"Our biological limitations often make us feel uncomfortable with our own humanity but at the end of the day we are forced to admit that we are human. For some of us this may be easier than others. Despite how we may feel mentally we are biologically human and we might as well embrace it. We are seeking to transcend into something greater so we will have more potential as human beings. We are finally in a position where augmentations are becoming a reality. With our brains being capable of so much It would be a shame to limit them to our current biology. We can start out with the basics like tattoos and piercings and remember how the first time we were modified we felt ourselves transforming. While some of us got tattoos and piercings for subcultural reasons there were those of us who got tattoos and piercings to look and feel like the people we truly were. I feel that this is what augmentations are all about and that we will continue to transform ourselves in the future to push our physical boundaries and become what we desire. A few months ago I had an idea of opening up a biohacking salon in LA. The idea was to get a bunch of people who were pushing the thresholds the of human body together in the same room. We would become engineers of our own bodies are reinvent ourselves on our own terms. It might look like something directly out of the book Snow Crash but it would be our actual lifestyle in 2012. Biopunk might replace steampunk as the dominant subculture and instead of blending the past with the future we would be blending our human bodies with the future of humanity. We would be enhancing ourselves as self-identified cyborgs and mutants who refused to let our biology limit our imaginations....."
"The informatics group at the Genome Institute at Washington University School of Medicine has released an integrated analysis and information-management system called the Genome Modeling System.
The system borrows concepts from traditional laboratory information-management systems — such as tracking methods and data-access interfaces, — and applies them to genomic analysis. The result is a standardized system that integrates both analysis and management capabilities, David Dooling, the assistant director of informatics at Wash U and one of the developers of GMS, explained to BioInform.
Dooling described the system during a presentation at the Genome Informatics conference hosted by Cold Spring Harbor Laboratory earlier this month.
During his talk, Dooling said that his group is working on integrating GMS with the Galaxy platform so that both systems can be accessed from each other.
Currently, users can download various analysis tools that Wash U researchers developed internally. However the team is working on packaging all the GMS capabilities into a single virtual machine image for the Ubuntu platform, a version of which they plan to release by the end of the year, Dooling told BioInform in a conversation this week..."
"PubMed Trend Analysis using Pipeline Pilot Keeping up to date with the explosion of published literature is virtually impossible these days. What are the hot topics and trends in science and industry? How are discoveries in one field of research impacting others, particularly yours? It's a catch-22 situation - you need to know what's going on in your field and related fields, but at the same time you need to be doing your own research. How can you most efficiently find the papers you need to read and keep abreast of developing fields of research? One way to help with this problem is to quickly and easily track trends and correlations in publications, for example to PubMed. These analyses can help reveal emerging topics and relationships in science, as well as those that are yesterday's news.
Trend Analysis
Trend and correlation analyses can be performed using the Text Analytics Collection (TAC) for Pipeline Pilot. TAC includes components dedicated for the search, retrieval, analysis and display of documents. To perform a trend analysis to PubMed, and show the results as a bar chart, set up a protocol similar to what is shown below..."
"The increasing ‘liveliness’ of machines and accessibility to the virtual world has raised questions about whether it is possible to uncouple the mind from the body in through a host of different strategies. The basic idea is that if we are able to escape the ties of our own flesh then we can upgrade them and even replace them with immortal ones. Performance artist Stelarc has made some of the most extreme and enduring work on this subject. The artist characteristically depersonalises his anatomy and claims that it is not only an object that can be subjected to re-designing but is also ‘obsolete’. During his performances, Stelarc mentally ‘vacates’ his own body to prove its obsolescence, and claims that his body is no more than a site for redesigning and re-engineering the human form.
In my view, Stelarc’s work paradoxically highlights the profound importance that embodiment holds for being human. When Stelarc dissociates his mind from his body he demonstrates its sheer plasticity and robustness. The artist then recolonizes the body with robots, communications technologies and soft prostheses as proof of this inbuilt physical redundancy. Yet the machines he hosts are given context by the presence of a body – for in its absence, they are just a collection of machines devoid of meaning. Moreover, redundancy is a characteristic of complex systems, which are a form of organization that does not obey the Cartesian, dualistic laws that govern machines. The artist’s rejection of these qualities simply highlights that the human body is not a machine."
Karmella A. Haynes, Francesca Ceroni, Daniel Flicker, Andrew Younger, and Pamela A. Silver
"RNA interference is a natural gene expression silencing system that appears throughout the tree of life. As the list of cellular processes linked to RNAi grows, so does the demand for tools to accurately measure RNAi dynamics in living cells. We engineered a synthetic RNAi sensor that converts this negative regulatory signal into a positive output in living mammalian cells, thereby allowing increased sensitivity and activation. Furthermore, the circuit’s modular design allows potentially any microRNA of interest to be detected. We demonstrated that the circuit responds to an artificial microRNA and becomes activated when the RNAi target is replaced by a natural microRNA target (miR-34) in U2OS osteosarcoma cells. Our studies extend the application of rationally designed synthetic switches to RNAi, providing a sensitive way to visualize the dynamics of RNAi activity rather than just the presence of miRNA molecules."
Rational Diversification of a Promoter Providing Fine-Tuned Expression and Orthogonal Regulation for Synthetic Biology by Benjamin A. Blount, Tim Weenink, Serge Vasylechko, Tom Ellis
"Yeast is an ideal organism for the development and application of synthetic biology, yet there remain relatively few well-characterised biological parts suitable for precise engineering of this chassis. In order to address this current need, we present here a strategy that takes a single biological part, a promoter, and re-engineers it to produce a fine-graded output range promoter library and new regulated promoters desirable for orthogonal synthetic biology applications. A highly constitutive Saccharomyces cerevisiae promoter, PFY1p, was identified by bioinformatic approaches, characterised in vivo and diversified at its core sequence to create a 36-member promoter library. TetR regulation was introduced into PFY1p to create a synthetic inducible promoter (iPFY1p) that functions in an inverter device. Orthogonal and scalable regulation of synthetic promoters was then demonstrated for the first time using customisable Transcription Activator-Like Effectors (TALEs) modified and designed to act as orthogonal repressors for specific PFY1-based promoters. The ability to diversify a promoter at its core sequences and then independently target Transcription Activator-Like Orthogonal Repressors (TALORs) to virtually any of these sequences shows great promise toward the design and construction of future synthetic gene networks that encode complex “multi-wire” logic functions."
E. coli neighborhood watch Nature Biotechnology "The bacterial signaling molecule indole is the direct cause of antibiotic resistance by some bacterial cells, reports a paper published online this week in Nature Chemical Biology. These findings improve our understanding of bacterial populations and point toward a potential new direction in the development of more effective antibacterial agents. Bacterial ‘persisters’ are cells that cannot be eradicated by existing antibiotic treatments even though the cells are genetically identical to cells that are killed by the treatment. Indole has been linked to cellular processes that are important in persisters, but its role was not clear. James Collins and colleagues show that indole serves as a signal for bacterial cells to enter a protected state. In particular, it decreases the impact of several antibiotics on E. coli, with cells that respond best to the molecule also demonstrating the highest level of protection. The authors also showed that indole activates two cellular pathways - oxidative stress and phage-shock responses - that are involved in persister formation. Importantly, another molecule that could also trigger these pathways causes the same formation of protected cells."http://bit.ly/GPyKJb
Science paper by Aleena R. Garner, David C. Rowland, Sang Youl Hwang1, Karsten Baumgaertel, Bryan L. Roth, Cliff Kentros, and Mark Mayford
"We investigated the effect of activating a competing, artificially generated, neural representation on encoding of contextual fear memory in mice. We used a c-fos–based transgenic approach to introduce the hM3Dq DREADD receptor (designer receptor exclusively activated by designer drug) into neurons naturally activated by sensory experience. Neural activity could then be specifically and inducibly increased in the hM3Dq-expressing neurons by an exogenous ligand. When an ensemble of neurons for one context (ctxA) was artificially activated during conditioning in a distinct second context (ctxB), mice formed a hybrid memory representation. Reactivation of the artificially stimulated network within the conditioning context was required for retrieval of the memory, and the memory was specific for the spatial pattern of neurons artificially activated during learning. Similar stimulation impaired recall when not part of the initial conditioning...."
Craig Venter, president and founder of the J. Craig Venter Institute, spoke to the California Institute for Regenerative Medicine governing board on January 17th, 2012, about the future of personalized medicine in which genomics, the study of genes and their function, is applied to pinpoint specific treatments for patients.
"The DNA sequence used to encode a polypeptide can have dramatic effects on its expression. Lack of readily available tools has until recently inhibited meaningful experimental investigation of this phenomenon. Advances in synthetic biology and the application of modern engineering approaches now provide the tools for systematic analysis of the sequence variables affecting heterologous expression of recombinant proteins. We here discuss how these new tools are being applied and how they circumvent the constraints of previous approaches, highlighting some of the surprising and promising results emerging from the developing field of gene engineering..."
"This is an ongoing project where we collect, analyze, and design microbial communities, exploring the bacterial connections between our bodies and our food. Shown below are cultures of skin bacteria donated by 71 individuals in March 2012..."
"Powerful modern technologies, including next-generation sequencing (NGS) and mass spectroscopy (MS), allow for rapid developments in systems biology and synthetic biology. These advances allow for an unprecedented approach for genomics, transcriptomics, epigenomics and proteomics, providing deeper insights into the interactions of genes, proteins and small molecules. Understanding how interacting biological systems regulate functional networks, chromatin, gene expression, signaling pathways and crucial cellular processes is essential for the future of systems medicine [1–8]. Although these innovative developments are considered pragmatic and funded by governments and industry, here the author discusses the latest advances and challenges in ‘rewiring’ cellular signaling circuits, and redesigning and editing genetic code for a systems medicine-based pragmatic revolution in health...."
"Yesterday, the Beijing Genomics Institute announced that they have used GPUs to speed up three genome data analysis tools: SOAP3 aligner, GSNP, and GAMA.
"We are drowning in the genome data that our high-throughput sequencing machines create every day," says Bingqiang Wang, head of high performance computing from BGI. "GPU acceleration of our genome analysis applications enables our scientists to crunch through data and gain insights into bacteria, plants and humans faster than was ever possible. It offers the potential for researchers and healthcare professionals to identify highly effective and affordable individualized medicines and treatments."..."
"Stanford doesn’t want me. I can say that because it’s a documented fact: I was once denied admission in writing. I took my last math class back in high school. Which probably explains why this quiz on how to get a computer to calculate an ideal itinerary is making my brain hurt. I’m staring at a crude map of Romania on my MacBook. Twenty cities are connected in a network of straight black lines. My goal is to determine the best route from Arad to Bucharest. A handful of search algorithms with names like breadth-first, depth-first, uniform-cost, and A* can be used. Each employs a different strategy for scanning the map and considering various paths. I’ve never heard of these algorithms or considered how a computer determines a route. But I’ll learn, because despite the utter lack of qualifications I just mentioned, I’m enrolled in CS221: Introduction to Artificial Intelligence, a graduate- level course taught by Stanford professors Sebastian Thrun and Peter Norvig...."
An interesting blog post. Thanks a lot for sharing. Something like this is on the horizon and the change might be quicker as we expect. I am still struggling with the question of the business model behind this all. In order to make people adapt to all these changes one need to tell them how to make a living. I disused this a lot the last days, but have no good answer. Ant further tips, advices, persons to contact... are very much appreciated.
C.DLT christopherdelatorre.com's comment March 29, 2012 9:29 PM
definitely will. and yes, a conundrum indeed.. I'm setting up an FB page for C.DLT over the weekend. I'll introduce my revised survey there, building on the preliminary survey u participated in last yr, with the aim of taking the pilot study a step further. the 'viable business model' is one of many engaging topics for the space! I'll tap u on the shoulder when the page is live.
Building novel applications with pipeline pilot to drive next generation sequencing
"Since the completion of the Human Genome Project nearly ten years ago, the science of genomics has undergone a transformation. Enabled by new DNA sequencing technologies, many more scientists and informaticians are interrogating larger and more complex data sets and are expanding the range of problems that can be addressed through sequencing. With the release of the Next Generation Sequencing (NGS) Collection for Pipeline Pilot , Accelrys is enabling scientists and informaticians to build and perform complex analyses of DNA sequence information in dramatically streamlined fashion. While the NGS Collection supports native data formats from all major sequencing platforms (including those from Illumina, Life Technologies, Roche/454), the system can adapt readily to new sequencing formats and analysis methods as they become available. Accelrys and Oxford Nanopore Technologies have been collaborating both on the development of pipelines that address general computational problems in NGS analysis, regardless of platform, as well as pipelines that support real-time nanopore based experimental analysis for use with the Oxford Nanopore product when it is commercially available. In this case study, collaborators from Oxford Nanopore describe features of the NGS Collection and how it will benefit genome researchers." “In no time at all and without requiring scientists to learn sophisticated analysis software, Pipeline Pilot helps scientists ask relevant, scientific questions about next generation sequencing data.” http://bit.ly/GOmDNP
"Kevin Warwick is Professor of Cybernetics at the University of Reading, where he carries out research in artificial intelligence, control, robotics and cyborgs. He is a Chartered Engineer and a Fellow of the IET.
Kevin was born in Coventry, UK and left school to join British Telecom, at the age of 16. He took his first degree at Aston University, followed by a PhD and research post at Imperial College, London. He subsequently held positions at Oxford, Newcastle and Warwick Universities before being offered the Chair at Reading.
As well as publishing over 500 research papers, Kevin's experiments into implant technology led to him being featured as the cover story on the US magazine, Wired. Kevin has been awarded higher doctorates (DSc) both by Imperial College and the Czech Academy of Sciences, Prague, and has received Honorary Doctorates from Aston University, Coventry University, Bradford University and Robert Gordon University. He was presented with The Future of Health Technology Award in MIT, was made an Honorary Member of the Academy of Sciences, St. Petersburg, and has received The IEE Senior Achievement Medal, the Mountbatten Medal and the Ellison-Cliffe Medal. In 2000 Kevin presented the Royal Institution Christmas Lectures, entitled "The Rise of the Robots".
Kevin's research involves the invention of an intelligent deep brain stimulator to counteract the effects of Parkinson Disease tremors. The tremors are predicted and a current signal is applied to stop the tremors before they start -- this is to be trialled in human subjects. Another project involves the use of cultured/biological neural networks to drive robots around -- the brain of each robot is made of neural tissue.
Kevin is perhaps best known for his pioneering experiments involving a neuro-surgical implantation into the median nerves of his left arm to link his nervous system directly to a computer to assess the latest technology for use with the disabled. He was successful with the first extra-sensory (ultrasonic) input for a human and with the first purely electronic telegraphic communication experiment between the nervous systems of two humans."
"Biochemical strategies that use a combination of synthetic oligonucleotides, thermostable DNA polymerases, and DNA ligases can produce large DNA constructs up to 1 megabase in length. Although these ambitious targets are feasible biochemically, comparable technologies for the chemical synthesis of long DNA strands lag far behind. The best available chemical approach is the solid-phase phosphoramidite method, which can be used to assemble DNA strands up to 150 bases in length. Beyond this point, deficiencies in the chemistry make it impossible to produce pure DNA. A possible alternative approach to the chemical synthesis of large DNA strands is to join together carefully purified synthetic oligonucleotides by chemical methods. Click ligation by the copper-catalyzed azide-alkyne (CuAAC) reaction could facilitate this process. In this Account, we describe the synthesis, characterization, and applications of oligonucleotides prepared by click ligation. The alkyne and azide oligonucleotide strands can be prepared by standard protocols, and the ligation reaction is compatible with a wide range of chemical modifications to DNA and RNA. We have employed click ligation to synthesize DNA constructs up to 300 bases in length and much longer sequences are feasible. When the resulting triazole linkage is placed in a PCR template, various DNA polymerases correctly copy the entire base sequence. We have also successfully demonstrated both in vitro transcription and rolling circle amplification through the modified linkage. This linkage has shown in vivo biocompatibility: an antibiotic resistance gene containing triazole linkages functions in E. coli . Using click ligation, we have synthesized hairpin ribozymes up to 100 nucleotides in length and a hammerhead ribozyme with the triazole linkage located at the substrate cleavage site. At the opposite end of the length scale, click-ligated, cyclic mini-DNA duplexes have been used as models to study base pairing. Cyclic duplexes have potential therapeutic applications. They have extremely high thermodynamic stability, have increased resistance to enzymatic degradation, and have been investigated as decoys for regulatory proteins. For potential nanotechnology applications, we have synthesized double stranded DNA catenanes by click ligation. Other researchers have studied covalently fixed multistranded DNA constructs including triplexes and quadruplexes."
"Bacterial cells that are genetically identical to members of their population that succumb to antibiotics can survive in a dormant state, thanks to chemical communication between bacteria.Surviving ‘persister’ cells have been implicated in chronic infections such as tuberculosis. James Collins and his team at Boston University in Massachusetts gave Escherichia coli the chemical indole, which the bacteria produce as a signalling molecule. Indole- treated E. coli were able to withstand higher levelsof several antibiotics than untreated bacteria. Moreover, the individual bacterial cells in a culture that were most responsive to indole were also those most resistant to antibiotics. Indole activates genes involved in responding to stress, and E. coli strains lacking stress-response genes produce fewer persisters. ....."Nature Research Highlights http://bit.ly/GJ7BqS
Original paper: Signaling-mediated bacterial persister formation by Nicole M Vega, Kyle R Allison, Ahmad S Khalil & James J Collins "Here we show that bacterial communication through indole signaling induces persistence, a phenomenon in which a subset of an isogenic bacterial population tolerates antibiotic treatment. We monitor indole-induced persister formation using microfluidics and identify the role of oxidative-stress and phage-shock pathways in this phenomenon. We propose a model in which indole signaling 'inoculates' a bacterial subpopulation against antibiotics by activating stress responses, leading to persister formation...." http://bit.ly/GVgfow #synbio #syntheticbiology
"It is commonplace to say teasingly of others that they live in an imaginary world. They go about their daily life much as others, but their thoughts and recollections have a surreal air—as if they lived in a world that is some combination of their imagination and the objective events of the physical world around them. Consider an experiment that deliberately creates this scenario, in which memories formed reflect not only the objective physical context of the study, but also imaginary “internal” stimuli that have somehow been artificially induced in the subject. Such a study could provide insights into the subtle interactions in cognition that occur between representations of the physical world and our internal thoughts. On page 1513 of this issue, Garner et al. (1) use elegant chemical and genetic engineering technology to peer into this aspect of the mind of a mouse."
"Scientist, inventor and human genome pioneer J. Craig Venter says advanced technologies exist to solve many of the world’s most pressing problems, like access to clean water and electricity, and many of them are also better for the environment than conventional energy and resource production techniques.
Transitioning to clean energy from fossil fuels is important in the fight against climate change, but increasing efficiencies and reducing waste in agriculture and other industries is just as important, particularly as global resources are stretched to meet a growing population, Venter says. Venter says he has developed microbial technology that can desalinate water while generating electricity at the same time.
“We don’t need one solution,” Venter says, speaking at The Wall Street Journal’s Eco:nomics conference in Santa Barbara, Calif. “We need to change how we produce food, find new ways to clean up water … or we’re going to be facing some tough challenges as we keep adding a billion people every few years.”.."
"Biological monitoring has failed to develop from simple binary assessment outcomes of the impacted/unimpacted type, towards more diagnostic frameworks, despite significant scientific effort over the past fifty years. It is our assertion that this is largely because of the limited information content of biological samples processed by traditional morphology-based taxonomy, which is a slow, imprecise process, focused on restricted groups of organisms. We envision a new paradigm in ecosystem assessment, which we refer to as ‘Biomonitoring 2.0’. This new schema employs DNA-based identification of taxa, coupled with high-throughput DNA sequencing on next-generation sequencing platforms. We discuss the transformational nature of DNA-based approaches in biodiversity discovery and ecosystem assessment and outline a path forward for their future widespread application."
"A couple weeks ago, we learned (thanks, Twitter!) that our Belly Button Biodiversity project had inspired another group of biologists and science communicators to explore body bacteria in interesting (and ahem, cheesy) new ways.
Christina Agapakis, a postdoctoral research fellow in synthetic biology at UCLA, and colleagues recently launched a new website Bacterially.org. They also set up shop at a local bar during SXSW (the annual music, film, and interactive conference and festival held in Austin) to get folks thinking, sampling and talking about their body microbes.
We asked Christina a few questions about Bacterially.org and her SXSW sampling experience:
What is Bacterially.org? Tell us about who you are and what your project is all about.
I’m a synthetic biologist so I’m interested in microbial ecology and symbiosis from more of an engineering perspective: what can organisms do as part of a community that they can’t do alone? I’m fascinated by how the biochemistry of individual bacteria changes when they are part of a community, especially because so much of what we know about microbes comes from bacteria studied in isolation and we still know so little about how microbes work together with other bacteria and with our bodies.
Bacterially.org is really a work in progress, a collaborative project that combines art and science where we explore these issues and collect images and data from the bacteria we’ve collected. We started the website because we wanted to be able to show people what their bacteria looked like and to learn along with us In many ways, we were inspired by what you did with the Belly Button Biodiversity project. We’re hoping to be complementary to your project, to learn from the diversity that you identify and sequence and to explore the chemistry and structure of microbial communities, and to perhaps recast bacterial ecologies as a substrate for design...."
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