Inter-subspecies mouse F1 hybrid embryonic stem cell lines newly established for studies of allelic imbalance in gene expression

Allele-specific monoallelic gene expression is a unique phenomenon and a great resource for analyzing gene regulation. To study this phenomenon, we established new embryonic stem (ES) cell lines derived from F1 hybrid blastocysts from crosses between four mouse subspecies (Mus musculus domesticus, C57BL/6; M. musculus molossinus, MSM/Ms; M. musculus, PWK; M. musculuscastaneus, HMI/Ms) and analyzed the expression levels of undifferentiated pluripotent stem cell markers and karyotypes of each line. To demonstrate the utility of our cell lines, we analyzed the allele-specific expression pattern of the Inpp5d gene as an example. The allelic expression depended on the parental alleles; this dependence could be a consequence of differences in compatibility between cis- and trans-elements of the Inpp5d gene from different subspecies. The use of parental mice from four subspecies greatly enhanced genetic polymorphism. The F1 hybrid ES cells retained this polymorphism not only in the Inpp5d gene, but also at a genome-wide level. As we demonstrated for the Inpp5d gene, the established cell lines can contribute to the analysis of allelic expression imbalance based on the incompatibility between cis- and trans-elements and of phenotypes related to this incompatibility.

Applications of synthetic yeast consortia for the production of native and non-native chemicals

The application of microbial consortia is a new approach in synthetic biology. Synthetic yeast consortia, simple or complex synthetic mixed cultures, have been used for the production of various metabolites. Cooperation between the members of a consortium and cross-feeding can be applied to create stable microbial communication. These consortia can: consume a variety of substrates, perform more complex functions, produce metabolites in high titer, rate, and yield (TRY), and show higher stability during industrial fermentations. Due to the new research context of synthetic consortia, few yeasts were used to build these consortia, including Saccharomyces cerevisiae, Pichia pastoris, and Yarrowia lipolytica. Here, application of the yeasts for design of synthetic microbial consortia and their advantages and bottlenecks for effective and robust production of valuable metabolites from bioresource, including: cellulose, xylose, glycerol and so on, have been reviewed. Key trends and challenges are also discussed for the future development of synthetic yeast consortia.

Microbial cell factories using Paenibacillus: status and perspectives

Considered a "Generally Recognized As Safe" (GRAS) bacterium, the plant growth-promoting rhizobacterium Paenibacillus has been widely applied in: agriculture, medicine, industry, and environmental remediation. Paenibacillus species not only accelerate plant growth and degrade toxic substances in wastewater and soil but also produce industrially-relevant enzymes and antimicrobial peptides. Due to a lack of genetic manipulation tools and methods, exploitation of the bioresources of naturally isolated Paenibacillus species has long been limited. Genetic manipulation tools and methods continue to improve in Paenibacillus, such as shuttle plasmids, promoters, and genetic tools of CRISPR. Furthermore, genetic transformation systems develop gradually, including: penicillin-mediated transformation, electroporation, and magnesium amino acid-mediated transformation. As genetic manipulation methods of homologous recombination and CRISPR-mediated editing system have developed gradually, Paenibacillus has come to be regarded as a promising microbial chassis for biomanufacturing, expanding its application scope, such as: industrial enzymes, bioremediation and bioadsorption, surfactants, and antibacterial agents. In this review, we describe the applications of Paenibacillus bioproducts, and then discuss recent advances and future challenges in the development of genetic manipulation systems in this genus. This work highlights the potential of Paenibacillus as a new microbial chassis for mining bioresources.

Bioresource-Functionalized Quantum Dots for Energy Generation and Storage: Recent Advances and Feature Perspective

The exponential increase in global energy demand in daily life prompts us to search for a bioresource for energy production and storage. Therefore, in developing countries with large populations, there is a need for alternative energy resources to compensate for the energy deficit in an environmentally friendly way and to be independent in their energy demands. The objective of this review article is to compile and evaluate the progress in the development of quantum dots (QDs) for energy generation and storage. Therefore, this article discusses the energy scenario by presenting the basic concepts and advances of various solar cells, providing an overview of energy storage systems (supercapacitors and batteries), and highlighting the research progress to date and future opportunities. This exploratory study will examine the systematic and sequential advances in all three generations of solar cells, namely perovskite solar cells, dye-sensitized solar cells, Si cells, and thin-film solar cells. The discussion will focus on the development of novel QDs that are economical, efficient, and stable. In addition, the current status of high-performance devices for each technology will be discussed in detail. Finally, the prospects, opportunities for improvement, and future trends in the development of cost-effective and efficient QDs for solar cells and storage from biological resources will be highlighted.

Metabolome Genome-Wide Association Study Identifies 74 Novel Genomic Regions Influencing Plasma Metabolites Levels

Metabolites are small products of metabolism that provide a snapshot of the wellbeing of an organism and the mechanisms that control key physiological processes involved in health and disease. Here we report the results of a genome-wide association study of 722 circulating metabolite levels in 8809 subjects of European origin, providing both breadth and depth. These analyses identified 202 unique genomic regions whose variations are associated with the circulating levels of 478 different metabolites. Replication with a subset of 208 metabolites that were available in an independent dataset for a cohort of 1768 European subjects confirmed the robust associations, including 74 novel genomic regions not associated with any metabolites in previous works. This study enhances our knowledge of genetic mechanisms controlling human metabolism. Our findings have major potential for identifying novel targets and developing new therapeutic strategies.

Shape-Memory and Anisotropic Carbon Aerogel from Biomass and Graphene Oxide

Biomass, as the most abundant and sustainable resource on the earth, has been regarded as an ideal carbon source to prepare various carbon materials. However, manufacturing shape-memory carbon aerogels with excellent compressibility and elasticity from biomass remains an open challenge. Herein, a cellulose-derived carbon aerogel with an anisotropic architecture is fabricated with the assistance of graphene oxide (GO) through a directional freeze-drying process and carbonization. The carbon aerogel displays excellent shape-memory performances, with high stress and height retentions of 93.6% and 95.5% after 1000 compression cycles, respectively. Moreover, the carbon aerogel can identify large ranges of compression strain (10–80%), and demonstrates excellent current stability during cyclic compression. The carbon aerogel can precisely capture a variety of biological signals in the human body, and thus can be used in wearable electronic devices.

Complete mitochondrial genome of Mekong fighting fish, Betta smaragdina (Teleostei: Osphronemidae)

Mekong fighting fish (Betta smaragdina) are found in Northeast Thailand. A complete mitochondrial genome (mitogenome) of B. smaragdina was assembled and annotated. Mitogenome sequences were 16,372 bp in length, with slight AT bias (59.8%), containing 37 genes with identical order to most teleost mitogenomes. Phylogenetic analysis of B. smaragdina showed closer relationship with B. splendens and B. mahachaiensis as the bubble-nesting group, compared to the mouthbrooder group (B. apollon, B. simplex, and B. pi). Results will allow the creation of a reference annotated genome that can be utilized to sustain biodiversity and eco-management of betta bioresources to improve conservation programs.

Mechanisms of Lignin-Degrading Enzymes

Lignin is abundant in nature. It is a potentially valuable bioresource, but, because of its complex structure, it is difficult to degrade. However, enzymatic degradation of lignin is effective. Major lignin-degrading enzymes include laccases, lignin peroxidases, and manganese peroxidases. In this paper, the mechanisms of degradation of lignin by these three enzymes is reviewed, and synergy between them is discussed.

Next-generation sequencing yields complete mitochondrial genome assembly of peaceful betta fish, Betta imbellis (Teleostei: Osphronemidae)

The complete mitochondrial genome (mitogenome) of the peaceful betta (Betta imbellis) was obtained using next-generation sequencing. The sample of B. imbellis was collected from its native habitat in Southern Thailand. The mitogenome sequence was 16,897 bp in length, containing 37 genes with identical order to most teleost mitogenomes. Overall nucleotide base composition of the complete mitogenome was determined as AT bias. Phylogenetic analysis of B. imbellis showed a closer relationship with bubble-nesting fighting fish. This annotated mitogenome reference can be utilized as a bioresource for phylogenetic studies to support betta conservation programs.

Complete mitochondrial genome of Mahachai betta, Betta mahachaiensis (Teleostei: Osphronemidae)

Mahachai bettas (Betta mahachaiensis) are distributed in areas of brackish water with Nipa Palms in Samut Sakhon, Thailand but urbanization is restricting their biodiversity. A complete mitochondrial genome (mitogenome) of B. mahachaiensis was determined to support conservation programs. Mitogenome sequences were 16,980 bp in length with slight AT bias (61.91%), containing 37 genes with identical order to most teleost mitogenomes. Phylogenetic analysis of B. mahachaiensis showed a closer relationship with B. splendens. Results will allow the creation of a reference annotated genome that can be utilized to sustain biodiversity and eco-management of the betta to improve conservation programs.

Diversity and Use of Edible Grasshoppers, Locusts, Crickets, and Katydids (Orthoptera) in Madagascar

Madagascar has a long history of using Orthoptera as food and feed. Our understanding of the biological diversity of this resource, its contemporary use, and its future potentials in Madagascar is extremely limited. The present study contributes basic knowledge of the biological diversity and local uses of edible Orthoptera in Malagasy food cultures. Data was collected with key informants in 47 localities covering most of the ecoregions of Madagascar and corresponding to 12 of the 19 ethnic groups. Orthoptera are consumed throughout Madagascar. We report 37 edible Orthoptera species, of which 28 are new species records of edible Orthoptera in Madagascar and 24 are new species records of edible Orthoptera in the world. Most species are endemic and occur in farming zones. Children are the primary collectors and consumers of edible Orthoptera. The insects are eaten both as snacks and main meals. Edible Orthoptera are primarily collected casually and marketing is rare, with the notable exceptions of the large cricket Brachytrupes membranaceus colosseus and during locust outbreaks (e.g., Locusta migratoria). The use of Orthoptera as feed seems rare. Further investigations of cultural and personal preferences are required to assess the future potential roles of Orthoptera in Malagasy food habits.

The Utilization of Biospecimens: Impact of the Choice of Biobanking Model

The term research "biobank" is one of multiple names (e.g., bioresource, biorepository,) used to designate an entity that receives, collects, processes, stores, and/or distributes biospecimens or other biospecimen-related products (e.g., data) to support research. There are multiple organizational models of biobanking used by bioresources, but the primary goal of all bioresources should not be simply to collect biospecimens, but ultimately to distribute almost all collected biospecimens and/or data to support scientific research; bioresources should serve as "biodistributors" rather than "biovaults." The appropriate choice of model is the first step in ensuring optimal biospecimen utilization by a bioresource. This article discusses some of the different models that may be used alone or in combination by a bioresource providing biospecimens for research; it describes the factors affecting the choice of the most appropriate model or models, the advantages and disadvantages of the various models, and a discussion of the impact of the choice of the model on biospecimen utilization. Frequently, problems with biospecimen utilization are not caused by any single model, but rather a mismatch between the choice of model and goals of the bioresource, and/or problems with the subsequent design, goals, operations, and management of the bioresource after a model is selected.

Anti‑photoaging effect of fermented agricultural by‑products on ultraviolet B‑irradiated hairless mouse skin

Processed products from agricultural produce generate a large number of agricultural by‑products that contain a number of functional substances. These are often discarded owing to the lack of suitable processing methods. The present study investigated the anti‑photoaging properties of fermented rice bran (FRB), soybean cake (FSB) and sesame seed cake (FSC) on ultraviolet B (UVB)‑irradiated hairless mouse skin. Results indicated that the oral administration of FRB, FSB and FSC effectively inhibited the UVB irradiation‑induced expression of matrix metalloproteinase (MMP)‑2, MMP‑9, MMP‑3 and MMP‑13. Reverse transcription‑quantitative polymerase chain reaction results also demonstrated that FRB, FSB and FSC significantly inhibited the UVB‑induced expression of the genes encoding tumor necrosis factor‑α, inducible nitric oxide synthase, interleukin (IL)‑6 and IL‑1β when compared with the UVB‑vehicle group (P<0.05). Additionally, collagen degradation and mast cell infiltration were reduced in hairless mouse skin. Furthermore, UVB‑induced wrinkle formation was also significantly reduced in mouse skin compared with the UVB‑vehicle group (P<0.05). These results reveal that fermented agricultural by‑products may serve as potential functional materials with anti‑photoaging activities.

The Importance of Human Tissue Bioresources in Advancing Biomedical Research

Medical research advances enabling the realization of precision medicine have relied heavily on the biospecimens provided by bioresources to identify the targets and biomarkers that are the focus of the new generation of more effective molecular-based therapies for specific subtypes of diseases. Through the biospecimens they have distributed, bioresources have permitted subtypes of cancers to be identified and molecular features of these subtypes to be effectively targeted. A prototype example is the human epidermal growth factor receptor type 2 (HER2), which currently is targeted in breast and gastric cancers. In the future, the use of biospecimens from bioresources will continue to increase the understanding of the molecular actions of drugs and how drugs may be more or less active in subpopulations of patients. Although the biospecimen inventories of the initial forms of bioresources may not have always been optimally planned and, therefore, utilized in supporting biomedical research, bioresources are evolving and overall, bioresource inventories and increasingly their prospective collection capabilities will continue to be a critical component of the research infrastructure.

Medaka Population Genome Structure and Demographic History Described via Genotyping-by-Sequencing

Medaka is a model organism in medicine, genetics, developmental biology and population genetics. Lab stocks composed of more than 100 local wild populations are available for research in these fields. Thus, medaka represents a potentially excellent bioresource for screening disease-risk- and adaptation-related genes in genome-wide association studies. Although the genetic population structure should be known before performing such an analysis, a comprehensive study on the genome-wide diversity of wild medaka populations has not been performed. Here, we performed genotyping-by-sequencing (GBS) for 81 and 12 medakas captured from a bioresource and the wild, respectively. Based on the GBS data, we evaluated the genetic population structure and estimated the demographic parameters using an approximate Bayesian computation (ABC) framework. The genome-wide data confirmed that there were substantial differences between local populations and supported our previously proposed hypothesis on medaka dispersal based on mitochondrial genome (mtDNA) data. A new finding was that a local group that was thought to be a hybrid between the northern and the southern Japanese groups was actually an origin of the northern Japanese group. Thus, this paper presents the first population-genomic study of medaka and reveals its population structure and history based on chromosomal genetic diversity.

Lessons Learned During Three Decades of Operations of Two Prospective Bioresources

Prospective collection is a model through which biospecimens are provided for research. Using this model, biospecimens are collected based on real-time requests from the research community instead of being collected based on the prediction of future requests. We describe the lessons learned by two bioresources that have operated successfully using a prospective model for over three decades. Our goal is to improve other bioresources by increasing utilization of biospecimens that honor consented donors who provide biospecimens to the research community; this provides strong evidence of stewardship of the public trust. The operation of these sites requires flexibility, close communication, and cooperation with the investigator in developing a standard operating procedure (protocol) based on the investigator's needs described in their initial request. If practicable, almost any preparation can be provided, including fresh (nonfrozen) biospecimens and tissue blots. A quality management system includes rigorous quality control of the specific biospecimens provided to an investigator. The informatics approach focuses on the investigator, the investigator's request, and the biospecimens collected for the investigator; the informatics focus of classic biobanks is on the biospecimens collected to match expected future requests. These lessons have been incorporated into our current operations. Standard investigator agreements (e.g., indemnification and no unapproved biospecimen transfers to third parties) replace material transfer agreements. We have operated under the prospective model of the Cooperative Human Tissue Network (CHTN), which has been successful and has provided over 1.2 million biospecimens since it began in 1987. These tissues have supported over 4300 peer-reviewed scientific articles. Since 2012, about 1000 publications have indicated support by CHTN tissues; their average citation rate is 31 with an H factor of 61. Also, during this period, 114 patents cited the CHTN. We also describe disadvantages of prospective bioresources (e.g., inadequate distribution of rare tissues, biospecimens not immediately available, and delayed clinical outcomes).

Subchondral bone derived mesenchymal stem cells display enhanced osteo-chondrogenic differentiation, self-renewal and proliferation potentials

Rabbit mesenchymal stem cells (MSCs) are important seed cells in regenerative medicine research, particularly in translational research. In the current study, we showed that rabbit subchondral bone is a reliable source of MSCs. First, we harvested subchondral bone (SCB) from the rabbit knee-joint and initiated the MSC culture by cultivating enzyme-treated SCB. Adherent fibroblast-like cells that outgrew from SCB fulfill the common immuno-phenotypic criteria for defining MSCs, but with low contamination of CD45+ hematopoietic cells. Interestingly, differentiated SCB-MSCs expressed osteogenic and chondrogenic markers at significantly higher levels than those in bone marrow cell suspension-derived MSCs (BMS-MSCs) (P<0.05). No differences in the expression of adipogenic markers between SCB-MSC and BMS-MSC (P>0.05) were observed. Moreover, the results of the colony forming unit-fibroblast assay and sphere formation assay demonstrated that the SCB-MSCs had increased self-renewal potential. SCB-MSCs expressed higher levels of the stemness markers Nanog, OCT4, and Sox-2 compared to in BMS-MSCs (P<0.05). Furthermore, the results of both the CCK-8-based assay and CFSE dilution assay showed that SCB-MSCs exhibited enhanced proliferative capacity. In addition, SCB-MSCs exhibited higher phosphorylation of extracellular signal-related kinase/mitogen-activated protein kinase signaling, which is closely related to MSC proliferation. In conclusion, we identified SCB-MSCs as a novel stem cell population that met the requirements of MSCs; the unique properties of SCB-MSC are important for the potential treatment of tissue damage resulting from disease and trauma.

Market-driven production of biospecimens and the role of NHS hospital-led biobanks

Biobanks are vital for biospecimen production in research, despite the regulatory, recruitment and commercial difficulties they face. We conducted interviews with clinicians, researchers, volunteers who recruit biobank participants, regulators and NHS managers about the integration of a biobank into an NHS hospital. We show that medical waste collected for biomedical research acquires its socio-ethical and economic value from the level of integration (both technologically and organisationally) of the biobank into the NHS hospital. There is extensive investment in a range of intellectual and commercial relationships and labour among stakeholders involved in the production of biospecimens. It is not only the boundaries of research, clinical care and commercialisation of biospecimens that blur but also those of volunteerism and citizenship. Hospital-led biobanks provide an opportunity to study the intertwining of biomedical innovation and healthcare.

Potential biotechnological capabilities of cultivable mycobiota from carwash effluents

Urban life has created man‐made extreme environments like carwashes. These environments have, however, not been sufficiently explored for mycobiota that can be sources of biotechnologically useful products, as has been the case with natural extreme environments. Using a combination of culture and molecular techniques, fungi from carwash effluents was characterized for production of lipase and cellulase enzymes, nonpolar and polar biotechnologically relevant secondary metabolites and hydrocarbon utilization. The isolated fungal strains belonged to the genera Alternaria, Cladosporium, Penicillium, Peyronellaea, Rhizopus, Spegazzinia, Trichoderma, Ulocladium and Yarrowia. Sixty‐six percent (66%) of the fungal isolates were found to be able to metabolize naphthalene and benzanthracene, showing potential for application in bioremediation of hydrocarbon polluted sites. Lipase production by the isolates Penicillium sp. BPS3 (2.61 U/ml), Trichoderma sp. BPS9 (2.01 U/ml), Rhizopus sp. CAL1 (2.05 U/ml), Penicillium sp. PCW1 (2.99 U/ml) and Penicillium sp. SAS1 (2.16 U/ml) compared well with previously recorded lipase production levels by other fungi. The highest producers of cellulase were Penicillium sp. SAS1 (12.10 U/ml), Peyronella sp. CAW5 (4.49 U/ml) and Cladosporium sp. SAS3 (4.07 U/ml), although these activities were lower than previously reported levels. GC‐MS analysis of the fungal secondary metabolites resulted in identification of 572 compounds, including azulene, methanamine, N‐pentylidene, metoclopramide, and mepivacaine while compounds determined by UHPLC‐MS included 10‐undecen‐1‐ol, piquerol A, 10‐undecyn‐1‐ol, cyclo(leucylprolyl) and rac‐etomidate. These compounds were previously determined to have various activities including anticancer, antibacterial, antifungal, antihypertensive, antidiabetic and anti‐inflammatory properties. The study demonstrated that fungi from carwash effluents are natural sources of some biotechnologically important products.

Business Planning in Biobanking: How to Implement a Tool for Sustainability

Worldwide, the sustainability of public health systems is challenged by the increasing number and cost of personalized therapies. Quality biological samples stored in biobanks are essential for the provision of appropriate health services and also act as a reservoir for the development of precision medicine and biotechnological innovation. Economic sustainability is a crucial factor in the maintenance of biobanking activities. Traditionally, management of biobanking is performed by health researchers and/or clinicians whose knowledge of economic issues is inadequate. On the other hand, familiarity with financial instruments used by economists is not often accompanied by a consolidated understanding of biobanking features. This article aims to be a guide for the implementation of business plans in biobanking and proposes models for the facilitation of their preparation, thus contributing to recognition of the importance of efficient management of resources of public health services.

Developing a guideline to standardize the citation of bioresources in journal articles (CoBRA)

BACKGROUND

Many biomedical publications refer to data obtained from collections of biosamples. Sharing such bioresources (biological samples, data, and databases) is paramount for the present governance of research. Recognition of the effort involved in generating, maintaining, and sharing high quality bioresources is poorly organized, which does not encourage sharing. At publication level, the recognition of such resources is often neglected and/or highly heterogeneous. This is a true handicap for the traceability of bioresource use. The aim of this article is to propose, for the first time, a guideline for reporting bioresource use in research articles, named CoBRA: Citation of BioResources in journal Articles.

METHODS

As standards for citing bioresources are still lacking, the members of the journal editors subgroup of the Bioresource Research Impact Factor (BRIF) initiative developed a standardized and appropriate citation scheme for such resources by informing stakeholders about the subject and raising awareness among scientists and in science editors' networks, mapping this topic among other relevant initiatives, promoting actions addressed to stakeholders, launching surveys, and organizing focused workshops.

RESULTS

The European Association of Science Editors has adopted BRIF's suggestion to incorporate statements on biobanks in the Methods section of their guidelines. The BRIF subgroup agreed upon a proposed citation system: each individual bioresource that is used to perform a study and that is mentioned in the Methods section should be cited as an individual "reference [BIORESOURCE]" according to a delineated format. The EQUATOR (Enhancing the QUAlity and Transparency Of health Research) network mentioned the proposed reporting guideline in their "guidelines under development" section.

CONCLUSIONS

Evaluating bioresources' use and impact requires that publications accurately cite such resources. Adopting the standard citation scheme described here will improve the quality of bioresource reporting and will allow their traceability in scientific publications, thus increasing the recognition of bioresources' value and relevance to research. Please see related article: http://dx.doi.org/10.1186/s12916-015-0284-9.

Quantifying the use of bioresources for promoting their sharing in scientific research

An increasing portion of biomedical research relies on the use of biobanks and databases. Sharing of such resources is essential for optimizing knowledge production. A major obstacle for sharing bioresources is the lack of recognition for the efforts involved in establishing, maintaining and sharing them, due to, in particular, the absence of adequate tools. Increasing demands on biobanks and databases to improve access should be complemented with efforts of end-users to recognize and acknowledge these resources. An appropriate set of tools must be developed and implemented to measure this impact.To address this issue we propose to measure the use in research of such bioresources as a value of their impact, leading to create an indicator: Bioresource Research Impact Factor (BRIF). Key elements to be assessed are: defining obstacles to sharing samples and data, choosing adequate identifier for bioresources, identifying and weighing parameters to be considered in the metrics, analyzing the role of journal guidelines and policies for resource citing and referencing, assessing policies for resource access and sharing and their influence on bioresource use. This work allows us to propose a framework and foundations for the operational development of BRIF that still requires input from stakeholders within the biomedical community.

The National BioResource Project (NBRP) Lotus and Glycine in Japan

The objective of the National BioResource Project (NBRP) in Japan is to collect, conserve and distribute biological materials for life sciences research. The project consists of twenty-eight bioresources, including animal, plant, microorganism and DNA resources. NBRP Lotus and Glycine aims to support the development of legume research through the collection, conservation, and distribution of these bioresources. Lotus japonicus is a perennial legume that grows naturally throughout Japan and is widely used as a model plant for legumes because of such advantages as its small genome size and short life cycle. Soybean (Glycine max) has been cultivated as an important crop since ancient times, and numerous research programs have generated a large amount of basic research information and valuable bioresources for this crop. We have also developed a "LegumeBase" a specialized database for the genera Lotus and Glycine, and are maintaining this database as a part of the NBRP. In this paper we will provide an overview of the resources available from the NBRP Lotus and Glycine database site, called "LegumeBase".