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51.
Benjamin Linard Ingo Ebersberger Shawn E McGlynn Natasha Glover Tomohiro Mochizuki Mateus Patricio Odile Lecompte Yannis Nevers Paul D Thomas Toni Gabaldn Erik Sonnhammer Christophe Dessimoz Ikuo Uchiyama QFO Consortium 《Molecular biology and evolution》2021,38(8):3033
Accurate determination of the evolutionary relationships between genes is a foundational challenge in biology. Homology—evolutionary relatedness—is in many cases readily determined based on sequence similarity analysis. By contrast, whether or not two genes directly descended from a common ancestor by a speciation event (orthologs) or duplication event (paralogs) is more challenging, yet provides critical information on the history of a gene. Since 2009, this task has been the focus of the Quest for Orthologs (QFO) Consortium. The sixth QFO meeting took place in Okazaki, Japan in conjunction with the 67th National Institute for Basic Biology conference. Here, we report recent advances, applications, and oncoming challenges that were discussed during the conference. Steady progress has been made toward standardization and scalability of new and existing tools. A feature of the conference was the presentation of a panel of accessible tools for phylogenetic profiling and several developments to bring orthology beyond the gene unit—from domains to networks. This meeting brought into light several challenges to come: leveraging orthology computations to get the most of the incoming avalanche of genomic data, integrating orthology from domain to biological network levels, building better gene models, and adapting orthology approaches to the broad evolutionary and genomic diversity recognized in different forms of life and viruses. 相似文献
52.
Toliopoulos IK Simos YV Daskalou TA Verginadis II Evangelou AM Karkabounas SC 《Indian journal of experimental biology》2011,49(12):904-908
Platelets aggregation around migrating tumor cells offers protection against the cytotoxic activity of the natural killers cells (NKC). The ascorbic acid in 3 x 10(-3) M concentration completely inhibited platelet aggregation, decreased thromboxane B2 levels, and inhibited the expression of platelet membranic receptor GpIIb/IIIa in non stimulated platelets, and increased the NKC cytotoxicity in an average rate of 105, 61, and 285% in the NKC/targets cells ratios 12.5:1, 25:1 and 50:1 respectively. The results suggest the role of ascorbic acid in increasing the susceptibility of tumor cells to NKC; the ascorbic acid could be used as part of a multidrug therapy to treat diseases which up to now have been treated only through chemotherapy. 相似文献
53.
Papastamatiou YP Cartamil DP Lowe CG Meyer CG Wetherbee BM Holland KN 《The Journal of animal ecology》2011,80(4):864-874
1. Animal search patterns reflect sensory perception ranges combined with memory and knowledge of the surrounding environment. 2. Random walks are used when the locations of resources are unknown, whereas directed walks should be optimal when the location of favourable habitats is known. However, directed walks have been quantified for very few species. 3. We re-analysed tracking data from three shark species to determine whether they were using directed walks, and if so, over which spatial scales. Fractal analysis was used to quantify how movement structure varied with spatial scale and determine whether the sharks were using patches. 4. Tiger sharks performed directed walks at large spatial scales (at least 6-8 km). Thresher sharks also showed directed movement (at scales of 400-1900 m), and adult threshers were able to orient at greater scales than juveniles, which may suggest that learning improves the ability to perform directed walks. Blacktip reef sharks had small home ranges, high site fidelity and showed no evidence of oriented movements at large scales. 5. There were inter- and intraspecific differences in path structure and patch size, although most individuals showed scale-dependent movements. Furthermore, some individuals of each species performed movements similar to a correlated random walk. 6. Sharks can perform directed walks over large spatial scales, with scales of movements reflecting site fidelity and home range size. Understanding when and where directed walks occur is crucial for developing more accurate population-level dispersal models. 相似文献
54.
Alizon S Michalakis Y 《Evolution; international journal of organic evolution》2011,65(12):3633-8; discussion 3639-41
55.
56.
Guillemin Y Cornut-Thibaut A Gillet G Penin F Aouacheria A 《Molecular biology and evolution》2011,28(12):3271-3283
Insertions or deletions (indels) of amino acids residues have been recognized as an important source of genetic and structural divergence between paralogous Bcl-2 family members. However, these signature sequences have not so far been extensively investigated amongst orthologous Bcl-2 family proteins. Bcl2l10 is an antiapoptotic member of the Bcl-2 family that has evolved rapidly throughout the vertebrate lineage and which shows conserved abundant expression in eggs and oocytes. In this paper, we have unraveled two major sites of divergence between human Bcl2l10 and its vertebrate homologs. The first one provides length variation at the N-terminus (before the BH4 domain) and the second one is located between the predicted α5-α6 pore-forming helices, providing an unprecedented case in the superfamily of helix-bundled pore-forming proteins. These two particular indels were studied phylogenetically and through biochemical and cell biological techniques, including truncation and site-directed mutagenesis. While deletion of the N-terminal extension had no significant functional impact in HeLa cells, our results suggest that the human Bcl2l10 protein evolved a calcium-binding motif in its α5-α6 interhelical region by acquiring critical negatively charged residues. Considering the reliance of female eggs on calcium-dependent proteins and calcium-regulated processes and the exceptional longevity of oocytes in the primate lineage, we propose that this microstructural variation may be an adaptive feature associated with high maternal expression of this Bcl-2 family member. 相似文献
57.
D. Nikitovic M. Mytilinaiou Ai. Berdiaki N.K. Karamanos G.N. Tzanakakis 《Biochimica et Biophysica Acta (BBA)/General Subjects》2014
Background
The solid melanoma tumor consists of transformed melanoma cells, and the associated stromal cells including fibroblasts, endothelial cells, immune cells, as well as, soluble macro- and micro-molecules of the extracellular matrix (ECM) forming the complex network of the tumor microenvironment. Heparan sulfate proteoglycans (HSPGs) are an important component of the melanoma tumor ECM. Importantly, there appears to be both a quantitative and a qualitative shift in the content of HSPGs, in parallel to the nevi–radial growth phase–vertical growth phase melanoma progression. Moreover, these changes in HSPG expression are correlated to modulations of key melanoma cell functions.Scope of review
This review will critically discuss the roles of HSPGs/heparin in melanoma development and progression.Major conclusions
We have correlated HSPGs' expression and distribution with melanoma cell signaling and functions as well as angiogenesis.General significance
The current knowledge of HSPGs/heparin biology in melanoma provides a foundation we can utilize in the ongoing search for new approaches in designing anti-tumor therapy. This article is part of a Special Issue entitled Matrix-mediated cell behaviour and properties. 相似文献58.
Carl G. Meyer Joseph M. O'Malley Yannis P. Papastamatiou Jonathan J. Dale Melanie R. Hutchinson James M. Anderson Mark A. Royer Kim N. Holland 《PloS one》2014,9(1)
Tiger sharks (Galecerdo cuvier) are apex predators characterized by their broad diet, large size and rapid growth. Tiger shark maximum size is typically between 380 & 450 cm Total Length (TL), with a few individuals reaching 550 cm TL, but the maximum size of tiger sharks in Hawaii waters remains uncertain. A previous study suggested tiger sharks grow rather slowly in Hawaii compared to other regions, but this may have been an artifact of the method used to estimate growth (unvalidated vertebral ring counts) compounded by small sample size and narrow size range. Since 1993, the University of Hawaii has conducted a research program aimed at elucidating tiger shark biology, and to date 420 tiger sharks have been tagged and 50 recaptured. All recaptures were from Hawaii except a single shark recaptured off Isla Jacques Cousteau (24°13′17″N 109°52′14″W), in the southern Gulf of California (minimum distance between tag and recapture sites = approximately 5,000 km), after 366 days at liberty (DAL). We used these empirical mark-recapture data to estimate growth rates and maximum size for tiger sharks in Hawaii. We found that tiger sharks in Hawaii grow twice as fast as previously thought, on average reaching 340 cm TL by age 5, and attaining a maximum size of 403 cm TL. Our model indicates the fastest growing individuals attain 400 cm TL by age 5, and the largest reach a maximum size of 444 cm TL. The largest shark captured during our study was 464 cm TL but individuals >450 cm TL were extremely rare (0.005% of sharks captured). We conclude that tiger shark growth rates and maximum sizes in Hawaii are generally consistent with those in other regions, and hypothesize that a broad diet may help them to achieve this rapid growth by maximizing prey consumption rates. 相似文献
59.
Mathias Rask-Andersen Ga?tan Philippot George Moschonis George Dedoussis Yannis Manios Claude Marcus Robert Fredriksson Helgi B. Schi?th 《PloS one》2014,9(4)
Five novel loci recently found to be associated with body mass in two GWAS of East Asian populations were evaluated in two cohorts of Swedish and Greek children and adolescents. These loci are located within, or in the proximity of: CDKAL1, PCSK1, GP2, PAX6 and KLF9. No association with body mass has previously been reported for these loci in GWAS performed on European populations. The single nucleotide polymorphisms (SNPs) with the strongest association at each loci in the East Asian GWAS were genotyped in two cohorts, one obesity case control cohort of Swedish children and adolescents consisting of 496 cases and 520 controls and one cross-sectional cohort of 2293 nine-to-thirteen year old Greek children and adolescents. SNPs were surveyed for association with body mass and other phenotypic traits commonly associated with obesity, including adipose tissue distribution, insulin resistance and daily caloric intake. No association with body mass was found in either cohort. However, among the Greek children, association with insulin resistance could be observed for the two CDKAL1-related SNPs: rs9356744 (β = 0.018, p = 0.014) and rs2206734 (β = 0.024, p = 0.001). CDKAL1-related variants have previously been associated with type 2 diabetes and insulin response. This study reports association of CDKAL1-related SNPs with insulin resistance, a clinical marker related to type 2 diabetes in a cross-sectional cohort of Greek children and adolescents of European descent. 相似文献
60.
Saskia J. te Velde Amika Singh Mai Chinapaw Ilse De Bourdeaudhuij Natasa Jan Eva Kovacs Elling Bere Froydis N. Vik Bettina Bringolf-Isler Yannis Manios Luis Moreno Johannes Brug 《PloS one》2014,9(11)