Scientists Have Drafted a Complete Tree of Life

Humans, bacteria, daffodils: We’re a diverse bunch on the surface, but trace each and every Earthling back far enough, and you’ll arrive at a common ancestor. For the first time, scientists have built a comprehensive tree of life that binds us all together.

A draft of the One Tree, published Friday in the Proceedings of the National Academies of Sciences, includes the roughly 2.3 million named species of animals, plants, fungi and microbes. It shows how all of the major branches relate to one another and traces each individual group back to its shared beginnings in a prebiotic soup 3.5 billion years ago.

“This is the first real attempt to connect the dots and put it all together,” said principal investigator Karen Cranston of Duke University in a statement. “Think of it as Version 1.0.”

This family tree of Earth’s lifeforms is considered a first draft of the 3.5-billion-year history of how life evolved and diverged. Image Credit: opentreeoflife.org

To build the tree of all life, researchers compiled thousands of smaller trees that had already been published online. One of the big challenges was simply accounting for the different taxonomic names, spellings and misspellings that crop up across scientific papers. For instance, in a strange fluke of taxonomy that I can only hope has inspired some fantastically weird artwork, spiny anteaters once shared their scientific name with moray eels.

The tree will continue to receive updates over time, of course — scientists are still discovering new species of plants, animals and fungi every year, and with our growing arsenal of genomic sequencing tools, we’re finally beginning to unlock the vast diversity of the microbial world. The team behind the tree is developing software tools that’ll enable researchers to log in and revise things as new data is collected.

In the meanwhile, the biology nerds in the room can start exploring all of this juicy data right now. The tree, along with the raw data and source code that built it, is available for free online at

https://tree.opentreeoflife.org.

[Read the full scientific paper at PNAS h/t phys.org]

Follow the author @themadstone

ORIGINAL: Gizmodo

Maddie Stone

9/19/15

Supercritical Sanitation Systems

ORIGINAL: Duke / U of Missouri

At supercritical water conditions, organics in sewage are converted to harmless carbon dioxide, clean water and energy in seconds.

Engineers at Duke University and the University of Missouri, with funding from the Bill & Melinda Gates Foundation, are investigating the potential of Supercritical Water Oxidation (SCWO) and Supercritical Water Gasification (SCWG) in helping solving the world’s sanitation challenges.

The team is designing and building a demonstration unit that fits into a 20 ft. shipping container and will be ready for testing in a developing country in 2014.

Neighborhood-Scale Sewage Treatment. Image: Duke

Project Overview

primer.pdf

A Shared Vision

According to the World Health Organization, “2.4 billion people do not have access to any type of improved sanitation facility. About 2 million people die every year due to diarrheal diseases; most of them are children less than 5 years of age.”[i] The United Nation’s Millennium Development Goals Report from 2012 states that “sanitation coverage increased from 36 per cent in 1990 to 56 per cent in 2010 in the developing regions as a whole. Despite progress, almost half of the population in those regions … still lack access to improved sanitation facilities.”[ii] As sanitation goals remain out of reach, the associated health hazards and poor living conditions persist.

Unfortunately, established sewage system standards in developed countries do not provide a feasible model for developing countries which do not have sewage infrastructure, lack the economic means to build and sustain such elaborate systems, and do not have the water required to operate them. Resolving the sanitation issue in developing countries will require new, innovative sanitation solutions.

The Water, Sanitation and Hygiene program of the Bill & Melinda Gates Foundation has identified the sanitation challenge as their top priority. The foundation fosters the development of new technologies and tools that can help deliver sustainable sanitation where it is needed. As part of this strategy it is funding numerous investigations into a wide variety of potential technologies by universities and commercial entities worldwide. In April, 2013, Duke University received a ‘Reinvent the Toilet Challenge’ grant from the Gates Foundation to develop a demonstration unit for community scale sewage treatment.

Our Project
The Gates Foundation diagram above depicts a sanitation solution that starts with the individual and the toilet, includes the storage, transportation and treatment of human waste, and ends, ideally, with safe, usable byproducts such as fertilizer, fuel or clean water. Engineers at Duke University and the University of Missouri are designing a unit that addresses the treatment of human waste and possible reuse of the system’s byproducts. It will sanitize the collected waste of approximately 1200 people—a neighborhood-scale solution. The goal of this project is to produce a demonstration unit that fits into a 20 ft. shipping container and will be ready for testing in a developing country by summer 2014. A successful design will have a running cost of less than 5 cents per person per day at commercial volumes.

The technology being employed to meet this challenge, supercritical water oxidation (SCWO), is promising because it works quickly and generates energy in the forms of hot water and steam from the treatment of human waste. Furthermore, it does not require prior dewatering or drying of fecal sludge, and it effectively eliminates all types of harmful organisms. SCWO technology has already been implemented in several research and commercial applications to treat waste products, including polychlorinated biphenyls (PCBs), chemical weapons and sewage sludge. Duke and the University of Missouri seek to demonstrate that both SCWO and supercritical water gasification (SCWG), a related technology, have prominent roles to play in solving the world’s sanitation challenges. In addition, we will produce a business model plan that quantifies and optimizes the economic, environmental and social benefits of the unit.

Our Team

Before and after pictures from a SCWO unit
at University of Missouri.

The project is being led by Marc Deshusses of Duke University’s Department of Civil and Environmental Engineering in collaboration with Jay Golden of Duke’s Center for Sustainability and Commerce. The Carbon Recycling Center, led by Bill Jacoby of the University of Missouri’s Biological Engineering Department, provides engineering expertise where the rubber meets the road. Some of the key challenges the team will be addressing include the corrosion associated with sewage at high temperature and pressure as well as designing a system that can be successfully operated in a low-tech environment. In parallel with the technology development, sustainability experts at Duke will be leading the environmental and socio-technological investigations of the value proposition and creating a business model for the sanitation solution. Throughout the project, existing research and first hand site visits to cities and neighborhoods in India, South Africa and possibly Ghana will be utilized to help inform the optimum design of the sewage treatment unit and lay out the best path toward commercial implementation.

Our Timeline
The experimentation and design phase, using process development units at Missouri, will take place in the spring and summer of 2013. Construction of the demonstration unit in an actual shipping container will take place at Duke in the late summer and fall of 2013. In the winter and early spring of 2014, the demonstration unit will be tested at a local sewage treatment plant near Duke University in North Carolina. By summer 2014, the unit should be ready for field testing in a chosen city in South Africa, India or Ghana.

Brain-to-brain interfaces have arrived, and they are absolutely mindblowing

ORIGINAL: io9

Robert T. Gonzalez

FEB 28, 2013

In a stunning first for neuroscience, researchers have created an electronic link between the brains of two rats, and demonstrated that signals from the mind of one can help the second solve basic puzzles in real time — even when those animals are separated by thousands of miles.

Here's how it works. An "encoder" rat in Natal, Brazil, trained in a specific behavioral task, presses a lever in its cage it knows will earn it a reward. A brain implant records activity from the rat's motor cortex and converts it into an electrical signal that is delivered via neural link to the brain implant of a second "decoder" rat.

Still with us? Here's where things get interesting. Rat number two is in an entirely different cage. In fact, it's in North Carolina. The second rat's motor cortex processes the signal from rat number one and — despite being unfamiliar with the behavioral task the first rat has been conditioned to perform — uses that information to press the same lever.

The experiment, the results of which are published free of charge in today's issue of Scientific Reports, was led by Duke neuroscientist Miguel Nicolelis, a pioneer in the field of brain-machine interfaces (BMIs). Back in 2011, Nicolelis and his colleagues unveiled the first such interface capable of a bi-directional link between a brain and a virtual body, allowing a monkey to not only mentally control a simulated arm, but receive and process sensory feedback about tactile properties like texture. Earlier this month, his team unveiled a BMI that enables rats to detect normally invisible infrared light via their sense of touch.

But an intercontinental mind-meld represents something new: a brain-to-brain interface between two live rats — one that enables realtime sharing of sensorimotor information. It's a scientific first, and while it's not telepathy, per se, it's certainly something close. Neither rat was necessarily aware of the other's existence, for example, but it's clear that their minds were, in fact, communicating. "It's not the Borg," Nicolelis tells Nature's Ed Yong. What he has created, he says, is "a new central nervous system made of two brains."

Said nervous system is far from perfect. Untrained decoder rats receiving input from a trained partner only chose the correct lever around two-thirds of the time. That's definitely better than random odds, but still a far cry from the 95% accuracy of the encoder rats.

What this two-brain system does do, Nicolelis argues, is enable the rats to work with one another in unprecedented ways. And while neural communication between two animals on entirely separate continents is certainly impressive in its own right, Nicolelis says the most groundbreaking application of this technology — a 3-, 4-, or n-mind "brain net" — are still to come.

"These experiments demonstrated the ability to establish a sophisticated, direct communication linkage between rat brains," he said in a statement, "so basically, we are creating an organic computer that solves a puzzle."

"We cannot predict what kinds of emergent properties would appear when animals begin interacting as part of a brain-net," he continues. "In theory, you could imagine that a combination of brains could provide solutions that individual brains cannot achieve by themselves."

The study is published in the latest issue of Scientific Reports. (No subscription required!) For more details on the study, including feedback from underwhelmed neuroscientists (seriously), check out this great overview over at Nature.

Images and video via Nicolelis lab

Animals Offer Clues to Regeneration

ORIGINAL: LiveScience

Chelsea Toledo, National Institutes of Health

15 February 2013

Injured fins that lack bone-forming cells use another type of cell to regenerate. CREDIT: : Ken Poss, Duke University Medical Center. 

With the goal of finding ways to regenerate lost or injured body parts, researchers funded by the National Institutes of Health are exploring the strategies that some organisms use to regrow missing cells, organs and appendages. Here are a few examples.

Re-Forming From Stem Cells

Planarians are tiny freshwater flatworms — about the size of toenail clippings — that can re-form from slivers 1/300th of their original size. To do this, planarians use stem cells, called cNeoblasts, that have the ability to become almost any cell type in the body. Researchers at the Whitehead Institute for Biomedical Research studied the genes that are active in these stem cells to determine which of them are key players.

Planarians are worms that can re-form from tiny segments. CREDIT: Alejandro Sánchez Alvarado, Stowers Institute for Medical Research

The researchers identified 10 “renewal” genes that help the stem cells create more like themselves. In addition, the scientists pinpointed two genes that trigger stem cells to become different types and also have roles in renewal. Because half of planarians’ genes have parallels in people, the scientists aim to use their findings to find regenerative genes in human embryonic stem cells.

Ringers in Regeneration

Zebrafish, blue-and-white-striped fish that grow to be about 1.5 inches long, can regrow fins. To study how, scientists at Duke University Medical Center generated zebrafish with depleted levels of cells responsible for creating bone. These cells, called osteoblasts, normally increase in number after a fish loses a fin. The researchers expected that when osteoblast-deficient fish lost fins, they wouldn’t be able to regenerate them as quickly as those with normal levels of osteoblasts, if they could regenerate their fins at all. Surprisingly, all of the fish in the experiment regrew their fins, with recovery occurring at normal rates. Learning more about this process could aid the development of therapies for bone injury or loss in humans.

About an inch and half, zebrafish can regrow lost fins. CREDIT: Wikimedia Commons.

Sticking with the Same

Scientists at Washington University in St. Louis identified another zebrafish regeneration strategy by tracking how individual cells behaved in the stump of an amputated fin. One possibility was that adult nerve, bone and skin cells that make up the fin would revert into stem cells with the potential to become other cell types. However, this study showed that adult cells maintained their identities during regeneration, with skin cells in the stump only giving rise to skin cells in the new fin. This discovery suggests that inducing the cells that are already present to grow again could be an additional approach to replacing lost or injured tissues. 

While ear tissue doesn't normally grow back completely in mice, the lack of one gene makes ears heal without scars. CREDIT: Ellen Heber-Katz, The Wistar Institute.

Gene Off, Healing On

Yet another technique for promoting regeneration might be found in turning genes off. Several years ago, researchers at The Wistar Institute discovered that inactivating a single gene allowed holes in mouse ears to close without scarring. The researchers determined that this breed of mice has an inactive version of a gene involved in regulating cell growth and division. The finding offers new insight into regeneration in a mammal and could guide the direction of future research.

While these results hold promise for the development of treatments to replace or repair human tissue, they also illustrate the complexity of regeneration and raise such questions as how organisms know what’s missing and how they prevent replacement tissues from cancerlike overgrowth.

Learn more:

Cool Video: Re-creating Kidney

Nobel de Química 2012: Robert J. Lefkowitz y Brian K. Kobilka

ORIGINAL: La Vanguardia

Josep Corbella. Barcelona

10/10/2012

La Real Academia de Ciencias de Suecia ha concedido el galardón a los científicos estadounidenses Robert Lefkowitz y Brian Kobilka por sus investigaciones sobre un tipo de receptores de la membrana de las células que regulan múltiples funciones biológicas

Los científicos estadounidenses Robert J. Lefkowitz y Brian K. Kobilka han sido galardonados con el Premio Nobel de Química 2012 AP / EFE / Archivo

Los científicos estadounidenses Brian Kobilka y Robert Lefkowitz han ganado el premio Nobel de Química 2012 por sus investigaciones sobre un tipo de receptores de la membrana de las células que regulan múltiples funciones biológicas.

De los receptores acoplados a proteínas G, como se denominan, depende la actividad de hormonas como la adrenalina o la leptina, así como de neurotransmisores como la serotonina o la dopamina. Regulan, por lo tanto, desde el apetito al estado de ánimo, pasando por la tensión arterial, el tono muscular o las reacciones ante situaciones de estrés.

Aproximadamente la mitad de los fármacos existentes actualmente basan su eficacia en la acción de estos receptores, ha destacado la Real Academia de Ciencias de Suecia al anunciar el galardón. Su conocimiento detallado, gracias a las investigaciones de Kobilka y Lefkowitz ayudará a desarrollar nuevos fármacos más eficaces y con menos efectos secundarios.

Kobilka (Little Falls, Minnesota,1955) es profesor de la Universidad de Stanford en California. Lefkowitz (Nueva Yordk, 1943) es profesor de la Universidad Duke en Durham (Carolina del Norte). Ambos compartirán los 8 millones de coronas suecas (unos 900.000 euros) del premio.

La presente edición de los Premios Nobel arrancó el lunes con la concesión al británico John B. Gurdon y al nipón Shinya Yamanaka del de Medicina, y prosiguió ayer con el anuncio de que el Nobel de Física recayó en el francés Serge Haroche y el estadounidense David J. Wineland.

En los próximos días, la Academia Sueca seguirá dando a conocer el nombre de los ganadores de los Premios Nobel por este orden: mañana jueves 11 será el turno del Nobel de Literatura, seguido por el Nobel de la paz, el viernes día 12.

Por último, el próximo 15 se conocerá el ganador del premio Nobel de Economía. El de Economía, por cierto, es el único de los galardones que no quedó estableció por Alfred Nobel en su testamento, sino que se incorporó a la lista en 1969.