Erik Bongcam-Rudloff

Swedish University of Agricultural Sciences | SLU · Department of Animal Breeding and Genetics

Cassava Brown Streak Virus (CBSV) and Ugandan Cassava Brown Streak Virus (UCBSV) are the two among six virus species speculated to cause the most catastrophic Brown Streak Disease of Cassava (CBSD) in Africa and Asia. For unknown reasons, Cassava Brown Streak Virus (CBSV) is hard to breed resistance for compared to Ugandan Cassava Brown Streak Viru...

The evaluation of the CGIAR Platform for Big Data in Agriculture responds to the request of CGIAR System Council as part of the approved 2021 workplan for the evaluation function under CGIAR Advisory Services Shared Secretariat (CAS Secretariat) to provide evaluative evidence to CGIAR for accountability and learning. The evaluation was conducted be...

The completion of the human genome sequence triggered worldwide efforts to unravel the secrets hidden in its deceptively simple code. Numerous bioinformatics projects were undertaken to hunt for genes, predict their protein products, function and post-translational modifications, analyse protein-protein interactions, etc. Many novel analytic and pr...

Effective control of ipomoviruses that cause cassava brown streak disease (CBSD) in Africa has remained problematic despite eight remarkable decades (1930-2021) of research efforts. Molecular mechanisms underlying resistance breakdown in genetically improved cassava are still unknown. The vast genetic diversity of cassava brown streak viruses, whic...

In this paper, we first summarise the 2020 International Conference of EMBnet (The Global Bioinformatics Network) on “Bioinformatics Approaches to Precision Research”, held on 23th-24th September 2020, and then briefly introduce the main topics and contributions presented at the Conference and published in this supplement issue. The Conference’s ma...

Coral reefs face an increased number of environmental threats from anthropomorphic climate change and pollution from agriculture, industries and sewage. Because environmental changes lead to their compositional and functional shifts, coral reef microbial communities can serve as indicators of ecosystem impacts through development of rapid and inexp...

Background The first month of life is the most critical in a child’s heath because it is associated with the highest risk of adverse health outcomes. In Tanzania the risk of adverse health outcomes in preterm infants is five times higher compared to term infants.The objective of this study was to assess common adverse health outcomes and compare th...

Today, academic researchers benefit from the changes driven by digital technologies and the enormous growth of knowledge and data, on globalisation, enlargement of the scientific community, and the linkage between different scientific communities and the society. To fully benefit from this development, however, information needs to be shared openly...

Test dataset for AcetoScan

Metagenomics has redefined many areas of microbiology. However, metagenome-assembled genomes (MAGs) are often fragmented, primarily when sequencing was performed with short reads. Recent long-read sequencing technologies promise to improve genome reconstruction. However, the integration of two different sequencing modalities makes downstream analys...

Host associated microbiome not only may affect the individual health-status or provide insights into the species- or group specific bacterial communities but may act as early warning signs in the assessment of zoonotic res-ervoirs, offering clues to predict, prevent and control possible episodes of emerging zoonoses. Bats may be carriers and reserv...

The Ebola virus disease is a severe hemorrhagic fever that affects humans and other primates. Ebola virus, the causative agent of the disease, is transmitted to humans from wild animals and is highly contagious and aggressive with an estimated fatality rate to be around 50%. Since 1976, 11 outbreaks of Ebola virus disease have been reported in tota...

Objective: To determine factors associated with risk of preterm delivery among pregnant women delivering at Muhimbili National Hospital in Tanzania. Methods: A 1:1 case-control study was conducted to assess maternal sociodemographic, lifestyle, and current and previous obstetric factors associated with risk of preterm delivery. Mothers of preter...

Today, academic researchers benefit from the changes driven by digital technologies and the enormous growth of knowledge and data, on globalisation, enlargement of the scientific community, and the linkage between different scientific communities and the society. To fully benefit from this development, however, information needs to be shared openly...

Anaerobic digestion (AD) has long been critical technology for green energy, but the majority of the microorganisms involved are unknown and are currently not cultivable, which makes abundance tracking difficult. Developments in nanopore long-read sequencing make it a promising approach for monitoring microbial communities via metagenomic sequencin...

The formyltetrahydrofolate synthetase (FTHFS) gene is a molecular marker of choice to study the diversity of acetogenic communities. However, current analyses are limited due to lack of a high-throughput sequencing approach for FTHFS gene amplicons and a dedicated bioinformatics pipeline for data analysis, including taxonomic annotation and visuali...

Background: Lipopolysaccharide (LPS) endotoxin stimulates pro-inflammatory pathways and is a key player in the pathological mechanisms involved in the development of endometritis. This study aimed to investigate LPS-induced DNA methylation changes in bovine endometrial epithelial cells (bEECs), which may affect endometrial function. Following in v...

Background: Anaerobic digestion (AD) has long been critical technology for green energy, but the majority of the microorganisms involved are unknown and are currently not cultivable, which makes abundance tracking difficult. Developments in nanopore long-read sequencing make it a promising approach for monitoring microbial communities via metagenom...

Host associated microbiome not only may affect the individual health-status or provide insights into the species- or group specific bacterial communities but may act as early warning signs in the assessment of zoonotic reservoirs, offering clues to predict, prevent and control possible episodes of emerging zoonoses. Bats may be carriers and reservo...

There is a lack of research on the benefits and risks of shoeing conditions in harness racing. Our objectives were thus to: 1) investigate whether velocity times (VT; s/km) are affected by racing unshod (N=76,932 records on 5247 horses); 2) determine the potential risks of galloping, being penalized and disqualification when competing unshod (N=111...

Coral reefs face increased environmental threats from anthropomorphic climate change and pollution, from agriculture, industries and tourism. They are economically vital for many people worldwide, and harbour a fantastically diverse ecosystem, being the home for many species of fish and algae. Surprisingly little is known about the microbial commun...

Metagenomics has redefined many areas of microbiology. However, metagenome-assembled genomes (MAGs) are often fragmented, primarily when sequencing was performed with short reads. Recent long-read sequencing technologies promise to improve genome reconstruction. However, the integration of two different sequencing modalities makes downstream analys...

Here we present the draft genome sequence of Setaria digitata, a parasitic nematode affecting cattle. Due to its similarity to Wuchereria bancrofti, the parasitic nematode that causes lymphatic filariasis in humans, S. digitata has been used as a model organism at the genomic level to find drug targets which can be used for the development of novel...

Harmonized embryo maternal relationships, are necessary at the beginning of pregnancy to insure the development of the young embryo and of the placenta. Specific mechanisms modulate the immune balance towards immune-tolerance for the embryo to be accepted by the endometrium. By the same time this tissue is submitted to intense remodelling, under co...

Reproducibility constitutes an important criterion for the evaluation of the quality of research and robustness of results. However, while big data are accumulating at a fast pace, data management, integration, sharing and interpretation become rather challenging. The massive amount of different kinds of data produced need standardised approaches f...

Background: Anaerobic digestion (AD) has long been critical technology for green energy, but the majority of the microorganisms involved are unknown and are currently not cultivable, which makes abundance tracking difficult. Developments in nanopore long-read sequencing make it a promising approach for monitoring microbial communities via metagenom...

Microbial communities are essential components of natural ecosystems. Of the global oceans, the Indian Ocean remains the least studied in terms of its microbial diversity, despite it being a highly dynamic tropical water body. Metagenomics methods have significantly advanced studies in marine microbial ecology in recent years. Preliminary metabarco...

Lipopolysaccharide (LPS) expressed on the surface of Gram-negative bacteria activates pro-inflammatory pathways, dys-regulates the function of endometrial cells and is a key player in the mechanisms involved in endometritis. This study aimed to investigate the effects of LPS on bovine endometrial epithelial cells (bEEC) from whole transcriptome wit...

CADASIL syndrome is a rare disease that belongs to a group of disorders called leukodystrophies. It is well established that NOTCH3 gene on chromosome 19 is primarily responsible for the development of the CADASIL syndrome. Herein, an attempt is made to shed light on the actual molecular mechanism underlying CADASIL syndrome, through insights extra...

Modern, high-throughput methods for the analysis of genetic information, gene and metabolic products and their interactions offer new opportunities to gain comprehensive information on life processes. The data and knowledge generated open diverse application possibilities with enormous innovation potential. To unlock that potential skills in genera...

p>Endogenous retroviruses (ervs) are sequences that derived from ancient retroviral infections of germ cells and integrated in humans, mammals and other vertebrates millions years ago. These ervs are inherited according to Mendelian expectations as all other genes in the genome. Coding sequences are flanked by two ltrs (long terminal repeat sequenc...

Open Science describes the ongoing transitions in the way research is performed, i.e. researchers collaborate, knowledge is shared, and science is organized. It is driven by digital technologies and by the enormous growth of data, globalization, enlargement of the scientific community and the need to address societal challenges [23]. It has now wid...

Motivation: The accurate in-silico simulation of metagenomic datasets is of great importance for benchmarking bioinformatics tools as well as for experimental design. Users are dependant on large-scale simulation to not only design experiments and new projects but also for accurate estimation of computational needs within a project. Unfortunately,...

Sponges belonging to genus Mycale are common and widely distributed across the oceans and represent a significant component of benthic communities in term of their biomass, which in many species is largely composed by bacteria. However, the microbial communities associated with Mycale species inhabiting different geographical areas have not been pr...

Microbial abundance List of the 25 most abundant OTUs in samples of Mycale (Oxymycale) acerata and Mycale (Aegogropila) magellanica as shown in Fig. 4.

OTUs in Mycale spp Relative abundance and taxonomy of 97% OTUs in samples of Mycale (Oxymycale) acerata and Mycale (Aegogropila) magellanica.

Microbial richness Observed (A) and estimated (B) microbial richness in samples of Mycale (Aegogropila) magellanica (blue) and Mycale (Oxymycale) acerata (red) from Rio Seco, Magallanes and from Fildes (King George Island) and South Bay (Doumer Island), WAP.

There is a severe shortage of statisticians and bioinformaticians available in research. As universities fail to cover the increasing need of graduates with the necessary skills, ad hoc training and workshops have become commonplace but are insufficient to cover the needs. Technical solutions that distribute the workload more efficiently between re...

Syntrophic acetate oxidation operates close to the thermodynamic equilibrium and very little is known about the participating organisms and their metabolism. Clostridium ultunense is one of the most abundant syntrophic acetate-oxidising bacteria (SAOB) that are found in engineered biogas processes operating with high ammonia concentrations. It has...

Syntrophic acetate oxidation operates close to the thermodynamic equilibrium and very little is known about the participating organisms and their metabolism. Clostridium ultunense is one of the most abundant syntrophic acetate-oxidising bacteria (SAOB) that are found in engineered biogas processes operating with high ammonia concentrations. It has...

Syntrophic acetate oxidation operates close to the thermodynamic equilibrium and very little is known about the participating organisms and their metabolism. Clostridium ultunense is one of the most abundant syntrophic acetate-oxidising bacteria (SAOB) found in engineered biogas processes operating with high ammonia concentrations. It has been prov...

For long-read sequencing applications, shearing of DNA is a significant issue as it limits the read-lengths generated by sequencing. During extraction and storage of DNA the DNA polymers are susceptible to physical and chemical shearing. In particular, the mechanisms of physical shearing are poorly understood in most laboratories as they are of lit...

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 ana...

Overview of the included courses in the eBioKit. Each course in the eBioKit comprises several lessons, which cover popular topics in bioinformatics analysis and introduce the students to the usage of the software and databases locally installed. (DOCX)

Summarized worldwide distribution for internet access, access to secure internet servers, pupil-teacher ratio, researchers in research and development (R&D), and technicians in R&D by country. Source: The World Bank databank and others [13, 16, 17]. (XLSX)

Worldwide distribution for internet access, access to secure internet servers, pupil-teacher ratio, researchers in research and development (R&D), and technicians in R&D by country. Source: The World Bank databank and others [13, 16, 17]. (XLSX)

This article briefly describes how bioinformatics research has been promoted in Pakistan, and its importance for the country’s development. Pivotal to this effort was the completion of a joint educational project between Pakistan’s Higher Education Commission (HEC) and the Swedish University of Agricultural Sciences (SLU).

When obtaining samples from biobanks, resolving ethical and legal concerns is a time-consuming task where researchers need to balance the needs of privacy, trust and scientific progress. The Biobanking and Biomolecular Resources Research Infrastructure-Large Prospective Cohorts project has resolved numerous such issues through intense communication...

During the past year, the EMBnet Executive Board (EB) had regular monthly meetings either via Skype or using Adobe Connect. These meetings were always carried out with the Interim Board (IB) composed by Teresa K. Attwood and Etienne de Villiers. The IB was indeed established during the Annual General Meeting 2015 to support the new EB to move its f...

There are several anecdotal reports of insertion sequence (IS)-element inactivation of verotoxin genes among enterohaemorrhagic Escherichia coli of the serotype O157:H7, a pathogen causing severe gastrointestinal disease in infected humans. These insertions can be expected to drastically reduce the virulence of the bacteria. IS-element inactivation...

Lipopolysaccharide (LPS) is a component of the outer membrane of gram-negative bacteria and is involved in postpartum uterine infection in cattle. Lipopolysaccharide causes inflammation of the endometrium and the activation of immune and pro-inflammatory pathways in uterine cells has been well documented. This study was performed to investigate the...

Syntrophaceticus schinkii is a mesophilic, anaerobic bacterium capable of oxidising acetate to CO2 and H2 in intimate association with a methanogenic partner, a syntrophic relationship which operates close to the energetic limits of microbial life. Syntrophaceticus schinkii has been identified as a key organism in engineered methane-producing proce...

Cofactor biosynthesis. (DOCX)

Comparison of the periplasmic [Ni-Fe] hydrogenase gene cluster. Comparison of the periplasmic [Ni-Fe] hydrogenase gene cluster predicted for S. schinkii strain Sp3 to the [Ni-Fe] hydrogenase gene clusters found in the genome of the SAOB T. phaeum, the hydrogen-producing Carboxidothermos hydrogenoformans and the sulphate reducer Desulfosporosinus or...

Gene clusters in Syntrophaceticus schinkii predicted to encode the Embden-Meyerhof-Parnas pathway. (DOC)

Genes associated to functions in the Wood-Ljungdahl pathway in Syntrophaceticus schinkii. (DOCX)

Bar graph showing the FPKM values of genes related to type IV pili and quorum sensing (QS). (PDF)

Genes predicted in Syntrophaceticus schinkii to be related to trimethylamine metabolism. (DOC)

General genome features. (DOCX)

Comparison of the putative Ferredoxin:NADH oxidoreductase/heterodisulphide reductase complex gene cluster to a similar gene cluster found in S. wolfei. Syntrophorhabdus aromaticivorans could not be included in the comparison since the gene sequences of the locus tags published are not publicly available. Percentage identity numbers of amino acid se...

Multiple sequence alignment of the deduced amino acid sequences of the putative archaeal-like ADP-forming acetyl-CoA synthase of S. schinkii and ADP-forming acetyl-CoA synthases of selected members of the domain Archaea. A comprehensive alignment file can be found in Additional file 15. (PNG)

Transporters predicted for the genome of Syntrophaceticus schinkii. (DOCX)

ClustalW alignment file of the deduced ADP-forming acetyl-CoA synthase including the closest 100 hits obtained by the BLASTP search algorithm using default parameters. (TXT)

Bar graph showing the FPKM values of genes related to heat shock proteins. (PDF)