Prototipe Low-Cost Shallow-ROV sebagai Alat Bantu pada Pemetaan Batimetri di Perairan Dangkal

Pengawasan dasar air dan kedalaman perairan yang dangkal (batimetri) baik di laut maupun sungai sangatlah penting sebagai antisipasi erosi, pendangkalan sungai dan pantai. Pada umumnya pengukuran dilakukan menggunakan sonar LIDAR dan echosounder, serta teknologi optic berbasis laser. Namun teknologi-teknologi tersebut membutuhkan biaya yang tidak sedikit dan akan kesulitan menjangkau daerah pengukuran yang cukup luas. Mengatasi hal tersebut dibuatlah Remote Operated Vehicle (ROV) yang mana akan difungsikan untuk membaca kedalaman air. ROV dilengkapi dengan perangkat navigasi berupa GPS (Global Positioning System) yang terintegrasi dengan perangkat intrumentasi menggunakan papan MultiWii SE. Sedangkan perangkat pengedali dan komunikasi menggunakan papan Arduino Uno v3. Pengukuran kedalaman menggunakan modul DT-SENSE Barometric Pressure & Temperature Sensor. SHALLOW-ROV juga dilengkapi sebuah kamera bertipe CMOS beresolusi VGA yang digunakan dalam pengendalian wahana. Pencatatan hasil pengukuran kedalaman dilakukan dengan menggunakan sebuah komputer yang dilangkapi program dan terhubung dengan database dan internet sehingga dapat langsung diamati secara onlin

antiSMASH 4.0—improvements in chemistry prediction and gene cluster boundary identification

Many antibiotics, chemotherapeutics, crop protection agents and food preservatives originate from molecules produced by bacteria, fungi or plants. In recent years, genome mining methodologies have been widely adopted to identify and characterize the biosynthetic gene clusters encoding the production of such compounds. Since 2011, the ‘antibiotics and secondary metabolite analysis shell—antiSMASH’ has assisted researchers in efficiently performing this, both as a web server and a standalone tool. Here, we present the thoroughly updated antiSMASH version 4, which adds several novel features, including prediction of gene cluster boundaries using the ClusterFinder method or the newly integrated CASSIS algorithm, improved substrate specificity prediction for non-ribosomal peptide synthetase adenylation domains based on the new SANDPUMA algorithm, improved predictions for terpene and ribosomally synthesized and post-translationally modified peptides cluster products, reporting of sequence similarity to proteins encoded in experimentally characterized gene clusters on a per-protein basis and a domain-level alignment tool for comparative analysis of trans-AT polyketide synthase assembly line architectures. Additionally, several usability features have been updated and improved. Together, these improvements make antiSMASH up-to-date with the latest developments in natural product research and will further facilitate computational genome mining for the discovery of novel bioactive molecules

MIBiG 2.0: a repository for biosynthetic gene clusters of known function

Fueled by the explosion of (meta)genomic data, genome mining of specialized metabolites has become a major technology for drug discovery and studying microbiome ecology. In these efforts, computational tools like antiSMASH have played a central role through the analysis of Biosynthetic Gene Clusters (BGCs). Thousands of candidate BGCs from microbial genomes have been identified and stored in public databases. Interpreting the function and novelty of these predicted BGCs requires comparison with a well-documented set of BGCs of known function. The MIBiG (Minimum Information about a Biosynthetic Gene Cluster) Data Standard and Repository was established in 2015 to enable curation and storage of known BGCs. Here, we present MIBiG 2.0, which encompasses major updates to the schema, the data, and the online repository itself. Over the past five years, 851 new BGCs have been added. Additionally, we performed extensive manual data curation of all entries to improve the annotation quality of our repository. We also redesigned the data schema to ensure the compliance of future annotations. Finally, we improved the user experience by adding new features such as query searches and a statistics page, and enabled direct link-outs to chemical structure databases. The repository is accessible online at https://mibig.secondarymetabolites.org/

Biosynthetic potential of the global ocean microbiome

Natural microbial communities are phylogenetically and metabolically diverse. In addition to underexplored organismal groups, this diversity encompasses a rich discovery potential for ecologically and biotechnologically relevant enzymes and biochemical compounds. However, studying this diversity to identify genomic pathways for the synthesis of such compounds and assigning them to their respective hosts remains challenging. The biosynthetic potential of microorganisms in the open ocean remains largely uncharted owing to limitations in the analysis of genome-resolved data at the global scale. Here we investigated the diversity and novelty of biosynthetic gene clusters in the ocean by integrating around 10,000 microbial genomes from cultivated and single cells with more than 25,000 newly reconstructed draft genomes from more than 1,000 seawater samples. These efforts revealed approximately 40,000 putative mostly new biosynthetic gene clusters, several of which were found in previously unsuspected phylogenetic groups. Among these groups, we identified a lineage rich in biosynthetic gene clusters ('Candidatus Eudoremicrobiaceae') that belongs to an uncultivated bacterial phylum and includes some of the most biosynthetically diverse microorganisms in this environment. From these, we characterized the phospeptin and pythonamide pathways, revealing cases of unusual bioactive compound structure and enzymology, respectively. Together, this research demonstrates how microbiomics-driven strategies can enable the investigation of previously undescribed enzymes and natural products in underexplored microbial groups and environments

MIBiG 3.0: a community-driven effort to annotate experimentally validated biosynthetic gene clusters

Microbial Biotechnolog

A chromosome-level Amaranthus cruentus genome assembly highlights gene family evolution and biosynthetic gene clusters that may underpin the nutritional value of this traditional crop

Traditional crops historically provided accessible and affordable nutrition to millions of rural dwellers but have been neglected, with most modern agricultural systems over reliant on a small number of internationally-traded crops. Traditional crops are typically well-adapted to local agro-ecological conditions and many are nutrient-dense. They can play a vital role in local food systems through enhanced nutrition (especially where diets are dominated by starch crops), food security and livelihoods for smallholder farmers, and a climate-resilient and biodiverse agriculture. Using short-read, long-read and phased sequencing technologies we generated a high-quality chromosome-level genome assembly for Amaranthus cruentus, an under-researched crop with micronutrient- and protein-rich leaves and gluten-free seed, but lacking improved varieties, with respect to productivity and quality traits. The 370.9 MB genome demonstrates a shared whole genome duplication with a related species, Amaranthus hypochondriacus. Comparative genome analysis indicates chromosomal loss and fusion events following genome duplication that are common to both species, as well as fission of chromosome 2 in A. cruentus alone, giving rise to a haploid chromosome number of 17 (versus 16 in A. hypochondriacus). Genomic features potentially underlying the nutritional value of this crop include two A. cruentus-specific genes with a likely role in phytic acid synthesis (an anti-nutrient), expansion of ion transporter gene families, and identification of biosynthetic gene clusters conserved within the amaranth lineage. The A. cruentus genome assembly will underpin much-needed research and global breeding efforts to develop improved varieties for economically viable cultivation and realisation of the benefits to global nutrition security and agrobiodiversity

The Moderation Effect of Uncertainty Environment on SME Business Performance

The Covid-19 pandemic has had an impact that has never been felt before by small and medium enterprises (SMEs) business actors in Indonesia. In business, this situation is called environmental uncertainty. Environmental uncertainty is a condition in which a person is constrained to predict the surrounding situation so he tries to do something to deal with the environmental uncertainty. Environmental dynamics with their uncertainties play a positive moderate role between strategic flexibility and firm performance, which is consistent with the results of previous studies. This research method used a mixed research design with a sequential explanatory strategy. The population of this research was SME's Sidorajo which has the following criteria: doing this business as the main job, running the business for at least 3 years and being active in community development activities and the department. The sample obtained was 100 respondents. The data collection technique was carried out by distributing online questionnaires via google form and FGD with SMEs and Koperindag Office. The results show that business strategy has a positive effect on business performance, strategic flexibility has a positive effect on business performance, environmental uncertainty has a negative effect on business performance and strategic flexibility has no effect on SMEs business performance in Indonesia when moderated by environmental uncertainty. Therefore, environmental uncertainty is not able to play a role as a moderating variable of the influence of strategic flexibility on the performance of SMEs businesses in Indonesi