Readings of an ec...
Follow
Find
879 views | +2 today
 
Rescooped by Fernan Aguero from Amazing Science
onto Readings of an eclectic biologist
Scoop.it!

How does Elon Musk’s SF-to-LA-in-30-minut

How does Elon Musk’s SF-to-LA-in-30-minut | Readings of an eclectic biologist | Scoop.it

In July of last year, Tesla and SpaceX founder Elon Musk let slip that he was working on the Hyperloop — an ultra-fast mode of transportation that will get you from downtown Los Angeles to downtown San Francisco is under 30 minutes. This is a distance of roughly 340 miles, and would require speeds of around 700 mph, or almost the speed of sound. Perhaps most importantly, though, Musk said the Hyperloop will only cost around $6 billion — compared to the $60 billion of the proposed high-speed rail link connecting the two cities. So far, so good, except for one niggling issue: Musk still hasn’t told us how he intends to build it.

 

Some of the world’s brightest minds have speculated that a vacuum tube is the only way to do it — but before that idea could even get off the ground, Musk said that the Hyperloop isnot based on an evacuated tunnel. With that possibility ruled out, there aren’t actually that many ways of safely and economically propelling carriages at 700 mph (1126 kph). Furthermore, when you factor in Musk’s comments that the Hyperloop “can never crash,” has no need for rails, and is “immune to weather,” the architecture of the system becomes a real head-scratcher. Oh, did I mention that Musk envisions the entire system being self-powered by solar panels, and that it somehow stores energy inside the system itself, without the need for batteries?

 

How, then, might the Hyperloop work? One possibility is by acoustic levitation. At that speed, the biggest enemy is always going to be air resistance, which is why a vacuum tunnel is usually the favored solution: In a vacuum there is no air resistance (drag), and thus you can essentially move as fast as you like — much like a spacecraft barreling through the great black expanse. But it isn’t an evacuated tube, so it must be something else. Not to mention, a vacuum tunnel would definitely not fulfill the “can never crash” factor; poke a hole in a vacuum tube, and the results would be very messy indeed. 

 

What we need is another way of efficiently reducing drag. Just recently, we wrote about a research group that levitated arbitrarily shaped objects in acoustic waves. This technique involves an acoustic phenomenon called standing waves — essentially, waves that are held in place by interference. If you imbue these waves with enough power (volume) and hit just the right frequency, you can levitate an object. Standing waves, as the name implies, don’t move — but Björn Smedman and Charles Alexander both theorize that, if you pump these waves into a loop (which we assume the Hyperloop is), and change up the acoustic parameters slightly, then it might be possible to carry vehicles on the edge of these waves as they travel around the loop.

 

It turns out that, by hitching a ride on the peak of a sound wave, you only really have to deal with drag caused by air density (linear), which is much less than drag caused by air velocity (square).If you pump enough power into the acoustic wave (i.e. increase the amplitude), the air density increases but the relative air velocity drops. In effect, the vehicle in the wave is stationary, in reference to its surroundings. Eventually, as the sound wave gets stronger and stronger, you achieve almost adiabatic travel — travel that loses no energy at all to the environment via drag or friction. In theory, this process is so efficient that solar panels on top of the loop (a very large surface area!) can power the system. The acoustic waves, traveling continuously around the loop, would effectively act as energy storage.

 

While acoustic waves neatly solve the traveling-at-almost-the-speed-of-sound bit, they don’t explain how you would embark and disembark from the Hyperloop. The best guess at the moment is that there will be an extra section at each end of the loop for managing acceleration and deceleration. To board the Hyperloop, you will hop into a carriage at the San Francisco or Los Angeles terminus, and then be accelerated up to speed using arailgun before entering the main loop. At the other end, you will be gently decelerated before disembarking. This neatly ties in with Musk’s comments that the Hyperloop will be a“cross between a Concorde and a railgun and an air hockey table.”


Via Dr. Stefan Gruenwald
more...
No comment yet.

From around the web

Your new post is loading...
Your new post is loading...
Scooped by Fernan Aguero
Scoop.it!

Genome-wide analysis of 3′-untranslated regions supports the existence of post-transcriptional regulons controlling gene expression in trypanosomes

Genome-wide analysis of 3′-untranslated regions supports the existence of post-transcriptional regulons controlling gene expression in trypanosomes | Readings of an eclectic biologist | Scoop.it

A group of messenger RNAs encoding functionally interrelated proteins together with the trans-acting factors that coordinately modulate their expression is termed a post-transcriptional regulon due to their partial analogy to a prokaryotic polycistron. In trypanosomes RNA motif discovery tools showed the presence of groups of functionally related trypanosomatid genes with common cis-regulatory elements. 

more...
No comment yet.
Rescooped by Fernan Aguero from Amazing Science
Scoop.it!

Genome editing: Improved technique makes it easier to add or delete genes in living cells

Genome editing: Improved technique makes it easier to add or delete genes in living cells | Readings of an eclectic biologist | Scoop.it

Earlier this year, MIT researchers developed a way to easily and efficiently edit the genomes of living cells. Now, the researchers have discovered key factors that influence the accuracy of the system, an important step toward making it safer for potential use in humans, says Feng Zhang, leader of the research team. 

With this technology, scientists can deliver or disrupt multiple genes at once, raising the possibility of treating human disease by targeting malfunctioning genes. To help with that process, Zhang’s team, led by graduate students Patrick Hsu and David Scott, has now created a computer model that can identify the best genetic sequences to target a given gene.

“Using this, you will be able to identify ways to target almost every gene. Within every gene, there are hundreds of locations that can be edited, and this will help researchers narrow down which ones are better than others,” says Zhang, the W.M. Keck Assistant Professor in Biomedical Engineering at MIT and senior author of a paper describing the new model, appearing in the July 21 online edition of Nature Biotechnology.

The genome-editing system, known as CRISPR, exploits a protein-RNA complex that bacteria use to defend themselves from infection. The complex includes short RNA sequences bound to an enzyme called Cas9, which slices DNA. These RNA sequences are designed to target specific locations in the genome; when they encounter a match, Cas9 cuts the DNA. 

This approach can be used either to disrupt the function of a gene or to replace it with a new one. To replace the gene, the researchers must also add a DNA template for the new gene, which would be copied into the genome after the DNA is cut. 

This technique offers a much faster and more efficient way to create transgenic mice, which are often used to study human disease. Current methods for creating such mice require adding small pieces of DNA to mouse embryonic cells. However, the process is inefficient and time-consuming. 

With CRISPR, many genes are edited at once, and the entire process can be done in three weeks, says Zhang, who is a core member of the Broad Institute and MIT’s McGovern Institute for Brain Research. The system can also be used to create genetically modified cell lines for lab experiments much more efficiently.


Via Dr. Stefan Gruenwald
more...
No comment yet.
Scooped by Fernan Aguero
Scoop.it!

Research | Discovery of Trypanosomatids as common associates of Drosophila

Research | Discovery of Trypanosomatids as common associates of Drosophila | Readings of an eclectic biologist | Scoop.it

"Symbiotic microbial communities in animals play important roles in human health, the pest status of agricultural insects, and the evolutionary potential and diversification of animal lineages..."

Fernan Aguero's insight:

When analyzing the Drosophila microbiota using next-generation sequencing to characterize the yeast communities associated with natural Drosophila populations, Angus Chandler and Pamela James serendipitously discovered new species (currently uncultred and uncharacterized) of trypanosomatids.

 

more...
No comment yet.
Scooped by Fernan Aguero
Scoop.it!

BMC Genomics | Full text | A genomic scale map of genetic diversity in Trypanosoma cruzi

BMC Genomics | Full text | A genomic scale map of genetic diversity in Trypanosoma cruzi | Readings of an eclectic biologist | Scoop.it

"This study provides the first look at the genetic diversity of T. cruzi at a genomic scale. The analysis covers an estimated ~ 60% of the genetic diversity present in the population, providing an essential resource for future studies on the development of new drugs and diagnostics, for Chagas Disease." 

Fernan Aguero's insight:

A story of a clonal parasite with infrequent mixing (hybridization)

 

The T. cruzi population is composed of 6 evolutionary lineages. However, two  of them (TcV, and TcVI) are composed of hybrid, highly heterozygous strains. And extant strains from another two lineages (TcII, and TcIII) are thought to be related to the ancestral cells that gave rise to the hybrid strains. 

 

Interestingly, based on all genome data available and a re-sequencing dataset, it is clear that about 42% of all single nucleotide polymorphisms identified could be discovered just by analyzing the hybrid (highly heterozygous) CL-Brener genome/strain, that belongs to lineage TcVI.

 

As expected, re-sequencing genes from TcII or TcIII strains only revealed few novel SNPs (3-4%)

 

However, re-sequencing genes from TcI or TcIV strains (lineages not involved in the 'hybridization hypothesis') allowed the identification of ~ 18% new SNPs in each case. 

 

 

 

 

more...
No comment yet.
Scooped by Fernan Aguero
Scoop.it!

PLOS ONE: Diagnostic Peptide Discovery: Prioritization of Pathogen Diagnostic Markers Using Multiple Features

PLOS ONE: Diagnostic Peptide Discovery: Prioritization of Pathogen Diagnostic Markers Using Multiple Features | Readings of an eclectic biologist | Scoop.it
The availability of complete pathogen genomes has renewed interest in the development of diagnostics for infectious diseases. Synthetic peptide microarrays provide a rapid, high-throughput platform for immunological testing of potential B-cell epitopes. However, their current capacity prevent the experimental screening of complete “peptidomes”. Therefore, computational approaches for prediction and/or prioritization of diagnostically relevant peptides are required. In this work we describe a computational method to assess a defined set of molecular properties for each potential diagnostic target in a reference genome. Properties such as sub-cellular localization or expression level were evaluated for the whole protein. At a higher resolution (short peptides), we assessed a set of local properties, such as repetitive motifs, disorder (structured vs natively unstructured regions), trans-membrane spans, genetic polymorphisms (conserved vs. divergent regions), predicted B-cell epitopes, and sequence similarity against human proteins and other potential cross-reacting species (e.g. other pathogens endemic in overlapping geographical locations). A scoring function based on these different features was developed, and used to rank all peptides from a large eukaryotic pathogen proteome. We applied this method to the identification of candidate diagnostic peptides in the protozoan Trypanosoma cruzi, the causative agent of Chagas disease. We measured the performance of the method by analyzing the enrichment of validated antigens in the high-scoring top of the ranking. Based on this measure, our integrative method outperformed alternative prioritizations based on individual properties (such as B-cell epitope predictors alone). Using this method we ranked 10 million 12-mer overlapping peptides derived from the complete T. cruzi proteome. Experimental screening of 190 high-scoring peptides allowed the identification of 37 novel epitopes with diagnostic potential, while none of the low scoring peptides showed significant reactivity. Many of the metrics employed are dependent on standard bioinformatic tools and data, so the method can be easily extended to other pathogen genomes.
Fernan Aguero's insight:
A bioinformatics method to help reduce a proteome down to a manageable set of peptides for inclusion into a peptide array.
more...
No comment yet.
Scooped by Fernan Aguero
Scoop.it!

PLOS Neglected Tropical Diseases: Interactive Multimedia to Teach the Life Cycle of Trypanosoma cruzi, the Causative Agent of Chagas Disease

PLOS Neglected Tropical Diseases: Interactive Multimedia to Teach the Life Cycle of Trypanosoma cruzi, the Causative Agent of Chagas Disease | Readings of an eclectic biologist | Scoop.it

The present work aims to use a cell biologic approach to create multimedia materials that present basic aspects of the life cycle of T. cruzi and the morphology of its various developmental stages, as well as some biological processes such a division, motility, and endocytic activity. In this report, we present new instructional material with modern schemes and dynamic models that include 3D animations. 

 

The parasite Trypanosoma cruzi, which is the causal agent of the human disease known as Chagas disease, affects approximately 8 million people and causes more than 14,000 deaths per year in Latin America.  T. cruzi has a complex life cycle involving both vertebrate and invertebrate hosts in three well-defined developmental stages: (1) amastigotes, which are the proliferative forms found inside the vertebrate host cells; (2) epimastigotes, which are the proliferative forms found in the intestine of the invertebrate host; and (3) trypomastigotes, which are highly infective and originate from the amastigotes at the end of the intracellular cycle following their release into the intercellular space and into bloodstream. Trypomastigotes also arise from epimastigotes in the posterior regions of the digestive tract of the invertebrate host.

more...
No comment yet.
Rescooped by Fernan Aguero from Readings of an eclectic biologist
Scoop.it!

The development of drugs for treatment of sleeping sickness: a historical review

The development of drugs for treatment of sleeping sickness: a historical review | Readings of an eclectic biologist | Scoop.it

" [...] German scientist Paul Ehrlich was the first to exploit the properties of dyes for the development of chemotherapies. In 1901, Ehrlich became interested in the chemotherapy of trypanosomiasis and tested more than 100 synthetic dyes against Trypanosoma equinum, a species that causes a disease in equids, and T. brucei brucei, which is responsible for Nagana, a disease of cattle. The only dye displaying trypanocidal activity was a benzopurpurine compound named Nagana Red. When trypanosome-infected mice were treated with Nagana Red, parasites became undetectable in the animals for a short period and the treated mice survived 2 days longer than control mice (5/6 days versus 3/4 days). Ehrlich thought that the poor efficacy of Nagana Red was due to its low solubility which impaired the absorption of the drug into the bloodstream from the subcutaneous inoculation site. In 1903, Ludwig Benda working for Cassella Farbwerke near Frankfurt synthesised a derivative of Nagana Red, called Trypan Red, with an extra sulphonic acid function and enhanced water solubility. Trypan Red proved to be both curative and prophylactic for T. equinum infections in mice [...]"

 

--

And so it was that modern drug discovery was born!

more...
No comment yet.
Rescooped by Fernan Aguero from Amazing Science
Scoop.it!

How does Elon Musk’s SF-to-LA-in-30-minut

How does Elon Musk’s SF-to-LA-in-30-minut | Readings of an eclectic biologist | Scoop.it

In July of last year, Tesla and SpaceX founder Elon Musk let slip that he was working on the Hyperloop — an ultra-fast mode of transportation that will get you from downtown Los Angeles to downtown San Francisco is under 30 minutes. This is a distance of roughly 340 miles, and would require speeds of around 700 mph, or almost the speed of sound. Perhaps most importantly, though, Musk said the Hyperloop will only cost around $6 billion — compared to the $60 billion of the proposed high-speed rail link connecting the two cities. So far, so good, except for one niggling issue: Musk still hasn’t told us how he intends to build it.

 

Some of the world’s brightest minds have speculated that a vacuum tube is the only way to do it — but before that idea could even get off the ground, Musk said that the Hyperloop isnot based on an evacuated tunnel. With that possibility ruled out, there aren’t actually that many ways of safely and economically propelling carriages at 700 mph (1126 kph). Furthermore, when you factor in Musk’s comments that the Hyperloop “can never crash,” has no need for rails, and is “immune to weather,” the architecture of the system becomes a real head-scratcher. Oh, did I mention that Musk envisions the entire system being self-powered by solar panels, and that it somehow stores energy inside the system itself, without the need for batteries?

 

How, then, might the Hyperloop work? One possibility is by acoustic levitation. At that speed, the biggest enemy is always going to be air resistance, which is why a vacuum tunnel is usually the favored solution: In a vacuum there is no air resistance (drag), and thus you can essentially move as fast as you like — much like a spacecraft barreling through the great black expanse. But it isn’t an evacuated tube, so it must be something else. Not to mention, a vacuum tunnel would definitely not fulfill the “can never crash” factor; poke a hole in a vacuum tube, and the results would be very messy indeed. 

 

What we need is another way of efficiently reducing drag. Just recently, we wrote about a research group that levitated arbitrarily shaped objects in acoustic waves. This technique involves an acoustic phenomenon called standing waves — essentially, waves that are held in place by interference. If you imbue these waves with enough power (volume) and hit just the right frequency, you can levitate an object. Standing waves, as the name implies, don’t move — but Björn Smedman and Charles Alexander both theorize that, if you pump these waves into a loop (which we assume the Hyperloop is), and change up the acoustic parameters slightly, then it might be possible to carry vehicles on the edge of these waves as they travel around the loop.

 

It turns out that, by hitching a ride on the peak of a sound wave, you only really have to deal with drag caused by air density (linear), which is much less than drag caused by air velocity (square).If you pump enough power into the acoustic wave (i.e. increase the amplitude), the air density increases but the relative air velocity drops. In effect, the vehicle in the wave is stationary, in reference to its surroundings. Eventually, as the sound wave gets stronger and stronger, you achieve almost adiabatic travel — travel that loses no energy at all to the environment via drag or friction. In theory, this process is so efficient that solar panels on top of the loop (a very large surface area!) can power the system. The acoustic waves, traveling continuously around the loop, would effectively act as energy storage.

 

While acoustic waves neatly solve the traveling-at-almost-the-speed-of-sound bit, they don’t explain how you would embark and disembark from the Hyperloop. The best guess at the moment is that there will be an extra section at each end of the loop for managing acceleration and deceleration. To board the Hyperloop, you will hop into a carriage at the San Francisco or Los Angeles terminus, and then be accelerated up to speed using arailgun before entering the main loop. At the other end, you will be gently decelerated before disembarking. This neatly ties in with Musk’s comments that the Hyperloop will be a“cross between a Concorde and a railgun and an air hockey table.”


Via Dr. Stefan Gruenwald
more...
No comment yet.
Rescooped by Fernan Aguero from Virology and Bioinformatics from Virology.ca
Scoop.it!

The alternative "what it takes to be a bioinformatician"

Inspired by this beautifully written piece over at the NY Genome Centre Blog, I thought I'd quickly write down the alternative version, according to yours truly :) ...


Via Chris Upton + helpers
Fernan Aguero's insight:

The day-to-day truth of being a bioinformatician!

more...
No comment yet.
Scooped by Fernan Aguero
Scoop.it!

Journal of Cheminformatics | Abstract | UniChem: a unified chemical structure cross-referencing and identifier tracking system

Journal of Cheminformatics | Abstract | UniChem: a unified chemical structure cross-referencing and identifier tracking system | Readings of an eclectic biologist | Scoop.it
UniChem is a freely available compound identifier mapping service on the internet, designed to optimize the efficiency with which structure-based hyperlinks may be built and maintained between chemistry-based resources.
Fernan Aguero's insight:

Badly needed web service ... congrats to the EBI team for making it happen!

more...
No comment yet.
Rescooped by Fernan Aguero from Virology and Bioinformatics from Virology.ca
Scoop.it!

T-705 (Favipiravir) Induces Lethal Mutagenesis in Influenza A H1N1 Viruses in Vitro


Via burkesquires
Fernan Aguero's insight:

Very interesting! The mechanism of action of the drug is through widespread increased transversion mutations, causing the virus to lose fitness (infectivity). But no resistant mutations have been observed ...

more...
burkesquires's curator insight, January 17, 2013 9:16 AM

Interesting in that the drug causes mutation rate to increase beyond extinction threshold of the virus

Scooped by Fernan Aguero
Scoop.it!

PLOS Neglected Tropical Diseases: Diverse Inhibitor Chemotypes Targeting Trypanosoma cruzi CYP51

PLOS Neglected Tropical Diseases: Diverse Inhibitor Chemotypes Targeting Trypanosoma cruzi CYP51 | Readings of an eclectic biologist | Scoop.it

The similarity between the membrane sterol requirements of pathogenic fungi and those of the parasitic protozoon Trypanosoma cruzi, the causative agent of Chagas human cardiopathy, has led to repurposing anti-fungal azole inhibitors of sterol 14α-demethylase (CYP51) for the treatment of Chagas Disease. To diversify the therapeutic pipeline of anti-Chagasic drug candidates we exploited an approach that included directly probing the T. cruzi CYP51 active site with a library of synthetic small molecules. Target-based high-throughput screening reduced the library of ~104,000 small molecules to 185 hits with estimated nanomolar KD values, while cross-validation against T. cruzi-infected skeletal myoblast cells yielded 57 active hits with EC50 <10 µM. Two pools of hits partially overlapped. The top hit inhibited T. cruzi with EC50 of 17 nM and was trypanocidal at 40 nM.

The hits are structurally diverse, demonstrating that CYP51 is a rather permissive enzyme target for small molecules. Cheminformatic analysis of the hits suggests that CYP51 pharmacology is similar to that of other cytochromes P450 therapeutic targets, including thromboxane synthase (CYP5), fatty acid ω-hydroxylases (CYP4), 17α-hydroxylase/17,20-lyase (CYP17) and aromatase (CYP19). Surprisingly, strong similarity is suggested to glutaminyl-peptide cyclotransferase, which is unrelated to CYP51 by sequence or structure. Lead compounds developed by pharmaceutical companies against these targets could also be explored for efficacy against T. cruzi.

 

more...
No comment yet.
Scooped by Fernan Aguero
Scoop.it!

Eclecticism - Wikipedia, the free encyclopedia

Eclecticism - Wikipedia, the free encyclopedia | Readings of an eclectic biologist | Scoop.it

"Eclecticism is a conceptual approach that does not hold rigidly to a single paradigm or set of assumptions, but instead draws upon multiple theories, styles, or ideas to gain complementary insights into a subject, or applies different theories in particular cases."

 

--

Science = Eclectic by nature

more...
No comment yet.
Scooped by Fernan Aguero
Scoop.it!

The development of drugs for treatment of sleeping sickness: a historical review

The development of drugs for treatment of sleeping sickness: a historical review | Readings of an eclectic biologist | Scoop.it

" [...] German scientist Paul Ehrlich was the first to exploit the properties of dyes for the development of chemotherapies. In 1901, Ehrlich became interested in the chemotherapy of trypanosomiasis and tested more than 100 synthetic dyes against Trypanosoma equinum, a species that causes a disease in equids, and T. brucei brucei, which is responsible for Nagana, a disease of cattle. The only dye displaying trypanocidal activity was a benzopurpurine compound named Nagana Red. When trypanosome-infected mice were treated with Nagana Red, parasites became undetectable in the animals for a short period and the treated mice survived 2 days longer than control mice (5/6 days versus 3/4 days). Ehrlich thought that the poor efficacy of Nagana Red was due to its low solubility which impaired the absorption of the drug into the bloodstream from the subcutaneous inoculation site. In 1903, Ludwig Benda working for Cassella Farbwerke near Frankfurt synthesised a derivative of Nagana Red, called Trypan Red, with an extra sulphonic acid function and enhanced water solubility. Trypan Red proved to be both curative and prophylactic for T. equinum infections in mice [...]"

 

--

And so it was that modern drug discovery was born!

more...
No comment yet.