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There is an urgent need to improve the infrastructure supporting the reuse of scholarly data. A diverse set of stakeholders-representing academia, industry, funding agencies, and scholarly publishers-have come together to design and jointly endorse a concise and measureable set of principles that we refer to as the FAIR Data Principles. The intent is that these may act as a guideline for those wishing to enhance the reusability of their data holdings. Distinct from peer initiatives that focus on the human scholar, the FAIR Principles put specific emphasis on enhancing the ability of machines to automatically find and use the data, in addition to supporting its reuse by individuals. This Comment is the first formal publication of the FAIR Principles, and includes the rationale behind them, and some exemplar implementations in the community.

Alkanes are oxidized in Acinetobacter sp. strain ADP1 through a three-component monooxygenase, composed of alkane hydroxylase, rubredoxin and rubredoxin reductase. The genes rubA and rubB encode rubredoxin and a NAD(P)H-dependent rubredoxin reductase. It is shown that single base pair substitutions in rubA or rubB lead to defects in alkane degradation, indicating that both genes are essential for alkane utilization.

Localized sets of random point mutations generated by polymerase chain reaction amplification can be transferred to the chromosome of Acinetobacter ADP1 strain in an efficient manner using natural transformation. The natural transformation method eliminates the need for cloning of PCR fragments in plasmids since PCR-amplified DNA fragments are internalized by cells and directly introduced into their genomes by homologous recombination. Results show that homologous recombination of the PCR-amplified DNA fragments into a specific chromosomal docking site from which they can be expressed is made possible by nucleotide sequence identity between the flanking regions and corresponding chromosomal segments in a cloned Acinetobacter recipient.

Acinetobacter PobR and PcaU are transcriptional activators which are very similar to each other based on main structure, DNA-binding sites, metabolic modulators and physiological activity. Mutants were isolated in which the pobR function has been deleted by nucleotide substitutions caused by mistakes during polymerase chain reaction amplification of the gene. Findings indicated that these mutations affect the ability of PobR to bind to its DNA target. PobR and PcaU have a linear domain structure similar to that of LysR transcriptional activators.

A method for the efficient random mutagenesis of selected genes in a bacterial chromosome is studied. The process is a combination of PCR replication errors with the uptake of PCR-amplified DNA via natural transformation. Mutations are also transferred directly to the chromosome through homologous recombination thereby eliminating the need to clone PCR fragments. It is shown that the method can by applied to other genes in Acinetobacter and other natural transformation systems.

16S rRNA gene probes were generated to monitor the growth of Bifidobacterium sp. strain LW420 in infant fecal samples. Sequencing and analysis of DNA from single-strain and mixed cultures of bifidobacteria and from heterogeneous feces samples revealed a significant homology of 16S rDNA of LW420 with known 16S rDNA sequences. PCR analyses showed that all fecal samples was positive for Bifidobacterium.

Expression of the lipA gene regulates lipase production in Acinetobacter calcoaceticus at the genetic level. This was gleaned from an investigation of the involvement of a fatty acyl-responsive DNA-binding protein in the regulation of expression of the A. calcoaceticus lipBA operon. It was also found that the level of active extracellular LipA may be influenced at the level of proteolytic stability or instability of the lipase.

Background and purpose -- The Taperloc Complete hip is the successor of the Taperloc hip, aiming to increase range of motion and optimizing femoral fit with intermediate stem sizes. We evaluated whether these design changes affect fixation, and this RSA study compares 2-year migration. Patients and methods -- In this prospective, multi-arm study, 100 patients were randomized to cementless total hip arthroplasty (THA) with Taperloc Complete full profile (TCFP), Taperloc Complete reduced distal (TCRD), Taperloc full profile (TFP), or Taperloc reduced distal (TRD). Migration was measured with model-based RSA postoperatively, and after 3, 12, and 24 months. Results -- Results based on mixed-model analysis on 2-year postoperative RSA data from 74 patients showed similar subsidence (mm) in the first 3 months (mean [95% CI] TCFP 0.44 [0.20--0.69], TCRD 0.91 [0.40--1.42], TFP 0.71 [0.22--1.19], TRD 1.25 [0.58--1.91]) and stabilization afterwards. The TCFP showed statistically significantly less retroversion (°) at 2-year postoperatively compared with TFP and TCRD (mean [95% CI] TCFP: --0.13 [--0.64 to 0.38], TCRD: 0.84 [0.35--1.33], TFP: 0.56 [0.12--1.00], TRD: 0.37 [--0.35 to 1.09]). Interpretation -- As expected in successful cementless THA, RSA shows stabilization after initial subsidence. Based on these results the Taperloc Complete stem is expected to have similar long-term fixation to the Taperloc stems. The reduced distal groups have larger, but statistically non-significant, initial migration compared with the TCFP group, which could be due to implantation in Dorr B, C femur types. It may be important to consider the femur shape for choosing a full profile or reduced distal stem to minimize migration. [ABSTRACT FROM AUTHOR]

Phenotypic analysis of five Acinetobacter calcoaceticus mutants lacking extracellular lipase, which were generated via insertion mutagenesis, revealed four lipolytic enzymes. Biochemical tests classified four mutants as export mutants, while the additional mutant, designated AAC302, exhibited showed mutation 0.84 kbp upstream of lipA, although it displayed the LipA- phenotype. DNA sequencing of the region revealed an open reading frame that encodes a protein required for the production of extracellular lipase. It is suggested that this protein acts as a lipase-specific chaperone.

The factors controlling the expression of growth-phase-dependent genes are investigated. The cloning of an Acinetobacter calcoaceticus BD413 esterase gene grown on N-broth plates provides more information on the positioning of the gene and its activity. A deletion plasmid is constructed to map the gene on a chromosomal DNA fragment.

This review provides a historical overview of the inception and development of bioinformatics research in the Netherlands. Rooted in theoretical biology by foundational figures such as Paulien Hogeweg (at Utrecht University since the 1970s), the developments leading to organizational structures supporting a relatively large Dutch bioinformatics community will be reviewed. We will show that the most valuable resource that we have built over these years is the close-knit national expert community that is well engaged in basic and translational life science research programmes. The Dutch bioinformatics community is accustomed to facing the ever-changing landscape of data challenges and working towards solutions together. In addition, this community is the stable factor on the road towards sustainability, especially in times where existing funding models are challenged and change rapidly. [ABSTRACT FROM AUTHOR]

There is an urgent need to improve the infrastructure supporting the reuse of scholarly data. A diverse set of stakeholders—representing academia, industry, funding agencies, and scholarly publishers—have come together to design and jointly endorse a concise and measureable set of principles that we refer to as the FAIR Data Principles. The intent is that these may act as a guideline for those wishing to enhance the reusability of their data holdings. Distinct from peer initiatives that focus on the human scholar, the FAIR Principles put specific emphasis on enhancing the ability of machines to automatically find and use the data, in addition to supporting its reuse by individuals. This Comment is the first formal publication of the FAIR Principles, and includes the rationale behind them, and some exemplar implementations in the community.

Examines the sequence analysis of the DNA downstream of the genes RubA and rubB in Acinetobacter sp. strain ADP1. Mutations determined for alkane mutants; Detection of oxyR gene transcripts; Regulation of the peroxide stress response in Acinetobacter by oxyR.

The extracellular lipase from Acinetobacter calco-aceticus BD413 was purified to homogeneity, via hydrophobic-interaction fast performance liquid chromatography (FPLC), from cultures grown in mineral medium with hexadecane as the sole carbon source. The enzyme has an apparent molecular mass of 32 kDa on SDS-polyacrylamide gels and hydrolyses long acyl chain p-nitrophenol (pNP) esters, like pNP palmitate (pNPP), with optimal activity between pH 7.8 and 8.8. Additionally, the enzyme shows activity towards triglycerides such as olive oil and tri-butyrin and towards egg-yolk emulsions. The N-terminal amino acid sequence of the mature protein was determined, and via reverse genetics the structural lipase gene was cloned from a gene library of A. calcoaceticus DNA in Escherichia coli phage M13. Sequence analysis of a 2.1 kb chromosomal DNA fragment revealed one complete open reading frame, lipA, encoding a mature protein with a predicted molecular mass of 32.1 kDa. This protein shows high similarity to known lipases, especially Pseudomonas lipases, that are exported in a two-step secretion mechanism and require a lipase-specific chaperone. The identification of an export signal sequence at the N-terminus of the mature lipase suggests that the lipase of Acineto-bacter is also exported via a two-step translocation mechanism. However, no chaperone-encoding gene was found downstream of lipA, unlike the situation in Pseudomonas. Analysis of an A. calcoaceticus mutant showing reduced lipase production revealed that a periplasmic disulphide oxidoreductase is involved in processing of the lipase. Via sequence alignments, based upon the crystal structure of the closely related Pseudomonas glumae lipase, a model has been made of the secondary-structure elements in AcLipA. The active site serine of AcLipA was changed to an alanine, via site-directed... [ABSTRACT FROM AUTHOR]

Three Acinetobacter calcoaceticus transformation-deficient mutants, obtained by insertional mutagenesis with the nptll gene, have been characterized physiologically. One mutant (AAC211) was found to be completely transformation deficient, while two others, AAC213 and AAC214, were severely impaired in transformation efficiency (100-1000 times lower than the wild type). The latter applied to both chromosomal as well as plasmid DNA. Analysis of the chromosomal ONA fragments flanking the nptll gene in the mutants showed that mutants AAC213 and AAC214 had an insertion of the nptll gene in the same chromosomal region, but that they were the result of two independent mutational events, whereas the insertion in mutant AAC211 was at a different position. None of the three mutants showed phenotypic or genotypic characteristics typical of a RecA-deficient strain. [ABSTRACT FROM AUTHOR]

We describe a new national organisation in scientific research that facilitates life scientists with technologies and technological expertise in an era where new projects often are data-intensive, multi-disciplinary, and multi-site. The Dutch Techcentre for Life Sciences (DTL, www.dtls.nl) is run as a lean not-for-profit organisation of which research organisations (both academic and industrial) are paying members. The small staff of the organisation undertakes a variety of tasks that are necessary to perform or support modern academic research, but that are not easily undertaken in a purely academic setting. DTL also represents the Netherlands in the ELIXIR ESFRI, and the office supports this task. The organisation is still being fine-tuned and this will probably continue over time, as it is crucial for this kind of organisation to adapt to a constantly changing environment. However, already being underway for several years on the path to professionalisation, our experiences can benefit researchers in other fields or other countries setting up similar initiatives.