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NIH Roadmap for Medical Research

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Abstract

The National Institutes of Health (NIH) Roadmap for Medical Research is a collection of far-reaching initiatives designed to transform the Nation's medical research capabilities and improve the translation of research into practice. As described below, the Roadmap consists of three major themes: new pathways to discovery, research teams of the future, and reengineering the clinical research enterprise.
NIH Roadmap for Medical Research
The National Institutes of Health (NIH) Roadmap
for Medical Research is a collection of far-reaching
initiatives designed to transform the Nations medical
research capabilities and improve the translation of
research into practice. As described below, the Roadmap
consists of three major themes: new pathways to dis-
covery, research teams of the future, and reengineering
the clinical research enterprise.
New Pathways to Discovery
The following initiatives within this theme aim to
improve the understanding of complex biological systems
and to develop tools that will advance biomedical research.
Building Blocks, Biological Pathways, and Networks.
Efforts are being made to develop new technologies to
help researchers studying the biological pathways and
networks that facilitate communication among genes,
molecules, and cells. One of the central components
of these networks is the set of proteins encoded by an
organisms genes (i.e., the proteome). Tools are being
developed that will enable researchers to determine, in
real time, the amounts, locations, physiological effects,
and interactions of large numbers of individual pro-
teins within a single cell.
Another focus of this initiative is to provide researchers
with new analytical tools to better understand the
metabolic components and networks within cells. For
example, new technologies may help researchers measure
local concentrations of carbohydrates, lipids, amino
acids, and other metabolites within a single cell or even
a specific part of a single cell. Specific areas of research
emphasis include approaches that are addressing the
widely fluctuating range of metabolite concentrations
and complexity of metabolite mixtures, the vast number
of unidentified compounds present within single sam-
ples, and the dynamic nature of the cell’s entire set of
metabolites. This type of comprehensive information
may pave the way for the development of better meth-
ods to detect metabolic differences between normal and
diseased cells.
Molecular Libraries and Imaging. Small molecules,
often with molecular weights of 500 or below, are
important for researchers studying molecular and cel-
lular functions. Such molecules are valuable for treat-
ing diseases, and most medicines marketed today are
from this class. With small-molecule libraries, biomed-
ical researchers in the public sector can have access to
the large-scale screening necessary to identify small
molecules that can be used as chemical probes for
genes, cells, and metabolic and biochemical pathways.
This will lead to new ways to explore the functions of
genes and signaling pathways in health and disease.
The imaging component of this initiative focuses
on the imaging of molecules or molecular events in
biological systems that span the scale from single cells
to whole organisms. Ultimately, this effort may enable
personalized profiles of cell and tissue function, which
may lead to more individualized approaches to diag-
nosing and treating disease.
Structural Biology. This effort aims to map the molec-
ular shapes of proteins in the body. This involves the
development of rapid, efficient, and dependable meth-
ods to produce protein samples that researchers can
use to determine the three-dimensional structure of a
protein. The new effort is catalyzing what currently is
a time-consuming process into a streamlined routine,
helping researchers clarify the role of protein shape in
health and disease.
Bioinformatics and Computational Biology. These
initiatives are creating a national software engineering
system to evaluate, combine, and visualize the large
amounts of data collected through biomedical research.
Through a computer-based grid, biologists, chemists,
physicists, computer scientists, and physicians any-
where in the country will be able to share and analyze
data using a common set of software tools.
Nanomedicine. An offshoot of nanotechnology,
nanomedicine refers to highly specific medical inter-
vention at the molecular level for curing disease or
repairing damaged tissues, such as bone, muscle, or
nerve. The Nanomedicine Roadmap Initiative calls for
the creation of Nanomedicine Development Centers,
which are focusing on gathering information about the
structures, processes, and networks inside cells. Researchers
will use this information to develop tools to detect and
correct biological defects in unhealthy cells.
The Human Microbiome Project. Little is known
about the communities of microbial cells that inhabit
healthy human bodies. The Human Microbiome
Project aims to study these cells and their role in human
health and disease. New DNA sequencing technologies
have created a field of research, called metagenomics,
that allows the comprehensive study of microbial
Alcohol Research & Health 12
NIH Roadmap for Medical Research
communities, even those composed of organisms that
cannot be cultivated experimentally. Instead of exam-
ining the genome of an individual bacterial strain that
has been grown in a laboratory, the metagenomic
approach allows analysis of genetic material derived
from complete microbial communities harvested
from natural environments. In the human micro-
biome project, this method will complement genetic
analyses of known isolated strains, providing unprece-
dented information about the complexity of human
microbial communities.
Epigenomics. Epigenetics involves the study of changes
in the regulation of gene activity and expression that
are not dependent on gene sequence. Epigenomics is
the global analyses of epigenetic changes across the
entire genome. The NIH Roadmap epigenomics program
is based on the hypothesis that the origins of health
and susceptibility to disease are, in part, the result of
epigenetic regulation of the genetic blueprint. In par-
ticular, this hypothesis suggests that epigenetic mecha-
nisms that control stem cell differentiation and organ
formation contribute to the biological response to
endogenous and exogenous forms of stimuli that result
in disease. The epigenomics program aims to develop
comprehensive reference epigenome maps and new
technologies for comprehensive epigenomic analyses.
Reengineering the Clinical Research Enterprise
The following initiatives within this theme are central
to the goal of moving research results more quickly
into clinical settings.
Clinical Research Networks. This initiative is focused
on improving and expanding existing clinical research
data networks and standardizing data reporting to
improve networking. Another goal is to determine
the feasibility of a National Electronic Clinical Trials/
Research Network (NECTAR), which will provide the
informatics infrastructure that will serve as the back-
bone for interconnected and interoperable research
networks.
Clinical Outcomes Assessment. This initiative aims to
develop new technologies to improve the assessment
of patient-reported clinical outcomes, such as fatigue,
pain, and mood changes.
Clinical Research Training. Efforts within this initia-
tive are designed to expand and strengthen the clinical
research workforce by supporting career development
for clinical researchers, increasing the number of clinical
researchers, diversifying the settings in which clinical
research is conducted, and providing clinical research
training for medical and dental students.
Clinical Research Policy Analysis and Coordination.
These initiatives address the difficulties clinical
researchers confront in satisfying the multiple require-
ments of diverse regulatory and policy agencies. NIH
is working to standardize reporting requirements and
streamline policies.
Translational Research. Initiatives in this group
are designed to accelerate the translation of research
findings to patient care, partly by fostering the devel-
opment of a new discipline of clinical and translational
science that will be broader and deeper than the cur-
rent separate domains of translational research and
clinical investigation.
See http://nihroadmap.nih.gov/ for more information
on the NIH Roadmap initiatives.
Research Teams of the Future
The following initiatives within this theme are designed
to encourage scientists and scientific institutions to test
a variety of models for conducting research.
High-Risk Research. The NIH Director’s Pioneer
Award program is designed to support individual
researchers with innovative approaches to major
challenges in biomedical research.
Interdisciplinary Research. A series of awards will
be established to make it easier for scientists to con-
duct interdisciplinary research. Other initiatives are
designed to change NIH policies and procedures. For
example, rather than recognizing only a single Principal
Investigator (PI) for every award, NIH is moving
toward recognition of multiple PIs for any award.
Public–Private Partnerships. Initiatives are promoting
and facilitating partnerships among researchers in
academia, the Government, and the private sector.
—Lori Wolfgang Kantor, M.A.
Science Editor for Alcohol Research & Health
Vol. 31, No. 1, 2008 13
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Thesis
This doctoral thesis has addressed specific aspects relating to the chemical machinery of the probiotic bacterium Lactobacillus fermentum, which is commonly found in different floras of the human body. The work focuses particularly on exploring the bacterium's reducing activity and ability to generate biofilms through exopolysaccharide (EPS) formation. The knowledge acquired can be applied to some health problems which directly or indirectly involve this bacterium. The results and discussions are presented in seven chapters. In the first chapter, basic concepts and motivation of this work has been stated. A bibliography review regarding the use of microorganisms for the synthesis of metallic nanoparticles has been performed. Furthermore, the EPS concept has been introduced and its high biotechnological interest has been highlighted and justified. We have focused on the use of EPS as a platform for the preparation of new nanomaterials. Finally, the Lactobacillus fermentum strain has been presented and the main applications in nutrition and medicine of this probiotic have been reviewed. The second chapter evaluates the reducing activity of L. fermentum through reactions with an electrochromic polyoxometalate, which changes from pale yellow to dark blue when reduced. We were able to demonstrate that the reducing activity of L. fermentum correlates to its metabolic strength. Hence, the method can be used to assess the effect of some different drugs on this probiotic. In particular, the effects of omeprazole and vancomycin were evaluated against the viability of the probiotic L. fermentum. Omeprazole is commonly used for treating ulcers and gastritis, while vancomycin, is one of the more widely used of all antibiotics. We have resolved the controversy over the effect of these drugs on bacterial flora. Our results show that omeprazole has no effect on the reducing capacity of L. fermentum, and in consequence to its metabolic strength. However, vancomycin severely decreased L. fermentum’s reducing capacity, leading to death or serious damage in this strain. In chapter three, we have developed a sensor for the diagnosis of bacterial vaginosis (BV) based on the theory that inhibition of the bacteria’s metabolic activity reduces metabolite secretion. BV infections affect approximately 10-15% of women in the general female population. In BV, the typical vaginal flora consisting of lactobacillus bacteria, which secrete lactic acid into the media, are altered by the growth of pathogenic anaerobic bacteria, which secrete short-chain fatty acids, where acetic acid is the most abundant. Current diagnostic methods are based on sample gathering to detect the presence of potentially pathogenic bacteria, which requires time, is expensive and difficult. Here we have developed a diagnostic method based on the detection of the metabolites typically secreted by the bacteria. An electrochromic polyoxometalate, which changes from yellow to blue when reduced in a sample containing lactic acid, is used to indicate the state of the vaginal flora. A more intense blue colour equals a higher concentration of lactic acid and, therefore, the “healthier” the sample is. This test is highly accurate, precise and economical, it provides a rapid diagnosis of the infection and can also be used to monitor treatment efficiency. Chapter four addresses the mechanism by which probiotic bacteria increase iron absorption in the gastrointestinal tract. Reduction of Fe(III) to Fe(II) is essential for iron absorption in the duodenum. It has been determined that the ferric-reducing activity of L. fermentum is due to an excreted molecule, p-hydroxyphenyllactic acid (HPLA). By reducing Fe(III), HPLA boosts Fe(II) absorption through the DMT1 channels of enterocytes – as mediated in the intestine by the ferric-reducing protein DcytB, a membrane protein that is linked to the DMT1 channels at enterocytes. HPLA was isolated from the supernatant of a L. fermentum culture using high-resolution liquid chromatography and then characterised with nuclear magnetic resonance (NMR) and mass spectroscopy techniques. In a second step, several experiments were carried out, one in vitro, to confirm that probiotics increase Fe absorption in the gastrointestinal tract due to the excretion of HPLA. For the first time, with these results we can propose a mechanism that explains why probiotics promote iron absorption: HPLA is a biomimetic molecule of DcytB. This discovery opens new avenues for the treatment of iron deficiency in humans, one of the most common and widespread nutritional disorders in the world. The fifth chapter, relates to the identification of the EPS from L. fermentum. Exopolysaccharides are the main components of bacterial biofilms and they are crucial for the development of bacterial functions. We isolated EPS from a culture containing sucrose as the carbon source and then identified it through NMR. The EPS consists of a mixture of the homopolysaccharides dextran and levan. Dextran is a glucose polymer and levan a fructose polymer. Both polymers have properties of interest for biotechnological applications in food and pharmaceutical industries. Chapter six explores the use of EPS from L. fermentum as a platform to support gold nanoparticles (AuNPs). The most typical AuNPS morphologies (spheres, rods and prisms) aggregated when deposited on the EPS. Moreover, EPS from L. fermentum produced gold aggregates from an Au(III) solution, which confirms its reducing and nucleation activity. UV-vis spectra of gold aggregates showed new absorbance peaks (Surface Plasmon Resonance, SPR) at lower energies compared to isolated nanoparticles. In the case of gold nanoprisms, the new absorption band appeared at a very low energy, centred at 1,100 nm. This increases our interest in the optical properties of these systems as well as expanding their possibilities in biomedical applications. As a first approach, we studied the Surface-enhanced Raman spectroscopy (SERS ) effect of gold aggregates on deposited rhodamine B (a model molecule for these kinds of study). In the case of gold nanoprism aggregates on EPS, the intensity of the rhodamine B Raman signal dramatically increased, whereas no effect was observed with the other morphologies. This fact was explained through TEM tomography, which revealed clear differences in the extension of the EPS coating across the AuNPs, in particular the higher exposure to rhodamine B of gold nanoparticle surface. Finally, the seventh chapter presents the general conclusions taken from this doctoral thesis.
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