Biomolecular Technology Research Articles

Chronic exposure to low levels of phenanthrene induces histological damage and carcinogenic risk in the uterus of female mice.

Phenanthrene (Phe), a polycyclic aromatic hydrocarbon with low molecular weight, is detected in the environment at high frequency. To study the toxic effects of Phe on the uterine structure and function, female Kunming mice were exposed to Phe (0.05, 0.5, 5ng/mL) for 270days by drinking water. Pathological alterations and their action pathways were analyzed using immunohistochemical and biomolecular technology. Phe significantly increased the percentage of blood vessel area, the number of endometrial neutrophils (indicating the occurrence of inflammation), collagen deposition (indicating fibrosis), and the percentage of Ki-67-positive cells (indicating carcinogenesis) in the uterus. Transcriptome sequencing identified differentially expressed genes that were mainly enriched in some signaling pathways, including inflammation and carcinogenesis, suggesting a carcinogenic risk in the Phe-exposed uterus. Elevated serum estrogen levels and decreased progesterone levels exhibited a disturbance of steroid hormone balance, which might be related to uterine damage. Upregulated protein levels of uterine androgen receptor and estrogen receptor α were linked to the pathological effects. Most of the effects exhibited a nonmonotonic dose response, which might be attributed to the corresponding change in the serum levels of Phe. The results suggest that exposure to low levels of Phe could exert adverse effects on the uterus.

Association study of polymorphisms in miRNA-1687 with growth traits of chickens

Polymorphisms within microRNAs can lead to phenotypic variations in organisms. The purpose of this research was to investigate the potential impact of the pre-miR-1687 single nucleotide polymorphism (SNP) on the economic characteristics of weight and body size in chickens. The SNP was genotyped using matrix-assisted laser desorption/ionization-time of flight mass spectrometry. A linear mixed model was utilized to analyse the associations between the SNP and chicken body size and growth traits. The SNP in the pre-miR-1687 gene was correlated with F2 chicken body weight (BW) at birth and at 4, 6, 8, and 10 weeks of age. The SNP in the gga-miR-1687 gene was correlated with shank length, shank girth, pectoral angle (at 4 weeks), and pelvic breadth (at 8 weeks). Different BW genotypes were observed in the studied flocks. The changes in the secondary structure of pre-miR-1687 and in the free energy values were estimated using online M-fold software. The results serve as a helpful resource for subsequent research on the mechanisms and functions of miRNAs. In addition, the study provides a credible basis for the application of biomolecular technology in poultry breeding.

Emerging Role of Precision Medicine in Diagnosis and Treatment of Chronic Respiratory Disease

Precision medicine is the current approach to managing chronic respiratory diseases, especially asthma and chronic obstructive pulmonary disease (COPD). It involves the evaluation of genetic, environmental, and lifestyle variations for each patient. It requires valid and specific biomarkers obtained through genetic studies, biomolecular technology, and omics-based technology to determine targeted therapies. Asthma and COPD have heterogeneous clinical phenotype variations, and giving one standard treatment for asthma and COPD may not necessarily provide the same effectiveness to other patients. The endotype, a specific molecular mechanism in disease pathogenesis, is essential in phenotype variation. The role of precision medicine in asthma and COPD is to determine endotypes through specific biomarkers and to provide specific targeted therapy for achieving personalized treatment in each patient. The application of precision medicine not only provides precise diagnosis and treatment but also enables early detection in individuals at risk and prevention of progression and exacerbation in asthma and COPD.

First person – François Tyckaert

ABSTRACT First Person is a series of interviews with the first authors of a selection of papers published in Journal of Cell Science, helping early-career researchers promote themselves alongside their papers. François Tyckaert is first author on ‘ Rac1, the actin cytoskeleton and microtubules are key players in clathrin-independent endophilin-A3-mediated endocytosis’, published in JCS. François conducted the research described in this article while a PhD student in Pierre Morsomme's lab at the Louvain Institute of Biomolecular Science and Technology (LIBST), UCLouvain, Louvain-la-Neuve, Belgium. He is now a postdoc in the lab of Henri-François Renard at Namur Research Institute for Life Sciences (NARILIS), UNamur, Namur, Belgium, investigating the regulation of unconventional endocytic mechanisms and their role in cellular physiology.

Case Study: CRISPR 101 – a novel online learning course harnessing innovative ways to teach a complex biomolecular technology

Complex biomolecular technologies revolutionise scientific research. Fully embedding scientific advances in the community requires innovative ways to educate learners on the molecular foundations upon which these technologies are based. In this case study, we present the conception and design of Walter and Eliza Hall Institute of Medical Research (WEHI’s) inaugural wholly online learning course focussed on explaining the revolutionary genome-editing technology, clustered regulatory interspaced palindromic repeats (CRISPR). Utilising WEHI’s strength in bringing science educators and world-leading CRISPR scientists together, we designed a multimodal online resource that introduces learners, without an extensive background in either science or genome editing, to the fundamental concepts of CRISPR technology. Using the online course creation tool, Articulate 360, we guided learners through three modules containing targeted lessons designed to focus on specific learning outcomes. Integrated videos, research articles, interviews, and other resources, allowed for self-paced learning that met various learning style needs. The extensive resources provided opportunities to delve deeper into the content for advanced learners. The effectiveness of the course, evaluated with survey responses collected upon completion of the course, highlighted the ease of use and functionality of the course, and an increased understanding of CRISPR technology after course completion. We anticipate future online learning course development to showcase complex molecular technology that will be valuable for tertiary education, as well as for those in the wider community interested in understanding important advances in biomedicine.

Immunocytochemistry and western blot test for the in-situ detection of biomarkers of osteogenesis

There are two ways that bones can form: intramembranous and endochondral ossification. Specific osteogenic markers, such as insulin-like growth factor (IGF-1), osteocalcin (OCN), Runt-related transcription factor 2 (RUNX2), and osterix (OSX), accompany osteoblast differentiation from an undifferentiated state to a functional state. IGF-1 hormones are the main regulators in growth, differentiation, and apoptosis in cells and tissues mediated by IGF-1 receptors (IGF-1R). Biomolecular technology aims to study nucleic acids and their regulation and expression of proteins. Techniques that can be used when analyzing proteins include the Bradford protein assay, immunocytochemistry, immunohistochemistry, sodium dodecyl sulfate–polyacrylamide gel electrophoresis, and the western blot test. To better understand the biomarkers of osteogenesis, the use of in-situ detection is suggested, such as immunocytochemistry and the western blot test. For this review, the author adhered to the Preferred Reporting Items for Systematic Reviews and Meta-analyses (PRISMA) standards. The research examined 50 articles; only 4 articles were selected for this review. In the immunocytochemical test, IGF-1 expression was found in the nucleus and IGF-1R expression in the cell membrane, and it was found that RUNX2, OSN, and OCN are important for osteogenesis. During the western blot test, it was found that the addition of IGF-1 in dental stem cells could increase the expression of RUNX2, OSX, and OCN proteins. Based on this information, it appears that both immunocytochemistry and western blot tests can detect the main biomarkers of osteogenesis.

The application of oncolytic viruses in cancer therapy.

Oncolytic therapy is a treatment method used to directly combat tumor cells by modifying the genes of naturally occurring low pathogenic viruses to form "rhizobia" virus. By taking the advantage of abnormal signal pathways in cancer cells, it selectively replicates in tumor cells leading to tumor cell lysis and death. At present, clinical studies widely employ biomolecular technology to transform oncolytic viruses to exert stronger oncolytic effects and reduce their adverse reactions. This review summarizes the current progresses and the molecular mechanism of oncolytic viruses towards tumor treatment and management.

Healing the Fundamental Unit of Heredity (Gene Therapy): Current Perspective and What the Future Holds

The ability to make precise adjustments to the human genome has been a goal of healing in which gene also introduces as the fundamental unit of heredity, in biomolecular technology in genetic diseases have opened new knowledge such as gene therapy. Gene therapy is a technique to repair DNA where its usage is to treat the malignancy and inherited genetic diseases. Gene therapy is a choice to the genetic cloth that goals to remedy a sickness this is hard to deal with or perhaps has no treatment. Currently, gene remedy is done in approaches to patients, specifically embryonic cells and somatic cells, every in vivo and ex vivo. Moral considerations with modification of the difficulty's cells and oversight of regulation and reagents want to be taken into consideration within the gene therapy project. Applications for using gene remedies have begun to be widely used, which include in case of maximum cancers, coronary heart disorder, infectious sicknesses, and others. Gene therapy has spread to a wide range of applications then go beyond the modification of genetic disorders. Advances in genetic modification of cancer cells and immunity and the use of viruses and bacteria to control cancer cells have resulted in many clinical trials and product developments for cancer treatment. The miracles and blessings of gene therapy are might believe, but even though they are being studied and developed now and, in the future, so that the desire for gene therapy may be even better future.Keywords: gene therapy, genetic recombination, gene therapy application

Data analysis in complex biomolecular systems

The biomolecular technology progress is directly related to the development of effective methods and algorithms for processing a large amount of information obtained by modern high-throughput experimental equipment. The priority task is the development of promising computational tools for the analysis and interpretation of biophysical information using the methods of big data and computer models. An integrated approach to processing large datasets, which is based on the methods of data analysis and simulation modelling, is proposed. This approach allows to determine the parameters of biophysical and optical processes occurring in complex biomolecular systems. The idea of an integrated approach is to use simulation modelling of biophysical processes occurring in the object of study, comparing simulated and most relevant experimental data selected by dimension reduction methods, determining the characteristics of the investigated processes using data analysis algorithms. The application of the developed approach to the study of bimolecular systems in fluorescence spectroscopy experiments is considered. The effectiveness of the algorithms of the approach was verified by analyzing of simulated and experimental data representing the systems of molecules and proteins. The use of complex analysis increases the efficiency of the study of biophysical systems during the analysis of big data.

Hazards and Detection Techniques of Veterinary Drug Residues in Animal-Origin Food

Veterinary drugs originally used to diagnose, prevent, control and treat animal diseases. However, now some of them can also be mixed into livestock feed as growth promoters. Although most countries have specified animal-derived veterinary drug residue standards, such as the maximum residue limit, withdrawal period and prohibition of some veterinary drugs as growth promoters, there are still some animal-derived products with illegal amount of drug residues. Consequently, long-term intake of products with excessive residues will result in irreversible impacts on human health, livestock industries and natural environment. To minimize these risks, the techniques of drug residues detection plays an important role in guarding food safety of animal products. Moreover, Veterinary drug residue detection technology, according to the author's opinion, can be divided into instrumental method, immunoassay method, biomolecular technology and bio-sensor technology. The purpose of this article is to collect and summarize the existing journal literature current about status, hazards and detection techniques of animal-origin veterinary drug residues so that ordinary readers can briefly understand the research status of the residue detection techniques, farmers can understand the importance of regulating and suitable handling of veterinary drugs, and relevant researchers may know about the emphasized difficulties that need to be overcome in drug residue detection techniques.

Metatranscriptomics: Monitoring Gut Microbiome Activity in Response to Diet

The study of the gut microbiome—the collection of microflora within the intestinal tract—is growing in popularity as associations are found between diet and nutrition, gut microflora activity, and host health and disease. However, current metagenomic and ribosomal profiling approaches are unable to capture changes in activity within the gut microbiome populations. In this environment, shifts in diet or nutritional intake may not result in microbiome population changes, but may instead influence the activity of the existing microbial community. Metatranscriptomics—the study of microbial population activity based on RNA‐seq data—offers detailed data on the gene expression of all microbes within the sampled community. Unfortunately, current approaches for processing raw metatranscriptome data rely either on restricted databases, a fully in‐house analysis server, or use metagenome‐based approaches that have not been fully evaluated for use in processing metatranscriptomic datasets.We have created a new bioinformatics pipeline, SAMSA (Simple Analysis of Metatranscriptome Sequence Annotations), designed specifically for metatranscriptome dataset analysis, with options for either in‐house or external server‐based computational processing. Designed for use by researchers with relatively little bioinformatics experience, SAMSA offers a breakdown of metatranscriptome activity by organism or transcript function, and is fully open source. We have also determined a series of “best practices” for metatranscriptome preprocessing and sequencing for the most accurate analysis results. Using publicly available data, we have demonstrated that SAMSA offers summary analysis of both the organism activity and transcript‐level expression within a metatranscriptome, as well as identifying the most significant expression changes between control and experimental populations. We expect that SAMSA will shed new light on expression changes within the gut microbiome, providing a deeper understanding of how this community reacts to dietary modulation.Support or Funding InformationFunded in part by the Peter J. Shields Endowed Chair in Dairy Food Science (D.M.) S.W. was supported by a fellowship under the Training Program in Biomolecular Technology (NIGMS‐NIH T32‐GM008799) at the University of California, Davis.

Cover Picture: Biotechnology Journal 4/2014

AbstractThis Special Issue on “Biomolecular Technology of Proteins – BioToP” compiles selected peer‐reviewed publications of students from the BioToP PhD program at the Vienna Institute of BioTechnology (VIBT) of the University of Natural Resources and Life Sciences, Vienna, Austria (BOKU) and is edited by Co‐Editorin‐Chief Prof. Alois Jungbauer. The cover represents the interdisciplinary and international character of BioToP. Idea: Andreas Maccani, Dagmar Brugger, Stefan Hofbauer, Vaibhav Jadhav, Gerald Klanert, Daniel Kracher, Iris Krondorfer, Irene Schaffner. Image: Dagmar Brugger.

Editorial: Biomolecular Technology of Proteins – BioToP

Current doctoral students who will be the driving force of science in the future. Christian Obinger, speaker of the BioToP Phd program "Biomolecular Technology of Proteins - BioToP", reviews the articles in this BioToP Special issue.

Biomolecular and clinical practice in malignant pleural mesothelioma and lung cancer: what thoracic surgeons should know

Today, molecular-profile-directed therapy is a guiding principle of modern thoracic oncology. The knowledge of new biomolecular technology applied to the diagnosis, prognosis, and treatment of lung cancer and mesothelioma should be part of the 21st century thoracic surgeons' professional competence. The European Society of Thoracic Surgeons (ESTS) Biology Club aims at providing a comprehensive insight into the basic biology of the diseases we are treating. During the 2013 ESTS Annual Meeting, different experts of the field presented the current knowledge about diagnostic and prognostic biomarkers in malignant pleural mesothelioma including new perspectives as well as the role and potential application of microRNA and genomic sequencing for lung cancer, which are summarized in the present article.

Antibody–Enzyme Fusion Proteins for Cancer Therapy

Advances in biomolecular technology have allowed the development of genetically fused antibody-enzymes. Antibody-enzyme fusion proteins have been used to target tumors for cancer therapy in two ways. In one system, an antibody-enzyme is pretargeted to the tumor followed by administration of an inactive prodrug that is converted to its active form by the pretargeted enzyme. This system has been described as antibody-directed enzyme prodrug therapy. The other system uses antibody-enzyme fusion proteins as direct therapeutics, where the enzyme is toxic in its own right. The key feature in this approach is that the antibody is used to internalize the toxic enzyme into the tumor cell, which activates cell-death processes. This antibody-enzyme system has been largely applied to deliver ribonucleases. This article addresses these two antibody-enzyme targeting strategies for cancer therapy from concept to (pre)clinical trials.

Pathology as the cornerstone of human tissue banking: experiences in the post-genomics era

Unprecedented advances in biomolecular technology have greatly increased the power and precision of analytical tools used in cancer research and have accelerated the drive toward personalised medicine. Human specimens that are analysed using these new and developing technology platforms have emerged as a critical resource for basic and translational research in cancer because they are a direct source of molecular data from which targets for therapy, detection, and prevention are identified. As a result this has stimulated a growing demand for carefully collected, appropriately stored and well-annotated tumour specimens worldwide. This requirement has put pathologists in the centre of the personalised medicine world as providers of information identifying tissues and also as decision makers on what materials should be biobanked, on the preservation conditions, and on the timeline of events that precede preservation and storage. This critical position in the research process places extraordinary demands on all aspects of pathology practice, in particular as pathology laboratories are ultimately key players in delivering new medicines through molecular diagnostics. We present a national biobank network infrastructure that promotes multi-disciplinary research and has pathology underpinning tumour banking in order to facilitate multi-institutional, high throughput genomic studies. This new era of medicine requires a strategic view of ways forward for better integration of pathology, not only as ‘tissue providers’ but also as essential participants in the design, performance, interpretation, and implementation of research and clinical trials.

Introduction

In November 2006, a discussion thread erupted on the online discussion list of the World Archaeological Congress (WAC) concerning the National Geographic Society's Genographic Project (which is also sponsored by IBM and the Waitt Family Foundation). Initiated in 2005, the Genographic Project is designed to study human population movements in the past based on the analysis of DNA samples voluntarily contributed from people around the world. This project was also designed to move beyond the kinds of ethical and other concerns relating to indigenous rights, appropriation, and group consent (to name a few) that led to the demise of its predecessor, the Human Genome Diversity Project, which began in 1991 and continued until the late 1990s. Such projects owe their origins to significant advancements in biomolecular research and technology studies, which have not only resulted in a genetic revolution in archaeology and related studies but also witnessed growing public interest in ancestry tracing through genetic means.

Biomolecular technology for detection, control, and toxicity assessment of EDCs, residual pharmaceutics, and nano-size materials

Prior to testing, soft tissues are usually maintained in different media and additives (solution, air, cryopreservant…) under various environment conditions (temperature, storage duration….). In many cases, results from mechanical tests performed on these stored tissues are supposed to be as closed as possible to the fresh ones. In the present work, cyclic tensile tests were performed with increasing values of strain on porcine skin tissues (excised following the Langer’s lines) to enhance tissues mechanical nonlinearity such as softening behavior and permanent set. Optical methods were used to follow the in-plane strains evolution. These latest values were used as data to simulate the structural behavior of these heterogeneous materials. The numerical simulation is based on the constitutive pseudo-elastic model accounting for the softening behavior as well as the permanent set. As a result, reliable material parameters were extracted from the experiments/model comparison for each storage solution. The result of this study reveals that preservation conditions must be carefully chosen: at low strain the tissues store in fridge in a saline solution during a short time, or in freezer (−80 °C) in water with cryopreservant and the fresh one lead to a similar mechanical response. For larger strain, the freezing (−80 °C) in water with cryopreservant is the only procedure for which the tissue recovers its initial behavior.

Differences of nucleotide and amino acid sequences of nucleoprotein (N) gene between wild-type measles virus and vaccine virus in Indonesia

Background Measles virus is a member of genus morbiliviruswhich belongs to family paramyxovirus with negative, single-strand RNA genome. RNA is packed by nucleocapsid (N) protein.The N protein is very important for RNA replication andtranslation. Abnormality in N protein will induce abnormality invirus replication.Objective This study aimed to explore the differences ofnucleotide sequence of N gene and amino acid sequences of Nprotein between wild-type measles virus (G2, G3 and D9) andvaccine virus (CAM-70, Schwarz and Edmonston-wt)Methods The exctraction and amplification of the gene wereconducted in the laboratory using biomolecular technology. Thegene and protein analysis were conducted using the bioinformatictechnology.Results The results showed that more differences were foundbetween nucleotide sequences of N gene of wild-type measlesvirus against CAM-70 vaccine virus (77 – 79 nucleotides)compared against Schwarz and Edmonston-wt vaccine virus (71-74 nucleotides). Likewise, more differences were also observedbetween amino acid sequences of N protein of wild-type measlesvirus against CAM-70 vaccine virus (18-24 residues) comparedagainst Schwarz and Edmonston-wt vaccine virus (17-23 residues).

Difference of hemaglutinins between wild-type and vaccine measles virus in Indonesia

Background Hemaglutinin (H) protein of measles virus is veryimportant in the process of host cell infection. H protein is alsoable to induce specific antibodies which can neutralize measlesvirus and block the cell infection.Objective This study aimed to explore the nucleotide and aminoacid sequence differences between wild-type measles virus (G2,G3 and D9) with CAM-70, Schwarz and Edmonston-wt vaccinevirus.Methods The exctration and amplification of the gene wereconducted in the laboratory using biomolecular technology. Thegene and protein analysis were conducted using the bioinformatictechnology.Results The results showed that the differences in nucleotidesequences were highest between wild-type virus and CAM-70vaccine virus (76-77 nucleotides), followed by Schwarz (61-64nucleotides) and Edmonston (60-63 nucleotides). The differencesin amino acid sequences were highest between wild-type virusand CAM-70 (24-29 residues), followed by Schwarz (13-20residues) and Edmonston (12-19 residues).Conclusion The Indonesian wild-type measles virus was geneticallycloser to Schwarz vaccine virus than CAM-70 vaccine virus,hence the neutralizing antibodies generated by Schwarz vaccinewere more specific against Indonesian wild-type virus comparedto CAM-70 vaccine.