A scalable and memory-efficient algorithm for de novo transcriptome assembly of non-model organisms

Abstract Background With increased availability of de novo assembly algorithms, it is feasible to study entire transcriptomes of non-model organisms. While algorithms are available that are specifically designed for performing transcriptome assembly from high-throughput sequencing data, they are very memory-intensive, limiting their applications to small data sets with few libraries. Results We develop a transcriptome assembly algorithm that recovers alternatively spliced isoforms and expression levels while utilizing as many RNA-Seq libraries as possible that contain hundreds of gigabases of data. New techniques are developed so that computations can be performed on a computing cluster with moderate amount of physical memory. Conclusions Our strategy minimizes memory consumption while simultaneously obtaining comparable or improved accuracy over existing algorithms. It provides support for incremental updates of assemblies when new libraries become available

Bacteria Mediate Oviposition by the Black Soldier Fly, \u3ci\u3eHermetia illucens\u3c/i\u3e (L.), (Diptera: Stratiomyidae)

Articl

Bacteria Mediate Oviposition by the Black Soldier Fly, Hermetia illucens (L.), (Diptera: Stratiomyidae)

There can be substantial negative consequences for insects colonizing a resource in the presence of competitors. We hypothesized that bacteria, associated with an oviposition resource and the insect eggs deposited on that resource, serve as a mechanism regulating subsequent insect attraction, colonization, and potentially succession of insect species. We isolated and identified bacterial species associated with insects associated with vertebrate carrion and used these bacteria to measure their influence on the oviposition preference of adult black soldier flies which utilizes animal carcasses and is an important species in waste management and forensics. We also ascertained that utilizing a mixture of bacteria, rather than a single species, differentially influenced behavioral responses of the flies, as did bacterial concentration and the species of fly from which the bacteria originated. These studies provide insight into interkingdom interactions commonly occurring during decomposition, but not commonly studied

Detection of Mycolactone A/B in Mycobacterium ulcerans–Infected Human Tissue

Skin infection with bacteria called Mycobacterium ulcerans causes Buruli ulcer, a disease common in West Africa and mainly affecting children. M. ulcerans is the only mycobacterium to cause disease by production of a toxin. This lipid molecule called mycolactone diffuses from the site of infection, killing surrounding cells and, at low concentration, suppressing the immune response. The aim of this study was to show that mycolactone can be detected among lipids extracted from human M. ulcerans lesions in order to study its role in the pathogenesis of M. ulcerans disease. Lipids were extracted from skin biopsies and tested for the presence of mycolactone using thin layer chromatography and mass spectrometry. The extracts were shown to kill cultured cells in a cytotoxicity assay. Mycolactone was detected in both pre-ulcerative and ulcerative forms of the disease and also in lesions during antibiotic treatment but with reduced bioactivity, suggesting a lower concentration compared to untreated lesions. These findings indicate that there is mycolactone in affected skin at all stages of M. ulcerans disease and it could be used as a biomarker for monitoring the clinical response to antibiotic treatment

Emergence of a unique group of necrotizing mycobacterial diseases.

Although most diseases due to pathogenic mycobacteria are caused by Mycobacterium tuberculosis, several other mycobacterial diseases-caused by M. ulcerans (Buruli ulcer), M. marinum, and M. haemophilum-have begun to emerge. We review the emergence of diseases caused by these three pathogens in the United States and around the world in the last decade. We examine the pathophysiologic similarities of the diseases (all three cause necrotizing skin lesions) and common reservoirs of infection (stagnant or slow-flowing water). Examination of the histologic and pathogenic characteristics of these mycobacteria suggests differences in the modes of transmission and pathogenesis, though no singular mechanism for either characteristic has been definitively described for any of these mycobacteria

Macrocheles species (Acari: Macrochelidae) associated with human corpses in Europe

The biology of macrochelid mites might offer new venues for the interpretation of the environmental conditions surrounding human death and decomposition. Three human corpses, one from Sweden and two from Spain, have been analysed for the occurrence of Macrochelidae species. Macrocheles muscaedomesticae females were associated with a corpse that was found in a popular beach area of southeast Spain. Their arrival coincides with the occurrence of one of their major carrier species, the filth fly Fannia scalaris, the activity of which peaks during mid-summer. M. glaber specimens were collected from a corpse in a shallow grave in a forest in Sweden at the end of summer, concurrent with the arrival of beetles attracted by odours from the corpse. M. perglaber adults were sampled from a corpse found indoors in the rural surroundings of Granada city, Spain. The phoretic behaviour of this species is similar to that of M. glaber, but being more specific to Scarabaeidae and Geotrupidae dung beetles, most of which favour human faeces. M. muscaedomesticae is known from urban and rural areas and poultry farms; M. glaber from outdoors, particularly the countryside; while M. perglaber from outdoor, rural, and remote, potentially mountainous locations. M. muscaedomesticae and M. perglaber are reported for the first time from the Iberian Peninsula. This is the first record of M. perglaber from human remains

Macrocheles species (Acari: Macrochelidae) associated with human corpses in Europe

The biology of macrochelid mites might offer new venues for the interpretation of the environmental conditions surrounding human death and decomposition. Three human corpses, one from Sweden and two from Spain, have been analysed for the occurrence of Macrochelidae species. Macrocheles muscaedomesticae females were associated with a corpse that was found in a popular beach area of southeast Spain. Their arrival coincides with the occurrence of one of their major carrier species, the filth fly Fannia scalaris, the activity of which peaks during mid-summer. M. glaber specimens were collected from a corpse in a shallow grave in a forest in Sweden at the end of summer, concurrent with the arrival of beetles attracted by odours from the corpse. M. perglaber adults were sampled from a corpse found indoors in the rural surroundings of Granada city, Spain. The phoretic behaviour of this species is similar to that of M. glaber, but being more specific to Scarabaeidae and Geotrupidae dung beetles, most of which favour human faeces. M. muscaedomesticae is known from urban and rural areas and poultry farms; M. glaber from outdoors, particularly the countryside; while M. perglaber from outdoor, rural, and remote, potentially mountainous locations. M. muscaedomesticae and M. perglaber are reported for the first time from the Iberian Peninsula. This is the first record of M. perglaber from human remains

FATAL HUMAN ASCARIASIS FOLLOWING SECONDARY MASSIVE INFECTION

More than \u27796 Ascaris lumbricoides worms weighing 550 g were recovered at autopsy from a 2-year-old black South African girl. Most of the worms were taken from necrotic small intestine, but worms were also in the stomach, esophagus, intrahepatic and extrahepatic bile ducts, and gallbladder. The worms had caused torsion and gangrene of the ileum, which was interpreted as the cause of death. Worms were formalin-fixed and individually weighed. There were 796 intact worms and 112 appreciably large (\u3e0.2 g) fragments of worms. Statistical analysis of the weights revealed 2 distinct populations of worms: 16 large worms (0.5-2.3 g) and 778 small worms (0.03-0.95 g). The difference in weight between these 2 groups of worms was significant (male and female worms treated separately; P \u3c 0.05 to P \u3c 0.001). These observations reveal that the patient acquired a massive and fatal infection with A. lumbricoides while hosting a relatively light worm burden