Molecular Phenotyping by Proteomic Pattern Analysis in Arabidopsis thaliana

We are conducting a large scale functional analysis of plant genes utilizing the promoter trap lines and proteomic analyses as a part of the Crop functional genomics research program of Korea. Here, I describe the progresses we have made during last 2.5 years and a future plan.     

Web Resources for Stem Cell Research

In this short review, we have presented a brief overview on major web resources relevant to stem cell research. To facilitate more efficient use of these resources, we have provided a preliminary rating based on our own user experience of the overall quality for each resource. We plan to update the information on an annual basis.     

Biological Databases for Hematology Research

With the advances of genome-wide sequencing technologies and bioinformatics approaches, a large number of datasets of normal and malignant erythropoiesis have been gener-ated and made public to researchers around the world. Collection and integration of these datasets greatly facilitate basic research and clinical diagnosis and treatment of blood disorders. Here we provide a brief introduction of the most popular omics data resources of normal and malignant hematopoiesis, including some integrated web tools, to help users get better equipped to perform common analyses. We hope this review will promote the awareness and facilitate the usage of public database resources in the hematology research.     

A dermatoglyphic study of the Kavalan aboriginal population of Taiwan

By the 1970s, a number of dermatoglyphic studies of Taiwan aborigines (Gaoshan nationality) had been published, however in each only a few dermatoglyphic variables were addressed. Since that time, little new research has been conducted. In this study, we collected and analyzed the dermatoglyphs of 100 individuals of Kavalan, a Taiwan aboriginal population, and we reported a wide range of dermatoglyphic variables including total finger ridge count (TFRC), a-b total ridge count (a-b RC), atd angle and axial triradius percent distance (tPD), and frequencies of fingerprint pattern, palmar thenar pattern, palmar interdigital pattern, palmar hypothenar pattern, and simian line. This study is the first comprehensive dermatoglyphic research of any Taiwan aboriginal population.     

Web Resources for Microbial Data

There are multitudes of web resources that are quite useful for the microbial scientific research community. Here, we provide a brief introduction on some of the most notable microbial web resources and an evaluation of them based upon our own user experience.     

The Methodology of Probe Design with Better Resolution and Less Resistive Donut Probe to Achieve the Best Performance

Probes are the interface between microsystems and bio-cells.The ideal interface is one-to-one interface.Though variousresearch groups have been able to establish some sort of interfaces after many years of research,they are very crude.Neurons aremillions in numbers,whereas the prostheses successfully built so far have only a few hundred probes at best.Creating an ef-fective interface is still far away.Though we have micro-and nano-technologies,we couldn’t build a prosthesis with an effectiveresolution.Main reasons behind it are the type of probe being used and the poor design of the probe.To address this problem,wedeveloped a methodology to design a probe and an array of probes with better resolution and less resistive donut probe.Thismethodology helps us to design a probe optimizing all the parameters.We presented our methodology through a design that iscapable of 70 μm penetration inside the tissue.The tissue heating by our designed probe is only 0.411 °C.We also characterizedthe donut probe,which could be used by any research group to design a donut probe of their specific need.     

Recent Progress Using High-throughput Sequencing Technologies in Plant Molecular Breeding

High-throughput sequencing is a revolutionary technological innovation in DNA sequencing.This technology has an ultra-low cost per base of sequencing and an overwhelmingly high data output.High-throughput sequencing has brought novel research methods and solutions to the research fields of genomics and post-genomics.Furthermore,this technology is leading to a new molecular breeding revolution that has landmark significance for scientific research and enables us to launch multi-level,multi-faceted,and multi-extent studies in the fields of crop genetics,genomics,and crop breeding.In this paper,we review progress in the application of high-throughput sequencing technologies to plant molecular breeding studies.     

The culture and establishment of embryonic germ （EG） cell lines from Chinese mini swine

As a part of a basic research project on Xeno-transplantion, we have been engaged in the derivation of embryonic stem cell lines from Chinese mini swine. Here, we reported for the first time the establishment of two porcine EG cell lines (BPEG1 and BPEG2) from primordial germ cells of genital ridges of a 28 anda 27 d embryos respectively. Their pluripotent nature has been identified by colony morphology, marker characterization as well as by in vitro and in vivo differentiation. These porcine EG cells are potentially useful for further basic studies.     

Foreword

正Between 2011-2013,Zoological Research has released 3 special issues on Primates and Animal Models of Human Diseases.Now,after a year of preparation,we are pleased to release this fourth special issue.In this issue,we compiled12 review,research articles and letters to the editor,each examining different aspects of scientific and medical research using non-primates as an animal model,with a special emphasis on recent developments in genetic,virological,behavioristic and methodological studies.     

THE EFFECT OF CYTOPLASM ON NUCLEAR ACTIVITY AND GENETIC CHARACTERS IN ANIMAL DEVELOPMENT

The present report is a summary of our works, published or unpublished, on the nucleo-cytoplasmic inter-reaction, performed in the past several years. As is well known, there is a tremendous amount of data from both basic and applied research showing nuclear control of development and genetics. On this matter, there is no argument at all. However, it would be a mistake if we belittle the contribution of cytoplasm and insist on that only the nucleus is involved in the control of     

Urimem,a membrane that can store urinary proteins simply and economically,makes the large-scale storage of clinical samples possible

By nature,biomarker is the measurable change associated with a physiological or pathophysiological process.Unlike blood which has mechanisms to minimize changes and to keep the internal environment homeostatic,urine is more likely to reflect changes of the body and is a better biomarker source.Because of its potential in biomarker discovery,urinary proteins should be preserved comprehensively as the duration of the patients’corresponding medical records.Here,we propose a method to adsorb urinary proteins onto a membrane we named Urimem.This simple and inexpensive method requires minimal sample handling,uses no organic solvents,and is environmentally friendly.Urine samples were filtered through the membrane,and urinary proteins were adsorbed onto the membrane.The proteins on the membrane were dried and stored in a vacuum bag,which keeps the protein pattern faithfully preserved.The membrane may even permit storage at room temperature for weeks.Using this simple and inexpensive method,it is possible to begin preserving urine samples from all consenting people.Thus,medical research especially biomarker research can be conducted more economically.Even more objective large-scale prospective studies will be possible.This method has the potential to change the landscape of medical research and medical practice.     

Effects of environmental stressors on stem cells

Environmental toxicants are ubiquitous,and many are known to cause harmful health effects.However,much of what we know or think we know concerning the targets and long-term effects of exposure to environmental stressors is sadly lacking.Toxicant exposure may have health effects that are currently mischaracterized or at least mechanistically incompletely understood.While much of the recent excitement about stem cells(SCs)focuses on their potential as therapeutic agents,they also offer a valuable resource to give us insight into the mechanisms and risks of toxicant effects.Not only as a response to the increasing ethical pressure to reduce animal testing,SC studies allow us valuable insight into the true effects of human exposure to environmental stressors under controlled conditions.We present a review of the history of publications on the effects of environmental stressors on SCs,followed by a consolidation of the literature over the past five years on a subset of key environmental stressors of importance to human health and their effects on both embryonic and tissue SCs.The review will make constructive suggestions as to areas of toxicant research where further studies are needed,as well as making indications of the potential utility for advancing knowledge and directing research on environmental toxicology.     

Activation and signaling of the p38 MAP kinase pathway

The family members of the mitogen-activated protein (MAP) kinases mediate a wide variety of cellular behaviors in response to extracellular stimuli. One of the four main sub-groups, the p38 group of MAP kinases, serve as a nexus for signal transduction and play a vital role in numerous biological processes. In this review, we highlight the known characteristics and components of the p38 pathway along with the mechanism and consequences of p38 activation. We focus on the role of p38 as a signal transduction mediator and examine the evidence linking p38 to inflammation, cell cycle, cell death, development, cell differentiation, senescence and tumorigenesis in specific cell types. Upstream and downstream components of p38 are described and questions remaining to be answered are posed. Finally, we propose several directions for future research on p38.     

Pluripotency of Induced Pluripotent Stem Cells

Induced pluripotent stem （iPS） cells can be generated by forced expression of four pluripotency factors in somatic cells. This has received much attention in recent years since it may offer us a promising donor cell source for cell transplantation therapy. There has been great progress in iPS cell research in the past few years. However, several issues need to be further addressed in the near future before the clinical application of iPS cells, like the immunogenieity of iPS cells, the variability of differentiation potential and most importantly tumor formation of the iPS derivative cells. Here, we review recent progress in research into the pluripotency of iPS cells.     

Pluripotent Stem Cells Models for Huntington＇s Disease： Prospects and Challenges

Pluripotent cellular models have shown great promise in the study of a number of neurological disorders.Several advantages of using a stem cell model include the potential for cells to derive disease relevant neuronal cell types,providing a system for researchers to monitor disease progression during neurogenesis,along with serving as a platform for drug discovery.A number of stem cell derived models have been employed to establish in vitro research models of Huntington’s disease that can be used to investigate cellular pathology and screen for drug and cell-based therapies.Although some progress has been made,there are a number of challenges and limitations that must be overcome before the true potential of this research strategy is achieved.In this article we review current stem cell models that have been reported,as well as discuss the issues that impair these studies.We also highlight the prospective application of Huntington’s disease stem cell models in the development of novel therapeutic strategies and advancement of personalized medicine.     

MicroRNAs in Common Human Diseases

MicroRNAs (miRNAs) are a class of short non-coding RNA molecules that have attracted tremendous attention from the biological and biomedical research communities over the past decade. With over 1900 miRNAs discovered in humans to date, many of them have already been implicated in common human disorders. Facilitated by high-throughput genomics and bioinformatics in conjunction with traditional molecular biology techniques and animal models, miRNA research is now positioned to make the transition from laboratories to clinics to deliver profound benefits to public health. Herein, we overview the progress of miRNA research related to human diseases, as well as the potential for miRNA to becoming the next generation of diagnostics and therapeutics.     

Urine—an untapped goldmine for biomarker discovery?

The past decade witnessed a few biomarkers discovered and validated;however,biomarker research as a whole has not been fruitful as expected.A majority of our efforts has been focused on blood,the dynamic tissue directly connecting every part of the body.Nevertheless,despite all the interest and endeavor spent on it,the blood has failed to deliver sufficient number of clinically valuable biomarkers.Is it possible that we have been barking up the wrong tree?     

Guest Editor＇s Forward

This is the special issue devoted to bioinformatics research in Singapore. Bioinformatics research in Singapore started largely in 1996 when the Bioinformatics Center, National University of Singapore, was formed. With the government＇s efforts to turn Singapore into a powerhouse of biomedical research, the Genome Institute of Singapore and the Bioinformatics Institute of Singapore have been established since 2000. Recently, a bioinformatics research center was also formed in the Nanyang Technological University. Currently, there are a large number of bioinformatics research teams in each of these institutions.