Structural basis of Rab effector specificity: crystal structure of the small G protein Rab3A complexed with the effector domain of rabphilin-3A

The small G protein Rab3A plays an important role in the regulation of neurotransmitter release. The crystal structure of activated Rab3A/GTP/Mg2+ bound to the effector domain of rabphilin-3A was solved to 2.6 A resolution. Rabphilin-3A contacts Rab3A in two distinct areas. The first interface involves the Rab3A switch I and switch II regions, which are sensitive to the nucleotide-binding state of Rab3A. The second interface consists of a deep pocket in Rab3A that interacts with a SGAWFF structural element of rabphilin-3A. Sequence and structure analysis, and biochemical data suggest that this pocket, or Rab complementarity-determining region (RabCDR), establishes a specific interaction between each Rab protein and its effectors. RabCDRs could be major determinants of effector specificity during vesicle trafficking and fusion.     

Content-specific working memory modulation of the attentional blink

Three experiments were conducted to investigate the effects of working memory content on temporal attention in a rapid serial visual presentation attentional blink paradigm. It was shown that categorical similarity between working memory content and the target stimuli pertaining to the attentional task (both digits) increased attentional blink magnitude compared to a condition in which this similarity was absent (colors and digits, respectively). This effect was only observed when the items in working memory were not presented as conjunctions of the involved categories (i.e., colored digits). This suggested that storage and retrieval from working memory was at least preferentially conjunctive in this case. It was furthermore shown that the content of working memory enhanced the identification rate of the second target, by means of repetition priming, when inter-target lag was short and the attentional blink was in effect. The results are incompatible with theories of temporal attention that assume working memory has no causal role in the attentional blink and support theories that do.     

A comparative genomics study of genetic products potentially encoding ladderane lipid biosynthesis

Background  

The fatty acids of anaerobic ammonium oxidizing (anammox) bacteria contain linearly concatenated cyclobutane moieties, so far unique to biology. These moieties are under high ring strain and are synthesised by a presently unknown biosynthetic pathway.     

Symmetric cyanine dyes for detecting nucleic acids

A novel approach to the design of sensitive fluorescent probes for nucleic acids detection is proposed. Suitable modifications of tri- and pentamethine cyanine dyes in the polymethine chain and/or in the heterocyclic residues can result in a significant decrease in unbound dye fluorescence intensity and an increase in dye emission intensity in the presence of DNA compared to the unsubstituted dye. The sharp enhancement in the fluorescence intensity upon dye interaction with double-stranded DNA permits the application of the modified tri- and pentamethine dyes as fluorescent probes in double-stranded DNA detection in homogeneous assays.     

The ecological integrity of the Lower Olifants River,Limpopo province,South Africa: 2009–2015 – Part A: Olifants River main stem

The major rivers of the South African ‘Lowveld’ (low-latitude savanna) suffer numerous impacts from upstream economic activities. Whereas monitoring these rivers is required to detect biodiversity losses, record pollution events and devise mitigation strategies, current monitoring programmes are inadequate. In 2009, the South African Earth Observation Network initiated an intensive long-term research programme on the Lowveld reaches of the Olifants River. Physico-chemical parameters, aquatic macroinvertebrates and fish abundances were recorded at four Lowveld sites in the Olifants River. We review six years of this programme. The results suggest deterioration in the ecological condition of the Olifants River with no discernible improvement through protected areas. Trends could not be detected. The parameters measured, sampling methods and/or sampling frequency might be responsible for the limited trends observed, or alternatively the results simply reflect stable conditions despite on-going pollution. Real time monitoring and an expansion in the parameters monitored would add value to the monitoring programme.     

Markerless Roentgen Stereophotogrammetric Analysis for in vivo implant migration measurement using three dimensional surface models to represent bone

Recent studies have shown that model-based RSA using implant surface models to detect in vivo migration is as accurate as the classical marker-based RSA method. Use of bone surface models would be a further advancement of the model-based method by decreasing complications arising from marker insertion. The aim of this pilot investigation was to assess the feasibility of a "completely markerless" model-based RSA in detecting migration of an implant using bone surface models instead of bone markers. A total knee arthroplasty (TKA) was performed on a human cadaver knee, which was subsequently investigated by repeated RSA measurements performed by one observer. The cadaver knee was CT scanned prior to implantation of the TKA. Tibia-fibular surface models were created using two different commercially available software packages to investigate the effect of segmentation software on the accuracy of repeated migration measures of zero displacement by one observer. Reverse engineered surface models of the TKA tibial component were created. The analysis of the RSA images was repeated 10 times by one individual observer. For the markerless method, the greatest apparent migration observed about the three anatomical axes investigated was between -2.08 and 1.35 mm (SD ≤ 0.88) for z-axis translation, and -4.57° to 7.86° (SD ≤ 3.17) for R(y)-axis rotation, which were well beyond out of the range of what is typically considered adequate for clinically relevant RSA measurements. Use of tibia-fibular surface models of the bone instead of markers could provide practical advantages in evaluating implant migration. However, we found the accuracy and precision of the markerless approach to be lower than that of marker-based RSA, to a degree which precludes the use of this method for measuring implant migration in its present form.     

K-SPMM: a database of murine spermatogenic promoters modules & motifs

Background  

Understanding the regulatory processes that coordinate the cascade of gene expression leading to male gamete development has proven challenging. Research has been hindered in part by an incomplete picture of the regulatory elements that are both characteristic of and distinctive to the broad population of spermatogenically expressed genes.