Annotation of primate miRNAs by high throughput sequencing of small RNA libraries

BACKGROUND: In addition to genome sequencing, accurate functional annotation of genomes is required in order to carry out comparative and evolutionary analyses between species. Among primates, the human genome is the most extensively annotated. Human miRNA gene annotation is based on multiple lines of evidence including evidence for expression as well as prediction of the characteristic hairpin structure. In contrast, most miRNA genes in non-human primates are annotated based on homology without any expression evidence. We have sequenced small-RNA libraries from chimpanzee, gorilla, orangutan and rhesus macaque from multiple individuals and tissues. Using patterns of miRNA expression in conjunction with a model of miRNA biogenesis we used these high-throughput sequencing data to identify novel miRNAs in non-human primates. RESULTS: We predicted 47 new miRNAs in chimpanzee, 240 in gorilla, 55 in orangutan and 47 in rhesus macaque. The algorithm we used was able to predict 64% of the previously known miRNAs in chimpanzee, 94% in gorilla, 61% in orangutan and 71% in rhesus macaque. We therefore added evidence for expression in between one and five tissues to miRNAs that were previously annotated based only on homology to human miRNAs. We increased from 60 to 175 the number miRNAs that are located in orthologous regions in humans and the four non-human primate species studied here. CONCLUSIONS: In this study we provide expression evidence for homology-based annotated miRNAs and predict de novo miRNAs in four non-human primate species. We increased the number of annotated miRNA genes and provided evidence for their expression in four non-human primates. Similar approaches using different individuals and tissues would improve annotation in non-human primates and allow for further comparative studies in the future

Zur Fauna der Zikaden, Wanzen und Augenfliegen des Kaiserstuhls: (Hemiptera: Auchenorrhyncha et Heteroptera; Diptera: Pipunculidae)

On the fauna of hemipteran bugs (Hemiptera: Auchenorrhyncha et Heteroptera) and big-headed flies (Diptera: Pipunculidae) of the Kaiserstuhl, southwestern Germany. – Field records of 157 Auchenorrhyncha species gathered on field excursionsto five sites in the Kaiserstuhl Hill during the 9th Auchenorrhyncha Meeting, June 14th - 15th 2002, are presented. Particularly noteworthy was the first German record of the leafhopper Arocephalus sagittarius Rib., which was so far only known from southwestern Europe, and the very rare Edwardsiana smreczynskii Dwor., which is known only from less than 10 localities in Poland, Slowakia, Germany, Switzerland and France. Two further species, which are known in Germany only from this locality, notably Cixidia pilatoi D'Urso & Gugl. and Phlepsius intricatus (H.-S.), were no more found

an observational study

Pulmonary tuberculosis (PTB) results in lung functional impairment and there are no surrogate markers to monitor the extent of lung involvement. We investigated the clinical significance of S100A12 and soluble receptor for advanced glycation end-products (sRAGE) for predicting the extent of lung involvement. We performed an observational study in India with 119 newly diagnosed, treatment naïve, sputum smear positive, HIV-negative PTB patients and 163 healthy controls. All patients were followed-up for six months. Sociodemographic variables and the serum levels of S100A12, sRAGE, esRAGE, HMGB-1, TNF-α, IFN-γ and CRP were measured. Lung involvement in PTB patients was assessed by chest radiography. Compared with healthy controls, PTB patients had increased serum concentrations of S100A12 while sRAGE was decreased. S100A12 was an independent predictor of disease occurrence (OR 1.873, 95%CI 1.212–2.891, p = 0.004). Under DOTS therapy, S100A12 decreased significantly after 4 months whereas CRP significantly decreased after 2 months (p < 0.0001). Importantly, although CRP was also an independent predictor of disease occurrence, only S100A12 was a significant predictor of lung alveolar infiltration (OR 2.60, 95%CI 1.35–5.00, p = 0.004). These results suggest that S100A12 has the potential to assess the extent of alveolar infiltration in PTB

Transcription Factors Are Targeted by Differentially Expressed miRNAs in Primates

MicroRNAs (miRNAs) are small RNA molecules involved in the regulation of mammalian gene expression. Together with other transcription regulators, miRNAs modulate the expression of genes and thereby potentially contribute to tissue and species diversity. To identify miRNAs that are differentially expressed between tissues and/or species, and the genes regulated by these, we have quantified expression of miRNAs and messenger RNAs in five tissues from multiple human, chimpanzee, and rhesus macaque individuals using high-throughput sequencing. The breadth of this tissue and species data allows us to show that downregulation of target genes by miRNAs is more pronounced between tissues than between species and that downregulation is more pronounced for genes with fewer binding sites for expressed miRNAs. Intriguingly, we find that tissue- and species-specific miRNAs target transcription factor genes (TFs) significantly more often than expected. Through their regulatory effect on transcription factors, miRNAs may therefore exert an indirect influence on a larger proportion of genes than previously thought

Historical biogeography of the leopard (Panthera pardus) and its extinct Eurasian populations

Background: Resolving the historical biogeography of the leopard (Panthera pardus) is a complex issue, because patterns inferred from fossils and from molecular data lack congruence. Fossil evidence supports an African origin, and suggests that leopards were already present in Eurasia during the Early Pleistocene. Analysis of DNA sequences however, suggests a more recent, Middle Pleistocene shared ancestry of Asian and African leopards. These contrasting patterns led researchers to propose a two-stage hypothesis of leopard dispersal out of Africa: an initial Early Pleistocene colonisation of Asia and a subsequent replacement by a second colonisation wave during the Middle Pleistocene. The status of Late Pleistocene European leopards within this scenario is unclear: were these populations remnants of the first dispersal, or do the last surviving European leopards share more recent ancestry with their African counterparts? Results: In this study, we generate and analyse mitogenome sequences from historical samples that span the entire modern leopard distribution, as well as from Late Pleistocene remains. We find a deep bifurcation between African and Eurasian mitochondrial lineages (~ 710 Ka), with the European ancient samples as sister to all Asian lineages (~ 483 Ka). The modern and historical mainland Asian lineages share a relatively recent common ancestor (~ 122 Ka), and we find one Javan sample nested within these. Conclusions: The phylogenetic placement of the ancient European leopard as sister group to Asian leopards suggests that these populations originate from the same out-of-Africa dispersal which founded the Asian lineages. The coalescence time found for the mitochondrial lineages aligns well with the earliest undisputed fossils in Eurasia, and thus encourages a re-evaluation of the identification of the much older putative leopard fossils from the region. The relatively recent ancestry of all mainland Asian leopard lineages suggests that these populations underwent a severe population bottleneck during the Pleistocene. Finally, although only based on a single sample, the unexpected phylogenetic placement of the Javan leopard could be interpreted as evidence for exchange of mitochondrial lineages between Java and mainland Asia, calling for further investigation into the evolutionary history of this subspecies

The effects of integrated inpatient health care on patient satisfaction and health-related quality of life: Results of a survey among heart disease patients in Germany

Objectives Since 2004 a large German health insurance company (Techniker Krankenkasse) has provided integrated inpatient health care (IHC) contracts to its members. The aim of the study was to evaluate the effects of this programme on patient satisfaction and health-related quality of life among heart disease patients.Methods A case-control study was conducted with patients in cardiologic and cardiosurgical units who were discharged in 2006. The cases included approximately 750 IHC patients from eight hospitals, whereas the controls were chosen both from the same and other hospitals. Data consisted of interviews in written form (overall response rate: 70.7%), and routine data of health insurances. Main assessment criteria were patient satisfaction with care measured by a modified standardised questionnaire (FK-P), and the SF-12 instrument for measuring health-related quality of life.Results In many respects, patient satisfaction with care was the highest among the IHC patients, followed by controls from the same hospitals, and by those from other hospitals. The process indicator of the lowest satisfaction across all three groups was the provision of competencies to deal with problems at home after discharge ("patient education"). Further benefits of IHC are the reduction of both the average length of hospital stay and the waiting time of patients for rehabilitation. By contrast, no statistically significant differences were found with regard to patient-reported health improvement and health-related quality of life.Conclusions Although the IHC programme did not seem to improve the patients' health-related quality of life and health status, positive effects on patient satisfaction and the efficiency of hospital care could be detected. For future research one ought to check the advantages and/or disadvantages of IHC for other disease groups, and should, if possible, use a prospective study design as well as integrate clinical parameters.Integrated health care Patient satisfaction Health-related quality of life Heart disease patients Hospital care