Can freshwater mites act as forensic tools?

Determination of post-mortem interval often employs analysis of age structure and diversity of saprophilic arthropods (including mites) that have colonized corpses. The majority of research has focused on decomposition processes in terrestrial situations, with relatively few studies on the utility of freshwater invertebrates as forensic agents. Most freshwater mites are predators, detritivores or algivores, and hence seem unlikely candidates as tools for aging or determining original placement of corpses or other bodily remains. The main exceptions to this are some aquatic Astigmata, which have occasionally been observed feeding on the tissues of moribund aquatic animals. Here I investigate Canadian law literature and published forensic research to determine how frequently freshwater mites are included in court cases or are found attending dead bodies. I found only one questionable report of aquatic mites in over 30 years of material from legal databases. Three published research papers reported mites associated with vertebrate flesh in fresh water. Only one paper provided an identification of mites finer than ‘Acari’ or ‘water mites’. In this case, the mites were identified as Hydrozetes (Oribatida). In none of these papers were mites reported to be high in abundance or biomass, and in two of the three publications methodological problems and/or poor reporting of data raised doubts about interpretation of results. I conclude that based on their biology, there is little expectation that freshwater mites should be of great value as forensic tools, and this survey of legal and scientific literature supports my argument.     

Advances in omics and bioinformatics tools for systems analyses of plant functions

Omics and bioinformatics are essential to understanding the molecular systems that underlie various plant functions. Recent game-changing sequencing technologies have revitalized sequencing approaches in genomics and have produced opportunities for various emerging analytical applications. Driven by technological advances, several new omics layers such as the interactome, epigenome and hormonome have emerged. Furthermore, in several plant species, the development of omics resources has progressed to address particular biological properties of individual species. Integration of knowledge from omics-based research is an emerging issue as researchers seek to identify significance, gain biological insights and promote translational research. From these perspectives, we provide this review of the emerging aspects of plant systems research based on omics and bioinformatics analyses together with their associated resources and technological advances.     

Systems Metabolic Engineering Meets Machine Learning: A New Era for Data‐Driven Metabolic Engineering

The recent increase in high‐throughput capacity of ‘omics datasets combined with advances and interest in machine learning (ML) have created great opportunities for systems metabolic engineering. In this regard, data‐driven modeling methods have become increasingly valuable to metabolic strain design. In this review, the nature of ‘omics is discussed and a broad introduction to the ML algorithms combining these datasets into predictive models of metabolism and metabolic rewiring is provided. Next, this review highlights recent work in the literature that utilizes such data‐driven methods to inform various metabolic engineering efforts for different classes of application including product maximization, understanding and profiling phenotypes, de novo metabolic pathway design, and creation of robust system‐scale models for biotechnology. Overall, this review aims to highlight the potential and promise of using ML algorithms with metabolic engineering and systems biology related datasets.     

CHOmics: A web-based tool for multi-omics data analysis and interactive visualization in CHO cell lines

Chinese hamster ovary (CHO) cell lines are widely used in industry for biological drug production. During cell culture development, considerable effort is invested to understand the factors that greatly impact cell growth, specific productivity and product qualities of the biotherapeutics. While high-throughput omics approaches have been increasingly utilized to reveal cellular mechanisms associated with cell line phenotypes and guide process optimization, comprehensive omics data analysis and management have been a challenge. Here we developed CHOmics, a web-based tool for integrative analysis of CHO cell line omics data that provides an interactive visualization of omics analysis outputs and efficient data management. CHOmics has a built-in comprehensive pipeline for RNA sequencing data processing and multi-layer statistical modules to explore relevant genes or pathways. Moreover, advanced functionalities were provided to enable users to customize their analysis and visualize the output systematically and interactively. The tool was also designed with the flexibility to accommodate other types of omics data and thereby enabling multi-omics comparison and visualization at both gene and pathway levels. Collectively, CHOmics is an integrative platform for data analysis, visualization and management with expectations to promote the broader use of omics in CHO cell research.     

Anesthesia, analgesia, and euthanasia of invertebrates

Invertebrate animals have long played an important role in biomedical research in such fields as genetics, physiology, and development. However, with few exceptions, scientists, veterinarians, and technicians have paid little attention to the anesthesia, analgesia, and euthanasia of these diverse creatures. Indeed, some standard research procedures are routinely performed without anesthesia. Yet various chemical agents are available for the immobilization or anesthesia of invertebrates, ranging from gases or volatile liquids that can be pumped into either an anesthetic chamber (for terrestrial species) or a container of water (aquatic species), to benzocaine and other substances for fish. Many invertebrates are not difficult to immobilize or anesthetize and the procedures recommended in this article appear to be safe; however, none should be considered totally risk-free. Analgesia of invertebrates is as yet a largely unexplored field; until scientific data are available, other measures can promote the well-being of these animals in the laboratory. For euthanasia, various methods (physical or chemical or a combination of both) have been recommended for different taxa of invertebrates, but most have not been properly studied under laboratory conditions and some can be problematic in the context of research procedures and tissue harvesting. Furthermore, relevant data are scattered, sometimes available only in languages other than English, and there is no international approach for seeking and collating such information. In this article I review various methods of anesthesia, analgesia, and euthanasia for terrestrial and aquatic invertebrates, as well as areas requiring further research.     

High‐Quality Biobanks: Pivotal Assets for Reproducibility of OMICS‐Data in Biomedical Translational Research

Human biospecimen samples (HBS) and associated data stored in biobanks (also called “biotrusts,” “biorepositories,” or “biodistributors”) are very critical resources for translational research. As HBS quality is decisive to the reproducibility of research results, biobanks are also key assets for new developments in precision medicine. Biobanks are more than infrastructures providing HBS and associated data. Biobanks have pioneered in identifying and standardizing sources of preanalytical variations in HBS, thus paving the way for the current biospecimen science. To achieve this milestone, biobankers have successively assumed the role of “detective,” and then “architect,” to identify new detrimental impact of preanalytical variables on the tissue integrity. While standardized methods in omics are required to be practiced throughout research communities, the accepted best practices and standards on biospecimen handling are generally not known nor applied by researchers. Therefore, it is mandatory to raise the awareness within omics communities regarding not only the basic concepts of collecting, storing, and utilizing HBS today, but also to suggest insights on biobanking in the cancer omics context.     

Marine antifouling laboratory bioassays: an overview of their diversity

In aquatic environments, biofouling is a natural process of colonization of submerged surfaces, either living or artificial, involving a wide range of organisms from bacteria to invertebrates. Antifouling can be defined as preventing the attachment of organisms onto surfaces. This article reviews the laboratory bioassays that have been developed for studying the control of algae and invertebrates by epibiosis (chemical ecology) and the screening of new active compounds (natural products and biocides) to inhibit settlement or adhesion, ie fouling-release coatings. The assays utilize a range of organisms (mainly marine bacteria, diatoms, algae, barnacles). The main attributes of assays for micro- and macroorganisms are described in terms of their main characteristics and depending on the biological process assessed (growth, adhesion, toxicity, behavior). The validation of bioassays is also discussed.     

A clustering method for next-generation sequences of bacterial genomes through multiomics data mapping

With various ‘omics’ data becoming available recently, new challenges and opportunities are provided for researches on the assembly of next-generation sequences. As an attempt to utilize novel opportunities, we developed a next-generation sequence clustering method focusing on interdependency between genomics and proteomics data. Under the assumption that we can obtain next-generation read sequences and proteomics data of a target species, we mapped the read sequences against protein sequences and found physically adjacent reads based on a machine learning-based read assignment method. We measured the performance of our method by using simulated read sequences and collected protein sequences of Escherichia coli (E. coli). Here, we concentrated on the actual adjacency of the clustered reads in the E. coli genome and found that (i) the proposed method improves the performance of read clustering and (ii) the use of proteomics data does have a potential for enhancing the performance of genome assemblers. These results demonstrate that the integrative approach is effective for the accurate grouping of adjacent reads in a genome, which will result in a better genome assembly.     

An omics perspective of protein disorder

Disordered regions within proteins have increasingly been associated with various cellular functions. Identifying the specific roles played by disorder in these functions has proved difficult. However, the development of reliable prediction algorithms has expanded the study of disorder from a few anecdotal examples to a proteome-wide scale. Moreover, the recent omics revolution has provided the sequences of numerous organisms as well as thousands of genome-wide data sets including several types of interactomes. Here, we review the literature regarding genome-wide studies of disorder and examine how these studies give rise to new characterizations and categories of this elusive phenomenon.     

Dispersal of freshwater invertebrates by large terrestrial mammals: a case study with wild boar (Sus scrofa) in Mediterranean wetlands

1. Many invertebrates inhabiting insular aquatic habitats rely on external agents or vectors to disperse. Besides water connections and wind, waterfowl and amphibians are known to mediate passive dispersal of freshwater invertebrates. However, the possibility of dispersal by terrestrial mammals has been largely overlooked. 2. We investigated the potential of both external and internal zoochorous dispersal of aquatic invertebrates by the wild boar (Sus scrofa) in Mediterranean wetlands in the Camargue (France). As wild boar frequently visit wetlands for feeding and wallowing purposes, we hypothesized that they may be important passive dispersal vectors of aquatic invertebrates at a local scale. Dried mud was collected from selected ‘rubbing trees’ used by boars to dispose of parasites. Additionally, faecal pellets were collected from different locations in the wetland area. 3. Seventeen freshwater invertebrate taxa including rotifers, cladocerans, copepods and ostracods hatched from sediment obtained from ‘rubbing trees’, while invertebrates hatching from dried faeces (10 taxa) were mainly rotifers. Dispersing invertebrates were collected up to 318 m from a nearest potential dispersal source. Both abundance and richness of invertebrates significantly decreased with dispersal distance. 4. Our results demonstrate that large mammals such as wild boar can act as dispersal vectors of aquatic invertebrates at a local scale in the wetland area of the Camargue and suggest that external transport may be quantitatively more important than internal transport. As wallowing (mud bathing) is common in many terrestrial mammals, this mode of dispersal may be quite widespread.     

整合分析多组学数据筛选疾病靶点的精准医学策略

随着高通量测序技术的不断发展与完善,对于不同层次和类型的生物组学数据的获取及分析方法也日趋成熟与完善。基于单组学数据的疾病研究已经发现了诸多新的疾病相关因子,而整合多组学数据研究疾病靶点的工作方兴未艾。生命体是一个复杂的调控系统,疾病的发生与发展涉及基因变异、表观遗传改变、基因表达异常以及信号通路紊乱等诸多层次的复杂调控机制,利用单一组学数据分析致病因子的局限性愈发显著。通过对多种层次和来源的高通量组学数据的整合分析,系统地研究临床发病机理、确定最佳疾病靶点已经成为精准医学研究的重要发展方向,将为疾病研究提供新的思路,并对疾病的早期诊断、个体化治疗和指导用药等提供新的理论依据。本文详细介绍了基因组、转录组和表观组等系统组学研究在疾病靶点筛选方面出现的新技术手段和研究进展,并对它们之间的整合分析新策略和优势进行了讨论。     

Addressing the Challenges of High‐Throughput Cancer Tissue Proteomics for Clinical Application: ProCan

The cancer tissue proteome has enormous potential as a source of novel predictive biomarkers in oncology. Progress in the development of mass spectrometry (MS)‐based tissue proteomics now presents an opportunity to exploit this by applying the strategies of comprehensive molecular profiling and big‐data analytics that are refined in other fields of ‘omics research. ProCan (ProCan is a registered trademark) is a program aiming to generate high‐quality tissue proteomic data across a broad spectrum of cancer types. It is based on data‐independent acquisition–MS proteomic analysis of annotated tissue samples sourced through collaboration with expert clinical and cancer research groups. The practical requirements of a high‐throughput translational research program have shaped the approach that ProCan is taking to address challenges in study design, sample preparation, raw data acquisition, and data analysis. The ultimate goal is to establish a large proteomics knowledge‐base that, in combination with other cancer ‘omics data, will accelerate cancer research.     

Fluorescent Proteins and Their Use in Marine Biosciences,Biotechnology, and Proteomics

This review explores the field of fluorescent proteins (FPs) from the perspective of their marine origins and their applications in marine biotechnology and proteomics. FPs occur in hydrozoan, anthozoan, and copepodan species, and possibly in other metazoan niches as well. Many FPs exhibit unique photophysical and photochemical properties that are the source of exciting research opportunities and technological development. Wild-type FPs can be enhanced by mutagenetic modifications leading to variants with optimized fluorescence and new functionalities. Paradoxically, the benefits from ocean-derived FPs have been realized, first and foremost, for terrestrial organisms. In recent years, however, FPs have also made inroads into aquatic biosciences, primarily as genetically encoded fluorescent fusion tags for optical marking and tracking of proteins, organelles, and cells. Examples of FPs and applications summarized here testify to growing utilization of FP-based platform technologies in basic and applied biology of aquatic organisms. Hydra, sea squirt, zebrafish, striped bass, rainbow trout, salmonids, and various mussels are only a few of numerous instances where FPs have been used to address questions relevant to evolutionary and developmental research and aquaculture.     

Diet partitioning in sympatric Atlantic salmon and brown trout in streams with contrasting riparian vegetation

Prey intake by Atlantic salmon Salmo salar and brown trout Salmo trutta was measured across different riparian vegetation types: grassland, open canopy deciduous and closed canopy deciduous, in upland streams in County Mayo, Western Ireland. Fishes were collected by electrofishing while invertebrates were sampled from the benthos using a Surber sampler and drifting invertebrates collected in drift traps. Aquatic invertebrates dominated prey numbers in the diets of 0+ year Atlantic salmon and brown trout and 1+ year Atlantic salmon, whereas terrestrial invertebrates were of greater importance for diets of 1+ and 2+ year brown trout. Terrestrial prey biomass was generally greater than aquatic prey for 1+ and 2+ year brown trout across seasons and riparian types. Prey intake was greatest in spring and summer and least in autumn apart from 2+ year brown trout that sustained feeding into autumn. Total prey numbers captured tended to be greater for all age classes in streams with deciduous riparian canopy. Atlantic salmon consumed more aquatic prey and brown trout more terrestrial prey with an ontogenetic increase in prey species richness and diversity. Atlantic salmon and brown trout diets were most similar in summer. Terrestrial invertebrates provided an important energy subsidy particularly for brown trout. In grassland streams, each fish age class was strongly associated with aquatic, mainly benthic invertebrates. In streams with deciduous riparian canopy cover, diet composition partitioned between conspecifics with older brown trout associated with surface drifting terrestrial invertebrates and older Atlantic salmon associated with aquatic invertebrates with a high drift propensity in the water column and 0+ year fish feeding on benthic aquatic invertebrates. Deciduous riparian canopy cover may therefore facilitate vertical partitioning of feeding position within the water column between sympatric Atlantic salmon and brown trout. Implications for riparian management are discussed.     

Active Interaction Mapping as a tool to elucidate hierarchical functions of biological processes

Increasingly, various ‘omics data are contributing significantly to our understanding of novel biological processes, but it has not been possible to iteratively elucidate hierarchical functions in complex phenomena. We describe a general systems biology approach called Active Interaction Mapping (AI-MAP), which elucidates the hierarchy of functions for any biological process. Existing and new ‘omics data sets can be iteratively added to create and improve hierarchical models which enhance our understanding of particular biological processes. The best datatypes to further improve an AI-MAP model are predicted computationally. We applied this approach to our understanding of general and selective autophagy, which are conserved in most eukaryotes, setting the stage for the broader application to other cellular processes of interest. In the particular application to autophagy-related processes, we uncovered and validated new autophagy and autophagy-related processes, expanded known autophagy processes with new components, integrated known non-autophagic processes with autophagy and predict other unexplored connections.     

Glucose-sulfate conjugates as a new phase II metabolite formed by aquatic crustaceans

We found that aquatic crustaceans, decapoda; atyidae (Caridina multidentata, Neocaridina denticulate, and Paratya compressa), metabolize pyrene to a new conjugation product. The results of deconjugation treatments indicated that glucose and sulfate combined with 1-hydroxypyrene. Further analysis by LC/ESI-MS/MS showed that the molecular weight of the product was 460 (m/z 459; deprotonated ion), and that it has a glucose-sulfate moiety (m/z 241; fragment ion). These results indicated that the new metabolite was the glucose-sulfate conjugate of 1-hydroxypyrene. The glucose-sulfate conjugate is a phase II product that has not been reported previously from any organism. Several studies have demonstrated that sulfation is an important pathway for metabolism of xenobiotics in aquatic invertebrates. Thus, glucose-sulfate conjugates may add an important signal for excretion or sequestration of xenobiotics for aquatic invertebrates.     

Opportunities for public aquariums to increase the sustainability of the aquatic animal trade

The global aquatic pet trade encompasses a wide diversity of freshwater and marine organisms. While relying on a continual supply of healthy, vibrant aquatic animals, few sustainability initiatives exist within this sector. Public aquariums overlap this industry by acquiring many of the same species through the same sources. End users are also similar, as many aquarium visitors are home aquarists. Here we posit that this overlap with the pet trade gives aquariums significant opportunity to increase the sustainability of the trade in aquarium fishes and invertebrates. Improving the sustainability ethos and practices of the aquatic pet trade can carry a conservation benefit in terms of less waste, and protection of intact functioning ecosystems, at the same time as maintaining its economic and educational benefits and impacts. The relationship would also move forward the goal of public aquariums to advance aquatic conservation in a broad sense. For example, many public aquariums in North America have been instrumental in working with the seafood industry to enact positive change toward increased sustainability. The actions include being good consumers themselves, providing technical knowledge, and providing educational and outreach opportunities. These same opportunities exist for public aquariums to partner with the ornamental fish trade, which will serve to improve business, create new, more ethical and more dependable sources of aquatic animals for public aquariums, and perhaps most important, possibly transform the home aquarium industry from a threat, into a positive force for aquatic conservation.