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Essays in Biochemistry

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https://www.readbyqxmd.com/read/27903826/synthetic-biology-approaches-to-biological-containment-pre-emptively-tackling-potential-risks
#1
REVIEW
Leticia Torres, Antje Krüger, Eszter Csibra, Edoardo Gianni, Vitor B Pinheiro
Biocontainment comprises any strategy applied to ensure that harmful organisms are confined to controlled laboratory conditions and not allowed to escape into the environment. Genetically engineered microorganisms (GEMs), regardless of the nature of the modification and how it was established, have potential human or ecological impact if accidentally leaked or voluntarily released into a natural setting. Although all evidence to date is that GEMs are unable to compete in the environment, the power of synthetic biology to rewrite life requires a pre-emptive strategy to tackle possible unknown risks...
November 30, 2016: Essays in Biochemistry
https://www.readbyqxmd.com/read/27903825/synthetic-biology-routes-to-bio-artificial-intelligence
#2
REVIEW
Darren N Nesbeth, Alexey Zaikin, Yasushi Saka, M Carmen Romano, Claudiu V Giuraniuc, Oleg Kanakov, Tetyana Laptyeva
The design of synthetic gene networks (SGNs) has advanced to the extent that novel genetic circuits are now being tested for their ability to recapitulate archetypal learning behaviours first defined in the fields of machine and animal learning. Here, we discuss the biological implementation of a perceptron algorithm for linear classification of input data. An expansion of this biological design that encompasses cellular 'teachers' and 'students' is also examined. We also discuss implementation of Pavlovian associative learning using SGNs and present an example of such a scheme and in silico simulation of its performance...
November 30, 2016: Essays in Biochemistry
https://www.readbyqxmd.com/read/27903824/societal-impact-of-synthetic-biology-responsible-research-and-innovation-rri
#3
REVIEW
Daniel Gregorowius, Anna Deplazes-Zemp
Synthetic biology is an emerging field at the interface between biology and engineering, which has generated many expectations for beneficial biomedical and biotechnological applications. At the same time, however, it has also raised concerns about risks or the aim of producing new forms of living organisms. Researchers from different disciplines as well as policymakers and the general public have expressed the need for a form of technology assessment that not only deals with technical aspects, but also includes societal and ethical issues...
November 30, 2016: Essays in Biochemistry
https://www.readbyqxmd.com/read/27903823/in%C3%A2-vitro-skin-models-and-tissue-engineering-protocols-for-skin-graft-applications
#4
REVIEW
Lucas B Naves, Chetna Dhand, Luis Almeida, Lakshminarayanan Rajamani, Seeram Ramakrishna
In this review, we present a brief introduction of the skin structure, a concise compilation of skin-related disorders, and a thorough discussion of different in vitro skin models, artificial skin substitutes, skin grafts, and dermal tissue engineering protocols. The advantages of the development of in vitro skin disorder models, such as UV radiation and the prototype model, melanoma model, wound healing model, psoriasis model, and full-thickness model are also discussed. Different types of skin grafts including allografts, autografts, allogeneic, and xenogeneic are described in detail with their associated applications...
November 30, 2016: Essays in Biochemistry
https://www.readbyqxmd.com/read/27903822/synthetic-biology-and-the-prospects-for-responsible-innovation
#5
REVIEW
Phil Macnaghten, Richard Owen, Roland Jackson
In this article we provide a short review of the debate on responsible innovation and its intersection with synthetic biology, focusing on initiatives we have witnessed and been involved with in the UK. First, we describe the ways in which responsibility in science has been reconfigured institutionally, from an internal focus on the provision of objective and reliable knowledge, to a more external view that embraces the ways in which it has an impact on society. Secondly, we introduce a framework for responsible innovation as a (partial) response to this shift, highlighting its constituent dimensions and the capacities and competencies that are needed to put it into practice...
November 30, 2016: Essays in Biochemistry
https://www.readbyqxmd.com/read/27903821/construction-of-a-minimal-genome-as-a-chassis-for-synthetic-biology
#6
REVIEW
Bong Hyun Sung, Donghui Choe, Sun Chang Kim, Byung-Kwan Cho
Microbial diversity and complexity pose challenges in understanding the voluminous genetic information produced from whole-genome sequences, bioinformatics and high-throughput '-omics' research. These challenges can be overcome by a core blueprint of a genome drawn with a minimal gene set, which is essential for life. Systems biology and large-scale gene inactivation studies have estimated the number of essential genes to be ∼300-500 in many microbial genomes. On the basis of the essential gene set information, minimal-genome strains have been generated using sophisticated genome engineering techniques, such as genome reduction and chemical genome synthesis...
November 30, 2016: Essays in Biochemistry
https://www.readbyqxmd.com/read/27903820/agent-based-modelling-in-synthetic-biology
#7
REVIEW
Thomas E Gorochowski
Biological systems exhibit complex behaviours that emerge at many different levels of organization. These span the regulation of gene expression within single cells to the use of quorum sensing to co-ordinate the action of entire bacterial colonies. Synthetic biology aims to make the engineering of biology easier, offering an opportunity to control natural systems and develop new synthetic systems with useful prescribed behaviours. However, in many cases, it is not understood how individual cells should be programmed to ensure the emergence of a required collective behaviour...
November 30, 2016: Essays in Biochemistry
https://www.readbyqxmd.com/read/27903819/towards-designing-new-nano-scale-protein-architectures
#8
REVIEW
Jana Aupič, Fabio Lapenta, Žiga Strmšek, Roman Jerala
The complexity of designed bionano-scale architectures is rapidly increasing mainly due to the expanding field of DNA-origami technology and accurate protein design approaches. The major advantage offered by polypeptide nanostructures compared with most other polymers resides in their highly programmable complexity. Proteins allow in vivo formation of well-defined structures with a precise spatial arrangement of functional groups, providing extremely versatile nano-scale scaffolds. Extending beyond existing proteins that perform a wide range of functions in biological systems, it became possible in the last few decades to engineer and predict properties of completely novel protein folds, opening the field of protein nanostructure design...
November 30, 2016: Essays in Biochemistry
https://www.readbyqxmd.com/read/27903818/properties-of-alternative-microbial-hosts-used-in-synthetic-biology-towards-the-design-of-a-modular-chassis
#9
REVIEW
Juhyun Kim, Manuel Salvador, Elizabeth Saunders, Jaime González, Claudio Avignone-Rossa, Jose Ignacio Jiménez
The chassis is the cellular host used as a recipient of engineered biological systems in synthetic biology. They are required to propagate the genetic information and to express the genes encoded in it. Despite being an essential element for the appropriate function of genetic circuits, the chassis is rarely considered in their design phase. Consequently, the circuits are transferred to model organisms commonly used in the laboratory, such as Escherichia coli, that may be suboptimal for a required function...
November 30, 2016: Essays in Biochemistry
https://www.readbyqxmd.com/read/27784777/the-immune-system
#10
REVIEW
Lindsay B Nicholson
All organisms are connected in a complex web of relationships. Although many of these are benign, not all are, and everything alive devotes significant resources to identifying and neutralizing threats from other species. From bacteria through to primates, the presence of some kind of effective immune system has gone hand in hand with evolutionary success. This article focuses on mammalian immunity, the challenges that it faces, the mechanisms by which these are addressed, and the consequences that arise when it malfunctions...
October 31, 2016: Essays in Biochemistry
https://www.readbyqxmd.com/read/27784776/photosynthesis
#11
REVIEW
Matthew P Johnson
Photosynthesis sustains virtually all life on planet Earth providing the oxygen we breathe and the food we eat; it forms the basis of global food chains and meets the majority of humankind's current energy needs through fossilized photosynthetic fuels. The process of photosynthesis in plants is based on two reactions that are carried out by separate parts of the chloroplast. The light reactions occur in the chloroplast thylakoid membrane and involve the splitting of water into oxygen, protons and electrons...
October 31, 2016: Essays in Biochemistry
https://www.readbyqxmd.com/read/27744339/chaperone-families-and-interactions-in-metazoa
#12
Yael Bar-Lavan, Netta Shemesh, Anat Ben-Zvi
Quality control is an essential aspect of cellular function, with protein folding quality control being carried out by molecular chaperones, a diverse group of highly conserved proteins that specifically identify misfolded conformations. Molecular chaperones are thus required to support proteins affected by expressed polymorphisms, mutations, intrinsic errors in gene expression, chronic insult or the acute effects of the environment, all of which contribute to a flux of metastable proteins. In this article, we review the four main chaperone families in metazoans, namely Hsp60 (where Hsp is heat-shock protein), Hsp70, Hsp90 and sHsps (small heat-shock proteins), as well as their co-chaperones...
October 15, 2016: Essays in Biochemistry
https://www.readbyqxmd.com/read/27744338/protein-quality-control-at-the-endoplasmic-reticulum
#13
Kathleen McCaffrey, Ineke Braakman
The ER (endoplasmic reticulum) is the protein folding 'factory' of the secretory pathway. Virtually all proteins destined for the plasma membrane, the extracellular space or other secretory compartments undergo folding and maturation within the ER. The ER hosts a unique PQC (protein quality control) system that allows specialized modifications such as glycosylation and disulfide bond formation essential for the correct folding and function of many secretory proteins. It is also the major checkpoint for misfolded or aggregation-prone proteins that may be toxic to the cell or extracellular environment...
October 15, 2016: Essays in Biochemistry
https://www.readbyqxmd.com/read/27744337/protein-quality-control-at-the-mitochondrion
#14
Wolfgang Voos, Witold Jaworek, Anne Wilkening, Michael Bruderek
Mitochondria are essential constituents of a eukaryotic cell by supplying ATP and contributing to many mayor metabolic processes. As endosymbiotic organelles, they represent a cellular subcompartment exhibiting many autonomous functions, most importantly containing a complete endogenous machinery responsible for protein expression, folding and degradation. This article summarizes the biochemical processes and the enzymatic components that are responsible for maintaining mitochondrial protein homoeostasis. As mitochondria lack a large part of the required genetic information, most proteins are synthesized in the cytosol and imported into the organelle...
October 15, 2016: Essays in Biochemistry
https://www.readbyqxmd.com/read/27744336/protein-quality-control-at-the-ribosome-focus-on-rac-nac-and-rqc
#15
Martin Gamerdinger
The biogenesis of new polypeptides by ribosomes and their subsequent correct folding and localization to the appropriate cellular compartments are essential key processes to maintain protein homoeostasis. These complex mechanisms are governed by a repertoire of protein biogenesis factors that directly bind to the ribosome and chaperone nascent polypeptide chains as soon as they emerge from the ribosomal tunnel exit. This nascent chain 'welcoming committee' regulates multiple co-translational processes including protein modifications, folding, targeting and degradation...
October 15, 2016: Essays in Biochemistry
https://www.readbyqxmd.com/read/27744335/epigenetic-inheritance-of-proteostasis-and-ageing
#16
Cheryl Li, Olivia Casanueva
Abundant evidence shows that the genome is not as static as once thought and that gene expression can be reversibly modulated by the environment. In some cases, these changes can be transmitted to the next generation even if the environment has reverted. Such transgenerational epigenetic inheritance requires that information be stored in the germline in response to exogenous stressors. One of the most elusive questions in the field of epigenetic inheritance is the identity of such inherited factor(s). Answering this question would allow us to understand how the environment can shape human populations for multiple generations and may help to explain the rapid rise in obesity and neurodegenerative diseases in modern society...
October 15, 2016: Essays in Biochemistry
https://www.readbyqxmd.com/read/27744334/shape-matters-the-complex-relationship-between-aggregation-and-toxicity-in-protein-misfolding-diseases
#17
Heidrun Maja Ries, Carmen Nussbaum-Krammer
A particular subgroup of protein-misfolding diseases, comprising Alzheimer's and Parkinson's disease, involves amyloidogenic proteins that can form alternative pathogenic conformations with a high tendency to self-assemble into oligomeric and fibrillar species. Although misfolded proteins have been clearly linked to disease, the exact nature of the toxic species remains highly controversial. Increasing evidence suggests that there is little correlation between the occurrence of macroscopic protein deposits and toxic phenotypes in affected cells and tissues...
October 15, 2016: Essays in Biochemistry
https://www.readbyqxmd.com/read/27744333/cellular-proteostasis-degradation-of-misfolded-proteins-by-lysosomes
#18
Matthew P Jackson, Eric W Hewitt
Proteostasis refers to the regulation of the cellular concentration, folding, interactions and localization of each of the proteins that comprise the proteome. One essential element of proteostasis is the disposal of misfolded proteins by the cellular pathways of protein degradation. Lysosomes are an important site for the degradation of misfolded proteins, which are trafficked to this organelle by the pathways of macroautophagy, chaperone-mediated autophagy and endocytosis. Conversely, amyloid diseases represent a failure in proteostasis, in which proteins misfold, forming amyloid deposits that are not degraded effectively by cells...
October 15, 2016: Essays in Biochemistry
https://www.readbyqxmd.com/read/27744332/the-function-of-small-heat-shock-proteins-and-their-implication-in-proteostasis
#19
Annika Strauch, Martin Haslbeck
All organisms rely on a conserved cellular machinery supporting and controlling the life cycle of proteins: the proteostasis network. Within this network, the main players that determine the fate of proteins are molecular chaperones, the ubiquitin-proteasome and the lysosome-autophagy systems. sHsps (small heat-shock proteins) represent one family of molecular chaperones found in all domains of life. They prevent irreversible aggregation of unfolded proteins and maintain proteostasis by stabilizing promiscuously a variety of non-native proteins in an ATP-independent manner...
October 15, 2016: Essays in Biochemistry
https://www.readbyqxmd.com/read/27744331/cellular-strategies-to-cope-with-protein-aggregation
#20
Annika Scior, Katrin Juenemann, Janine Kirstein
Nature has evolved several mechanisms to detoxify intracellular protein aggregates that arise upon proteotoxic challenges. These include the controlled deposition of misfolded proteins at distinct cellular sites, the protein disaggregation and refolding by molecular chaperones and/or degradation of misfolded and aggregated protein species by cellular clearance pathways. In this article, we discuss cellular the strategies of prokaroytes and eukaryotes to control protein aggregation.
October 15, 2016: Essays in Biochemistry
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