Category Archives: Transhuman News

New capabilities for genome-wide engineering of yeast Science Daily "The goal of the work was really to develop a genome-scale engineering tool for yeast . . . traditional metabolic engineering focused on just a few genes and the few existing genome-scale engineering tools are only applicable to bacteria, not ...

Read the original here:
New capabilities for genome-wide engineering of yeast - Science Daily

May 5, 2017 by Jessica Sieff By understanding how species of Daphnia respond to toxic elements like industrial contaminants, toxic algae blooms or thermal stress, scientists can look at how environmental changes caused by agriculture and road runoff or warming temperatures and climate change could impact populations in lakes, rivers and standing bodies of water. Credit: Matt Cashore/University of Notre Dame

For many, experience with Daphnia, commonly known as water fleas, ends in high school. The organism is often used for science experiments exploring water toxicity, because of its sensitivity to environmental factors. But the tiny, transparent microcrustaceans have been studied intensively for more than 150 years, and new research published and featured on the cover of the journal G3 reveals scientists can now take a closer look at its genome.

Researchers have completed a new and improved genome sequence of Daphnia pulex (D. pulex), providing a clearer roadmap of the organism's genome so they can identify the genes and pathways that make this organism so successful in freshwater ecosystems.

Populations of Daphnia, barely visible to the naked eye, can be found in virtually every standing body of water on the planet, including Antarctica. They evolve quickly and are masters of responding to the conditions in their environment. Sensing the chemical cues of nearby predators, some species of Daphnia develop elaborate defensive structures such as spines and helmets that make them harder to eat. While scientists have gained a thorough understanding of what these tiny water fleas do to adapt to varying conditions, they don't yet know how they do it.

"That's why a system like this is so powerful," said Michael E. Pfrender, director of the Genomics & Bioinformatics Core Facility and associate professor in the Department of Biological Sciences and the Environmental Change Initiative at the University of Notre Dame. "We need this genomic infrastructure to add to the ecological context we already have to gain a better understanding of how Daphnia adapt. Because we have an improved genome sequence, we can get a more accurate catalog of genes and when thinking about response to the environment and chemical cues, it's the turning on and off of genes and pathways that's important. The picture is much more complete than it was before."

Calling it the "Portland Arch" genome after the Indiana Nature Preserve where the Daphnia was collected, the new assembly comes six years after the first sequence of D. pulex in 2011. The current study describes how scientists used the latest technology as part of a thorough and methodical process the result of which led to the identification of 18,440 genes.

D. pulex plays a vital role in Earth's ecology. Feeding off of algae and phytoplankton in standing freshwaters, they are the primary grazer in those environments, the "cows of lakes," said Pfrender. They're also primary forage, transferring all of that energy to the fish that eat them. By understanding how species of Daphnia respond to toxic elements like industrial contaminants, toxic algae blooms or thermal stress, scientists can look at how environmental changes caused by agriculture and road runoff or warming temperatures and climate change could impact populations in lakes, rivers and standing bodies of water.

"What happens to this vital part of the ecosystem when conditions change very rapidly? What genes allow some populations to cope with these changes while others fail?" Pfrender said. "That's what we want to find out. This genome sequence provides the toolkit."

Explore further: Study of the evolution of the micro-crustacean group Cladocera

More information: Zhiqiang Ye et al. A New Reference Genome Assembly for the Microcrustacean, G3: Genes|Genomes|Genetics (2017). DOI: 10.1534/g3.116.038638

Scientists of the Senckenberg Institute have studied the evolutionary history of the so-called "water fleas." These tiny crustaceans from the order Cladocera form the basis of the trophic pyramid and therefore play an important ...

Water fleas can thwart their enemies by growing defensive structures such as helmets and spines. What's more, this predator-induced 'arming' process is not a one-size-fits-all approach - they can even tailor their defensive ...

A common species of zooplanktonthe smallest animals in the freshwater food webcan evolve genetic tolerance to moderate levels of road salt in as little as two and a half months, according to new research published online ...

The key to helping animals evolve quickly in response to climate change could actually be their predators, according to a new UBC study.

A University of Michigan biologist combined the techniques of "resurrection ecology" with the study of dated lake sediments to examine evolutionary responses to heavy-metal contamination over the past 75 years.

There are many different kinds of crustaceans, ranging from the shellfish Swedish people eat at traditional crayfish parties every August to tiny relatives found in their millions in both freshwater and saltwater. One of ...

Much is known about flu viruses, but little is understood about how they reproduce inside human host cells, spreading infection. Now, a research team headed by investigators from the Icahn School of Medicine at Mount Sinai ...

For many, experience with Daphnia, commonly known as water fleas, ends in high school. The organism is often used for science experiments exploring water toxicity, because of its sensitivity to environmental factors. But ...

Researchers in dermatology at Lund University in Sweden believe they have cracked the mystery of why we are able to quickly prevent an infection from spreading uncontrollably in the body during wounding. They believe this ...

Vladimir Lukhtanov, entomologist and evolutionary biologist at the Zoological Institute in St. Petersburg, Russia, made a startling discovery: what people had thought was a population of a common species, turned out to be ...

(Phys.org)A team of researchers with the Howard Hughes Medical Institute has found that a ring of cells in the middle of the fruit fly brain acts as a compass, helping the insect understand where it is, where it has been ...

New research helps answer a long-standing mystery of how honeybees sense the size and strength of their colony, a critical cue for the bees to switch from investing solely in survival to also investing in reproduction.

Please sign in to add a comment. Registration is free, and takes less than a minute. Read more

Follow this link:
Scientists reveal new and improved genome sequence of Daphnia pulex - Phys.Org

From a single species of plant comes many teas. The tea tree, a shrub called Camellia sinensis, produces white, green, black and oolong teas. The tea's destiny is a matter of variables.

The final drink reflects the tea cultivar, the growing environment and how the leaves are processed - dried, crushed, steamed, blended. Farmers pluck 'baby' leaves, as one Snapple commercial put it in the mid-2000s, to begin making white tea.

And yet scientists in China, South Korea and the United States say there is another way to further tea's potential, beyond altering the dirt or the stages of harvest or processing.

DNA analysis could lead to "a more diversified set of tea flavours" by tracing the genes responsible for taste, according to Lizhi Gao, a botany professor at the Chinese Academy of Sciences' Kunming Institute of Botany.

He and colleagues have completed the "first high-quality" genome of the tea tree shrub, published this week in the journal Molecular Plant.

The plant took five years to analyse, thanks to the sheer number of DNA sequences involved.

"The tea tree genome is extremely large," Gao wrote in an email to The Washington Post - counting 3 billion base pairs, about four times the size of coffee's genome.

Of hot and invigorating drinks, coffee gets most of the buzz, at least in the United States: this country is home to 140 million daily coffee drinkers and the Starbucks Unicorn Frappuccino, and Americans consume more coffee than people anywhere else.

Researchers sequenced the genome of robusta coffee in 2014, hinting at a future of genetically modified coffees, as The Post reported at the time.

Scientists followed up with the arabica coffee genome in January.

Monday marked the tea tree's turn. It was a long time coming. Dried plants, recently found in a Chinese mausoleum, revealed that emperors in the Han Dynasty enjoyed tea 2,100 years ago, possibly as part of a soup.

The sovereigns were onto something. Today, 3 billion people drink tea, and by one estimate, for every mug of coffee consumed on the planet, humans drink three cups of tea.

Gao and his colleagues had to churn through the tea tree's huge levels of retrotransposons. These repeated DNA sequences, about 80 percent of the tea genome, duplicated themselves into the genome again and again over 50 million years of tea tree evolution.

"It is a mystery why retrotransposon sequences are abundant in this plant but not in another," Gao said.

But the researchers were most interested not in size but in the way tea produces tasty molecules.

"The tea-processing industries in tea-drinking countries, especially in China, have developed numerous tea products with diverse tea flavour," Gao said.

But processing techniques alone aren't enough, he said. Tea also depends on developing new plant varieties, containing unique combinations of flavourful molecules.

Three types of chemicals are most responsible for tea's taste. One is an amino acid only found in tea, called l-theanine, which in the last decade has been added to drinks that promote focus and concentration. (Such focus drinks are of dubious efficacy and lack supporting research.)

The second type of chemical is a class of flavonoid, or plant pigment molecule, called catechins. The third is caffeine, which evolved in tea independently of cacao and coffee, akin to the way both sea turtles and dolphins evolved flippers separately.

There are several theories as to why plants produce caffeine. Caffeine at high doses is a natural pesticide. But at low doses, as in some nectars, it may be giving insects a memorable jolt.

Caffeine was one tool in tea's repertoire of "disease defense and environmental stress tolerance" methods to help it adapt globally to diverse habitats, Gao said.

The tea genome answered a question the scientist had long pondered: Why can't we make tea from close Camelliasinensis cousins, such as the tea oil plant Camellia oleifera?

It turns out that C. oleifera and its 100 other Camellia relatives do not produce high amounts of the caffeine or catechin family of genes. (Caffeine and catechins are not proteins but secondary metabolites, which means many genes are required to construct them.)

Put another way, Gao said, the expression levels of caffeine- and catechin-related genes "determines the tea processing suitability".

The chief horticulturist at Britain's Royal Horticultural Society, Guy Barter, said plant breeders would welcome this work.

"Once you understand the basis for the flavours and the processing quality of the tea, you can then have genetic markers that breeders can look for when trying to produce new varieties," he told the BBC.

2017 Washington Post

This article was originally published by The Washington Post.

Excerpt from:
The Tea Plant's Genome Has Been Unlocked - And It's 4 Times That of Coffee - ScienceAlert

Indian company to collect genomic code of 1 lakh Asians, including over 30,000 Indians from various parts of the country

Hyderabad: Imagine a repository of over 30,000 Indian genomes covering a wide variety of groups from various regions and ethnic backgrounds accessible to researchers and healthcare providers.

Such a large Indian genomic data will not only enable researchers in finding the patterns of how genes are expressed but also can help in spotting mutations, which could be the answer for personalized therapy protocols for cancer patients, cardio-vascular ailments, end-stage kidney ailments and many more.

An Indian company along with several others in Asia has taken up this amibtious project to collect the genomic code of a whopping 1 lakh Asians, which also includes over 30,000 Indians from various parts of the country.

In the past, there have been isolated attempts at finding genomic sequence of one or two Indian groups but this is for the first time that a concerted effort is being taken up to collect the genome sequence of such a large set of population.

Standard genome Indian researchers need to have access to standard Indian genomic data to isolate the genes responsible for causing ailments among Indians. Almost all the medical standards, for instance ideal BP levels, sugar levels or anything else is based on Caucasian population. In the coming years, we intend to sequence genome of Indians and hopefully reach towards a standardized Indian genome, says CEO (India), MedGenome, Girish Mehta.

Talking to Telangana Today, Mehta said that MedGenome, a Bengaluru-based company, has already committed US$ 10 million for the project. The overall cost of the 1 lakh Asian genome is close to Rs. 100 crore or over 120 million US dollars.

We are collaborating with Singapore and South East Asian biotech companies to take part in preparing this genomic sequence. This will be very important because we will not only get to know the standard Indian genome but also the Asian genomic sequence, which is vital to form new treatment protocols, Mehta said, during a visit to Hyderabad.

Back in 2014, the United Kingdom had launched its own 1 lakh genome project and similar projects are under way in Qatar, Europe and the US.

Unfortunately, we are second largest population but we still do not have our own standard genome code. Earlier, genome sequencing of a single human being was very expensive but technology is rapidly making it very affordable. This is a four-year project and hopefully it should be completed in time, Mehta added.

Visit link:
Towards India's own standard genome sequence - Telangana Today