Teixobactin – New Antibiotic Attacks Ability of Bacteria to Build Cell Walls

Posted on January 31, 2015  Comments (0)

New class of antibiotic could turn the tables in battle against superbugs

The antibiotic, called teixobactin, kills a wide range of drug-resistant bacteria, including MRSA and bugs that cause TB and a host of other life-threatening infections.

It could become a powerful weapon in the battle against antimicrobial resistance, because it kills microbes by blocking their capacity to build their cell walls, making it extremely difficult for bacteria to evolve resistance.

It would be great if the exciting results carried through to real world results similar to the hope. Medical research is full of promising initial results that fail to deliver, however. We are at great risk if some new miracle anti-biotic isn’t found. Many people are investigating potential solutions.

Most antibiotics are isolated from bacteria or fungi that churn out lethal compounds to keep other microbes at bay. But scientists have checked only a tiny fraction of bugs for their ability to produce potential antibiotics because 99% cannot be grown in laboratories.

Lewis’s group found a way around the problem by developing a device called an iChip that cultures bacteria in their natural habitat. The device sandwiches the bugs between two permeable sheets. It is then pushed back into the ground where the microbes grow into colonies.

Working with a Massachusetts-based company, NovoBiotic, and researchers at the University of Bonn, [Kim] Lewis’s group screened 10,000 soil bacteria for antibiotics and discovered 25 new compounds. Of these, teixobactin was the most promising.

Though promising, Lewis said that years more work lie ahead before the drug could be available. Human clinical trials could begin within two years to check its safety and efficacy, but more development would follow that.

It is wonderful to read about the great work so many scientists are making in researching potential life saving drugs. Hopefully this antibiotic will save us from what will be catastrophic harm if some new antibiotic is not available soon.

Related: Search for Antibiotic Solutions Continues: Killing Sleeper Bacteria Cells (2013)New Family of Antibacterial Agents Discovered (2009)Potential Antibiotic Alternative to Treat Infection Without Resistance (2012)

Ranking Countries by Scientific Publication Citations: USA, UK, Germany…

Posted on January 24, 2015  Comments (1)

The SCImago Journal and Country Rank provides journal and country scientific indicators developed from the information contained in the Scopus database. I posted about this previously (in 2014, 2011 and 2008).

The data in the post is based on their data from 1996 through 2013. The web site also lets you look at these ranking by very specific categories. For example biotechnology #1 USA, #2 Germany, #3 UK, #4 Japan, #12 China or human computer interaction #1 USA, #2 Germany, #3 UK #4 Japan, #13 China).

I like looking at data and country comparisons but in doing so it is wise to remember this is the results of a calculation that is interesting but hardly definative. We don’t have the ability to measure the true scientific research output by country.

The table shows the top 6 countries by h-index and then some others I chose to list.

Country h-index 2010
h-index
2007
h-index
% of World
Population
% of World GDP total cites
USA 1,518 1,139 793     4.5%   22.2% 152,984,430
United Kingdom 918 689 465  0.9  3.5 37,450,384
Germany 815 607 408  1.1  5.0  30,644,118
France 742 554 376  0.9  3.8  21,193,343
Canada 725 536 370  0.5  2.4 18,826,873
Japan 635 527 372  1.8  7.8 23,633,462
Additional countries of interest (with 2013 country rank)
16) China 436 279 161  19.2  11.7  14,752,062
19) South Korea 375 258 161    .7  1.7  5,770,844
22) Brazil 342 239 148  2.8  3.0 4,164,813
23) India 341 227 146  17.5  2.6 5,666,045

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Manufacture Biological Sensors Using Silk and Looms

Posted on January 18, 2015  Comments (1)

The fabric chip platform from Achira Labs in India uses looms to manufacture biological sensors.

Image of process for creating silk test strips

image by Achira Labs

Yarn coated with appropriate biological reagents like antibodies or enzymes is woven into a piece of fabric at the desired location. Strips of fabric are then cut out, packaged and can form the substrate for di erent biological assays. Even a simple handloom could produce thousands of these sensors at very low cost.

The resulting fabrics can be used to test for pregnancy, diabetes, chronic diseases, etc.. Achira Labs, an Indian start-up, received $100,000 in Canadian funding in 2013 to develop a silk strip that can diagnose rotavirus, a common cause of diarrhea and can be used in diapers.

The company is planing to start selling silk diabetes test strips using there process this year and expects costs to be about 1/3 of the existing test strips using conventional manufacturing processes.

Related: Appropriate Technology Health Care Solution Could Save 72,000 Lives a YearWater WheelUsing Drones to Deliver Medical Supplies in Roadless AreasAppropriate Technology: Self Adjusting Glasses

20 Most Popular Post on Curious Cat Science and Engineering Blog in 2014

Posted on January 10, 2015  Comments (0)

Here are the most popular (by number of page views) posts on our blog in 2014.

I think it is interesting to see the distribution over the years of publication

2014: 1
2013: 2

2011: 2
2010: 5
2009: 3
2008: 4
2007: 2

2005: 1

Related: 10 Most Popular Posts on the Curious Cat Management Blog in 2014

Defying Textbook Science, Study Finds Proteins Built Without DNA Instructions

Posted on January 3, 2015  Comments (1)

Open any introductory biology textbook and one of the first things you’ll learn is that our DNA spells out the instructions for making proteins, tiny machines that do much of the work in our body’s cells. Results from a recent study show for the first time that the building blocks of a protein, called amino acids, can be assembled without blueprints – DNA and an intermediate template called messenger RNA (mRNA). A team of researchers has observed a case in which another protein specifies which amino acids are added.

“This surprising discovery reflects how incomplete our understanding of biology is,” says first author Peter Shen, Ph.D., a postdoctoral fellow in biochemistry at the University of Utah. “Nature is capable of more than we realize.”

To put the new finding into perspective, it might help to think of the cell as a well-run factory. Ribosomes are machines on a protein assembly line, linking together amino acids in an order specified by the genetic code. When something goes wrong, the ribosome can stall, and a quality control crew is summoned to the site. To clean up the mess, the ribosome is disassembled, the blueprint is discarded, and the partly made protein is recycled.

Yet this study reveals a surprising role for one member of the quality control team, a protein conserved from yeast to man named Rqc2. Before the incomplete protein is recycled, Rqc2 prompts the ribosomes to add just two amino acids (of a total of 20) – alanine and threonine – over and over, and in any order. Think of an auto assembly line that keeps going despite having lost its instructions. It picks up what it can and slaps it on.

“In this case, we have a protein playing a role similar to that filled by mRNA,” says Adam Frost, M.D., Ph.D., assistant professor at University of California, San Francisco (UCSF) and adjunct professor of biochemistry at the University of Utah. He shares senior authorship with Jonathan Weissman, Ph.D., a Howard Hughes Medical Institute investigator at UCSF, and Onn Brandman, Ph.D., at Stanford University. “I love this story because it blurs the lines of what we thought proteins could do.”

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Virgin Births in the Animal Kingdom

Posted on December 25, 2014  Comments (1)

Spectacular and Real Virgin Births

Scientists are discovering that virgin births occur in many different species; amphibians, reptiles, cartilaginous and bony fish and birds and it happens for reasons we don’t quite understand.

Initially, a virgin birth, also known as parthenogenesis, was thought to be triggered by extreme situations; it was only documented among captive animals, for example, perhaps by the stress, or isolation. A way to continue the bloodline when all other options had gone, when there was no other choice.

Not necessarily. It now appears that some virgin females produce offspring even in the presence of males.

Another interesting area of research for scientists. The value of sex to aid a species’ success is well understood. The value of being able to produce offspring when no males are around seems obvious also. But how this all works is quite interesting and again shows how much we have to learn.

Related: Fungus-gardening Ant Species Has Given Up Sex Completely (2010)Some Female Sharks Can Reproduce All by Themselves (2007)Amazon Molly Fish are All Female (2008)Bdelloid Rotifers Abandoned Sex 100 Million Years Ago (2007)

The Downside of Adopting the Metric System

Posted on December 9, 2014  Comments (4)

The only downside of adopting the metric system is less control over room temperature (based on my experience). Every ºC = ºF * 1.8 so have less control (when using only integers to control temperature as is the case in my experience).

Granted this could be solved easily by using .5 (option in air conditioning and heating controllers but in my experience they don’t) for Celsius. For Fahrenheit this works out to enough control for me. For Celsius in a fair number (lets say 15%) of systems it is a bit uncomfortable.

The specific circumstances add greatly to creating a problem. My guess is those that annoy me swing even further than 1 ºC, they move further in one direction in order to not turn on and off all the time. So maybe that moves to swings of 2 or 3 ºC at the measurement point. But that is another issue, the measurement on home (or hotel) systems is often 1 reader so the variation is often greater in other locations.

Add to that the imprecision of their measures, I don’t have good data, but I am confident that the measurement error is fairly high. I am pretty comfortable at about 25ºC for air conditioning. But in some places I am cold at 27º and others I am warm at 23º. It could be me, but I don’t think so (most of the time – sometimes it is me).

A long time ago I had some imprecise portable temperature gauge and while I wouldn’t stake my life on results based on it, it confirmed my feelings (when I felt it was warmer than the local reading said my device agreed and when I felt it was colder my device agreed). Hardly scientifically valid proof, but it made me more comfortable trusting my opinion on this matter anyway.

My guess is in a unit using ºF you often can be 4 or 5 degrees off (or more) in different locations. For some people that might be ok. But for me that often starts to be uncomfortable. If you convert the issue to that time 1.8 it is noticably worse.

Now in reality I don’t think it expands quite that much. While the manufactures balance the confusion of adding .5 to a Celsius controller and decide not to, I would think they don’t swing 1.8 times as far (in heating or cooling in order to not turn on and off all the time), but it is still let precise than using Fahrenheit integers. I believe (hope) they set their internal dynamics not based only on integers but could say for example turn off .5º past the setting and turn on when the conditions are .5º worse than the setting (so .5º too warm in the case of air conditioning, for example).

It is still lame the USA fails to adopt the metric system, but reducing this problem in the USA is one small benefit of holding off :-) I wonder if 1 in a million, 1 in 10 million… up to 1 in 7.2 billion people (just me, all alone in the world) have my concern for the lack of precision of heating and air conditioners when using the metric system.

Related: Google Lets Servers Stay Hot, Saving Air Conditioning CostsDo It Yourself Solar Furnace for Home HeatingUsing Algae Filled Window Panes to Provide Passive and Active Solar

Leslie Lamport Receives 2013 ACM Turing Award

Posted on November 22, 2014  Comments (1)

Leslie Lamport, a Principal Researcher at Microsoft Research, has been named as the recipient of the 2013 ACM A.M. Turing Award for imposing clear, well-defined coherence on the seemingly chaotic behavior of distributed computing systems, in which several autonomous computers communicate with each other by passing messages. He devised important algorithms and developed formal modeling and verification protocols that improve the quality of real distributed systems. These contributions have resulted in improved correctness, performance, and reliability of computer systems.

ACM (Association for Computing Machinery) announced that the funding level for the ACM Turing Award is now $1,000,000 (to be provided by Google). The new amount is four times its previous level. It seems to me the 14th of November 2014 is a bit late to announce the 2013 award winner, but for an extra $750,000 I would gladly wait a year (or a decade for that matter).

The new award level brings the computer science award to the level of Nobel Prizes and the Fields medal.

Leslie Lamport’s 1978 paper, “Time, Clocks, and the Ordering of Events in a Distributed System,” one of the most cited in the history of computer science.

Read more about the work of Leslie Lamport.

Related: Barbara Liskov wins Turing Award (2009)Donald Knuth, Computer Scientist (2006)Google 2006 Anita Borg Scholarship2008 Draper Prize for Engineering

Biology: How Wounds to Our Skin Heal

Posted on November 15, 2014  Comments (2)

This is an interesting webcast looking at how our bodies heal wounds to our skin.

Related: Science Explained: How Cells React to Invading VirusesTissue Regeneration in AnimalsScience Explained: Cool Video of ATP Synthase, Which Provides Usable Energy to UsLooking Inside Living CellsA Healthy Lifestyle is More About Health Care than the Sickness Management That We Call Health Care Is

Deinocheirus is a Totally Bizarre Dinosaur

Posted on November 8, 2014  Comments (0)

A very strange dinosaur has been uncovered, studied and explained by scientists. The dinosaur is from Mongolia about 70 million years ago.

“Deinocheirus is a totally bizarre dinosaur,” explains Phil Currie, professor and Canada Research Chair in Dinosaur Paleobiology at the University of Alberta. At 11 meters long and with an estimated weight of 6.4 tons, Deinocheirus was a behemoth to be sure—but hardly the giant tyrannosaur its massive arms may have suggested. Rather, the apparently disproportionately large forearms were more likely used for digging and gathering plants in freshwater habitats, or for fishing. Among its other unusual attributes are tall dorsal spines, truncated hoof-like claws on the feet to prevent sinking into muddy ground, and bulky hind legs that indicate it was a slow mover.

“Although the arms have been known since 1965 and have always aroused speculation because of their enormous size and sharp, recurving claws, we were completely unprepared for how strange this dinosaur looks,” says Currie. “It almost appears to be a chimera, with its ornithomimid-like arms, its tyrannosaurid-like legs, its Spinosaurus-like vertebral spines, its sauropod-like hips, and its hadrosaur-like duckbill and foot-hooves.”

Currie notes that Deinocheirus is a descendant of ostrich-like dinosaurs that were only slightly larger than humans, so its evolution into a giant, multi-tonne creature is almost certainly responsible for most of its unusual characteristics. “Its great size probably gave it some protection from the tyrannosaurid Tarbosaurus, which appears to have been relatively common in that part of Mongolia some 70 million years ago,” says Currie. To feed its great bulk, Deinocheirus was apparently an omnivore that ingested both plants and fish, as evident from fish remains found in its stomach contents.

“The study of this specimen has shown that even in dinosaurs like Deinocheirus, an animal that has been known for almost half a century, we can still learn surprising things about their anatomy,” says Currie. “Furthermore, it underlines the fact that even today, dinosaurs are still relatively poorly known. The fact that Deinocheirus is from the Nemegt Formation of Mongolia, one of the richest and most diverse dinosaur faunas known, hints that there are probably thousands of dinosaurs that we still do not know about from the majority of dinosaur localities in the world.”

Including poached dinosaur bones (stealing bones has long been a problem to the advancement of science) with the existing bones available to scientists allowed the new understanding of this amazing dinosaur. The now near-complete Deinocheirus specimen has been returned to its home for further study in the Mongolia Centre for Paleontology.

Full press release

Related: Ancient Whale Uncovered in Egyptian DesertNigersaurus, the Mesozoic CowDinosaur Remains Found with Intact Skin and TissueLobopodians from China (“the walking cactus” – an animal)Korea-Mongolia International Dinosaur Project

RoboBoat 2014 – Student Designed Autonomous Boats

Posted on November 1, 2014  Comments (10)

The first video gives a recap of RoboBoat 2014. In 2014, Embry-Riddle Aeronautical University took 1st place. University of Florida was 2nd, followed by the Robotics Club at UCF and in 4th place the Georgia Institute of Technology.

The teams must design and build an autonomous boat to compete in challenges. During the competition, student teams race their autonomous surface vehicles through an aquatic obstacle course. This includes littoral area navigation, channel following, and autonomous docking. The competition provides an opportunity for students to develop skills in system engineering by accomplishing realistic missions with autonomous vehicles in the maritime environment.

A team participated from Diponegoro University, Semarang, Indonesia, which is next to me – though about as far from the finals as you can be on the globe.

Related: 9th International Autonomous Underwater Vehicle Competition20th Annual US First Robotics CompetitionBotball 2009 FinalsRobo-One Grand Championship in Tokyo (2007)Eco-Vehicle Student Competition

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