DeltaProt: a software toolbox for comparative genomics

Background  

Statistical bioinformatics is the study of biological data sets obtained by new micro-technologies by means of proper statistical methods. For a better understanding of environmental adaptations of proteins, orthologous sequences from different habitats may be explored and compared. The main goal of the DeltaProt Toolbox is to provide users with important functionality that is needed for comparative screening and studies of extremophile proteins and protein classes. Visualization of the data sets is also the focus of this article, since visualizations can play a key role in making the various relationships transparent. This application paper is intended to inform the reader of the existence, functionality, and applicability of the toolbox.     

Conformational features of the full-length HIV and SIV Nef proteins determined by mass spectrometry

The Nef protein from human or simian immunodeficiency virus enhances viral replication, downregulates immune cell receptors, and activates multiple host cell signaling pathways. Conformational information about full-length Nef has been difficult to obtain as the full-length protein is not readily amenable to NMR or X-ray crystallography due to aggregation at high concentrations. As an alternative, full-length HIV and SIV Nef were probed with hydrogen exchange mass spectrometry, a method compatible with the low concentration requirements of Nef. The results showed that HIV Nef contains a solvent-protected core, as previously demonstrated with both NMR and X-ray crystallography. SIV Nef, for which there is no structural information, had a similar protected core, although it was more flexible and dynamic than its HIV counterpart. Many of the regions outside the core in both SIV and HIV Nef were highly solvent exposed. However, limited protection from exchange was observed in both N- and C-terminal regions, suggesting the presence of structured elements. Protection from exchange was also observed in a large loop emanating from the core that was deleted for NMR and X-ray analysis. These data show that while the majority of Nef was highly solvent exposed, regions outside the core may have structural attributes which may contribute to Nef functions known to map to these regions.     

Markov Model of Haploid Random Mating with Given Distribution of Population Size

An exact Markov chain model is formulated and computed for random mating in a haploid gamete pool. There are two versions of the gamete, and there is a finite number of diploid monoecious organisms. The founder population is given, and the subsequent generations allow a prescribed statistical distribution over different population sizes. The non-homogeneous Markov chain works on the haploid gamete level provided the probability of self-fertilization is 1/n, where n is the number of diploid individuals. Standard deviations of gamete frequencies and fixation probabilities are calculated. Effective population sizes for different population size distributions are estimated, including periodic bottlenecks.     

Telomerase peptide vaccination: a phase I/II study in patients with non-small cell lung cancer

PURPOSE: A phase I/II study was conducted to investigate the safety, tolerability and clinical response to vaccination with a combination of telomerase peptides GV1001 (hTERT: 611-626) and HR2822 (hTERT: 540-548) in patients with non-small cell lung cancer. EXPERIMENTAL DESIGN: Twenty-six patients with non-small cell lung cancer received intradermal administrations of either 60 nmole (112 microg) or 300 nmole (560 microg) GV1001 in combination with 60 nM (68.4 microg) HR2822 and granulocyte macrophage-colony stimulating factor. The treatment period was 10 weeks. Booster vaccinations with 300 nM GV1001 were offered as follow-up. Monitoring of blood samples, clinical examination and radiological staging were performed regularly. Immune responses were measured as delayed-type hypersensitivity skin reaction and in vitro T cell proliferation. Bone marrow function was monitored in long time survivors. RESULTS: The treatment was well tolerated with minor side effects. No bone marrow toxicities were observed in long time survivors with immune responses. Immune responses against GV1001 were detected in 11 of 24 evaluable patients during the primary regimen and in additional two patients following booster injections. Two patients responded to HR2822. Cloned GV1001-specific CD4+ T cells displayed a Th1 cytokine profile and recognized autologous antigen presenting cells pulsed with recombinant telomerase protein. A complete tumor response was observed in one patient who developed GV1001-specific cytotoxic T cells that could be cloned from peripheral blood. CONCLUSION: The results demonstrate that GV1001 and HR2822 are immunogenic and safe to use in patients with NSCLC. Induction of GV1001-specific immune responses may result in objective tumor responses. Based on these initial encouraging results, further clinical studies of GV1001 in NSCLC patients are warranted.     

Seasonal cycles of species diversity and similarity in a tropical butterfly community

1. Studies of seasonality in ecological diversity rarely extend over more than a few years, and few studies of seasonal diversity have explicitly investigated the influence of environmental factors on seasonal community composition, especially in tropical communities. 2. Our 10 years of monthly sampling in Amazonian Ecuador yielded 20 996 individuals of 137 fruit-feeding butterfly species. Seasonal cycles of rainfall drive annual cycles in species diversity and community similarity. Undetermined processes operating most strongly during the dry season maintain species diversity and high community similarity across years. 3. Seasonal cycles in community diversity and similarity are superimposed on a gradual decline in similarity between community samples on a decadal time-scale because of long-term changes in species abundances. 4. Monitoring and analysis of changes in community composition over a range of time-scales can be used to refine models of community dynamics by incorporating environmental factors necessary to predict the ecological impact of future climate change.     

Reproductive Performance,Udder Health,and Antibiotic Resistance in Mastitis Bacteria isolated from Norwegian Red cows in Conventional and Organic Farming

Background  

The objectives of this study were to investigate whether there were differences between Norwegian Red cows in conventional and organic farming with respect to reproductive performance, udder health, and antibiotic resistance in udder pathogens.     

Harvesting strategies for Norwegian spring-spawning herring

The overfishing of an increasing number of fish populations has put focus on the need for development of robust sustainable harvest strategies that can be easily implemented. This requires estimates and modelling of the deterministic and stochastic components of the population dynamics as well as an evaluation of the contribution of different harvest strategies to future population fluctuations. Here we present an example of such an approach, using the collapse of Norwegian spring-spawning herring stock as a case. We demonstrate that the collapse probably was due to overfishing, and that the large influence of the environmental stochasticity could only influence the timing of the collapse. We suggest that a proportional threshold strategy with a threshold around 14 billion individuals (4 200 000 tons), combined with a harvest of 30–40% of the individuals above this threshold will give a sustainable yield with little annual variation. The choice of harvest strategy should also be strongly influenced by the uncertainty in the assessment of stock size. When the population stock is estimated with uncertainty, the proportional threshold strategy give a mean annual yield close to the optimum for known population size.     

There are more small amino acids and fewer aromatic rings in proteins of ionizing radiation-resistant bacteria

The identification of specific amino acids (AAs) or groups of functionally important AA residues in ionizing radiation-resistant bacteria (IRRB) is an important challenge in understanding the biological basis of resistance to ionizing radiation (IR; X-rays and gamma-rays). To address this problem, we compared homologous sites in multiple alignments of proteins of IRRB and IR-sensitive bacteria (IRSB) using the DeltaProt Toolbox. Substitution patterns were used as evidence for selection of certain AAs over others. Our results show that, in contrast to aromatic AAs, small/tiny AAs tend to be preferred in IRRB compared to IRSB. In agreement with previous experimental data showing that oxidation of AA residues is causative in the killing of irradiated cells and that IR resistance is correlated with the accumulation of divalent manganese ions (Mn²⁺)–peptide–orthophosphate (Pi) complexes, we proposed a chemical interpretation based on the Hard and Soft (Lewis) Acids and Bases (HSAB) concept. These findings should assist future efforts in selecting mutations for rational design of proteins with enhanced IR tolerance properties.     

Performance Comparison of Digital microRNA Profiling Technologies Applied on Human Breast Cancer Cell Lines

MicroRNA profiling represents an important first-step in deducting individual RNA-based regulatory function in a cell, tissue, or at a specific developmental stage. Currently there are several different platforms to choose from in order to make the initial miRNA profiles. In this study we investigate recently developed digital microRNA high-throughput technologies. Four different platforms were compared including next generation SOLiD ligation sequencing and Illumina HiSeq sequencing, hybridization-based NanoString nCounter, and miRCURY locked nucleic acid RT-qPCR. For all four technologies, full microRNA profiles were generated from human cell lines that represent noninvasive and invasive tumorigenic breast cancer. This study reports the correlation between platforms, as well as a more extensive analysis of the accuracy and sensitivity of data generated when using different platforms and important consideration when verifying results by the use of additional technologies. We found all the platforms to be highly capable for microRNA analysis. Furthermore, the two NGS platforms and RT-qPCR all have equally high sensitivity, and the fold change accuracy is independent of individual miRNA concentration for NGS and RT-qPCR. Based on these findings we propose new guidelines and considerations when performing microRNA profiling.