Bioinformatics analysis has become an integral part of research in biology. However, installation and use of scientific software can be difficult and often requires technical expert knowledge. Reasons are dependencies on certain operating systems or required third-party libraries, missing graphical user interfaces and documentation, or nonstandard input and output formats. In order to make bioinformatics software easily accessible to researchers, we here present a web-based platform. The Center for Bioinformatics Tuebingen (ZBIT) Bioinformatics Toolbox provides web-based access to a collection of bioinformatics tools developed for systems biology, protein sequence annotation, and expression data analysis. Currently, the collection encompasses software for conversion and processing of community standards SBML and BioPAX, transcription factor analysis, and analysis of microarray data from transcriptomics and proteomics studies. All tools are hosted on a customized Galaxy instance and run on a dedicated computation cluster. Users only need a web browser and an active internet connection in order to benefit from this service. The web platform is designed to facilitate the usage of the bioinformatics tools for researchers without advanced technical background. Users can combine tools for complex analyses or use predefined, customizable workflows. All results are stored persistently and reproducible. For each tool, we provide documentation, tutorials, and example data to maximize usability. The ZBIT Bioinformatics Toolbox is freely available at https://webservices.cs.uni-tuebingen.de/.

Paired sample t-test of contigs produced by SPAdes, Velvet, ABySS and SOAPdenovo assemblers. Our optimised ‘SPAdes K15-17-19_cap3’ (SPAdes assembly; dataset = 21–22 nt; kmer set =15,17 and 19; and scaffolded with CAP3) (SP22_K15-17-19_cap3) assembly was compared against all other kmer settings and/or tools. A) SPAdes - Longest assembled contigs (21–22 nt pipeline); B) SPAdes - Total number of assembled bases for contigs > =100 nt (21–22 nt pipeline); C) SPAdes - Longest assembled contigs (21–25 nt pipeline); D) SPAdes - Total number of assembled bases for contigs > =100 nt (21–25 nt pipeline); E) Comparison of longest assembled contig using Velvet against SP22_K15-17-19_cap3; F) Comparison of longest assembled contig using ABySS against SP22_K15-17-19_cap3; G) Comparison of longest assembled contig using SOAPdenovo against SP22_K15-17-19_cap3. (XLSX 19 kb)

Bioinformatics skills have become essential for many research areas; however, the availability of qualified researchers is usually lower than the demand and training to increase the number of able bioinformaticians is an important task for the bioinformatics community. When conducting training or hands-on tutorials, the lack of control over the analysis tools and repositories often results in undesirable situations during training, as unavailable online tools or version conflicts may delay, complicate, or even prevent the successful completion of a training event. The eBioKit is a stand-alone educational platform that hosts numerous tools and databases for bioinformatics research and allows training to take place in a controlled environment. A key advantage of the eBioKit over other existing teaching solutions is that all the required software and databases are locally installed on the system, significantly reducing the dependence on the internet. Furthermore, the architecture of the eBioKit has demonstrated itself to be an excellent balance between portability and performance, not only making the eBioKit an exceptional educational tool but also providing small research groups with a platform to incorporate bioinformatics analysis in their research. As a result, the eBioKit has formed an integral part of training and research performed by a wide variety of universities and organizations such as the Pan African Bioinformatics Network (H3ABioNet) as part of the initiative Human Heredity and Health in Africa (H3Africa), the Southern Africa Network for Biosciences (SAnBio) initiative, the Biosciences eastern and central Africa (BecA) hub, and the International Glossina Genome Initiative.

Statistics of the viral sequences assembled using 21–25 nt, 21–22 nt and 24 nt small RNA subsets. *Virus name: GRSPaV = Grapevine rupestris stem pitting-associated virus; GVB = Grapevine virus B; GFkV = Grapevine fleck virus; GLRaV-3 = Grapevine leafroll-associated virus; HSVd = Hop stunt viroid; PNRSV = Prunus necrotic ringspot virus; RBDV = Raspberry bushy dwarf virus; RYNV = Rubus yellow net virus; SPSMV-1 = Sweetpotato symptomless mastrevirus 1; SMoV = Strawberry mottle virus; MsiMV = Miscanthus sinensis mosaic virus; CTV = Citrus tristeza virus; CVd-VI = Citrus viroid VI; MCDV = Maize chlorotic dwarf virus; AcVB = Actinidia virus B; TVCV = Tobacco vein-clearing virus. **Virus type: RT = retro-transcribing virus; ssRNA + = ssRNA positive-strand virus; ssDNA = single-stranded DNA virus; dsRNA = double-strand RNA virus; V = viroid. (XLSX 49 kb)

Presented at the ECCB2016, den Haag, NL, Sept 2016Africa is not unique in its need for basic bioinformatics training for individuals from a molecular biology background. However, unique logistical challenges in Africa, most notably access to bioinformatics expertise and internet stability, must be addressed in order to meet this need on the continent. H3ABioNet (www.h3abionet.org), the Pan African Bioinformatics Network for H3Africa, has therefore developed an innovative, free Introduction to bioinformatics course taking these challenges into account. A distance-based learning model has been selected for this 3 month course (July-September 2016) to increase access to expert African and European Bioinformatics trainers covering several bioinformatics topics, including: databases and resources; genomics; Linux; sequence alignment; and phylogenetics. Classrooms with a total of >350 participants are hosted at 20 institutions, across 11 African countries, in order to provide local administrative and academic support. Classroom selection was based on certain infrastructure criteria, including: computer resources; Internet access; and availability of local teaching assistants. Although lectures are delivered live to remote sites via an online platform, to ensure that classroom success does not rely on stable Internet, classrooms can watch pre-recorded and pre-downloaded lecture videos, as well as work through practical assignments on the lecture content, during biweekly contact sessions. Lecture recordings are available on the course website http://training.h3abionet.org/IBT_2016/. While trainers are available via video conferencing to take questions during contact sessions, online ‘question and discussion’ forums, hosted on the course management platform, are also available. This distance based model, developed for a resource limited setting, could easily be adapted to other settings.

International Journal of Engineering and Advanced Technology Acceptance Rate - ResearchHelpDesk - International Journal of Engineering and Advanced Technology (IJEAT) is having Online-ISSN 2249-8958, bi-monthly international journal, being published in the months of February, April, June, August, October, and December by Blue Eyes Intelligence Engineering & Sciences Publication (BEIESP) Bhopal (M.P.), India since the year 2011. It is academic, online, open access, double-blind, peer-reviewed international journal. It aims to publish original, theoretical and practical advances in Computer Science & Engineering, Information Technology, Electrical and Electronics Engineering, Electronics and Telecommunication, Mechanical Engineering, Civil Engineering, Textile Engineering and all interdisciplinary streams of Engineering Sciences. All submitted papers will be reviewed by the board of committee of IJEAT. Aim of IJEAT Journal disseminate original, scientific, theoretical or applied research in the field of Engineering and allied fields. dispense a platform for publishing results and research with a strong empirical component. aqueduct the significant gap between research and practice by promoting the publication of original, novel, industry-relevant research. seek original and unpublished research papers based on theoretical or experimental works for the publication globally. publish original, theoretical and practical advances in Computer Science & Engineering, Information Technology, Electrical and Electronics Engineering, Electronics and Telecommunication, Mechanical Engineering, Civil Engineering, Textile Engineering and all interdisciplinary streams of Engineering Sciences. impart a platform for publishing results and research with a strong empirical component. create a bridge for a significant gap between research and practice by promoting the publication of original, novel, industry-relevant research. solicit original and unpublished research papers, based on theoretical or experimental works. Scope of IJEAT International Journal of Engineering and Advanced Technology (IJEAT) covers all topics of all engineering branches. Some of them are Computer Science & Engineering, Information Technology, Electronics & Communication, Electrical and Electronics, Electronics and Telecommunication, Civil Engineering, Mechanical Engineering, Textile Engineering and all interdisciplinary streams of Engineering Sciences. The main topic includes but not limited to: 1. Smart Computing and Information Processing Signal and Speech Processing Image Processing and Pattern Recognition WSN Artificial Intelligence and machine learning Data mining and warehousing Data Analytics Deep learning Bioinformatics High Performance computing Advanced Computer networking Cloud Computing IoT Parallel Computing on GPU Human Computer Interactions 2. Recent Trends in Microelectronics and VLSI Design Process & Device Technologies Low-power design Nanometer-scale integrated circuits Application specific ICs (ASICs) FPGAs Nanotechnology Nano electronics and Quantum Computing 3. Challenges of Industry and their Solutions, Communications Advanced Manufacturing Technologies Artificial Intelligence Autonomous Robots Augmented Reality Big Data Analytics and Business Intelligence Cyber Physical Systems (CPS) Digital Clone or Simulation Industrial Internet of Things (IIoT) Manufacturing IOT Plant Cyber security Smart Solutions – Wearable Sensors and Smart Glasses System Integration Small Batch Manufacturing Visual Analytics Virtual Reality 3D Printing 4. Internet of Things (IoT) Internet of Things (IoT) & IoE & Edge Computing Distributed Mobile Applications Utilizing IoT Security, Privacy and Trust in IoT & IoE Standards for IoT Applications Ubiquitous Computing Block Chain-enabled IoT Device and Data Security and Privacy Application of WSN in IoT Cloud Resources Utilization in IoT Wireless Access Technologies for IoT Mobile Applications and Services for IoT Machine/ Deep Learning with IoT & IoE Smart Sensors and Internet of Things for Smart City Logic, Functional programming and Microcontrollers for IoT Sensor Networks, Actuators for Internet of Things Data Visualization using IoT IoT Application and Communication Protocol Big Data Analytics for Social Networking using IoT IoT Applications for Smart Cities Emulation and Simulation Methodologies for IoT IoT Applied for Digital Contents 5. Microwaves and Photonics Microwave filter Micro Strip antenna Microwave Link design Microwave oscillator Frequency selective surface Microwave Antenna Microwave Photonics Radio over fiber Optical communication Optical oscillator Optical Link design Optical phase lock loop Optical devices 6. Computation Intelligence and Analytics Soft Computing Advance Ubiquitous Computing Parallel Computing Distributed Computing Machine Learning Information Retrieval Expert Systems Data Mining Text Mining Data Warehousing Predictive Analysis Data Management Big Data Analytics Big Data Security 7. Energy Harvesting and Wireless Power Transmission Energy harvesting and transfer for wireless sensor networks Economics of energy harvesting communications Waveform optimization for wireless power transfer RF Energy Harvesting Wireless Power Transmission Microstrip Antenna design and application Wearable Textile Antenna Luminescence Rectenna 8. Advance Concept of Networking and Database Computer Network Mobile Adhoc Network Image Security Application Artificial Intelligence and machine learning in the Field of Network and Database Data Analytic High performance computing Pattern Recognition 9. Machine Learning (ML) and Knowledge Mining (KM) Regression and prediction Problem solving and planning Clustering Classification Neural information processing Vision and speech perception Heterogeneous and streaming data Natural language processing Probabilistic Models and Methods Reasoning and inference Marketing and social sciences Data mining Knowledge Discovery Web mining Information retrieval Design and diagnosis Game playing Streaming data Music Modelling and Analysis Robotics and control Multi-agent systems Bioinformatics Social sciences Industrial, financial and scientific applications of all kind 10. Advanced Computer networking Computational Intelligence Data Management, Exploration, and Mining Robotics Artificial Intelligence and Machine Learning Computer Architecture and VLSI Computer Graphics, Simulation, and Modelling Digital System and Logic Design Natural Language Processing and Machine Translation Parallel and Distributed Algorithms Pattern Recognition and Analysis Systems and Software Engineering Nature Inspired Computing Signal and Image Processing Reconfigurable Computing Cloud, Cluster, Grid and P2P Computing Biomedical Computing Advanced Bioinformatics Green Computing Mobile Computing Nano Ubiquitous Computing Context Awareness and Personalization, Autonomic and Trusted Computing Cryptography and Applied Mathematics Security, Trust and Privacy Digital Rights Management Networked-Driven Multicourse Chips Internet Computing Agricultural Informatics and Communication Community Information Systems Computational Economics, Digital Photogrammetric Remote Sensing, GIS and GPS Disaster Management e-governance, e-Commerce, e-business, e-Learning Forest Genomics and Informatics Healthcare Informatics Information Ecology and Knowledge Management Irrigation Informatics Neuro-Informatics Open Source: Challenges and opportunities Web-Based Learning: Innovation and Challenges Soft computing Signal and Speech Processing Natural Language Processing 11. Communications Microstrip Antenna Microwave Radar and Satellite Smart Antenna MIMO Antenna Wireless Communication RFID Network and Applications 5G Communication 6G Communication 12. Algorithms and Complexity Sequential, Parallel And Distributed Algorithms And Data Structures Approximation And Randomized Algorithms Graph Algorithms And Graph Drawing On-Line And Streaming Algorithms Analysis Of Algorithms And Computational Complexity Algorithm Engineering Web Algorithms Exact And Parameterized Computation Algorithmic Game Theory Computational Biology Foundations Of Communication Networks Computational Geometry Discrete Optimization 13. Software Engineering and Knowledge Engineering Software Engineering Methodologies Agent-based software engineering Artificial intelligence approaches to software engineering Component-based software engineering Embedded and ubiquitous software engineering Aspect-based software engineering Empirical software engineering Search-Based Software engineering Automated software design and synthesis Computer-supported cooperative work Automated software specification Reverse engineering Software Engineering Techniques and Production Perspectives Requirements engineering Software analysis, design and modelling Software maintenance and evolution Software engineering tools and environments Software engineering decision support Software design patterns Software product lines Process and workflow management Reflection and metadata approaches Program understanding and system maintenance Software domain modelling and analysis Software economics Multimedia and hypermedia software engineering Software engineering case study and experience reports Enterprise software, middleware, and tools Artificial intelligent methods, models, techniques Artificial life and societies Swarm intelligence Smart Spaces Autonomic computing and agent-based systems Autonomic computing Adaptive Systems Agent architectures, ontologies, languages and protocols Multi-agent systems Agent-based learning and knowledge discovery Interface agents Agent-based auctions and marketplaces Secure mobile and multi-agent systems Mobile agents SOA and Service-Oriented Systems Service-centric software engineering Service oriented requirements engineering Service oriented architectures Middleware for service based systems Service discovery and composition Service level

VirFind BLASTX results for contigs with sequence simalrity to viruses or viroids. (XLSX 50Â kb)

International Journal of Engineering and Advanced Technology - ResearchHelpDesk - International Journal of Engineering and Advanced Technology (IJEAT) is having Online-ISSN 2249-8958, bi-monthly international journal, being published in the months of February, April, June, August, October, and December by Blue Eyes Intelligence Engineering & Sciences Publication (BEIESP) Bhopal (M.P.), India since the year 2011. It is academic, online, open access, double-blind, peer-reviewed international journal. It aims to publish original, theoretical and practical advances in Computer Science & Engineering, Information Technology, Electrical and Electronics Engineering, Electronics and Telecommunication, Mechanical Engineering, Civil Engineering, Textile Engineering and all interdisciplinary streams of Engineering Sciences. All submitted papers will be reviewed by the board of committee of IJEAT. Aim of IJEAT Journal disseminate original, scientific, theoretical or applied research in the field of Engineering and allied fields. dispense a platform for publishing results and research with a strong empirical component. aqueduct the significant gap between research and practice by promoting the publication of original, novel, industry-relevant research. seek original and unpublished research papers based on theoretical or experimental works for the publication globally. publish original, theoretical and practical advances in Computer Science & Engineering, Information Technology, Electrical and Electronics Engineering, Electronics and Telecommunication, Mechanical Engineering, Civil Engineering, Textile Engineering and all interdisciplinary streams of Engineering Sciences. impart a platform for publishing results and research with a strong empirical component. create a bridge for a significant gap between research and practice by promoting the publication of original, novel, industry-relevant research. solicit original and unpublished research papers, based on theoretical or experimental works. Scope of IJEAT International Journal of Engineering and Advanced Technology (IJEAT) covers all topics of all engineering branches. Some of them are Computer Science & Engineering, Information Technology, Electronics & Communication, Electrical and Electronics, Electronics and Telecommunication, Civil Engineering, Mechanical Engineering, Textile Engineering and all interdisciplinary streams of Engineering Sciences. The main topic includes but not limited to: 1. Smart Computing and Information Processing Signal and Speech Processing Image Processing and Pattern Recognition WSN Artificial Intelligence and machine learning Data mining and warehousing Data Analytics Deep learning Bioinformatics High Performance computing Advanced Computer networking Cloud Computing IoT Parallel Computing on GPU Human Computer Interactions 2. Recent Trends in Microelectronics and VLSI Design Process & Device Technologies Low-power design Nanometer-scale integrated circuits Application specific ICs (ASICs) FPGAs Nanotechnology Nano electronics and Quantum Computing 3. Challenges of Industry and their Solutions, Communications Advanced Manufacturing Technologies Artificial Intelligence Autonomous Robots Augmented Reality Big Data Analytics and Business Intelligence Cyber Physical Systems (CPS) Digital Clone or Simulation Industrial Internet of Things (IIoT) Manufacturing IOT Plant Cyber security Smart Solutions – Wearable Sensors and Smart Glasses System Integration Small Batch Manufacturing Visual Analytics Virtual Reality 3D Printing 4. Internet of Things (IoT) Internet of Things (IoT) & IoE & Edge Computing Distributed Mobile Applications Utilizing IoT Security, Privacy and Trust in IoT & IoE Standards for IoT Applications Ubiquitous Computing Block Chain-enabled IoT Device and Data Security and Privacy Application of WSN in IoT Cloud Resources Utilization in IoT Wireless Access Technologies for IoT Mobile Applications and Services for IoT Machine/ Deep Learning with IoT & IoE Smart Sensors and Internet of Things for Smart City Logic, Functional programming and Microcontrollers for IoT Sensor Networks, Actuators for Internet of Things Data Visualization using IoT IoT Application and Communication Protocol Big Data Analytics for Social Networking using IoT IoT Applications for Smart Cities Emulation and Simulation Methodologies for IoT IoT Applied for Digital Contents 5. Microwaves and Photonics Microwave filter Micro Strip antenna Microwave Link design Microwave oscillator Frequency selective surface Microwave Antenna Microwave Photonics Radio over fiber Optical communication Optical oscillator Optical Link design Optical phase lock loop Optical devices 6. Computation Intelligence and Analytics Soft Computing Advance Ubiquitous Computing Parallel Computing Distributed Computing Machine Learning Information Retrieval Expert Systems Data Mining Text Mining Data Warehousing Predictive Analysis Data Management Big Data Analytics Big Data Security 7. Energy Harvesting and Wireless Power Transmission Energy harvesting and transfer for wireless sensor networks Economics of energy harvesting communications Waveform optimization for wireless power transfer RF Energy Harvesting Wireless Power Transmission Microstrip Antenna design and application Wearable Textile Antenna Luminescence Rectenna 8. Advance Concept of Networking and Database Computer Network Mobile Adhoc Network Image Security Application Artificial Intelligence and machine learning in the Field of Network and Database Data Analytic High performance computing Pattern Recognition 9. Machine Learning (ML) and Knowledge Mining (KM) Regression and prediction Problem solving and planning Clustering Classification Neural information processing Vision and speech perception Heterogeneous and streaming data Natural language processing Probabilistic Models and Methods Reasoning and inference Marketing and social sciences Data mining Knowledge Discovery Web mining Information retrieval Design and diagnosis Game playing Streaming data Music Modelling and Analysis Robotics and control Multi-agent systems Bioinformatics Social sciences Industrial, financial and scientific applications of all kind 10. Advanced Computer networking Computational Intelligence Data Management, Exploration, and Mining Robotics Artificial Intelligence and Machine Learning Computer Architecture and VLSI Computer Graphics, Simulation, and Modelling Digital System and Logic Design Natural Language Processing and Machine Translation Parallel and Distributed Algorithms Pattern Recognition and Analysis Systems and Software Engineering Nature Inspired Computing Signal and Image Processing Reconfigurable Computing Cloud, Cluster, Grid and P2P Computing Biomedical Computing Advanced Bioinformatics Green Computing Mobile Computing Nano Ubiquitous Computing Context Awareness and Personalization, Autonomic and Trusted Computing Cryptography and Applied Mathematics Security, Trust and Privacy Digital Rights Management Networked-Driven Multicourse Chips Internet Computing Agricultural Informatics and Communication Community Information Systems Computational Economics, Digital Photogrammetric Remote Sensing, GIS and GPS Disaster Management e-governance, e-Commerce, e-business, e-Learning Forest Genomics and Informatics Healthcare Informatics Information Ecology and Knowledge Management Irrigation Informatics Neuro-Informatics Open Source: Challenges and opportunities Web-Based Learning: Innovation and Challenges Soft computing Signal and Speech Processing Natural Language Processing 11. Communications Microstrip Antenna Microwave Radar and Satellite Smart Antenna MIMO Antenna Wireless Communication RFID Network and Applications 5G Communication 6G Communication 12. Algorithms and Complexity Sequential, Parallel And Distributed Algorithms And Data Structures Approximation And Randomized Algorithms Graph Algorithms And Graph Drawing On-Line And Streaming Algorithms Analysis Of Algorithms And Computational Complexity Algorithm Engineering Web Algorithms Exact And Parameterized Computation Algorithmic Game Theory Computational Biology Foundations Of Communication Networks Computational Geometry Discrete Optimization 13. Software Engineering and Knowledge Engineering Software Engineering Methodologies Agent-based software engineering Artificial intelligence approaches to software engineering Component-based software engineering Embedded and ubiquitous software engineering Aspect-based software engineering Empirical software engineering Search-Based Software engineering Automated software design and synthesis Computer-supported cooperative work Automated software specification Reverse engineering Software Engineering Techniques and Production Perspectives Requirements engineering Software analysis, design and modelling Software maintenance and evolution Software engineering tools and environments Software engineering decision support Software design patterns Software product lines Process and workflow management Reflection and metadata approaches Program understanding and system maintenance Software domain modelling and analysis Software economics Multimedia and hypermedia software engineering Software engineering case study and experience reports Enterprise software, middleware, and tools Artificial intelligent methods, models, techniques Artificial life and societies Swarm intelligence Smart Spaces Autonomic computing and agent-based systems Autonomic computing Adaptive Systems Agent architectures, ontologies, languages and protocols Multi-agent systems Agent-based learning and knowledge discovery Interface agents Agent-based auctions and marketplaces Secure mobile and multi-agent systems Mobile agents SOA and Service-Oriented Systems Service-centric software engineering Service oriented requirements engineering Service oriented architectures Middleware for service based systems Service discovery and composition Service level agreements (drafting,

Food web dynamics are vital in shaping the functional ecology of ecosystems. However, trophic ecology is still in its infancy in groundwater ecosystems due to the cryptic nature of these environments. To unravel trophic interactions between subterranean biota, we applied an interdisciplinary Bayesian mixing model design (multi-factor BMM) based on the integration of faunal C and N bulk tissue stable isotope data (δ13C and δ15N) with radiocarbon data (Δ14C), and prior information from metagenomic analyses. We further compared outcomes from multi-factor BMM with a conventional isotope double proxy mixing model (SIA BMM), triple proxy (δ13C, δ15N and Δ14C, multi-proxy BMM) and double proxy combined with DNA prior information (SIA+DNA BMM) designs. Three species of subterranean beetles (Paroster macrosturtensis, Paroster mesosturtensis and Paroster microsturtensis) and their main prey items Chiltoniidae amphipods (AM1: Scutachiltonia axfordi and AM2: Yilgarniella sturtensis), cyclopoids and harpacticoids from a calcrete in Western Australia were targeted. Diet estimations from stable isotope only models indicated homogeneous patterns with modest preferences for amphipods as prey items. Multi-proxy BMM suggested increased - and species-specific - predatory pressures on amphipods coupled with high rates of scavenging/predation on sister species. SIA+DNA BMM showed marked preferences for amphipods AM1 and AM2 and reduced interspecific scavenging/predation on Paroster species. Multi-factorial BMM revealed the most precise estimations (lower overall SD and very marginal beetles’ interspecific interactions), indicating consistent preferences for amphipods AM1 in all the beetles’ diets. Incorporation of genetic priors allowed crucial refining of the feeding preferences, while integration of more expensive radiocarbon data as a third proxy (when combined with genetic data) produced more precise outcomes but close dietary reconstruction to that from SIA+DNA BMM. Further multidisciplinary modelling from other groundwater environments will help elucidate the potential behind these designs and bring light to the feeding ecology of one the most vital ecosystems worldwide.

Methods Supporting information Sacco et al., 2020 Ecology and Evolution

Extraction of DNA: a total of 15 individuals for each of the three Paroster species (P. macrosturtensis (B), P. mesosturtensis (M), P. microsturtensis (S)) were sorted into triplicate stygobitic pools (i.e. 5 individuals per pool) for DNA extraction. Prior to DNA extraction, stygobitic animals (5 individuals per pool; n=18) were placed in a petri dish containing ultrapure water and UV sterilised for 10 minutes to eliminate any potential eDNA that may be contained on the exoskeleton. Immediately post-UV treatment, the animals were placed into tissue lysis tubes with 180 µL ATL and 20 µL Proteinase K and homogenised using Minilys® tissue homogeniser (ThermoFisher Scientific, Australia) at high speed for 30 seconds. Lysis tubes, inclusive of one laboratory control, were incubated at 56°C using an agitating heat block (Eppendorf ThermoStat™ C, VWR, Australia) for 5 hours. Following incubation, DNA extraction was carried out using DNeasy Blood and Tissue Kit (Qiagen; Venlo, Netherlands eluted off the silica column in 50 µL AE buffer.

PCR: The quality and quantity of DNA extracted from each stygobitic pool was measured using quantitative PCR (qPCR), insect 16S and COI genes. PCR reactions to assess the quality and quantity of the DNA target of interest were carried out via qPCR (Applied Biosystems [ABI], USA) in 25 µL reaction volumes consisting of 2 mM MgCl2 (Fisher Biotec, Australia), 1 x PCR Gold Buffer (Fisher Biotec, Australia), 0.4 µM dNTPs (Astral Scientific, Australia), 0.1 mg bovine serum albumin (Fisher Biotec, Australia), 0.4 µM of each primer (MZArtF and MZArtR Zeale, Butlin, & Jones 2011; Ins16S_1shortF and Ins16S_1shortR Clarke, Soubrier, & Cooper 2014), 0.2 µL of AmpliTaq Gold (AmpliTaq Gold, ABI, USA), and 2 µL of template DNA (Neat, 1/10, 1/100 dilutions). The cycling conditions were: initial denaturation at 95°C for 5 minutes, followed by 40 cycles of 95°C for 30 seconds, 52°C for 30 seconds, 72°C for 30 seconds, and a final extension at 72°C for 10 minutes.

DNA extracts that successfully yielded DNA of sufficient quality, free of inhibition, as determined by the initial qPCR screen (detailed above), were assigned a unique 6-8bp multiplex identifier tag (MID-tag) with the 16S and COI primer set. Independent MID-tag qPCR for each stygobitic pool were carried out in 25 µL reactions containing 1 x PCR Gold Buffer, 2.5 mM MgCl2, 0.4 mg/mL BSA, 0.25 mM of each dNTP, 0.4 µM of each primer, 0.2 µL AmpliTaq Gold and 2-4 µL of DNA as determined by the initial qPCR screen. The cycling conditions for qPCR using the MID-tag primer sets were as described above. MID-tag PCR amplicons were generated in duplicate and the library was pooled in equimolar ratio post-PCR for DNA sequencing. The final library was size selected (160-600bp) using Pippin Prep (Sage Sciences, USA) to remove any MID-tag primer-dimer products that may have formed during amplification. The final library concentration was determined using a QuBitTM 4 Fluorometer (Thermofischer, Australia) and sequenced using a 300 cycle V2 kit on an Illumina MiSeq platform (Illumina, USA).

MID-tag sequence reads obtained from the MiSeq were sorted (filtered) back to the stygobitic pool based on the MID-tags assigned to each DNA extract using Geneious v10.2.5. MID-tag and primer sequences were trimmed from the sequence reads allowing for no mismatch in length or base composition. Each stygobitic pool for the two genes amplified were searched using BLASTn (Altschul, Gish, & Lipman 1990), against the NCBI GenBank nucleotide database to enable taxonomic identification. This was automated in the internet-based bioinformatics workflow environment through Pawsey Supercomputing (REF). The BLAST results obtained were imported into MEtaGenome Analyzer v4 (MEGAN; Huson, Auch, & Schuster 2007), where they were taxonomically assigned using the LCA-assignment algorithm (min. bit score = 65.0, top percentage = 5%, min. support = 5).

Additional references

Altschul, S. F., Gish, W., Miller, W., Myers, E. W., & Lipman, D. J. (1990). Basic local alignment search tool. Journal of molecular biology, 215(3), 403-410.

Clarke, L. J., Soubrier, J., Weyrich, L. S., & Cooper, A. (2014). Environmental metabarcodes for insects: in silico PCR reveals potential for taxonomic bias. Molecular ecology resources, 14(6), 1160-1170.

Huson, D. H., Auch, A. F., Qi, J., & Schuster, S. C. (2007). MEGAN analysis of metagenomic data. Genome research, 17(3), 377-386.

Zeale, M. R., Butlin, R. K., Barker, G. L., Lees, D. C., & Jones, G. (2011). Taxon‐specific PCR for DNA barcoding arthropod prey in bat faeces. Molecular ecology resources, 11(2), 236-244.

The data consists of five Protein Data Bank (PDB) structure files of the complex formed by FtsQ, FtsL, FtsB, FtsW, and FtsI of the divisome of Escherichia coli (FtsQLBWI). The five PDB files consist of an original AlphaFold2 model, partially validated through mutagenesis in vivo, and a series of derivatives remodeled seeking insight into the potential structural transitions that lead to activation of the FtsWI complex, which produced peptidoglycan during cell division. In the original model (file FtsQLBWI_protomer_original.pdb), FtsLB serves as a support for FtsI, placing its periplasmic domain in an extended and possibly active conformation. We remodeled the periplasmic domain of FtsI to assess it the model is compatible with a compact and possibly inactive conformation (file FtsQLBWI_protomer_compact.pdb). Additionally, the complex was remodeled to assume an Fts[QLBWI]2 diprotomeric configuration, using FtsLB as a central hub (file FtsQLBWI_diprotomer_clashing.pdb). This was performed by applying the C2 symmetry operation (180° rotation) to the Fts[QLBWI]1 complex that reconstructs the Fts[LB]2 complex in the Y-model configuration from the Fts[LB]1 AlphaFold2 prediction. In this model, a severe steric overlap occurs between FtsQ and FtsI, which occupy the same region of space adjacent to FtsLB. To address whether this clash could be solved by providing flexibility to a hinge in the CCD region of FtsLB, we used a procedure, based on docking of FtsQ with HADDOCK followed by loop reconstruction with Rosetta (file FtsQLBWI_diprotomer_extended.pdb). Finally, we reconfigured the initial diprotomeric model in a compact state (file FtsQLBWI_diprotomer_compact.pdb). Methods The original data was obtained by submitting the sequences of FtsQ, FtsL, FtsB, FtsW, and FtsI to AlphaFold2 (ColaFold) (1). The monoprotomeric FtsQLBWI complex was reconfigured using homology modeling using the SWISS-MODEL webserver (2). The reconfiguration in a diprotomeric configuration was performed using a program written with MSL (3). Remodeling of FtsQ in the diprotomeric extended state was performed with HADDOCK (4) and Rosetta (5). References: 1. Mirdita M, Ovchinnikov S, Steinegger M. ColabFold - Making protein folding accessible to all [Internet]. Bioinformatics; 2021 Aug [cited 2021 Sep 14]. 2. Waterhouse A, Bertoni M, Bienert S, Studer G, Tauriello G, Gumienny R, et al. SWISS-MODEL: homology modelling of protein structures and complexes. Nucleic Acids Res. 2018 Jul 2;46(W1):W296–303. 3. Kulp DW, Subramaniam S, Donald JE, Hannigan BT, Mueller BK, Grigoryan G, et al. Structural informatics, modeling, and design with an open-source Molecular Software Library (MSL). J Comput Chem. 2012 Jul 30;33(20):1645–61. 4. Dominguez C, Boelens R, Bonvin AMJJ. HADDOCK: A Protein−Protein Docking Approach Based on Biochemical or Biophysical Information. J Am Chem Soc. 2003 Feb 19;125(7):1731–7. 5. Huang PS, Ban YEA, Richter F, Andre I, Vernon R, Schief WR, et al. RosettaRemodel: A Generalized Framework for Flexible Backbone Protein Design. Uversky VN, editor. PLoS ONE. 2011 Aug 31;6(8):e24109.

Adaptor clipped and quality trimmed read statistics of small RNA-Seq datasets. Clean reads = Adaptor clipped small RNA reads provided by BGI service provider; QC = Quality Control consisting of adaptor clipping and poor base call trimming; n.a. = not available. (XLSX 44 kb)

VirFind contigs annotated with hits to viruses were run through the Yabi VSD toolkit pipeline. Top BLASTX hits (Evalue = < 1e-5) to a combined plant and virus protein database are reported. VirFind assembled contigs with a top hit to a plant virus are highlighted in green background. (XLSX 59 kb)

Transcriptome analysis experiments enable researchers to gain extensive insights into the molecular mechanisms underlying cell physiology and disease. Oxford Nanopore Technologies (ONT) has recently been developed as a fast, miniaturized, portable, and cost-effective alternative to next-generation sequencing (NGS). However, RNA-Seq data analysis software that exploits ONT portability and allows scientists to easily analyze ONT data everywhere without bioinformatics expertise is not widely available. We developed DuesselporeTM, an easy-to-follow deep sequencing workflow that runs as a local webserver and allows the analysis of ONT data everywhere without requiring additional bioinformatics tools or internet connection. DuesselporeTM output includes differentially expressed genes and further downstream analyses, such as variance heatmap, disease and gene ontology plots, gene concept network plots, and exports customized pathways for different cellular processes. We validated DuesselporeTM by analyzing the transcriptomic changes induced by PCB126, a dioxin-like PCB, and a potent aryl hydrocarbon receptor (AhR) agonist in human HaCaT keratinocytes, a well-characterized model system. DuesselporeTM was specifically developed to analyze ONT data, but we also implemented NGS data analysis. DuesselporeTM is compatible with Linux, Microsoft, and Mac operating systems and allows convenient, reliable, and cost-effective analysis of ONT and NGS data.