Deep sequencing approach for investigating infectious agents causing fever.

Acute undifferentiated fever (AUF) poses a diagnostic challenge due to the variety of possible aetiologies. While the majority of AUFs resolve spontaneously, some cases become prolonged and cause significant morbidity and mortality, necessitating improved diagnostic methods. This study evaluated the utility of deep sequencing in fever investigation. DNA and RNA were isolated from plasma/sera of AUF cases being investigated at Cairns Hospital in northern Australia, including eight control samples from patients with a confirmed diagnosis. Following isolation, DNA and RNA were bulk amplified and RNA was reverse transcribed to cDNA. The resulting DNA and cDNA amplicons were subjected to deep sequencing on an Illumina HiSeq 2000 platform. Bioinformatics analysis was performed using the program Kraken and the CLC assembly-alignment pipeline. The results were compared with the outcomes of clinical tests. We generated between 4 and 20 million reads per sample. The results of Kraken and CLC analyses concurred with diagnoses obtained by other means in 87.5 % (7/8) and 25 % (2/8) of control samples, respectively. Some plausible causes of fever were identified in ten patients who remained undiagnosed following routine hospital investigations, including Escherichia coli bacteraemia and scrub typhus that eluded conventional tests. Achromobacter xylosoxidans, Alteromonas macleodii and Enterobacteria phage were prevalent in all samples. A deep sequencing approach of patient plasma/serum samples led to the identification of aetiological agents putatively implicated in AUFs and enabled the study of microbial diversity in human blood. The application of this approach in hospital practice is currently limited by sequencing input requirements and complicated data analysis.

Ultrastructure and fertilizing ability of Limousin bull sperm after storage in CEP-2 extender with and without egg yolk.

Sperm can change physiology and structure during storage in refrigerator temperature or frozen temperature that caused by cold shock or free radical. The aim of this study to evaluate ultrastructure and fertilizing ability of Limousin bull sperm after storage in cauda epididymal plasma-based (CEP-2) extender with or without 20% egg yolk concentration at refrigerator temperature. Semen sample collected from three Limousin bull were diluted with CEP-2 with 20% egg yolk and CEP-2 without egg yolk, cooled and stored at 4-5 degrees C during eight days. Sperm ultrastructure were observed with scanning electron microscopy (SEM). Fertilizing ability of Limousin bull sperm were assessed on cleavage rate of embryo using in vitro fertilization method. The percentage data were transformed into arcsine before being analysis with ANOVA and Duncan's multiple comparison test. The result of study showed morphologically normal sperm after storage in CEP-2 with 20% egg yolk, whereas in CEP-2 without egg yolk morphologically abnormal sperm especially neck was fractured and head was destroyed. Fertilizing ability of Limousin bull sperm were significantly higher in CEP-2 extender with egg yolk 20% (74.29 +/- 4.95%; p < 0.05) than without egg yolk (30.00 +/- 12.02%; p < 0.05). Egg yolk 20% in CEP-2 extender protected ultrastructure and fertilizing ability after storage during eight days.

Paternally inherited markers in bovine hybrid populations.

The genetic integrity of crossfertile bovine- or cattle-like species may be endangered by species hybridization. Previously, amplified fragment length polymorphism, satellite fragment length polymorphism and microsatellite assays have been used to analyze the species composition of nuclear DNA in taurine cattle, zebu, banteng and bison populations, while mitochondrial DNA reveals the origin of the maternal lineages. Here, we describe species-specific markers of the paternally transmitted Y-chromosome for the direct detection of male-mediated introgression. Convenient PCR-restriction fragment length polymorphism and competitive PCR assays are shown to differentiate the Y-chromosomes of taurine cattle, American bison and European bison, and to detect the banteng origin of Indonesian Madura and Bali cattle bulls.