NHLBI plans for the promise of cell-based therapies

This article presents the National Heart, Lung and Blood Institute (NHLBI) perspective on the status of cell-based therapies. A summary of current and future NHLBI/National Institutes of Health (NIH) programs is given along with a history of the development of NHLBI/NIH resources to aid the advancement of cell-based therapies. A brief discussion of clinical research programs to utilize cell-based therapies is also included.     

Structural Genomics of Eukaryotic Targets at a Laboratory Scale

Structural genomics programs are distributed worldwide and funded by large institutions such as the NIH in United-States, the RIKEN in Japan or the European Commission through the SPINE network in Europe. Such initiatives, essentially managed by large consortia, led to technology and method developments at the different steps required to produce biological samples compatible with structural studies. Besides specific applications, method developments resulted mainly upon miniaturization and parallelization. The challenge that academic laboratories faces to pursue structural genomics programs is to produce, at a higher rate, protein samples. The Structural Biology and Genomics Department (IGBMC – Illkirch – France) is implicated in a structural genomics program of high eukaryotes whose goal is solving crystal structures of proteins and their complexes (including large complexes) related to human health and biotechnology. To achieve such a challenging goal, the Department has established a medium-throughput pipeline for producing protein samples suitable for structural biology studies. Here, we describe the setting up of our initiative from cloning to crystallization and we demonstrate that structural genomics may be manageable by academic laboratories by strategic investments in robotic and by adapting classical bench protocols and new developments, in particular in the field of protein expression, to parallelization.     

Summary and critique of the new NIH guidelines for recombinant DNA research.

New NIH Guidelines for research involving recombinant DNA (R-DNA) molecules were issued on December 15, 1978. These are composed of four main parts, the first defining R-DNA and specifying prohibitions and exemptions, the second describing physical and biological containment, the third assigning the containment levels for many R-DNA experiments, and the fourth detailing the roles and responsibilities of the investigator, research institutions and NIH. Although the new Guidelines reduce restrictions, principally on those R-DNA experiments that use Escherichia coli K-12 host-vector systems, and exempt from the Guidelines several classes of experiments on prokaryotes that naturally exchange their DNA, most of their provisions are unjustified by the present assessment of the absence of any practical risks; many totally innocuous experiments are unnecessarily restricted and even virtually prohibited mainly because no host-vector systems were officially certified. The term Guidelines is a misnomer since they are mandatory regulations, even without any statutory basis. They impose large but unnecessary bureaucratic burdens on scientists, research institutions, research committees and NIH, and represent unwarranted censorship of basic research, which is antithetical to the creativity of human thought, thus posing serious dangers to the traditional freedom of inquiry.     

National Institutes of Health--supported opportunities in Comparative Medicine

The Comparative Medicine (CM) area of the National Institutes of Health (NIH) is a major source of support for research on laboratory animals, training of laboratory animal specialists, and support of shared, regional animal resources. We present a brief history of CM at NIH and the major mechanisms by which it accomplishes its goals in programs located across the United States.     

Associative brain systems as the behavioral control apparatus based on the dominant and conditioned reflex

The main statements of author's conception concerning the associative brain systems (thalamoparietal and thalamofrontal) as the behaviour control systems are presented. The participation of associative systems in performance of the high brain functions ensures due to the entrance of the whole information spectrum of biological and signal significance into them and to the presence of neuronal plastic mechanisms, the mechanisms for retrieval the whole behaviour programs from the long-term memory and the ability of short-term storing of behaviour programs and estimation of their adequacy on the ground of dominant and conditioning mechanisms.     

A public domain image-analysis program for the single-cell gel-electrophoresis (comet) assay

The single-cell gel electrophoresis (or comet) assay has gained widespread acceptance as a cheap and simple genotoxicity test, but it requires a computer-assisted image-analysis system. As commercial programs are expensive and inflexible, we decided to develop an image-analysis system based on public domain programs and make it publicly available for the scientific community. Our system is based on the scientific image-processing program NIH Image, and was written in its Pascal-like macro language. User interaction was kept as simple as possible, to enable the measurement of a large number of cells with a few keystrokes. Therefore, the time for image analysis is very low, even on slow computers. The comet macro can be obtained from http://mailbox.univie.ac.at/christoph.helma++ +/comet/, NIH Image is available at http://rsb.info.nih.gov/nih-image/. Both programs are free of charge.     

脑源性神经营养因子受体trkB在NIH 3T3细胞上的表达

构建了克隆有大鼠脑源性神经营养因子（BDNF）受体trkB全长基因的真核表达载体pcDNA3.1( )-rat trkB.用脂质体介导法将重组载体转入小鼠NIH3T3细胞,在mRNA和蛋白质水平检测到了trkB基因在用G418筛选到的抗性NIH 3T3细胞中的表达,表达的trkB蛋白定位于细胞膜上。BDNF能够剂量依赖性地促进NIH 3T3－trkB细胞的增殖,说明表达的trkB是有功能的。该表达trkB和NIH3T3细胞为研究BDNF的生理功能、活性测定和从噬菌体展示肽库中筛选BDNF肽提供了一个简便的细胞模型。     

Prospects for using genetic transformation for improved SIT and new biocontrol methods

The genetic manipulation of non-drosophilid insect species is possible by the creation of recombinant DNA constructs that can be integrated into host genomes by several transposon-based vector systems. This technology will allow the development and testing of a variety of systems that can improve existing biological control methods, and the development of new highly efficient methods. For programs such as sterile insect technique (SIT), transgenic strains may include fluorescent protein marker genes for detection of released insects, and conditional gene expression systems that will result in male sterility and female lethality for genetic sexing. Conditional expression systems include the yeast GAL4 system and the bacterial Tet-off and Tet-on systems that can, respectively, negatively or positively regulate expression of genes for lethality or sterility depending on a dietary source of tetracycline. Importantly, strains for male sterility must also incorporate an effective system for genetic sexing, since typically, surviving females would remain fertile. Models for the use of these expression systems and associated genetic material come from studies in Drosophila and, while many of these systems should be transferable to other insects, continued research will be necessary in insects of interest to clone genes, optimize germ-line transformation, and perform vector stability studies and risk assessment for their release as transgenic strains.     

The possible role of information technology in radiotherapy II. The development of a biological dose distribution model in the 3-dimensional treatment planning of brain tumours

OBJECTIVE: Developing a new medical software based on the utilisation of information technology required in 3-dimensional treatment planning and modern radiotherapy. METHODS: The physical dose distribution programs were converted into biological meaning with the insertion of biological equivalence equations based on LQ model. Biological dose distributions and biological dose-volume histograms were generated. The treatment plans of a brain tumour patient were investigated to determine the dose burdening of the normal central nervous system tissues. RESULTS: Employing 3D conformal method, the dose of the vital mid-line structures decreased significantly, which possesses a more meaningful biological importance. Different treatment plans and different fractionation regimens could be compared to each other by utilising this kind of biological model. CONCLUSION: By employing information technology we succeeded in establishing a theoretical biological dose distribution system that could be visualised. The advantages of 3D treatment planning proved unambiguous. In the future this method will probably be suitable to choose the best therapeutic regimens.     

Two accurate sequence,structure, and phylogenetic template-based RNA alignment systems

Background

The analysis of RNA sequences, once a small niche field for a small collection of scientists whose primary emphasis was the structure and function of a few RNA molecules, has grown most significantly with the realizations that 1) RNA is implicated in many more functions within the cell, and 2) the analysis of ribosomal RNA sequences is revealing more about the microbial ecology within all biological and environmental systems. The accurate and rapid alignment of these RNA sequences is essential to decipher the maximum amount of information from this data.

Methods

Two computer systems that utilize the Gutell lab's RNA Comparative Analysis Database (rCAD) were developed to align sequences to an existing template alignment available at the Gutell lab's Comparative RNA Web (CRW) Site. Multiple dimensions of cross-indexed information are contained within the relational database - rCAD, including sequence alignments, the NCBI phylogenetic tree, and comparative secondary structure information for each aligned sequence. The first program, CRWAlign-1 creates a phylogenetic-based sequence profile for each column in the alignment. The second program, CRWAlign-2 creates a profile based on phylogenetic, secondary structure, and sequence information. Both programs utilize their profiles to align new sequences into the template alignment.

Results

The accuracies of the two CRWAlign programs were compared with the best template-based rRNA alignment programs and the best de-novo alignment programs. We have compared our programs with a total of eight alternative alignment methods on different sets of 16S rRNA alignments with sequence percent identities ranging from 50% to 100%. Both CRWAlign programs were superior to these other programs in accuracy and speed.

Conclusions

Both CRWAlign programs can be used to align the very extensive amount of RNA sequencing that is generated due to the rapid next-generation sequencing technology. This latter technology is augmenting the new paradigm that RNA is intimately implicated in a significant number of functions within the cell. In addition, the use of bacterial 16S rRNA sequencing in the identification of the microbiome in many different environmental systems creates a need for rapid and highly accurate alignment of bacterial 16S rRNA sequences.

     

Constraints to the implementation of biological control in Sri Lanka

Sri Lanka is a tropical island with a rich diversity of arthropods, with many species of indigenous natural enemies of economic pests. However, no extensive island wide surveys have been carried out for natural enemies of major crop ecosystems and only a few of the indigenous natural enemies are reported useful for augmentation biological pest control by massive field releases of laboratory-produced insects. Most successful biological control programs on the island are importation (i.e. classical) biological control programs, where established exotic natural enemies control certain pest populations in valuable crops. There is growing interest in the use of native natural enemies in pest management, thus creating a need for intensive research on the ecology of indigenous natural enemies and development of infrastructure and technology to produce natural enemies for augmentation. This paper examines constraints and opportunities for implementation of biological control in Sri Lanka.     

干细胞因子逆转录病毒表达载体的构建及体外性质研究

目的通过逆转录病毒介导两种类型人干细胞因子在NIH3T3细胞中稳定表达,并研究它们对白血病细胞的作用。方法用DNA重组技术构建并鉴定可溶型及膜结合型干细胞因子的重组逆转录病毒表达载体MSCV—PGK—GFP—sSCF、MSCV—PGK—GFP—mSCF,与空载体对照MSCV—PGK—GFP分别转染Phoenix细胞包装病毒,并感染NIH3T3细胞,流式分选术获得3种阳性细胞,CCK8法分别检测与其共培养的K562细胞的增殖情况。结果成功构建了sSCF、mSCF逆转录病毒表达载体;经Phoenix包装的重组及对照逆转录病毒成功感染NIH3T3细胞,获得了稳定表达细胞株NIH3T3-S、NIH3T3-M和对照细胞株NIH3T3-V。共培养中NIH3T3-S、NIH3T3-M均可促进K562细胞的增殖,且在低血清条件下,NIH3T3-M的作用高于NIH3T3-S。结论可溶性及膜结合SCF分别通过旁分泌和并置性作用促进白血病细胞的增殖。     

Plant volatiles: new perspectives for research in Brazil

Agroecosystems consist on complex trophic relationships among host plants, herbivores and their natural enemies. This article reviews the research of plant volatiles in Brazil, in order to determine multiple resistance mechanisms of economically important crops and to contribute to the understanding of insect-plant interactions. Most pest management programs, including chemical and biological control, do not consider the impact of these chemicals on herbivores and their natural enemies. Alternative control methods are being developed in order to improve our understanding on the endogenous mechanisms of plant induced defenses against phytophagous arthropods. The use of plant volatiles technology as an additional tool in integrated pest management programs would offer a new and environmentally sound approach to crop protection. This technique involves the development of baits that attract beneficial organisms and the manipulation of biochemical processes that induce and regulate plant defenses, key factors in the improvement of control programs against economically important pests. The elucidation of the mechanisms involved in the indirect defenses of plants will result in useful tools for biological control of crop pests.     

Mitochondrial DNA from colorectal cancer cells promotes the malignant phenotype of NIH3T3 cells

We investigated the potential role of mitochondrial DNA (mtDNA) in colorectal carcinogenesis by constructing a eukaryotic expression vector of the mitochondrial D-loop gene from colorectal cancer cell SW480 and transfected NIH3T3 cells. The NIH3T3/SW480 cells exhibited a significantly increased growth rate and colony formation rate, and also had a decreased apoptotic rate. Polyploidy and aberrant chromosomes were detected in the NIH3T3/SW480 cells by chromosome karyotype analysis. Our results suggested that mtDNA from colorectal cancer cells promotes the malignant phenotype of NIH3T3 cells. Further study of the biological functions of NIH3T3/SW480 cells might be helpful in understanding the role of mtDNA in colorectal carcinogenesis.     

Synthetic biology: ethical ramifications 2009

During 2007 and 2008 synthetic biology moved from the manifesto stage to research programs. As of 2009, synthetic biology is ramifying; to ramify means to produce differentiated trajectories from previous determinations. From its inception, most of the players in synthetic biology agreed on the need for (a) rationalized design and construction of new biological parts, devices, and systems as well as (b) the re-design of natural biological systems for specified purposes, and that (c) the versatility of designed biological systems makes them suitable to address such challenges as renewable energy, the production of inexpensive drugs, and environmental remediation, as well as providing a catalyst for further growth of biotechnology. What is understood by these goals, however, is diverse. Those assorted understandings are currently contributing to different ramifications of synthetic biology. The Berkeley Human Practices Lab, led by Paul Rabinow, is currently devoting its efforts to documenting and analyzing these ramifications as they emerge.     

PSP94-TNFαD11a融合基因在NIH3T3细胞中的表达及其产物活性分析

 为了分析 PSP94- TNFαD1 1 a融合基因的表达和表达产物的生物学活性 ,将含该融合基因的质粒 pc DNA- PSP94- TNFα D1 1 a转染 NIH3T3细胞 ,72 h后收集细胞培养上清 ,并提取细胞总RNA,经 RT- PCR,得到与目的基因长度相符合的 c DNA片段 ;以 PSP94c DNA为探针 ,对 RT-PCR产物进行 Southern印迹分析 .结果表明 :转染 PSP94- TNFαD1 1 a融合基因的 NIH3T3细胞 ,其 RT- PCR产物杂交信号为阳性 .细胞培养上清用 TNF抗体行 Western印迹和 ELISA分析 ,检测结果为阳性 .生物学活性分析表明 ,细胞培养上清不仅具有 PSP94抑制人前列腺癌细胞 PC- 3生长的活性 ,而且显示出 TNFα对 L92 9细胞的细胞毒作用 .以上结果表明 ,pc DNA- PSP94- TNFαD1 1 a质粒能够正确表达目的基因 PSP94- TNFα D1 1 a,且表达的 PSP94- TNFαD1 1 a融合蛋白具有预期的双重生物学活性 .     

Interactome Mapping: Using Protein Microarray Technology to Reconstruct Diverse Protein Networks

A major focus of systems biology is to characterize interactions between cellular components, in order to develop an accurate picture of the intricate networks within biological systems. Over the past decade, protein microarrays have greatly contributed to advances in proteomics and are becoming an important platform for systems biology. Protein microarrays are highly flexible, ranging from large-scale proteome microarrays to smaller customizable microarrays, making the technology amenable for detection of a broad spectrum of biochemical properties of proteins. In this article, we will focus on the numerous studies that have utilized protein microarrays to reconstruct biological networks including protein-DNA interactions, posttranslational protein modifications (PTMs), lectin-glycan recognition, pathogen-host interactions and hierarchical signaling cascades. The diversity in applications allows for integration of interaction data from numerous molecular classes and cellular states, providing insight into the structure of complex biological systems. We will also discuss emerging applications and future directions of protein microarray technology in the global frontier.     

NIH Image to ImageJ: 25 years of image analysis

For the past 25 years NIH Image and ImageJ software have been pioneers as open tools for the analysis of scientific images. We discuss the origins, challenges and solutions of these two programs, and how their history can serve to advise and inform other software projects.