Crystal Structure and Size-Dependent Neutralization Properties of HK20, a Human Monoclonal Antibody Binding to the Highly Conserved Heptad Repeat 1 of gp41

The human monoclonal antibody (mAb) HK20 neutralizes a broad spectrum of primary HIV-1 isolates by targeting the highly conserved heptad repeat 1 (HR1) of gp41, which is transiently exposed during HIV-1 entry. Here we present the crystal structure of the HK20 Fab in complex with a gp41 mimetic 5-Helix at 2.3 Å resolution. HK20 employs its heavy chain CDR H2 and H3 loops to bind into a conserved hydrophobic HR1 pocket that is occupied by HR2 residues in the gp41 post fusion conformation. Compared to the previously described HR1-specific mAb D5, HK20 approaches its epitope with a different angle which might favor epitope access and thus contribute to its higher neutralization breadth and potency. Comparison of the neutralization activities of HK20 IgG, Fab and scFv employing both single cycle and multiple cycle neutralization assays revealed much higher potencies for the smaller Fab and scFv over IgG, implying that the target site is difficult to access for complete antibodies. Nevertheless, two thirds of sera from HIV-1 infected individuals contain significant titers of HK20-inhibiting antibodies. The breadth of neutralization of primary isolates across all clades, the higher potencies for C-clade viruses and the targeting of a distinct site as compared to the fusion inhibitor T-20 demonstrate the potential of HK20 scFv as a therapeutic tool

Architecture consistency: state of the practice, challenges and requirements

Architecture Consistency (AC) aims to align implemented systems with their intended architectures. Several AC approaches and tools have been proposed and empirically evaluated, suggesting favourable results. In this paper, we empirically examine the state of practice with respect to Architecture Consistency, through interviews with nineteen experienced software engineers. Our goal is to identify 1) any practises that the companies these architects work for, currently undertake to achieve AC; 2) any barriers to undertaking explicit AC approaches in these companies; 3) software development situations where practitioners perceive AC approaches would be useful, and 4) AC tool needs, as perceived by practitioners. We also assess current commercial AC tool offerings in terms of these perceived needs. The study reveals that many practitioners apply informal AC approaches as there are barriers for adopting more formal an

Prostatic specific antigen for prostate cancer detection

Prostate-specific antigen (PSA) has been used for prostate cancer detection since 1994. PSA testing has revolutionized our ability to diagnose, treat, and follow-up patients. In the last two decades, PSA screening has led to a substantial increase in the incidence of prostate cancer (PC). This increased detection caused the incidence of advanced-stage disease to decrease at a dramatic rate, and most newly diagnosed PC today are localized tumors with a high probability of cure. PSA screening is associated with a 75% reduction in the proportion of men who now present with metastatic disease and a 32.5% reduction in the age-adjusted prostate cancer mortality rate through 2003. Although PSA is not a perfect marker, PSA testing has limited specificity for prostate cancer detection, and its appropriate clinical application remains a topic of debate. Due to its widespread use and increased over-detection, the result has been the occurrence of over-treatment of indolent cancers. Accordingly, several variations as regards PSA measurement have emerged as useful adjuncts for prostate cancer screening. These procedures take into consideration additional factors, such as the proportion of different PSA isoforms (free PSA, complexed PSA, pro-PSA and B PSA), the prostate volume (PSA density), and the rate of change in PSA levels over time (PSA velocity or PSA doubling time). The history and evidence underlying each of these parameters are reviewed in the following article

Ranging patterns of bottlenose dolphins living in oceanic waters : implications for population structure

Author Posting. © The Author(s), 2008. This is the author's version of the work. It is posted here by permission of Springer for personal use, not for redistribution. The definitive version was published in Marine Biology 156 (2008): 179-192, doi: 10.1007/s00227-008-1075-z.Very little is known about the ecology of common bottlenose dolphins (Tursiops truncatus) living in oceanic waters. This study investigated the ranging and residence pattern, of bottlenose dolphins occurring in the Azores (Portugal), the most isolated archipelago in the North Atlantic. Data were collected during standardized boat-based surveys conducted over a 6-year period in an area of approximately 5,400 km2 (main study area). To investigate the extent of movements of individual animals. non-systematic surveys were also conducted outside this area. Only 44 individuals out of 966 identified were frequently sighted within and between years. The remaining individuals were either temporary migrants from within or outside the archipelago, or transients. Resident dolphins showed strong geographic fidelity to the area. Long-distance movements (of almost 300 km), consistent with foraging or exploratory trips. were observed among non-resident dolphins. Home range size was estimated for 31 individuals sighted ≥ 10 times. Range areas of these dolphins varied in size and location, but considerable overlap was observed in the areas used, suggesting the absence of habitat partitioning between resident and non-resident dolphins. Estimates of home range size of bottlenose dolphins in the Azores were found to be considerably larger than those previously reported for this species. It is hypothesized that dolphins living in the Azores carry out extensive movements and have large home ranges in response to the lower density and patchy distribution of prey compared to other areas. The extensive ranging behaviour and the lack of territoriality provide an opportunity for interbreeding between dolphins associated with different islands, thus preventing genetic differentiation within the population of the Azores.This researd was funded by the Portuguese Science and Technology Foundation (FCT). under the CETAMARH project (POCTI/BSF/38991/01 ), by an EU-LlFE program (B4-3200/98/ 509), and by an Interreg program (Interreg IIIBMAC/4.2/A2). We are also grateful to FCT for funding M. A. S. doctoral grant (SFRH/BD/ 8609/2002) and post-doctoral grams (SFRH/BPD/29841/2006), and S. M. M. and M. I. S. research grams through the CETAMARH projec

Intron creation and DNA repair

Ragg H. Intron creation and DNA repair. Cell. Mol. Life Sci. 2011;68(2):235-242.The genesis of the exon-intron patterns of eukaryotic genes persists as one of the most enigmatic questions in molecular genetics. In particular, the origin and mechanisms responsible for creation of spliceosomal introns have remained controversial. Now the issue appears to have taken a turn. The formation of novel introns in eukaryotes, including some vertebrate lineages, is not as rare as commonly assumed. Moreover, introns appear to have been gained in parallel at closely spaced sites and even repeatedly at the same position. Based on these discoveries, novel hypotheses of intron creation have been developed. The new concepts posit that DNA repair processes are a major source of intron formation. Here, after summarizing the current views of intron gain mechanisms, I review findings in support of the DNA repair hypothesis that provides a global mechanistic scenario for intron creation. Some implications on our perception of the mosaic structure of eukaryotic genes are also discussed

Effect of Cigarette Smoking on a Marker for Neuroinflammation: A [11C]DAA1106 Positron Emission Tomography Study.

In the brain, microglia continuously scan the surrounding extracellular space in order to respond to damage or infection by becoming activated and participating in neuroinflammation. When activated, microglia increase the expression of translocator protein (TSPO) 18 kDa, thereby making the TSPO expression a marker for neuroinflammation. We used the radiotracer [11C]DAA1106 (a ligand for TSPO) and positron emission tomography (PET) to determine the effect of smoking on availability of this marker for neuroinflammation. Forty-five participants (30 smokers and 15 non-smokers) completed the study and had usable data. Participants underwent a dynamic PET scanning session with bolus injection of [11C]DAA1106 (with smokers in the satiated state) and blood draws during PET scanning to determine TSPO affinity genotype and plasma nicotine levels. Whole-brain standardized uptake values (SUVs) were determined, and analysis of variance was performed, with group (smoker vs non-smoker) and genotype as factors, thereby controlling for genotype. Smokers and non-smokers differed in whole-brain SUVs (P=0.006) owing to smokers having 16.8% lower values than non-smokers. The groups did not differ in injected radiotracer dose or body weight, which were used to calculate SUV. An inverse association was found between whole-brain SUV and reported cigarettes per day (P<0.05), but no significant relationship was found for plasma nicotine. Thus, smokers have less [11C]DAA1106 binding globally than non-smokers, indicating less microglial activation. Study findings are consistent with much prior research demonstrating that smokers have impaired inflammatory functioning compared with non-smokers and that constituents of tobacco smoke other than nicotine affect inflammatory processes