Conserved intron positions in ancient protein modules

Background  

The timing of the origin of introns is of crucial importance for an understanding of early genome architecture. The Exon theory of genes proposed a role for introns in the formation of multi-exon proteins by exon shuffling and predicts the presence of conserved splice sites in ancient genes. In this study, large-scale analysis of potential conserved splice sites was performed using an intron-exon database (ExInt) derived from GenBank.     

Morbidity in acute virus hepatitis B on the territory of Kabardin-Balkaria

Morbidity in acute virus hepatitis B (AVHB) in Kabardin-Balkaria during the period of 1992 to 2003 was analyzed. The dynamics of changes in the age groups of AVHB patients, as well as in the structure of the transmission routes of the disease, was analyzed. The level of AVHB morbidity in the Kabardin-Balkar Republic was lower in recent years than the average level of such morbidity in the whole of Russia. The sharply defined irregularity in the territorial distribution of AVHB cases was established. The highest morbidity rates in AVHB were registered in Nalchik, as well as in Chegem and Prokhladnensk regions. The leading role in the formation of the morbidity in acute virus hepatitis B on the territory of Kabardin-Balkaria belongs to Nalchik, where 56.8% of AVHB cases were registered. In the structure of the transmission routes of AVHB the prevalence of artificial paths was noted; among them, the highest proportion belonged to parenteral medical manipulations in outpatient clinics (32.9%). The proportion of AVHB cases associated with the intravenous use of drugs was 6.9%. In the age structure of AVHB patients adults prevailed, and among them the highest number of cases was registered in the age groups of 20 - 29 years and 30 - 39 years. In 2002 the total proportion of AVHB cases among the patients of these age groups reached 68.3%.     

Sepsis progression and outcome: a dynamical model

Background  

Sepsis (bloodstream infection) is the leading cause of death in non-surgical intensive care units. It is diagnosed in 750,000 US patients per annum, and has high mortality. Current understanding of sepsis is predominately observational and correlational, with only a partial and incomplete understanding of the physiological dynamics underlying the syndrome. There exists a need for dynamical models of sepsis progression, based upon basic physiologic principles, which could eventually guide hourly treatment decisions.     

A novel approach for multi-domain and multi-gene family identification provides insights into evolutionary dynamics of disease resistance genes in core eudicot plants

Background

Recent advances in DNA sequencing techniques resulted in more than forty sequenced plant genomes representing a diverse set of taxa of agricultural, energy, medicinal and ecological importance. However, gene family curation is often only inferred from DNA sequence homology and lacks insights into evolutionary processes contributing to gene family dynamics. In a comparative genomics framework, we integrated multiple lines of evidence provided by gene synteny, sequence homology and protein-based Hidden Markov Modelling to extract homologous super-clusters composed of multi-domain resistance (R)-proteins of the NB-LRR type (for NUCLEOTIDE BINDING/LEUCINE-RICH REPEATS), that are involved in plant innate immunity.

Results

To assess the diversity of R-proteins within and between species, we screened twelve eudicot plant genomes including six major crops and found a total of 2,363 NB-LRR genes. Our curated R-proteins set shows a 50% average for tandem duplicates and a 22% fraction of gene copies retained from ancient polyploidy events (ohnologs). We provide evidence for strong positive selection and show significant differences in molecular evolution rates (Ka/Ks-ratio) among tandem- (mean = 1.59), ohnolog (mean = 1.36) and singleton (mean = 1.22) R-gene duplicates. To foster the process of gene-edited plant breeding, we report species-specific presence/absence of all 140 NB-LRR genes present in the model plant Arabidopsis and describe four distinct clusters of NB-LRR “gatekeeper” loci sharing syntenic orthologs across all analyzed genomes.

Conclusion

By curating a near-complete set of multi-domain R-protein clusters in an eudicot-wide scale, our analysis offers significant insight into evolutionary dynamics underlying diversification of the plant innate immune system. Furthermore, our methods provide a blueprint for future efforts to identify and more rapidly clone functional NB-LRR genes from any plant species.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-966) contains supplementary material, which is available to authorized users.     

Allelic Combinations of Immune Response Genes and Risk of Development of Myocardial Infarction

Myocardial infarction (MI) is a multifactorial polygenic disease. It develops because of the complex interaction between many environmental and genetic factors. In this paper, we have studied associations of MI and allele combinations of 17 polymorphic markers of immune response genes in an ethnically homogeneous group of Tatars. The material for analysis was DNA samples of patients (286 men) with onset of MI at the age of 30 to 60 years and 301 essentially healthy men of the control group. Using the APSampler algorithm, we obtained allele combinations with the increased risk of MI in which allele variants CX3CR1*M (rs3732378), VCAM1*C (rs3917010), ICAM1*E (rs5498), LTA*A (rs909253), and TNFRSF1B*M (rs1061622) occurred the most often.     

Human alveolar macrophage fibronectin: synthesis, secretion, and ultrastructural localization during gelatin-coated latex particle binding

Human pulmonary alveolar macrophages synthesized and secreted several characteristic high molecular weight proteins for at least 7 d in vitro. Immunoprecipitates of medium and cell lysates from metabolically labeled cultures with specific anti-human plasma fibronectin IgG contained one major labeled polypeptide of molecular weight 440,000 (unreduced) or 220,000 (reduced). An identical polypeptide in conditioned medium from radiolabeled macrophages bound specifically to gelatin-Sepharose, demonstrating that alveolar macrophages synthesized and secreted a molecule immunologically and functionally similar to fibronectin. Fibronectin was the major newly synthesized and secreted polypeptide of freshly harvested alveolar macrophages. Pulse-chase experiments revealed that newly synthesized fibronectin was rapidly secreted into medium, approximately 50 percent appearing by 1 h and 80 percent by 8 h. Immunoperoxidase staining using antifibronectin F(ab’)(2)-peroxidase conjugates revealed the majority of immunoreactive fibronectin to be intracellular, localized to endoplasmic reticulum and Golgi apparatus. No extracellular matrix fibronectin was visualized, and cell surface staining was rarely seen, usually appearing only at sites where cells were closely apposed and not at sites of macrophage-substrate attachment. Similar immunostaining of fibroblast cultures revealed cell surface-associated fibrillar fibronectin. Ultrastructural localization of fibronectin during binding and phagocytosis of gelatin-coated and plain latex particles revealed fibronectin only on gelatin-latex beads and at their cell binding sites. Neigher plain latex beads nor their cell membrane binding sites stained for fibronectin. These results demonstrate that fibronectin is a major product of human alveolar macrophages, is rapidly secreted, and is localized at cell membrane binding sites for gelatin-coated particles. In view of the known binding properties of fibronectin, it may serve as an endogenous opsonic factor promoting the binding of staphylococcus, denatured collagen, fibrin, or other macromolecules to macrophages in the lower respiratory tract.     

Survival of amphibian embryos after continuous ultrasound treatment

The influence of continuous ultrasound on the embryonic development of grass frog Rana temporaria has been investigated. Intact embryos at the blastula stage were treated by ultrasound of different frequency (0.88 and 2.64 MHz), intensity (0.05-1.0 W/cm2), and duration (1-15 min). The treatment with ultrasound of frequency 0.88 MHz and intensity 0.05 W/cm2 for 1-5 min tended to increase the proportion of normally developing embryos up to hatch (10-25% of control). Increasing the intensity of ultrasound (0.88 MHz) to 0.7-1.0 W/cm2 and the duration of its action to 5-15 min induced the death of almost all of treated embryos. No significant differences were found between the development of control embryos and embryos treated with ultrasound of middle intensity (0.2-0.7 W/cm2) for 1-5 min. The exposure of amphibian embryos to ultrasound of frequency 2.64 MHz and intensity 0.05-0.7 W/cm2 for 1-5 min did not change their survival. Increasing the intensity of ultrasound (2.64 MHz) to 1.0 W/cm2 and the duration of its action to 5 min decreased the number of normal developing embryos (by 35%).     

Evaluation of the system for controlling the quality of the HBsAg detection in the system of screening laboratories

The two-stage control system, ensuring the high quality of serological investigations in the network of screening laboratories in Moscow was developed and introduced into practice. At the first stage the entry control of the quality of the test system for the detection of HbsAg, coming to the screening laboratories, is made in the reference laboratory with the use of specially developed "representative" panels, as well as the test systems for comparison ("reference" test systems). Then "minipanels" are formed from specimens included into the "representative" panels, which are used for the evaluation of the quality of laboratory investigations made in the screening laboratories. The high quality of such system for controlling the quality of the detection of HBsAg in the screening laboratories of Moscow is shown.