Nanoscale Analysis of Frozen Water by Atom Probe Tomography Using Graphene Encapsulation and Cryo-Workflows.

There has been an increasing interest in atom probe tomography (APT) to characterize hydrated and biological materials. A major benefit of APT compared to microscopy techniques more commonly used in biology is its combination of outstanding three-dimensional (3D) spatial resolution and mass sensitivity. APT has already been successfully used to characterize biominerals, revealing key structural information at the atomic scale, however there are many challenges inherent to the analysis of soft hydrated materials. New preparation protocols, often involving specimen preparation and transfer at cryogenic temperature, enable APT analysis of hydrated materials and have the potential to enable 3D atomic scale characterization of biological materials in the near-native hydrated state. In this study, samples of pure water at the tips of tungsten needle specimens were prepared at room temperature by graphene encapsulation. A comparative study was conducted where specimens were transferred at either room temperature or cryo-temperature and analyzed by APT by varying the flight path and pulsing mode. The differences between the analysis workflows are presented along with recommendations for future studies, and the compatibility between graphene coating and cryogenic workflows is demonstrated.

Comprehensive Two-Dimensional Gas Chromatography with Peak Tracking for Screening of Constituent Biodegradation in Petroleum UVCB Substances.

Petroleum substances, as archetypical UVCBs (substances of unknown or variable composition, complex reaction products, or biological substances), pose a challenge for chemical risk assessment as they contain hundreds to thousands of individual constituents. It is particularly challenging to determine the biodegradability of petroleum substances since each constituent behaves differently. Testing the whole substance provides an average biodegradation, but it would be effectively impossible to obtain all constituents and test them individually. To overcome this challenge, comprehensive two-dimensional gas chromatography (GC × GC) in combination with advanced data-handling algorithms was applied to track and calculate degradation half-times (DT50s) of individual constituents in two dispersed middle distillate gas oils in seawater. By tracking >1000 peaks (representing ∼53-54% of the total mass across the entire chromatographic area), known biodegradation patterns of oil constituents were confirmed and extended to include many hundreds not currently investigated by traditional one-dimensional GC methods. Approximately 95% of the total tracked peak mass biodegraded after 64 days. By tracking the microbial community evolution, a correlation between the presence of functional microbial communities and the observed progression of DT50s between chemical classes was demonstrated. This approach could be used to screen the persistence of GC × GC-amenable constituents of petroleum substance UVCBs.

Methods and Research Hotspots of Forensic Kinship Testing.

Kinship testing is widely needed in forensic science practice. This paper reviews the definitions of common concepts, and summarizes the basic principles, advantages and disadvantages, and application scope of kinship analysis methods, including identity by state (IBS) method, likelihood ratio (LR) method, method of moment (MoM), and identity by descent (IBD) segment method. This paper also discusses the research hotspots of challenging kinship testing, complex kinship testing, forensic genetic genealogy analysis, and non-human biological samples.

Collection and use of human materials during TB clinical research; a review of practices.

BACKGROUND: Human biological materials are usually stored for possible future use in research because they preserve valuable biological information, save time and resources, which would have been spent on collection of fresh samples. However, use of these materials may pose ethical challenges such as unauthorized disclosure of genetic information, which can result in dire consequences for individuals or communities including discrimination, stigma, and psychological harm; has biosecurity implications; and loss of control or ownership of samples or data. To understand these problems better, we evaluated the extent to which tuberculosis (TB) clinical research protocols that were used to collect and store biological materials for future use conform to the requirements stated in the Uganda national guidelines for research involving humans as participants. METHODS: This was a retrospective review of TB clinical research projects approved by the Uganda National Council for Science and Technology (UNCST) from 2011 to 2015, to examine whether they fulfilled the requirements for ethical collection and use of human materials. Data were abstracted through review of the project protocols using a template developed based on the informed consent and the Materials Transfer Agreement (MTA) requirements in the national guidelines. RESULTS: Out of 55 research protocols reviewed, most of the protocols 83.6% had been used to collect the stored samples (sputum, blood and sometimes urine), 28% had a section on specimen collection and 24% mentioned ownership of the biological materials. With respect to review of the consent forms used in the studies that stored materials for future use, only 9% of the protocols had a separate consent form for storage of materials, 4.5% of the consent forms explained the risks, 11.4% explained the purpose of the study while 6.8% mentioned the place of storage for the collected materials. CONCLUSION: Many of the studies reviewed did not meet the requirements for collection and storage of biological materials contained in the national guidelines, which indicates a need to additional training on this topic.

Calcite Nanotuned Chitinous Skeletons of Giant Ianthella basta Marine Demosponge.

Marine sponges were among the first multicellular organisms on our planet and have survived to this day thanks to their unique mechanisms of chemical defense and the specific design of their skeletons, which have been optimized over millions of years of evolution to effectively inhabit the aquatic environment. In this work, we carried out studies to elucidate the nature and nanostructural organization of three-dimensional skeletal microfibers of the giant marine demosponge Ianthella basta, the body of which is a micro-reticular, durable structure that determines the ideal filtration function of this organism. For the first time, using the battery of analytical tools including three-dimensional micro-X-ray Fluorescence (3D-µXRF), X-ray diffraction (XRD), infra-red (FTIR), Raman and Near Edge X-ray Fine Structure (NEXAFS) spectroscopy, we have shown that biomineral calcite is responsible for nano-tuning the skeletal fibers of this sponge species. This is the first report on the presence of a calcitic mineral phase in representatives of verongiid sponges which belong to the class Demospongiae. Our experimental data suggest a possible role for structural amino polysaccharide chitin as a template for calcification. Our study suggests further experiments to elucidate both the origin of calcium carbonate inside the skeleton of this sponge and the mechanisms of biomineralization in the surface layers of chitin microfibers saturated with bromotyrosines, which have effective antimicrobial properties and are responsible for the chemical defense of this organism. The discovery of the calcified phase in the chitinous template of I. basta skeleton is expected to broaden the knowledge in biomineralization science where the calcium carbonate is regarded as a valuable material for applications in biomedicine, environmental science, and even in civil engineering.

Ethical issues of the research and practice in forensic genetics.

Forensic genetics mainly uses human biological samples as the objects, solves the identification of biological materials related to law by detecting genetic information, provides clues for investigation and evidences for trial, thus facing many ethical issues. This paper put forward the ethical principles in forensic genetics research and practice, and discussed the ethical issues in sample collection, forensic DNA phenotyping, forensic genetic genealogy analysis, forensic DNA database development, paternity and kinship testing, and research data sharing. We suggest that specific ethical requirements should be formulated, the ethical review system should be established for forensic genetics and ethical training for practitioners should be strengthened.

Detection of tumor suppressor protein p53 with special emphasis on biosensors: A review.

Cancer is a general word, which specifies a cluster of diseases affecting almost every-body part. Cancer is a second leading cause of death, globally. The tumor suppressor protein p53 is known to play a vital role in prevention of cancer. The enhanced and active form of p53 controls target gene expression through binding with DNA response elements (REs) and thus inhibits tumor cell growth. p53 is found mutated in more than 50% of the cancers. The wide mutation spectrum of p53 gene underlies the process of tumor development. Hence, the accurate quantification of p53 protein levels has great importance in early diagnosis of cancer. The biosensors are the tools, which convert biological interactions into readout signals. These are the most simple, sensitive, specific, rapid and precise devices used for determination of altered protein levels. Hence, Bio sensing methods have great potential as a diagnostic tool for determination of p53 protein. This review describes the screening of most recent and different types of bio sensing approaches, reported for detection of p53. The review also discusses the necessity of biomarker based bio-sensing methods for early diagnosis of cancer. The overall aim of this review is to advance the future analytical approaches of p53 biosensors.

Electrochemical Approach for Isolation of Chitin from the Skeleton of the Black Coral Cirrhipathes sp. (Antipatharia).

The development of novel and effective methods for the isolation of chitin, which remains one of the fundamental aminopolysaccharides within skeletal structures of diverse marine invertebrates, is still relevant. In contrast to numerous studies on chitin extraction from crustaceans, mollusks and sponges, there are only a few reports concerning its isolation from corals, and especially black corals (Antipatharia). In this work, we report the stepwise isolation and identification of chitin from Cirrhipathes sp. (Antipatharia, Antipathidae) for the first time. The proposed method, aiming at the extraction of the chitinous scaffold from the skeleton of black coral species, combined a well-known chemical treatment with in situ electrolysis, using a concentrated Na2SO4 aqueous solution as the electrolyte. This novel method allows the isolation of α-chitin in the form of a microporous membrane-like material. Moreover, the extracted chitinous scaffold, with a well-preserved, unique pore distribution, has been extracted in an astoundingly short time (12 h) compared to the earlier reported attempts at chitin isolation from Antipatharia corals.

Biosynthesis of Polyhydroxyalkanoates (PHAs) by the Valorization of Biomass and Synthetic Waste.

Synthetic pollutants are a looming threat to the entire ecosystem, including wildlife, the environment, and human health. Polyhydroxyalkanoates (PHAs) are natural biodegradable microbial polymers with a promising potential to replace synthetic plastics. This research is focused on devising a sustainable approach to produce PHAs by a new microbial strain using untreated synthetic plastics and lignocellulosic biomass. For experiments, 47 soil samples and 18 effluent samples were collected from various areas of Punjab, Pakistan. The samples were primarily screened for PHA detection on agar medium containing Nile blue A stain. The PHA positive bacterial isolates showed prominent orange-yellow fluorescence on irradiation with UV light. They were further screened for PHA estimation by submerged fermentation in the culture broth. Bacterial isolate 16a produced maximum PHA and was identified by 16S rRNA sequencing. It was identified as Stenotrophomonas maltophilia HA-16 (MN240936), reported first time for PHA production. Basic fermentation parameters, such as incubation time, temperature, and pH were optimized for PHA production. Wood chips, cardboard cutouts, plastic bottle cutouts, shredded polystyrene cups, and plastic bags were optimized as alternative sustainable carbon sources for the production of PHAs. A vital finding of this study was the yield obtained by using plastic bags, i.e., 68.24 ± 0.27%. The effective use of plastic and lignocellulosic waste in the cultivation medium for the microbial production of PHA by a novel bacterial strain is discussed in the current study.

Bacterially Produced, Nacre-Inspired Composite Materials.

The impressive mechanical properties of natural composites, such as nacre, arise from their multiscale hierarchical structures, which span from nano- to macroscale and lead to effective energy dissipation. While some synthetic bioinspired materials have achieved the toughness of natural nacre, current production methods are complex and typically involve toxic chemicals, extreme temperatures, and/or high pressures. Here, the exclusive use of bacteria to produce nacre-inspired layered calcium carbonate-polyglutamate composite materials that reach and exceed the toughness of natural nacre, while additionally exhibiting high extensibility and maintaining high stiffness, is introduced. The extensive diversity of bacterial metabolic abilities and the possibility of genetic engineering allows for the creation of a library of bacterially produced, cost-effective, and eco-friendly composite materials.

The French glioblastoma biobank (FGB): a national clinicobiological database.

BACKGROUND: Glioblastomas (GB) are the most common and lethal primary brain tumors. Significant progress has been made toward identifying potential risk factors for GB and diagnostic and prognostic biomarkers. However, the current standard of care for newly diagnosed GB, the Stupp protocol, has remained unchanged for over a decade. Large-scale translational programs based on a large clinicobiological database are required to improve our understanding of GB biology, potentially facilitating the development of personalized and specifically targeted therapies. With this goal in mind, a well-annotated clinicobiological database housing data and samples from GB patients has been set up in France: the French GB biobank (FGB). METHODS: The biobank contains data and samples from adult GB patients from 24 centers in France providing written informed consent. Clinical and biomaterial data are stored in anonymized certified electronic case report forms. Biological samples (including frozen and formalin-fixed paraffin-embedded tumor tissues, blood samples, and hair) are conserved in certified biological resource centers or tumor tissue banks at each participating center. RESULTS: Clinical data and biological materials have been collected for 1087 GB patients. A complete set of samples (tumor, blood and hair) is available for 66%, and at least one frozen tumor sample is available for 88% of the GB patients. CONCLUSIONS: This large biobank is unique in Europe and can support the large-scale translational projects required to improve GB care. Additional biological materials, such as peritumoral brain zone and fecal samples, will be collected in the future, to respond to research needs.

New Source of 3D Chitin Scaffolds: The Red Sea Demosponge Pseudoceratina arabica (Pseudoceratinidae, Verongiida).

The bioactive bromotyrosine-derived alkaloids and unique morphologically-defined fibrous skeleton of chitin origin have been found recently in marine demosponges of the order Verongiida. The sophisticated three-dimensional (3D) structure of skeletal chitinous scaffolds supported their use in biomedicine, tissue engineering as well as in diverse modern technologies. The goal of this study was the screening of new species of the order Verongiida to find another renewable source of naturally prefabricated 3D chitinous scaffolds. Special attention was paid to demosponge species, which could be farmed on large scale using marine aquaculture methods. In this study, the demosponge Pseudoceratina arabica collected in the coastal waters of the Egyptian Red Sea was examined as a potential source of chitin for the first time. Various bioanalytical tools including scanning electron microscopy (SEM), fluorescence microscopy, FTIR analysis, Calcofluor white staining, electrospray ionization mass spectrometry (ESI-MS), as well as a chitinase digestion assay were successfully used to confirm the discovery of α-chitin within the skeleton of P. arabica. The current finding should make an important contribution to the field of application of this verongiid sponge as a novel renewable source of biologically-active metabolites and chitin, which are important for development of the blue biotechnology especially in marine oriented biomedicine.

Using the samples of human biological materials in the criminal procedure: the practice of the european court of human rights

Introduction: The use of modern advances in medicine to investigate crimes has caused a number of problems that require scientific reflection. In particular, today there are quite acute questions: medical intervention without the person's consent; forced sampling of human biological materials; clinical methods, the use of which in the biological samples taking will not be regarded as violation of international standards of human rights protection; the correlation of the need for the formation of DNA profile databases and the right of the person to non-disclosure of medical information. The aim: The aim of this work is to identify and analyze the key points of the European Court of Human Rights (hereinafter referred to as the ECHR) regarding the peculiarities of retention and use of human biological material samples in the investigation of crimes, and the retention of such materials after the completion of the investigation and trial. Material and methods: In the preparation of the article, scientific works, the provisions of international normative acts regulating the use of human biological materials as well as the practice of the ECHR concerning the use of human biological materials in the investigation of crimes were used (8 decisions were analyzed in which the ECHR concerned the use of biological samples or related issues). In the research process to achieve the goal, a complex of general scientific and special methods of cognition was used, in particular, the comparative legal method, the system and structural method, the method of generalization, the method of analysis and synthesis, etc. Review: The positions of the ECHR concerning the following were distinguished and generalized: a) the criteria for the permissibility of compulsory medical intervention for taking of human biological material within the framework of the crime investigation; b) the possibilities of spreading the right not to incriminate oneself on the compulsory taking of human biological materials samples; c) the retention features of cell samples and DNA information in the context of respect for the right to non-interference in the person's private life. Conclusions: Obtaining and using the human material for the investigation of crimes are not a violation of the European Convention on Human Rights (hereinafter ­ the Convention), subject to the requirements stated in the practice of the ECHR.

Determination of thiocyanate as a biomarker of tobacco smoke constituents in selected biological materials of human origin.

In order to protect human health, it is necessary to biomonitor toxic substances originating from tobacco smoke in biological materials sampled from persons with different exposures to tobacco smoke constituents. Thiocyanate anion is a biomarker of exposure to tobacco smoke components which is characterized by a relatively long half-life in the human body, i.e. 6 days. In this work, we present the results of thiocyanate determinations performed on samples of placenta, meconium, saliva, breast milk, sweat and blood. The placenta samples were subjected to accelerated solvent extraction with water. The thiocyanate concentrations were determined using ion chromatography. The analyzed biological materials were compared with regard to their applicability for biomonitoring toxic substances originating from tobacco smoke. The highest mean concentrations of thiocyanate were observed in the samples of biological materials collected from active smokers.

Quantitative analysis of hydrogen peroxide with special emphasis on biosensors.

Determination of hydrogen peroxide (H2O2) has become essential in pharmaceutical, biological, clinical and environmental studies. The conventional detection methods of H2O2 such as colourimetry, titration, chromatography, spectrophotometry, fluorimetry, chemiluminescence have limited success, due to their poor selectivity and sensitivity, long analysis time and lack of long-term reliability and reproducibility. The biosensors overcome these limitations because of their simplicity, rapidity, selectivity and high sensitivity. This review describes the principle, analytic parameters, merits and demerits of various methods of H2O2 determination with special emphasis on biosensors. The classification of biosensors based on various materials/nanomaterials and electrodes have been described in detail. The recent advances in vivo sensing and bio-sensing of H2O2 by hemoglobin nanoparticles are also presented. The significant challenges and future perspective for highly selective H2O2 detection are discussed.

The biomechanics of seed germination.

From a biomechanical perspective, the completion of seed (and fruit) germination depends on the balance of two opposing forces: the growth potential of the embryonic axis (radicle-hypocotyl growth zone) and the restraint of the seed-covering layers (endosperm, testa, and pericarp). The diverse seed tissues are composite materials which differ in their dynamic properties based on their distinct cell wall composition and water uptake capacities. The biomechanics of embryo cell growth during seed germination depend on irreversible cell wall loosening followed by water uptake due to the decreasing turgor, and this leads to embryo elongation and eventually radicle emergence. Endosperm weakening as a prerequisite for radicle emergence is a widespread phenomenon among angiosperms. Research into the biochemistry and biomechanics of endosperm weakening has demonstrated that the reduction in puncture force of a seed's micropylar endosperm is environmentally and hormonally regulated and involves tissue-specific expression of cell wall remodelling proteins such as expansins, diverse hydrolases, and the production of directly acting apoplastic reactive oxygen. The endosperm-weakening biomechanics and its underlying cell wall biochemistry differ between the micropylar (ME) and chalazal (CE) endosperm domains. In the ME, they involve cell wall loosening, cell separation, and programmed cell death to provide decreased and localized ME tissue resistance, autolysis, and finally the formation of an ME hole required for radicle emergence. Future work will further unravel the molecular mechanisms, environmental regulation, and evolution of the diverse biomechanical cell wall changes underpinning the control of germination by endosperm weakening.

Past, Present, and Future of Informed Consent in Pain and Genomics Research: Challenges Facing Global Medical Community.

In recent decades, there has been a revision of the role of institutional review boards with the intention of protecting human subjects from harm and exploitation in research. Informed consent aims to protect the subject by explaining all of the benefits and risks associated with a specific research project. To date, there has not been a review published analyzing issues of informed consent in research in the field of genetic/Omics in subjects with chronic pain, and the current review aims to fill that gap in the ethical aspects of such investigation. Despite the extensive discussion on ethical challenges unique to the field of genetic/Omics, this is the first attempt at addressing ethical challenges regarding Informed Consent Forms for pain research as the primary focus. We see this contribution as an important one, for while ethical issues are too often ignored in pain research in general, the numerous arising ethical issues that are unique to pain genetic/Omics suggest that researchers in the field need to pay even greater attention to the rights of subjects/patients. This article presents the work of the Ethic Committee of the Pain-Omics Group (www.painomics.eu), a consortium of 11 centers that is running the Pain-Omics project funded by the European Community in the 7th Framework Program theme (HEALTH.2013.2.2.1-5-Understanding and controlling pain). The Ethic Committee is composed of 1 member of each group of the consortium as well as key opinion leaders in the field of ethics and pain more generally.

Nanoelectromechanical Chip (NELMEC) Combination of Nanoelectronics and Microfluidics to Diagnose Epithelial and Mesenchymal Circulating Tumor Cells from Leukocytes.

An integrated nano-electromechanical chip (NELMEC) has been developed for the label-free distinguishing of both epithelial and mesenchymal circulating tumor cells (ECTCs and MCTCs, respectively) from white blood cells (WBCs). This nanoelectronic microfluidic chip fabricated by silicon micromachining can trap large single cells (>12 µm) at the opening of the analysis microchannel arrays. The nature of the captured cells is detected using silicon nanograss (SiNG) electrodes patterned at the entrance of the channels. There is an observable difference between the membrane capacitance of the ECTCs and MCTCs and that of WBCs (measured using SiNG electrodes), which is the key indication for our diagnosis. The NELMEC chip not only solves the problem of the size overlap between CTCs and WBCs but also detects MCTCs without the need for any markers or tagging processes, which has been an important problem in previously reported CTC detection systems. The great conductivity of the gold-coated SiNG nanocontacts as well as their safe penetration into the membrane of captured cells, facilitate a precise and direct signal extraction to distinguish the type of captured cell. The results achieved from epithelial (MCF-7) and mesenchymal (MDA-MB231) breast cancer cells circulated in unprocessed blood suggest the significant applications for these diagnostic abilities of NELMEC.

Synthetic biology meets bioprinting: enabling technologies for humans on Mars (and Earth).

Human exploration off planet is severely limited by the cost of launching materials into space and by re-supply. Thus materials brought from Earth must be light, stable and reliable at destination. Using traditional approaches, a lunar or Mars base would require either transporting a hefty store of metals or heavy manufacturing equipment and construction materials for in situ extraction; both would severely limit any other mission objectives. Long-term human space presence requires periodic replenishment, adding a massive cost overhead. Even robotic missions often sacrifice science goals for heavy radiation and thermal protection. Biology has the potential to solve these problems because life can replicate and repair itself, and perform a wide variety of chemical reactions including making food, fuel and materials. Synthetic biology enhances and expands life's evolved repertoire. Using organisms as feedstock, additive manufacturing through bioprinting will make possible the dream of producing bespoke tools, food, smart fabrics and even replacement organs on demand. This new approach and the resulting novel products will enable human exploration and settlement on Mars, while providing new manufacturing approaches for life on Earth.

Managing Human Tissue Transfer Across National Boundaries - An Approach from an Institution in South Africa.

With biobank research on the increase and the history of exploitation in Africa, it has become necessary to manage the transfer of human tissues across national boundaries. There are many accepted templates of Material Transfer Agreements (MTAs) that currently exist internationally. However, these templates do not address the specific concerns of South Africa and even of Africa as a continent. This article will examine three significantly important ethico-legal concepts that were deliberated and carefully adapted by a South African Institution to suit the transfer of Human Biological Materials (HBMs) and associated data for biobank research, namely: informed consent; benefit sharing arrangements; and ownership together with intellectual property rights in human tissues. The discussion includes an analysis of current practice; the ethico-legal challenges in the South African/African context; the decisions made with regard to how the related ethico-legal challenges were addressed in the MTA; and justifications for implementing these decisions. The processes considered could be of benefit to other developing world countries who consider it necessary to manage the transfer of HBMs across national boundaries.