Tag Archives: molecular biology

cells in cages

cells in cages

Scientists have created nanometer-scale cages to hold living cells and better study their behavior. Check it out! 

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Crystal structure of 40S ribosomal subunit determined

The structure fo the 40S ribosomal subunit of eukaryotic ribosomes has recently been determined through x-ray crystallography, a method that allows scientists to reconstruct a 3-dimensional model of a protein in its native conformation. This discovery represents a significant breakthrough that scientists are hopeful will lead to an understanding of the evolution of ribosomes and eukaryote-specific mechanisms of protein synthesis.

Ribosomes, the small organelles that exist in millions of copies in all living cells, are responsible for one of life’s most essential processes- the creation of specific proteins with millions of different functions. Composed of a small and a large “subunit”, ribosomes are essentially tiny factories that process RNA and match specific RNA sequences with the amino acids necessary for building a particular protein. Because of this vital role, they have remained relatively highly conserved over evolutionary time. However, enough changes have accrued in ribosomes that, over time, they have become important biomarkers for distinguishing species. This technique has proved incredibly useful in describing the diversity of microbial communities. In particular, when  scientists want to get a sense of the ” species diversity” in a particular environmental sample, extraction and genetic sequencing of the small ribosomal subunit has become the gold standard.

Compared to prokaryotes, less is known about the structure and function of the eukaryotic ribosome. Not only are eukaryotic ribsomes larger and somewhat more complex, eukaryotic protein synthesis involves complex regulation and feedback pathways that are not present in prokaryotes. For example, the new crystal structure of the 40S subunit, or small eukaryotic ribosome subunit, reveals an interaction with a small protein known as an “initiation factor” that helps signal the ribsome to begin produciton of a new protein. The small subunit is responsible for binding numerous such initiation factors, and the new 3D structure promises to provide insight into eukaryotic-specific aspects of proteins synthesis, as well insight into the evolution of ribsomes by comparison of structures across a diverse range of species.

HydroTropi teaches scientists how to grow plants in space

In the zero gravity conditions aboard the International Space Station, scientists get to play around with plant growth in ways not possible on Earth. NASA has strongly supported zero-gravity plant research since the beginning, given its crucial importance to any sustainable long-term space exploration.

Recent research from ‘Hydrotropism and Auxin-Inducible Gene expression in Roots Grown Under Microgravity Conditions’, or  the HydroTropi experiment, promises to provide new insights into plant growth on a molecular level in response to water (hydrotropism) and gravity (gravitropism). Scientists are growing cucumber seedlings ‘in microgravity’ conditions, providing controlled levels of water to determine the magnitude of root growth responses. They are specifically looking at auxins, a suite of plant growth hormones that, when induced, stimulate cell division at a growing root tip. Understanding how environmental parameters such as water induce auxins in zero gravity will allow scientists to refine their understanding of plant gene expression and how to optimize plant growth in such an alien environment.

GeoChip: linking genetics with environmental processes

Over the past decade, environmental scientists have been casting a wider net in their attempts to understand complex environmental processes on a molecular scale. Once fascinating new line of research involves co-opting techniques developed by geneticists, largely for the biomedical industry, in order to understand how genes are important regulators of earth-scale processes as carbon and nitrogen cycling.

The GeoChip is a clear example of this search for new methods to answer old questions. Microbiologists  are working on remote Antarctic islands to understand some of the simplest nutrient cycling pathways in the world. The ecosystems they study are often composed of only a handful of fungal and microbial species. These simple food chains allow resarchers to contruct basic models of how energy and nutrients (such as carbon and nitrogen) are transferred.

This is where GeoChip comes in. GeoChip is a gene microarray chip designed to identify “functional genes” involved in important nutrient cycles. It allows the identification of genes in an environmental sample that regulate carbon fixation, decomposition, and atmospheric nitrogen fixation, to name a few.  Understanding what functional genes are available in a system allows scientists to both understand the potential of that system for cycling nutrients and better predict how that system will respond to environmental change.

Imagine a glass floor divided into hundreds of indentical squares. Each of these squares contains a different fragment of DNA, reconstructed by geneticists from known DNA sequences. When scientists want to probe an environmental sample for specific DNA sequences, they “wash” their sample over the floor. Fragments of DNA will stick to their complementary sequence on the floor, causing a square to light up. Scientists can “read” a GeoChip by identifying fluroescently lit spots where environmental DNA has attached. They use this information to develop a picture of the functional genes present in that system.

In Antarctica, GeoChip is already been used to answer important ecological questions. For example, scientists are finding that genes for nitrogen fixation, the crucial ecosystem process that produces plant-useable nitrogen in the soil, occur in lichen-rich areas. Lichens are believed to be among the earliest land colonizers, and the ability of lichen-dominated systems to add nitrogen to the soil may be an important finding in reconstructing the early colonization of terrestrial systems. Other findings include carbon-fixation genes in plots that lack vegetation, indicating microbial communities that are able to perform some sort of photosythesis in the absence of plants.

Citation:

Yergeau et al. 2007. Functional microarray analysis of nitrogen and carbon cycling genes across an Antarctic latitudinal transect. The ISME Journal 1: 163–179