Sensitivity of Arthropod and Microbial Communities Associated with Vertebrate Carrion in Response to Delayed Blow Fly Access: Implication for Carrion Ecology and Forensic Entomology

The objectives of this study were to determine the sensitivity of microbial metabolic community profiles, terrestrial and soil arthropod community structures and function, and soil chemistry dynamics associated with carrion experiencing delayed Diptera colonization. Bacterial metabolism profiles indicate a significant difference between carrion with immediate insect access (Control) and carrion with delayed insect colonization for seven days and 14 days (Treatments). In contrast, soil samples demonstrated no significant change in soil microbial metabolic profiles in 2013, but exhibited significant difference in 2014 trial. These results suggest high sensitivity of microbial community function on pig carrion, but a stochastic response in the soil microbial ecosystem. This phenomenon may be due to the significant abiotic change in the temperatures as well as the differences in the amount of precipitation between trials. Soil chemistry profiles were significantly different between Control and Treatment carcasses. Furthermore, significant differences were found between days of decomposition (temporal sensitive) and soil regions (spatial sensitive). Soil nutrients, such as ammonium, phosphate, non-purgeable organic carbon and total nitrogen were sensitive to treatment effects, but nitrate was not. The treatment effects, community divergence, convergence and resilience for aboveground and belowground arthropods depended on trial, sampling methods (sticky traps, pitfall traps, and sweep nets), taxonomic resolutions (Order, Family, and Genus) and ecological indices (richness, Simpson’s diversity, Shannon-Wiener’s diversity, evenness, and effective number of species) tested. In general, soil arthropod (including acari) community structures were sensitive to treatment effects only at the Family level. The total abundance of acari was not significantly different across treatments in all-sampling days. For aboveground arthropod community structure and function trapped by sticky traps, significant differences in treatments were detected at the Order and Genus levels for both pitfall traps and sweep nets. The present study demonstrated that insect succession on carrion by family level is predictable. However, insect succession by genus level demonstrated stochasticity when dealing with disturbances. Hence, both Clementsian and Gleasonian models explained insect succession and scale matters with regards to these ecological phenomena. These data are valuable for a host of applications, such as forensic sciences, disease ecology, and conservation biology

Aural myiasis in a neonate in peninsular Malaysia

Myiasis is a pathological condition in humans and animals caused by various species of dipterous larvae. Myiasis which occurs in a newborn baby is referred as neonatal myiasis. It is a rare condition and there are only a few reports to date. A case of neonatal aural myiasis in a two day old infant is reported in this paper

Effect of microbial inoculant on the oviposition and completion of life cycle of Chrysomya megacephala (Fabricius) and Chrysomya rufifacies (Macquart) infesting rabbit carcasses

This research was conducted to assess the influence of microbial inoculant (EM.1®) on the initial oviposition and developmental pattern of two prevalent necrophagous flies (Chrysomya megacephala and Chrysomya rufifacies) in Malaysia. Nine rabbit carcasses were equally divided into control and two treated groups. The control carcasses were sprayed with deionized water (about 100 mL), whereas the two other treated groups were individually sprayed with two concentrations of EM.1® at 1:500 and 1:100, respectively. Results revealed that the single application of EM.1® on both treated carcasses did not statistically impede oviposition by both necrophagous species, as well as their subsequent developmental patterns (P > 0.05) when compared with that of controls. Therefore, estimating the minimum post-mortem interval (mPMI) using empirical baseline data for the control animal model would remain appropriate for estimating mPMI in cases involving carcasses with a single application of EM.1

Pan-cancer analysis of whole genomes

Cancer is driven by genetic change, and the advent of massively parallel sequencing has enabled systematic documentation of this variation at the whole-genome scale(1-3). Here we report the integrative analysis of 2,658 whole-cancer genomes and their matching normal tissues across 38 tumour types from the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA). We describe the generation of the PCAWG resource, facilitated by international data sharing using compute clouds. On average, cancer genomes contained 4-5 driver mutations when combining coding and non-coding genomic elements; however, in around 5% of cases no drivers were identified, suggesting that cancer driver discovery is not yet complete. Chromothripsis, in which many clustered structural variants arise in a single catastrophic event, is frequently an early event in tumour evolution; in acral melanoma, for example, these events precede most somatic point mutations and affect several cancer-associated genes simultaneously. Cancers with abnormal telomere maintenance often originate from tissues with low replicative activity and show several mechanisms of preventing telomere attrition to critical levels. Common and rare germline variants affect patterns of somatic mutation, including point mutations, structural variants and somatic retrotransposition. A collection of papers from the PCAWG Consortium describes non-coding mutations that drive cancer beyond those in the TERT promoter(4); identifies new signatures of mutational processes that cause base substitutions, small insertions and deletions and structural variation(5,6); analyses timings and patterns of tumour evolution(7); describes the diverse transcriptional consequences of somatic mutation on splicing, expression levels, fusion genes and promoter activity(8,9); and evaluates a range of more-specialized features of cancer genomes(8,10-18).Peer reviewe

Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples

Funder: NCI U24CA211006Abstract: The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC) curated consensus somatic mutation calls using whole exome sequencing (WES) and whole genome sequencing (WGS), respectively. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2,658 cancers across 38 tumour types, we compare WES and WGS side-by-side from 746 TCGA samples, finding that ~80% of mutations overlap in covered exonic regions. We estimate that low variant allele fraction (VAF < 15%) and clonal heterogeneity contribute up to 68% of private WGS mutations and 71% of private WES mutations. We observe that ~30% of private WGS mutations trace to mutations identified by a single variant caller in WES consensus efforts. WGS captures both ~50% more variation in exonic regions and un-observed mutations in loci with variable GC-content. Together, our analysis highlights technological divergences between two reproducible somatic variant detection efforts

Comprehensive analysis of chromothripsis in 2,658 human cancers using whole-genome sequencing

Chromothripsis is a mutational phenomenon characterized by massive, clustered genomic rearrangements that occurs in cancer and other diseases. Recent studies in selected cancer types have suggested that chromothripsis may be more common than initially inferred from low-resolution copy-number data. Here, as part of the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA), we analyze patterns of chromothripsis across 2,658 tumors from 38 cancer types using whole-genome sequencing data. We find that chromothripsis events are pervasive across cancers, with a frequency of more than 50% in several cancer types. Whereas canonical chromothripsis profiles display oscillations between two copy-number states, a considerable fraction of events involve multiple chromosomes and additional structural alterations. In addition to non-homologous end joining, we detect signatures of replication-associated processes and templated insertions. Chromothripsis contributes to oncogene amplification and to inactivation of genes such as mismatch-repair-related genes. These findings show that chromothripsis is a major process that drives genome evolution in human cancer

Insect succession associated with a hanging pig carcass placed in an oil palm plantation in Malaysia

This study was carried out in an oil palm plantation in Tanjung Sepat, Selangor in September 2007 by using pigs (Sus scrofa L.) as a carcass model in a forensic entomological research. A 2.5 month old pig (10 kg) which died naturally was hanged on a palm tree to observe the insect succession and decomposition stages. Observation was made for 16 days; one afternoon visit per day and all climatological data were recorded. On the first day, adult muscids of Ophyra spinigera Stein and Musca domestica L. were observed, however no blowfly (Calliphoridae) activities were sighted. Fly eggs wer seen on the second day on both sides of the face, inside nostrils and genitourinary area. Adults of Chrysomya megacephala Fabricius and Chrysomya rufifacies (Macquart) congregated on the head and anal areas. Adult flies and maggots (first and second instars) were observed in the mouth and anus of the pig on the third day of hanging. Adult yellow jackets (Vespidae) and spiders (Arachnida) were found preying on some adult flies. Rove beetles (Staphilinidae) were also discovered on the pig carcass. Only a few ants (Formicidae) were sighted. Maggot masses were found in eye orbits, neck, and genital organs on the fourth day of hanging and some maggots were seen falling down to the ground. The dominant maggot species identified on this day was Ch. megacephala. On the sixth day, the head, neck, and anus were in the stage of active decay. Maggots of Ch. rufifacies were abundant on the seventh day and was the dominant species. On day eight the carcass fell onto the ground. Chrysomya rufifacies maggots were found underneath the pig carcass and they started to migrate and pupated under the soil. On the tenth day, third instar Op. spinigera maggots were found under the carcass. The rate of carcass decomposition slowed down and became stable from tenth day onwards to the sixteenth day of decomposition. Thereafter, most of the remaining parts of the body remained dried and devoid of any insects

First report of liposcelis bostrychophila badonnel (Psocoptera: Liposcelidae) as a museum insect pest in Malaysia

This paper reports the infestation of psocid, Liposcelis bostrychophila Badonnel (Psocoptera: Liposcelidae) in the insect museum at Medical Entomology Unit, Institute for Medical Research, Kuala Lumpur. These tiny organisms were recognised as museum insect pest and found frequently in the insect boxes containing mosquitoes, flies, cockroaches and butterflies. They feed on dead insect specimens and cause severe physical damages to the valuable reference specimens collected in the early 20th century. Hence, it is important to control their population immediately to prevent them from causing further deterioration to the museum collection

Opportunistic insects associated with pig carrions in Malaysia

Flies from the family Calliphoridae, Sarcophagidae and Muscidae are usually found on human cadavers or animal carcasses. However, there are many other families of Diptera and Coleoptera that were found associated with animal carcasses, which have not been reported in Malaysia. In this paper, we report dipterans from the family Micropezidae: Mimegralla albimana Doleschall, 1856, Neriidae: Telostylinus lineolatus (Wiedemann 1830); Sepsidae: Allosepsis indica (Wiedemann 1824), Ulidiidae: Physiphora sp. and a beetle (Coleoptera: Hydrophilidae: Sphaeridium sp.) as opportunist species feeding on oozing fluid during the decomposition process. They did not oviposit on the pig carcasses, therefore, their role in estimation of time of death is of little importance. However, they could provide clues such as locality and types of habitats of the crime scene