An Introductory Guide to Aligning Networks Using SANA, the Simulated Annealing Network Aligner.

Sequence alignment has had an enormous impact on our understanding of biology, evolution, and disease. The alignment of biological networks holds similar promise. Biological networks generally model interactions between biomolecules such as proteins, genes, metabolites, or mRNAs. There is strong evidence that the network topology-the "structure" of the network-is correlated with the functions performed, so that network topology can be used to help predict or understand function. However, unlike sequence comparison and alignment-which is an essentially solved problem-network comparison and alignment is an NP-complete problem for which heuristic algorithms must be used.Here we introduce SANA, the Simulated Annealing Network Aligner. SANA is one of many algorithms proposed for the arena of biological network alignment. In the context of global network alignment, SANA stands out for its speed, memory efficiency, ease-of-use, and flexibility in the arena of producing alignments between two or more networks. SANA produces better alignments in minutes on a laptop than most other algorithms can produce in hours or days of CPU time on large server-class machines. We walk the user through how to use SANA for several types of biomolecular networks

Biorefining Twin Transition: Digitalisation for Bio-based Chemicals/Materials - Discovery, Design and Optimisation

The article discusses the production of platform chemicals from various biological sources, including glycerol, lignin, cellulose, bio-oils, and sea products. It presents the results of catalytic and downstream processes involved in the conversion of these biomass-derived feedstocks. The experimental approaches are complemented by numerical descriptions, ranging from density functional theory (DFT) calculations to kinetic modellingof the experimental data. This multi-scale modelling approach helps to understand the underlying mechanisms and optimize the production of platform chemicals from renewable resources

The occurrence of germline BRCA1 and BRCA2 sequence alterations in Slovenian population

<p>Abstract</p> <p>Background</p> <p>The <it>BRCA1 </it>and <it>BRCA2 </it>mutation spectrum and mutation detection rates according to different family histories were investigated in 521 subjects from 322 unrelated Slovenian cancer families with breast and/or ovarian cancer.</p> <p>Methods</p> <p>The <it>BRCA1 </it>and <it>BRCA2 </it>genes were screened using DGGE, PTT, HRM, MLPA and direct sequencing.</p> <p>Results</p> <p>Eighteen different mutations were found in <it>BRCA1 </it>and 13 in <it>BRCA2 </it>gene. Mutations in one or other gene were found in 96 unrelated families. The mutation detection rates were the highest in the families with at least one breast and at least one ovarian cancer - 42% for <it>BRCA1 </it>and 8% for <it>BRCA2</it>. The mutation detection rate observed in the families with at least two breast cancers with disease onset before the age of 50 years and no ovarian cancer was 23% for <it>BRCA1 </it>and 13% for <it>BRCA2</it>. The mutation detection rate in the families with at least two breast cancers and only one with the disease onset before the age of 50 years was 11% for <it>BRCA1 </it>and 8% for <it>BRCA2</it>. In the families with at least two breast cancers, all of them with disease onset over the age of 50 years, the detection rate was 5% for <it>BRCA2 </it>and 0% for <it>BRCA1</it>.</p> <p>Conclusion</p> <p>Among the mutations detected in Slovenian population, 5 mutations in <it>BRCA1 </it>and 4 mutations in <it>BRCA2 </it>have not been described in other populations until now. The most frequent mutations in our population were c.181T > G, c.1687C > T, c.5266dupC and c.844_850dupTCATTAC in <it>BRCA1 </it>gene and c.7806-2A > G, c.5291C > G and c.3978insTGCT in <it>BRCA2 </it>gene (detected in 69% of <it>BRCA1 </it>and <it>BRCA2 </it>positive families).</p

Lichen flora of Žumberak-Samoborsko gorje Nature Park, NW Croatia

During 2007 and 2008 epiphytic and terrestrial lichen communities were surveyed in the Žumberak-Samoborsko gorje Nature Park (NW Croatia); 84 taxa were recorded including, Lecanora thysanophora, which was new to Croatia, and four, Bryoria fuscescens, Lobaria pulmonaria, Usnea subfloridana and Usnea hirta, which are red data species in Croatia

Genome-wide meta-analysis identifies five new susceptibility loci for cutaneous malignant melanoma.

Thirteen common susceptibility loci have been reproducibly associated with cutaneous malignant melanoma (CMM). We report the results of an international 2-stage meta-analysis of CMM genome-wide association studies (GWAS). This meta-analysis combines 11 GWAS (5 previously unpublished) and a further three stage 2 data sets, totaling 15,990 CMM cases and 26,409 controls. Five loci not previously associated with CMM risk reached genome-wide significance (P < 5 × 10(-8)), as did 2 previously reported but unreplicated loci and all 13 established loci. Newly associated SNPs fall within putative melanocyte regulatory elements, and bioinformatic and expression quantitative trait locus (eQTL) data highlight candidate genes in the associated regions, including one involved in telomere biology.[Please see the Supplementary Note for acknowledgments.]This is the author accepted manuscript. The final version is available from NPG via http://dx.doi.org/10.1038/ng.337

Bismuth modified gold nanoelectrode ensemble for stripping voltammetric determination of lead

The preparation of bismuth modified ensembles of gold nanoelectrodes (Bi-NEE) is described for the first time. Bi-NEEs are characterized and successfully applied for anodic stripping voltammetric measurement of trace Pb(II). Optimization of the experimental parameters provided low detection limits of 60 ng L−1 and 30 ng L−1 by using in-situ and ex-situ bismuth film deposition, respectively, after a 3 min accumulation step

Birth cohort-specific trends of sun-related behaviors among individuals from an international consortium of melanoma-prone families.

Funder: Coordenação de Aperfeiçoamento de Pessoal de Nível Superior; doi: http://dx.doi.org/10.13039/501100002322Funder: Radiumhemmets Forskningsfonder; doi: http://dx.doi.org/10.13039/501100007232Funder: Swedish Cancer SocietyFunder: Lunds Universitet Paulsson TrustFunder: CIBER de Enfermedades Raras of the Instituto de Salud Carlos IIIFunder: European Regional Development Fund; doi: http://dx.doi.org/10.13039/501100008530Funder: DiagnopticsFunder: CERCA Programme Generalitat de CatalunyaFunder: Esther Koplowitz Center, Barcelona, SpainFunder: Comision Honoraria de Lucha Contra el Cancer, CSIC, Fundacion Manuel Perez, Montevideo, UruguayBACKGROUND: Individuals from melanoma-prone families have similar or reduced sun-protective behaviors compared to the general population. Studies on trends in sun-related behaviors have been temporally and geographically limited. METHODS: Individuals from an international consortium of melanoma-prone families (GenoMEL) were retrospectively asked about sunscreen use, sun exposure (time spent outside), sunburns, and sunbed use at several timepoints over their lifetime. Generalized linear mixed models were used to examine the association between these outcomes and birth cohort defined by decade spans, after adjusting for covariates. RESULTS: A total of 2407 participants from 547 families across 17 centers were analyzed. Sunscreen use increased across subsequent birth cohorts, and although the likelihood of sunburns increased until the 1950s birth cohort, it decreased thereafter. Average sun exposure did not change across the birth cohorts, and the likelihood of sunbed use increased in more recent birth cohorts. We generally did not find any differences in sun-related behavior when comparing melanoma cases to non-cases. Melanoma cases had increased sunscreen use, decreased sun exposure, and decreased odds of sunburn and sunbed use after melanoma diagnosis compared to before diagnosis. CONCLUSIONS: Although sunscreen use has increased and the likelihood of sunburns has decreased in more recent birth cohorts, individuals in melanoma-prone families have not reduced their overall sun exposure and had an increased likelihood of sunbed use in more recent birth cohorts. These observations demonstrate partial improvements in melanoma prevention and suggest that additional intervention strategies may be needed to achieve optimal sun-protective behavior in melanoma-prone families