From the cell cycle to the circadian rhythm, oscillations permeate life. However, natural biological oscillations typically emerge from the interaction between a large set of components, and detangling the underlying mechanism of oscillation is a highly nontrivial affair. Synthetic oscillators much more readily provide insight into the basic principles of biological oscillations, with the caveat that one should not expect all of the refined properties present in natural oscillators to emerge from a minimal synthetic system. The aim of this chapter is to provide an overview of experimentally realized synthetic oscillators, with an emphasis on the common core design features throughout. The mathematical basis behind the conclusions will not be dwelt upon, as several such reviews exist. Keywords: systems and synthetic biology; biological oscillators; entrainment; ClpXP protease; queuing theory
Emerging clinical data suggest that cancer immunotherapy is likely to become a key part of the clinical management of cancer. Knowledge of the basic mechanisms of the immune system as they relate to cancer has been increasing rapidly, and such developments have accelerated the translation of novel immunotherapy techniques into medical breakthroughs for many cancer patients. The development of checkpoint-blocking antibodies, against cytotoxic T-lymphocyte antigen 4 (CTLA-4) and the programmed death 1 receptor (PD-1), has recently demonstrated significant promise in the treatment of malignancies. Ipilimumab (to block CTLA-4) and pembrolizumab (to block PD-1) have been approved by the US Food and Drug Administration for the treatment of advanced melanoma, and additional regulatory approvals are expected for a variety of other agents such as nivolumab (to block PD-1). To combine checkpoint inhibitors approaches with other therapies such as immunomodulators (cytokines, indoleamine 2,3-dioxygenase inhibitors), cytotoxic chemotherapy, radiation therapy or molecularly targeted therapies, may hold the key to the true potential of immunotherapy in the future management of cancer patients. Keywords: T cell; cancer; CTLA-4; immunotherapy; PD-1/PD-L1
In this review we summarize current understanding of the development of autonomic neurons in vertebrates. The mechanisms controlling the development of sympathetic and enteric neurons have been studied in considerable detail in laboratory mammals, chick and zebrafish, and there are also limited data about the development of sympathetic and enteric neurons in amphibians. Little is known about the development of parasympathetic neurons apart from the ciliary ganglion in chicks. Although there are considerable gaps in our knowledge, some of the mechanisms controlling sympathetic and enteric neuron development appear to be conserved between mammals, avians and zebrafish. For example, some of the transcriptional regulators involved in the development of sympathetic neurons are conserved between mammals, avians and zebrafish, and the requirement for Ret signalling in the development of enteric neurons is conserved between mammals (including humans), avians and zebrafish. However, there are also differences between species in the migratory pathways followed by sympathetic and enteric neuron precursors and in the requirements for some signalling pathways.
During recent years, the reduced use of chemical processes to produce commodity chemicals, and their substitution with microbiological alternatives, has been frequently observed. However, because of the low efficiency of these biotechnological synthetic materials, investigations are constantly being performed to increase their productivity by controlling the metabolism of bacterial cells. One solution to this problem would be to modify the environmental conditions of the culture of microorganisms or, alternatively, to control the composition of the culture medium by using additional and important enzymes that serve as cofactors in metabolite production. Such production by microorganisms can be also improved by employing genetic engineering tools, whereby modified bacteria are able to synthesize several-fold more desirable metabolites than can wild-type strains. The biotechnological synthesis of diols such as 1,2-propanediol (1,2-PD), 1,3-propanediol (1,3-PD) and 2,3-butanediol (2,3-BD) by the direct microbial bioconversion of renewable feedstocks, and even from waste materials of biofuel production, has been well described. These diols are widely used in many branches of industry, including the production of chemicals, food products, cosmetics and pharmaceuticals. As the methods used to increase the efficiency of their production are still being investigated, recent developments in the production of 1,2-PD, 1,3-PD and 2,3-BD, with regards to the metabolic engineering of production strains and the optimization of fermentation processes, are reviewed and discussed in this chapter. Keywords: 1,2-Propanediol (1,2-PD); 1,3-Propanediol (1,3-PD); 1,4-Butanediol (1,4-PD); 2,3-Butanediol (2,3-PD); culture conditions; medium composition; metabolic engineering
Mammalian cortical development is a multifaceted process that is under the control of precise transcriptional programs. During embryonic neurogenesis, neural progenitor cells undergo defined steps of differentiation to generate functional neurons at distinct stages of development. It is becoming increasingly clear that epigenetic mechanisms, including histone modifications, DNA methylation, chromatin remodeling and noncoding RNAs, play critical roles in specifying and maintaining cell-fates during neurogenesis. Furthermore, these mechanisms function in concert with each other and with sequence-specific transcription factors, emphasizing the collaboration between genetic and epigenetic mechanisms in driving neuronal fate. In this chapter, a comprehensive overview is provided of the epigenetic layers that underlie neurogenesis, along with prospective for future challenges in this exciting field. Keywords: histones; chromatin; post-translational modification of histones; DNA methylation; noncoding RNA; epigenetics; corticogenesis; neural progenitors; neurons
Increasing demand of biofuels is inevitable today considering the adverse impact of fossil fuels on environment, issue of its sustainability, rising price, and dependence on foreign countries. However, the question remains on how to produce biofuels in cost effective manner from the non-food resources. The non-food agricultural and forestry residues have recalcitrant biomass that is difficult to hydrolyze via enzymes, and presence of non-conventional pentose sugars and inhibitors makes the sugar fermentation into ethanol a formidable task. Besides, ethanol has its inherent issue of having low energy density and hygroscopic nature, encouraging scientists to look for alternative fuels, such as butanol and hydrocarbons. Algae are another non-food feedstock that is being explored for fuel production, but its low growth rate and low lipid yield in fluctuating environmental growth condition is of great concern. Synthetic biology with its new tools and applications is likely to play a central role in addressing these issues.Keywords:synthetic biology;biofuels;lignocellulosic biomass;metabolic engineering;feedstock engineering;microbial engineering;hydrolytic enzymes;algal fuels
Hit-to-Lead medicinal chemistry is the process through which “hits” are converted into “leads.” Fundamental to the process is to gain confidence, first that a hit compound can be developed into a robust (lead) series, and second that the leads have the potential to be converted into drug candidates. Such confidence is gained in a stepwise fashion: initially, hit compounds must have their activity confirmed, and second it must be demonstrated that structural modification of the hit can result in changes in biological activity, thus generating a series. Third, members of the series must pass a series of so-called “developability filters,” thus ensuring that there is a high chance of success in the subsequent phase of lead optimization. The hit-to-lead phase is highly important, as chemists are frequently presented with multiple hits from which to identify a small number of series to take forward. Selection at this point will have a direct impact on the success of lead optimization. Keywords: hit; lead; lead optimization; fragment; ligand efficiency
Retinoblastoma is a rare, malignant, childhood tumor that is primarily initiated by the inactivation of both alleles of the retinoblastoma tumor susceptibility gene, RB1, in a developing human retinal cell. A rare subset of retinoblastoma is initiated by somatic amplification of the MYCN oncogene in a predisposing retinal cell. Surprisingly the retinoblastoma protein (pRB), encoded by RB1, is an important transcription factor. Cell-cycle control by pRB is mainly accomplished by transcriptional repression of the genes required for cell-cycle progression. Control of differentiation by pRB is achieved by the activation of transcription. Through extensive post-translational modifications and interactions with other proteins, pRB and family members also influence senescence, chromosomal stability, and apoptosis. Almost every type of tumor has disruption in the retinoblastoma pathway associated with tumor progression, but germline mutation of the RB1 gene predisposes children to a 95% specific risk of developing retinoblastoma and a significantly increased risk of second primary tumors, such as osteosarcoma and melanoma. However, retinoblastoma is also characterized by other genomic changes subsequent to RB1 mutation. Keywords: aneuploidy; apoptosis; chromosome instability (CIN); E2F ; LOH ; MYCN ; proband; RB1 ; retinoblast; retinoma; SV40 ; TAg ; tumor suppressor
In The Origin of Species, Charles Darwin described the formation of new species as the “mystery of mysteries”. More than 150 years after Darwin first posed the problem much progress has been made in discerning what creates the great diversity of life. Speciation is the evolutionary process where a group of inbreeding populations diverges into two or more reproductively isolated groups. In this chapter, we summarize the current understanding of speciation in sexually reproductive organisms. In particular, we describe how barriers to gene flow evolve and focus on the most important factors promoting speciation. Further, we integrate different perspectives by describing recent progress from many different model systems for the study of speciation. Building on this work, we emphasize new genomic approaches to the study of speciation and how advances in DNA sequencing methods will revolutionize our understanding of the genetic basis of the speciation process. We conclude by summarizing our current understanding of speciation and show that although much of Darwin's mystery is solved, many important questions remain. Keywords: speciation; genomics; gene flow; reproductive isolation; symbiosis
Multicellular organisms develop from fertilized eggs or asexual propagules. In the case of animals the developmental processes by which their bodies take form originated in several phases beginning between 600 and 700 million years ago, in the Ediacaran period. Genes and signaling pathways, many of which were present in unicellular ancestors, came to mediate morphogenesis and cell pattern formation by virtue of bringing into play physical effects that were newly relevant on the scale of cell aggregates. Focusing on “liquid-like” properties of cell clusters and their capacity to act as “excitable media,” this review explores how the products of ancient and some novel genes of what became the “developmental toolkit” were variously employed to mobilize well-characterized physical effects and processes (cohesivity, phase separation and disaggregation, surface and shape polarization of cells, chemical oscillation, reaction–diffusion coupling) in the cell aggregates that eventually evolved into animal bodies and organs. This interplay of physics and genetics led to the generation of morphological motifs such as the tissue layering of gastrulation, lumen formation, body elongation, triploblasty, segmentation, and patterning of endoskeletal elements. Since not all founding lineages had identical sets of toolkit genes, not all morphogenetic and patterning processes were equally present in their descendents. These “physico-genetic” factors collectively account for the conservation and diversity of body plans seen in the present-day animal phyla. Keywords: “basal” metazoans; basal lamina; convergent extension; diploblasts; liquid tissue; lumen formation; multilayering; saltational evolution; segmentation; triploblasts; tetrapod limbs
Graphene is currently a “shining star” in nanomedicine on account of its good biocompatibility, low cytotoxicity, and ease of functionalization. The versatile nature of modifiable graphene leads to a novel horizon with promising application opportunities in a wide range of technologies and markets. The unique applications of graphene and its derivatives in biosensing, bioimaging, therapeutics, and genetic engineering are discussed in this chapter. Keywords: graphene; graphene derivative; molecular imaging; theranostics; genetic engineering
As a therapeutic strategy, small interfering RNA (siRNA) has a remarkable potential to treat genetic diseases driven by mutated or aberrantly expressed genes, including cancer, inflammatory conditions, neurodegenerative disorders, and viral infections. Since the discovery of the RNA interference (RNAi) pathway in 1998, a multitude of siRNA delivery methods have been designed and tested. However, siRNA-based therapeutics are currently limited by the inability to safely and robustly deliver nucleic acids to target cells and tissues. With the development of nanocarriers composed of organic (lipids, liposomes, conjugated polymers) and inorganic (iron oxide, gold) materials, nanotechnology has emerged as a discipline that offers one of the most powerful solutions to enable the stable and safe delivery of siRNA oligonucleotides. Many of these nanocarriers demonstrate acceptable safety profiles, enhance the in-vivo stability of siRNA, promote robust tissue penetration, and can be modified with a targeting ligand to allow for tissue-specific uptake. In this chapter, the challenges of delivering siRNA are reviewed, and the most important advances in the development of nanoparticle-based siRNA delivery systems currently in preclinical and clinical development will be highlighted.
With the majority of cancer patients succumbing to the metastatic form of the disease, there is an ongoing search for ways to block metastatic spread and render patients free from cancer. Radiovirotherapy involves the use of viruses to deliver radioisotopic treatment into infected cells, and several types of virus (e.g., measles virus, herpes simplex type 1 virus, adenovirus, and vaccinia virus), all of which possess oncolytic properties, have been utilized to deliver transgenes encoding for the human sodium iodide symporter (NIS). As the virus does not carry any radioactivity, radiovirotherapy is always a two-step strategy, with viral gene delivery followed by systemic administration of the radionuclide. The NIS transports 131I, which is used to treat thyroid diseases, and radiovirotherapy has been investigated using this radionuclide in experimental cancers, with encouraging results. In spite of some problems with viral delivery, radiovirotherapy has been consistently more efficient in treating experimental cancers than virotherapy alone. Yet another approach to radioactive microbe cancer therapy, radioactive bacteria (radiolisteria), employs a combinatorial agent capable of selectively infecting tumor cells and delivering a therapeutic radionuclide inside the tumor cells. The tumoricidal effect of such therapy results from the Listeria organisms killing tumor cells via the production of reactive oxygen species and a direct impact of radiation on cancer cells. Whilst the field of radioactive microbes for cancer therapy is still in its infancy, it is hoped that radioactive microbe therapy will be extended to clinical trials in the near future, hopefully with encouraging results. Keywords: radiovirotherapy; sodium iodide symporter (NIS); oncolytic virus/bacterium; 131iodine
The aim of proteomics is to identify, characterize and map gene functions at the protein level for whole cells or organisms. A typical experimental scheme for a large-scale proteomics inquiry involves the fractionation of a complex protein mixture by electrophoretic or chromatographic means, followed by subsequent identification of the components in individual fractions, using mass spectrometry (MS). Owing to continuous and rapid improvements in instrument sensitivity, throughput capacity, software versatility, and techniques of statistical validation, MS-based approaches have during recent years become mainstream methods for proteome analysis. Keywords: 2D PAGE ; MS/MS ; MudPIT ; quantitative proteomics; orbitrap
Recent advances in knowledge of the human microbiome's composition and function have generated a flood of new information, technologies, and capabilities that have increased the present understanding of the impact that the microflora has on the initiation, progression, and treatment of cancer. Revealing the molecular mechanisms by which the gastrointestinal microflora can affect carcinogenesis will help to identify both potential new therapeutic targets and microflora–drug interactions that may either disrupt or improve therapeutic efficacy. Clinical translation of this new information is in its infancy, and will be critical to the development of novel strategies for improved therapies based on the rational targeting and manipulation of microbiome function for the treatment of human tumors. Keywords: microbiome; dysbiosis; probiotic; prebiotic; synbiotic; endobiotic and xenobiotic; microbial metabolites; drug metabolism; cancer therapeutic
Recently, the biosynthesis of peptides and proteins harboring chemical functionalities not found within the canonical 20 amino acids has been accomplished by harnessing natural post-translational modifications (PTMs) or by expanding the genetic repertoire with unnatural amino acids. These methods have vastly increased the chemical space that can be explored in directed evolution experiments, resulting in peptides and proteins with new or improved function. Although this area of synthetic biology is relatively new, it is rapidly emerging as a transformative research tool across multiple disciplines. Ultimately, the convergence of methodologies using PTM and expanded genetic repertoires will allow the biosynthesis of custom-tailored peptides and proteins with a rich variety of structures and functions. Keywords: directed evolution; post-translational modification (PTM); ribosomally synthesized post-translationally modified peptides (RiPPs); post-ribosomal peptide synthesis (PRPS); unnatural amino acids (uAAs); orthogonal aminoacyl-tRNA synthetase/tRNA (aaRS/tRNA) pairs
Cytokines are proteins or glycoproteins which are produced by cells and act on other cells that display on their surface specific cytokine receptors. Cytokines are used by cells to communicate. Within a determined sequence, these mediators lead the responding cells to modify their function (e.g., secretion, proliferation, induction, inhibition, enhanced or reduced function, migration, apoptosis). Despite cytokines having mainly been discovered by immunologists as a product of cells of leukocyte lineage, they are now recognized as elements of a universal language used by most cells of any other lineage. Accordingly, they are essential for many events through life, such as reproductive tissue remodeling, embryogenesis, steady-state and adaptive hematopoiesis, surveillance and maintenance of tissue structure, functions of the immune system, inflammation, cell survival, and cell death. Cytokines also allow a dialog with the central nervous system, and some may modify different behaviors (e.g., fever, anorexia, sleep). Cytokines usually act within their vicinity, but they can also act via an endocrine fashion. Their production is tightly controlled within a complex network of positive and negative loops. They are a prerequisite for the control of infection by invasive microorganisms, though their exacerbated production may be deleterious at local or systemic levels. Their “half-angel/half-devil” aspect has rendered cytokines difficult to use for therapeutic purposes, though some recombinant cytokines or cytokine-neutralizing strategies have been used successfully in different pathological conditions.
The crux of targeted therapy is the inhibition, enhancement, correction, reversal, or negation of events to overcome pathological processes, by targeting features or entities specific to the pathology. Genomics has been a critical component of target identification, and has greatly amplified the impact and potential of targeted therapy. Incredibly, genomics has only scratched the surface of this endeavor. Today, progress is driven by pan-omics, integrating genomics, epigenomics, transcriptomics, proteomics, metabolomics, and metagenomics data using bioinformatics and system biology approaches. The advent of advanced “-omics” has provided the molecular foundation for the development of new-targeted therapeutics, including small molecules, biologicals, tools for genomic editing, and more. Targeted therapy is used to treat an array of diverse diseases, ranging from cancer and HIV to atherosclerosis and malaria. In this chapter, the essential aspects of targeted therapy are discussed, including many of the remarkable successes as well as some of the shortcomings. How “-omics” approaches have contributed to the evolution of targeted therapy and what can be expected in the future is also described.Keywords:targeted therapy;precision medicine;genomics;epigenomics;transcriptomics;metabolomics;proteomics;metagenomics;bioinformatics
