DESM: portal for microbial knowledge exploration systems

Microorganisms produce an enormous variety of chemical compounds. It is of general interest for mi-crobiology and biotechnology researchers to have means to explore information about molecular and genetic basis of functioning of different microor-ganisms and their ability for bioproduction. To en-able such exploration, we compiled 45 topic-specific knowledgebases (KBs) accessible through DESM portal (www.cbrc.kaust.edu.sa/desm). The KBs con-tain information derived through text-mining of PubMed information and complemented by informa-tion data-mined from various other resources (e.g. ChEBI, Entrez Gene, GO, KOBAS, KEGG, UniPath-ways, BioGrid). All PubMed records were indexed us

Biosilica from deep-sea marine sponge Geodia barretti for the development of 3D printed scaffolds for bone tissue regeneration applications

Os oceanos sempre foram um grande instigador da curiosidade humana e, desde os tempos das grandes navegações até os dias atuais. Estima-se que a biodiversidade dos oceanos seja maior do que a das florestas tropicais, sendo ainda pouco conhecida e considerada a última barreira às descobertas científicas no planeta. As esponjas marinhas são um dos animais invertebrados mais antigos neste ambiente, sendo estudadas mais recentemente por várias áreas de investigação, pela sua interação com outros microrganismos e propriedades estruturais. As esponjas marinhas apresentam composições fisiológicas, que podem ser utilizados em abordagens terapêuticas, nomeadamente na medicina regenerativa. Além disso, a biossílica de esponjas marinhas tornou-se atraente por sua aplicação em estratégias de engenharia de tecido ósseo. A biossílica de Geodia barretti (GB) foi um material alvo em nosso estudo em comparação com Diatomaceous Earth (DE) e Bioglass® 45S5 (BG) na produção de tintas à base de alginato para fabricação de andaimes de impressão 3D. A obtenção das partículas cerâmicas à base de GB foi realizada através do processo de calcinação. Antes da formulação da tinta, a produção das partículas de sílica de GB, DE e BG foram padronizadas por tamanho na faixa de 36 a 63 µm e caracterizadas físico-quimicamente com o uso de espectroscopia de infravermelho por transformada de Fourier (FTIR), difração de raios-X (XRD) e Microscopia Eletrônica de Varredura - Espectroscopia Dispersiva de Raios-X (MEV / EDS). As “tintas” foram desenvolvidas pela mistura de materiais à base de sílica com solução de alginato e a respetiva avaliação reológica apresentou módulos viscosos e elásticos estáveis, apoiando o avanço para a impressão 3D para produção de scaffolds. A porosidade e distribuição de tamanho de poro dos scaffolds obtidos foram avaliados pela técnica de imagem de micro-TC de raios-X, mostrando sua alta porosidade e interconectividade. A bioatividade dos scaffolds foi analisada por imersão em fluido corporal simulado por até 21 dias seguida pela deteção da formação de fosfato de cálcio em sua superfície, usando MEV / EDS. Os resultados dos testes mecânicos apontam para propriedades de compressão insuficientes quando comparadas às exibidas pelo tecidoalvo. A avaliação biológica dos scaffolds de sílica-alginato com e sem recobrimento de colágeno mostrou que as formulações com biossílica GB tiveram desempenho igual ou melhor que as demais, com a adição de colágeno melhorando a adesão e proliferação celular nos scaffolds

DES-mutation : system for exploring links of mutations and diseases

During cellular division DNA replicates and this process is the basis for passing genetic information to the next generation. However, the DNA copy process sometimes produces a copy that is not perfect, that is, one with mutations. The collection of all such mutations in the DNA copy of an organism makes it unique and determines the organism's phenotype. However, mutations are often the cause of diseases. Thus, it is useful to have the capability to explore links between mutations and disease. We approached this problem by analyzing a vast amount of published information linking mutations to disease states. Based on such information, we developed the DES-Mutation knowledgebase which allows for exploration of not only mutation-disease links, but also links between mutations and concepts from 27 topic-specific dictionaries such as human genes/proteins, toxins, pathogens, etc. This allows for a more detailed insight into mutation-disease links and context. On a sample of 600 mutation-disease associations predicted and curated, our system achieves precision of 72.83%. To demonstrate the utility of DES-Mutation, we provide case studies related to known or potentially novel information involving disease mutations. To our knowledge, this is the first mutation-disease knowledgebase dedicated to the exploration of this topic through text-mining and data-mining of different mutation types and their associations with terms from multiple thematic dictionaries

Redox control of vascular biology

Redox control is lost when the antioxidant defense system cannot remove abnormally high concentrations of signaling molecules, such as reactive oxygen species (ROS). Chronically elevated levels of ROS cause oxidative stress that may eventually lead to cancer and cardiovascular and neurodegenerative diseases. In this review, we focus on redox effects in the vascular system. We pay close attention to the subcompartments of the vascular system (endothelium, smooth muscle cell layer) and give an overview of how redox changes influence those different compartments. We also review the core aspects of redox biology, cardiovascular physiology, and pathophysiology. Moreover, the topic-specific knowledgebase DES-RedoxVasc was used to develop two case studies, one focused on endothelial cells and the other on the vascular smooth muscle cells, as a starting point to possibly extend our knowledge of redox control in vascular biology. © 2019 The Authors. BioFactors published by Wiley Periodicals, Inc. on behalf of International Union of Biochemistry and Molecular Biology

Sponge Community Biocomplexity, Competition, and Functional Significance in Hard-Bottom Habitats of the Florida Keys, FL (USA)

Sponges can have powerful effects on ecosystem processes in shallow, tropical marine ecosystems and are an integral component of the bentho-pelagic cycle of nutrients, via filtering of dissolved and particulate organic matter from the water column. The diversity of marine communities is thought to play a determining role in intensity of ecosystem processes; thus the loss of taxa alters community function and by extension ecosystem processes. Coastal sponge populations worldwide are increasingly exposed to declining water quality that in several regions has resulted in mass sponge mortalities and reduced sponge diversity. In the Florida Keys (Florida, USA), for example, frequent cyanobacteria blooms have decimated coastal sponge communities. There were two objectives for this research. First, to experimentally establish the baseline effects of Florida Keys sponges, at ecologically relevant biomass levels, on various shallow water ecosystem processes and functions, and richness on water column properties. The results of this work demonstrated the importance of sponge biomass and species-specific filtration rates on the intensity of water column nutrient cycling, and its constituents. The second objective of this research was to develop an understanding of how sponges might interact in the wild, ultimately affecting the ecosystem processes and functions measured previously. The results of field manipulations, and sponge measurements plus water column sampling, conducted at multiple sites within Florida Bay showed clearly that the sponges of these back-water lagoons competed intensely for food, particularly in areas of higher biomass and slower water movement. Overall, this dissertation highlighted how reductions in the abundance and diversity of sponges in coastal ecosystems can drastically alter water column properties

DES-ncRNA: A knowledgebase for exploring information about human micro and long noncoding RNAs based on literature-mining

Noncoding RNAs (ncRNAs), particularly microRNAs (miRNAs) and long ncRNAs (lncRNAs), are important players in diseases and emerge as novel drug targets. Thus, unraveling the relationships between ncRNAs and other biomedical entities in cells are critical for better understanding ncRNA roles that may eventually help develop their use in medicine. To support ncRNA research and facilitate retrieval of relevant information regarding miRNAs and lncRNAs from the plethora of published ncRNA-related research, we developed DES-ncRNA (www.cbrc.kaust.edu.sa/des_ncrna). DES-ncRNA is a knowledgebase containing text- and data-mined information from public scientific literature and other public resources. Exploration of mined information is enabled through terms and pairs of terms from 19 topic-specific dictionaries including, for example, antibiotics, toxins, drugs, enzymes, mutations, pathways, human genes and proteins, drug indications and side effects, mutations, diseases, etc. DES-ncRNA contains approximately 878,000 associations of terms from these dictionaries of which 36,222 (5,373) are with regards to miRNAs (lncRNAs). We provide several ways to explore information regarding ncRNAs to users including controlled generation of association networks as well as hypotheses generation. We show an example how DES-ncRNA can aid research on Alzheimer disease and suggest potential therapeutic role for Fasudil. DES-ncRNA is a powerful tool that can be used on its own or as a complement to the existing resources, to support research in human ncRNA. To our knowledge, this is the only knowledgebase dedicated to human miRNAs and lncRNAs derived primarily through literature-mining enabling exploration of a broad spectrum of associated biomedical entities, not paralleled by any other resource

Literature-Based Enrichment Insights into Redox Control of Vascular Biology

In cellular physiology and signaling, reactive oxygen species (ROS) play one of the most critical roles. ROS overproduction leads to cellular oxidative stress. This may lead to an irrecoverable imbalance of redox (oxidation-reduction reaction) function that deregulates redox homeostasis, which itself could lead to several diseases including neurodegenerative disease, cardiovascular disease, and cancers. In this study, we focus on the redox effects related to vascular systems in mammals. To support research in this domain, we developed an online knowledge base, DES-RedoxVasc, which enables exploration of information contained in the biomedical scientific literature. The DES-RedoxVasc system analyzed 233399 documents consisting of PubMed abstracts and PubMed Central full-text articles related to different aspects of redox biology in vascular systems. It allows researchers to explore enriched concepts from 28 curated thematic dictionaries, as well as literature-derived potential associations of pairs of such enriched concepts, where associations themselves are statistically enriched. For example, the system allows exploration of associations of pathways, diseases, mutations, genes/proteins, miRNAs, long ncRNAs, toxins, drugs, biological processes, molecular functions, etc. that allow for insights about different aspects of redox effects and control of processes related to the vascular system. Moreover, we deliver case studies about some existing or possibly novel knowledge regarding redox of vascular biology demonstrating the usefulness of DES-RedoxVasc. DES-RedoxVasc is the first compiled knowledge base using text mining for the exploration of this topic