of similar effect size remain to be discovered.     

Genome-wide association study identifies a second prostate cancer susceptibility variant at 8q24

Prostate cancer is the most prevalent noncutaneous cancer in males in developed regions, with African American men having among the highest worldwide incidence and mortality rates. Here we report a second genetic variant in the 8q24 region that, in conjunction with another variant we recently discovered, accounts for about 11%-13% of prostate cancer cases in individuals of European descent and 31% of cases in African Americans. We made the current discovery through a genome-wide association scan of 1,453 affected Icelandic individuals and 3,064 controls using the Illumina HumanHap300 BeadChip followed by four replication studies. A key step in the discovery was the construction of a 14-SNP haplotype that efficiently tags a relatively uncommon (2%-4%) susceptibility variant in individuals of European descent that happens to be very common (approximately 42%) in African Americans. The newly identified variant shows a stronger association with affected individuals who have an earlier age at diagnosis.     

A threshold of transmembrane potential is required for mitochondrial dynamic balance mediated by DRP1 and OMA1

As an organellar network, mitochondria dynamically regulate their organization via opposing fusion and fission pathways to maintain bioenergetic homeostasis and contribute to key cellular pathways. This dynamic balance is directly linked to bioenergetic function: loss of transmembrane potential across the inner membrane (Δψ _m) disrupts mitochondrial fission/fusion balance, causing fragmentation of the network. However, the level of Δψ _m required for mitochondrial dynamic balance, as well as the relative contributions of fission and fusion pathways, have remained unclear. To explore this, mitochondrial morphology and Δψ _m were examined via confocal imaging and tetramethyl rhodamine ester (TMRE) flow cytometry, respectively, in cultured 143B osteosarcoma cells. When normalized to the TMRE value of untreated 143B cells as 100%, both genetic (mtDNA-depleted ρ⁰) and pharmacological [carbonyl cyanide m-chlorophenyl hydrazone (CCCP)-treated] cell models below 34% TMRE fluorescence were unable to maintain mitochondrial interconnection, correlating with loss of fusion-active long OPA1 isoforms (L-OPA1). Mechanistically, this threshold is maintained by mechanistic coordination of DRP1-mediated fission and OPA1-mediated fusion: cells lacking either DRP1 or the OMA1 metalloprotease were insensitive to loss of Δψ _m, instead maintaining an obligately fused morphology. Collectively, these findings demonstrate a mitochondrial ‘tipping point’ threshold mediated by the interaction of Δψ _m with both DRP1 and OMA1; moreover, DRP1 appears to be required for effective OPA1 maintenance and processing, consistent with growing evidence for direct interaction of fission and fusion pathways. These results suggest that Δψ _m below threshold coordinately activates both DRP1-mediated fission and OMA1 cleavage of OPA1, collapsing mitochondrial dynamic balance, with major implications for a range of signaling pathways and cellular life/death events.     

Natural history of mesenchymal stem cells,from vessel walls to culture vessels

Mesenchymal stem/stromal cells (MSCs) can regenerate tissues by direct differentiation or indirectly by stimulating angiogenesis, limiting inflammation, and recruiting tissue-specific progenitor cells. MSCs emerge and multiply in long-term cultures of total cells from the bone marrow or multiple other organs. Such a derivation in vitro is simple and convenient, hence popular, but has long precluded understanding of the native identity, tissue distribution, frequency, and natural role of MSCs, which have been defined and validated exclusively in terms of surface marker expression and developmental potential in culture into bone, cartilage, and fat. Such simple, widely accepted criteria uniformly typify MSCs, even though some differences in potential exist, depending on tissue sources. Combined immunohistochemistry, flow cytometry, and cell culture have allowed tracking the artifactual cultured mesenchymal stem/stromal cells back to perivascular anatomical regions. Presently, both pericytes enveloping microvessels and adventitial cells surrounding larger arteries and veins have been described as possible MSC forerunners. While such a vascular association would explain why MSCs have been isolated from virtually all tissues tested, the origin of the MSCs grown from umbilical cord blood remains unknown. In fact, most aspects of the biology of perivascular MSCs are still obscure, from the emergence of these cells in the embryo to the molecular control of their activity in adult tissues. Such dark areas have not compromised intents to use these cells in clinical settings though, in which purified perivascular cells already exhibit decisive advantages over conventional MSCs, including purity, thorough characterization and, principally, total independence from in vitro culture. A growing body of experimental data is currently paving the way to the medical usage of autologous sorted perivascular cells for indications in which MSCs have been previously contemplated or actually used, such as bone regeneration and cardiovascular tissue repair.     

Flora of the Stansbury Mountains, Utah

Normal 0 false false false EN-US X-NONE X-NONE MicrosoftInternetExplorer4 st1\:*{behavior:url(#ieooui) } /* Style Definitions */ table.MsoNormalTable {mso-style-name:"Table Normal"; mso-tstyle-rowband-size:0; mso-tstyle-colband-size:0; mso-style-noshow:yes; mso-style-priority:99; mso-style-qformat:yes; mso-style-parent:""; mso-padding-alt:0in 5.4pt 0in 5.4pt; mso-para-margin:0in; mso-para-margin-bottom:.0001pt; mso-pagination:widow-orphan; font-size:11.0pt; font-family:"Calibri","sans-serif"; mso-ascii-font-family:Calibri; mso-ascii-theme-font:minor-latin; mso-fareast-font-family:"Times New Roman"; mso-fareast-theme-font:minor-fareast; mso-hansi-font-family:Calibri; mso-hansi-theme-font:minor-latin; mso-bidi-font-family:"Times New Roman"; mso-bidi-theme-font:minor-bidi;} The Stansbury Mountains of north central Utah rise over 2000 m above surrounding desert valleys to a maximum elevation of 3362 m on Deseret Peak. Because of the great variety of environmental conditions that can be found in the Stansburys, a wide range of plant species and vegetation types (from shadscale desert to alpine meadow) exist there. This paper presents an annotated list of 594 vascular plant species in 315 genera and 78 families. The largest families are Asteraceae (98 species), Poaceae (71), Brassicaceae (33), Fabaceae (27), and Rosaceae (26). Elymus flavescens was previously unreported from Utah. Statistical comparison of the Stansbury flora with neighboring mountain floras indicates that the Wasatch Mountains lying 65 km to the east have probably been the primary source area for development of the Stansbury flora. Many lowland species, especially those inhabiting sandy areas, apparently have migrated to the area from the south.     

Mutations in the pre-replication complex cause Meier-Gorlin syndrome

Meier-Gorlin syndrome (ear, patella and short-stature syndrome) is an autosomal recessive primordial dwarfism syndrome characterized by absent or hypoplastic patellae and markedly small ears1?3. Both pre- and post-natal growth are impaired in this disorder, and although microcephaly is often evident, intellect is usually normal in this syndrome. We report here that individuals with this disorder show marked locus heterogeneity, and we identify mutations in five separate genes: ORC1, ORC4, ORC6, CDT1 and CDC6. All of these genes encode components of the pre-replication complex, implicating defects in replication licensing as the cause of a genetic syndrome with distinct developmental abnormalities.