Ph.D in Molecular Biology

What is molecular Biology?

Molecular biology is the study of biology at a molecular level. The field overlaps with other areas of biology and chemistry, particularly genetics and biochemistry. Molecular biology chiefly concerns itself with understanding the interactions between the various systems of a cell, including the interactions between DNA, RNA and protein biosynthesis as well as learning how these interactions are regulated.

Relationship to other biological sciences

Researchers in molecular biology use specific techniques native to molecular biology, but increasingly combine these with techniques and ideas from genetics and biochemistry. There is not a defined line between these disciplines. The figure above is a schematic that depicts one possible view of the relationship between the fields:

• ''Biochemistry'' is the study of the chemical substances and vital processes occurring in living organisms. Biochemists focus heavily on the role, function, and structure of biomolecules. The study of the chemistry behind biological processes and the synthesis of biologically active molecules are examples of biochemistry.
• ''Genetics'' is the study of the effect of genetic differences on organisms. Often this can be inferred by the absence of a normal component (e.g. one gene). The study of "mutants" – organisms which lack one or more functional components with respect to the so-called "wild type" or normal phenotype. Genetic interactions (epistasis) can often confound simple interpretations of such "knock-out" studies.
• ''Molecular biology'' is the study of molecular underpinnings of the process of replication, transcription and translation of the genetic material. The central dogma of molecular biology where genetic material is transcribed into RNA and then translated into protein, despite being an oversimplified picture of molecular biology, still provides a good starting point for understanding the field. This picture, however, is undergoing revision in light of emerging novel roles for RNA.

Much of the work in molecular biology is quantitative, and recently much work has been done at the interface of molecular biology and computer science in bioinformatics and computational biology. As of the early 2000s, the study of gene structure and function, molecular genetics, has been amongst the most prominent sub-field of molecular biology.

Increasingly many other loops of biology focus on molecules, either directly studying their interactions in their own right such as in cell biology and developmental biology, or indirectly, where the techniques of molecular biology are used to infer historical attributes of populations or species, as in fields in evolutionary biology such as population genetics and phylogenetics. There is also a long tradition of studying biomolecules "from the ground up" in biophysics.

Molecular Biology: Research Topics

Microbiology

Microbiology includes the study of a huge variety of microscopic organisms that come from all three domains of life, Bacteria, Archaea, and Eukaryota, and the viruses.

Microorganisms and viruses are found everywhere on Earth and play important roles in the environment, in the health of plants and animals, including humans, and in biotechnology. Several faculty members in the Section of Molecular Biology have research interests related to microbiology and they study a range of topics including: the bacterial cytoskeleton and chromosome partitioning; mechanisms of biological clocks and circadian gene regulation; bacterial development, communication and signaling; microbial genomics and metagenomics; quantitative and systems biology; evolution of bacterial membrane transporters; genetics and regulation of microalgae; interactions between microbial pathogens and hosts; and molecular structures of viruses. Several faculty members actively participate in the San Diego Center for Algae Biotechnology and have research projects related to the use of algae for the production of bioproducts and biofuels. Microbiology has a close relationship to immunology, another strength within the Section of Molecular Biology. Molecular Biology faculty members also use microorganisms as model organisms to study fundamental properties common to all life. For example, several faculty members use bacteria and yeast as model systems to study topics including signal transduction pathways, mechanisms of RNA splicing, chromatin dynamics, gene regulation and gene networks, and synthetic genetic circuits.

RNA Biology

The primary product of the genes of our genome is RNA.

In addition to protein-coding mRNAs, genomes produce a wide variety of non-coding RNAs, which function in a vast array of cellular processes, including all aspects of gene expression and its regulation. The study of RNA Biology focuses on understanding the functions, processing, and regulation of these numerous classes of RNA molecules. The RNA Biologists within the Division of Biological Sciences explore a variety of aspects of RNA-mediated regulation of gene expression, including mechanisms of pre-mRNA processing, regulation of mRNA turnover and translation, and the processing and activity of microRNAs and other noncoding RNAs that play central roles in gene regulatory pathways, including those involved in organismal and immune system development.

Gene Regulation

The proper regulation of gene expression is essential for the growth, development, and survival of organisms.

Research in the Section of Molecular Biology includes the analysis of the fundamental mechanisms by which gene activity is controlled at the levels of transcription, chromatin dynamics, RNA stability and function, and gene networks as well as the investigation of the critical roles of gene expression in the context of signal transduction, cancer, immunology, stem cell biology, and circadian rhythms.

Immunology

The immune system is continuously adapting to defend the host against invading pathogens.

In parallel, microorganisms evolve to paralyze the immune response, leading to a race between microbe (virulence) and immune system (resistance). Despite major efforts, numerous viruses and bacteria continue to affect the lives of millions of people globally. The immunologists in the Molecular Biology section study the development and function of both the innate and adaptive immune system with a particular emphasis on the cellular and molecular aspects of host-pathogen interactions.

Quantitative Biology

Over the past decade, scientists and engineers have begun to define the path forward in the genomic era.

Systems Biology has arisen as the deduction of interaction networks from -omics data generated in the wake of remarkable technological achievements. Likewise, DNA synthesis technologies are driving the development of Synthetic Biology, whereby engineered circuitry and even entire genomes can be reconstituted from chemical building blocks. These two emerging areas have catalyzed the growth of Quantitative Biology, whereby the central goal is the deduction of quantitative principles that can be used to construct predictive models for biological phenomena.

Cancer Biology

Cancer is a group of diseases affecting various organs of the human body

Despite extensive efforts in the war against cancer, there have been few successful treatments to cure advanced stage cancer. Taking advantage of the state-of-art model systems including transgenic mouse models and human pluripotent stem cells, members of the Molecular Biology Section are investigating the roles of tumor suppressors and oncogenic proteins as well as different cellular and molecular immune regulators in human tumorigenesis. These studies will help to identify new diagnostic and therapeutic targets to treat human cancers more effectively.