Structures of proteins and cofactors: X-ray crystallography

Protein crystallography is the predominately used technique for the determination of the three-dimensional structures of proteins and other macromolecules. In this article, the methodology utilized for the measurement and analysis of the diffraction data from crystals is briefly reviewed. As examples of both the usefulness and difficulties of this technique, the determination of the structures of several photosynthetic pigment–protein complexes is described, namely, the reaction center from purple bacteria, photosystem I and photosystem II from cyanobacteria, the light-harvesting complex II from purple bacteria, and the FMO protein from green bacteria.     

An ��Escape Clock�� for Estimating the Turnover of SIV DNA in Resting CD4+ T Cells

Persistence of HIV DNA presents a major barrier to the complete control of HIV infection under current therapies. Most studies suggest that cells with latently integrated HIV decay very slowly under therapy. However, it is much more difficult to study the turnover and persistence of HIV DNA during active infection. We have developed an “escape clock” approach for measuring the turnover of HIV DNA in resting CD4+ T cells. This approach studies the replacement of wild-type (WT) SIV DNA present in early infection by CTL escape mutant (EM) strains during later infection. Using a strain-specific real time PCR assay, we quantified the relative amounts of WT and EM strains in plasma SIV RNA and cellular SIV DNA. Thus we can track the formation and turnover of SIV DNA in sorted resting CD4+ T cells. We studied serial plasma and PBMC samples from 20 SIV-infected Mane-A*10 positive pigtail macaques that have a signature Gag CTL escape mutation. In animals with low viral load, WT virus laid down early in infection is extremely stable, and the decay of this WT species is very slow, consistent with findings in subjects on anti-retroviral medications. However, during active, high level infection, most SIV DNA in resting cells was turning over rapidly, suggesting a large pool of short-lived DNA produced by recent infection events. Our results suggest that, in order to reduce the formation of a stable population of SIV DNA, it will be important either to intervene very early or intervene during active replication.     

The membrane effect of 1-anilino-8-naphthalene sulfonate on transferrin and iron uptake by rabbit reticulocytes

Studies on the effect of 1-anilino-8-naphthalene sulfonate on uptake of transferrin and iron by rabbit reticulocytes show that the inhibitory action of ANS is localized at the membrane level. The intravesicular pH and cellular ATP level were not affected by this anionic probe. ANS shifted the transition temperature and reduced the enthalpy changes of iron uptake by rabbit reticulocytes. These suggested that the drug reduced the membrane fluidity. Hence, ANS disturbed the physicochemical environment of the receptor for transferrin resulting in the perturbation of receptor-mediated endocytosis.     

The wildlife snaring crisis: an insidious and pervasive threat to biodiversity in Southeast Asia

Southeast Asia, a region supporting more threatened species than any other comparable continental area, is in the midst of a conservation crisis. Hunting constitutes the greatest current threat to the region’s threatened vertebrates and has resulted in many areas of largely intact forest losing much of their former vertebrate diversity and abundance. Though numerous hunting methods are used, capture with home-made snares is a major driver of this defaunation. Snares are cheaply constructed and easy to set but can be difficult to detect and are highly damaging to vertebrate populations due to their indiscriminate and wasteful nature. The primary response to snaring is the removal of snares by patrol teams: more than 200,000 snares were removed from just five of the region’s protected areas between 2010 and 2015. However due to the low opportunity costs of replacing snares, removal alone is largely ineffective. Without the proactive search, arrest and prosecution of snare-setters, along with incentives not to hunt, snares will continue to be replaced. Legislative reform that criminalises the possession of snares, and the materials used for their construction, inside and immediately adjacent to protected areas is also required. Consistent enforcement of such legislation is essential. This must be combined with longer-term demand reduction activities aimed at changing cultural attitudes and behaviors related to the consumption of wildlife products in Southeast Asia.     

Adaptation to different climates results in divergent phenotypic plasticity of wing size and shape in an invasive drosophilid

The phenotypic plasticity of wing size and wing shape of Zaprionus indianus was investigated in relation to growth temperature (17°C to 31°C) in two natural populations living under different climates, equatorial and subtropical. The two populations were clearly distinguished not only by their wing size (the populations from the colder climate being bigger in size), but also by the shape of the response curves to growth temperature i.e., their reaction norms. In this respect, the temperature at which the size of the wing was maximum was about 3°C higher in the equatorial population. Such a difference in size plasticity is already found in two other nonclosely related species, might be a general evolutionary pattern in drosophilids. Wing shape was investigated by calculating an ellipse included into the wing blade, then by considering the ratio of the two axes, and also by analysing the angular position of 10 wing-vein landmarks. For an overall shape index (ratio of the two axes of the ellipse), a regular and almost linear increase was observed with increasing temperature i.e., a more round shape at high temperatures. Wing shape was also analysed by considering the variations of the various angles according to temperature. A diversity of response curves was observed, revealing either a monotonous increase or decrease with increasing temperature, and sometimes a bell shape curve. An interesting conclusion is that, in most cases, a significant difference was observed between the two populations, and the difference was more pronounced at low temperatures. These angular variations are difficult to interpret in an evolutionary context. More comparative studies should be undertaken before reaching some general conclusions.     

A Fuzzy-C-Means-Clustering Approach: Quantifying Chromatin Pattern of Non-Neoplastic Cervical Squamous Cells

Despite the effectiveness of Pap-smear test in reducing the mortality rate due to cervical cancer, the criteria of the reporting standard of the Pap-smear test are mostly qualitative in nature. This study addresses the issue on how to define the criteria in a more quantitative and definite term. A negative Pap-smear test result, i.e. negative for intraepithelial lesion or malignancy (NILM), is qualitatively defined to have evenly distributed, finely granular chromatin in the nuclei of cervical squamous cells. To quantify this chromatin pattern, this study employed Fuzzy C-Means clustering as the segmentation technique, enabling different degrees of chromatin segmentation to be performed on sample images of non-neoplastic squamous cells. From the simulation results, a model representing the chromatin distribution of non-neoplastic cervical squamous cell is constructed with the following quantitative characteristics: at the best representative sensitivity level 4 based on statistical analysis and human experts’ feedbacks, a nucleus of non-neoplastic squamous cell has an average of 67 chromatins with a total area of 10.827μm ²; the average distance between the nearest chromatin pair is 0.508μm and the average eccentricity of the chromatin is 0.47.     

Evidence for an opiomelanotropin acetyltransferase in the rat pituitary neurointermediate lobe

Results of this study demonstrate two distinct forms of acetyltransferase activity which will acetylate α-MSH. These acetyltransferases are distinguished by pH optima, subcellular distribution and sensitivity to magnesium and several solubilizing detergents. A general acetyltransferase, as characterized in the rat pituitary anterior lobe and lens, has a pH optima of 7.4 and is inhibited by magnesium. Subcellular fractionation of anterior and neurointermediate lobes revealed that this acetyltransferase is primarily localized in the cytosol fraction of these tissues. An α-MSH acetyltransferase (MAT) and a β-endorphin acetyltransferase (EAT) have a pH opitma of 6.0–6.6, are inhibited by detergents, and are specifically localized in the secretory granules of the neurointermediate lobe. Comparative studies of MAT and EAT suggest a single enzyme responsible for the acetylation of opioid and melanotropin peptides, and we term this enzyme opiomelanotropin acetyltransferase (OMAT).     

Biodeterioration of external architectural paint films - A review

This paper presents a review of the biodeterioration of architectural paint films by bacteria, fungi and algae, concentrating on external films. 107 references are cited in the following sections: 1. Microbiota of paint films - resident microflora, colonization and biofilm formation; 2. Effects of environment on biofilm formation and survival; 3. Influence of paint formulation on colonization - basic paint components, pigment volume content (PVC), pigments, biocides; 4. Effects of painted substrate on susceptibility; 5. Instrumental methods used in the analysis of paint film biodeterioration - vibrational spectroscopy, laser-induced breakdown spectroscopy, HPLC, image analysis, FTIR spectroscopy, GC-MS; 6. New technologies in the coatings industry - photocatalytic layers, cool paints, silver nanoparticles, silicon-containing paints.