Biomolecular machines

White Blood Cell Uses DNA 'Catapult' To Fight Infection
U.S. and Swiss scientists have made a breakthrough in understanding how a type of white blood cell called the eosinophil may help the body to fight bacterial infections in the digestive tract, according to research published online in Nature Medicine.

Hans-Uwe Simon, from the University of Bern, Switzerland, Gerald J.Gleich, M.D., from the University of Utah School of Medicine, and their colleagues discovered that bacteria can activate eosinophils to release mitochondrial DNA in a catapult-like fashion to create a net that captures and kills bacteria.

Dang, how cool is that. Like catching fish (bacteria) with a DNA net.
"This is a fascinating finding," says Gleich, professor of dermatology and internal medicine at the University of Utah and a co-author of the study. "The DNA is released out of the cell in less than a second."

Eosiniphils, which comprise only 1 to 3 percent of human white blood cells, are known to be useful in the body's defense mechanisms against parasites. But their exact role in the immune system is not clear. Unlike other white blood cells, which are distributed throughout the body, eosinophils are found only in selected areas, including the digestive tract. Mitochondria – often referred to as the power plants of the cell – are components within cells that are thought to descend from ancient bacteria. Although most cellular DNA is contained in the nucleus, mitochondria have their own DNA.

The researchers hope to learn more about how eosiniphils expel mitochondrial DNA. They speculate that the explosive mechanism might rely on stored energy, similar to the way plants release pollen into the air. "We don't know how eosinophils are capable of catapulting mitochondrial DNA so quickly," says Gleich.

Future investigation may focus on how this energy is generated and how this new knowledge can be applied to the treatment of bacterial infections and inflammatory diseases related to eosinophils.



More functions for previously thought Darwinian junk DNA.
How DNA Repairs Can Reshape Genome, Spawn New Species
Researchers at Duke University Medical Center and at the National Institute of Environmental Health Sciences (NIEHS) have shown how broken sections of chromosomes can recombine to change genomes and spawn new species.

"People have discovered high levels of repeated sequences in the genomes of most higher species and spun theories about why there are so many repeats," said Lucas Argueso, Ph.D., a research scholar in Duke's Department of Molecular Genetics and Microbiology. "We have been able to show with yeast that these repeated sequences allow the formation of new types of chromosomes (chromosome aberrations), and represent one important way of diversifying the genome."

The scientists used X-rays to break yeast chromosomes, and then studied how the damage was repaired. Most of the chromosome aberrations they identified resulted from interactions between repeated DNA sequences located on different chromosomes rather than from a simple re-joining of the broken ends on the same chromosome.

Chromosome aberrations are a change in the normal chromosome complement because of deletion, duplication, or rearrangement of genetic material. On rare occasions, the development of one of these new chromosome structures is beneficial, but more often DNA changes can be detrimental, leading to problems like tumors.

"Every so often the rearrangements may be advantageous," Argueso said. "Those particular differences may prove to be more successful in natural selection and eventually you may get a new species.

Repeat sequences aid in chromosome aberration repair and contributes to introduction of variability. :cool:
 
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Cell division: Cross-talk between DNA replication, DNA repair, cell cycle signaling and programmed cell death pathways​

The cell cycle is a highly regulated process and "takes micromanagement to the extreme". Various positive- and negative-feedback systems ensure that cells divide in a controlled manner. The process consists of a sequence of events by which a growing cell duplicates all its components and divides into two daughter cells, each with sufficient machinery to repeat the process. In eukaryotic cells, one round of cell division consists of two “gap” phases termed G1- and G2-, an S-phase during which duplication of all DNA happen, and an M-phase where proper segregation of duplicated chromosomes and chromatid separation occur. During each of these phases, regulatory signaling pathways monitor the successful completion of events in each phase before proceeding to the next phase. These regulatory pathways are commonly referred to as cell cycle checkpoints. Cell cycle checkpoints are activated in response the following (Figure 1):

  • Cellular damage
  • Exogenous cellular stress signals
  • Lack of availability of nutrients, hormones and essential growth factors.

During the G1 phase many signals intervene to influence cell division and the deployment of a cell’s developmental program (Figure 1). Crucial "decisions" are made to pass the G1 restriction point as commitment to replicate DNA and divide is irreversible until the next G1 phase. Failure to meet the correct conditions results in a failed attempt to divide. Signaling events converge to affect the phosphorylation status of the retinoblastoma protein (pRB) family (pRB, p107, and p130). Cyclin dependent kinases (CDKs) play a crucial role in pRB phosphorylation status and their activity is in turn controlled by cell stress and growth inhibitory signaling pathways. Sufficient phosphorylation (hyper-phosphorylation) of pRB causes it to dissociate from the elongation factor 2 (e2F) family of transcription factors. Dissociated e2F transcription factors mediate the transcription and activity of genes required for DNA replication during the S-phase.

As soon as the restriction point (G1/S transition checkpoint) is passed, initiation of DNA replication takes place at multiple sites on the chromosomes, called the origins of replication. The origin recognition complex (ORC) marks the position of replication origins in the genome and serves as the landing pad for the assembly of a multiprotein, pre-replicative complex (pre-RC) at the origins, consisting of ORC, cell division cycle 6 (Cdc6), Cdc10-dependent transcript (Cdt1), mini-chromosome maintenance (MCM) proteins, clamp-loaders, sliding clamps, helicases, DNA polymerases etc. The MCM proteins serve as key participants in the mechanism that limits eukaryotic DNA replication to once-per-cell-cycle and its binding to the chromatin marks the final step of pre-RC formation. Once the replisome is assembled, the transition to DNA replication is irreversibly completed and the cell enters the S-phase.

After successful completion of DNA replication the mitosis promoting factor (MPF) complex forms and plays a crucial role in nuclear envelope breakdown, centrosome separation, spindle assembly, chromosome condensation and Golgi fragmentation during mitosis. Cells only enter mitosis (G2/M transition) after the completion of the above events.

When a cell is unable to address the above circumstances, cell division is permanently halted and the cell either enters senescence or programmed cell death is activated (Figure 1). Programmed cell death (particularly apoptosis) removes potentially hazardous cells from a population of cells, resulting in the controlled destruction of the cells designated for destruction. Two checkpoints during the cell cycle exist.

  1. The DNA structure checkpoint
  2. The spindle checkpoint

The DNA structure checkpoint operates between the G1/S transition, the S-phase and the G2/M transition (Figure 1). The DNA structure checkpoint during the G1/S and G2/M transitions ensure that DNA damage is minimal while the S-phase DNA structure checkpoint also recognizes and deals with replication intermediates, stalled replication forks and unreplicated DNA. Whenever the criteria are not met during a checkpoint, a cell will not proceed to the next phase. Various signaling networks are activated and operate to ensure these criteria are met. DNA structure checkpoint signaling has the same pattern during any phase of the cell cycle (Figure 1):

  • Detection: Sensor proteins include proliferating cell nuclear antigen (PCNA)-like and replication factor C (RFC)-like protein complexes (see Sliding clamps, clamp-loaders and helicases), which are able to bind to damaged DNA to form a scaffold for downstream repair proteins. The Rad50/Mre11/NBS1 complex is also loaded onto damaged DNA sites and mediates downstream checkpoint and repair proteins.
  • Signal transduction: Activated sensor proteins in turn activate several signaling proteins which in turn activates DNA repair mechanisms and downstream effector proteins that controls cell cycle checkpoint signal transduction and programmed cell death signaling. Some examples include, ataxia telangiectasia mutated (ATM), ataxia telangiectasia and Rad3 related (ATR) p53 binding protein (53bp), the topoisomerase binding protein TopBP1, mediator of DNA damage checkpoint (MDC1), breast cancer 1 (BRCA 1) etc.
  • Effect: Downstream of the signal transducers include the the effector serine/threonine protein kinases CHK1 and CHK2. CHK’s transfer the signal of DNA damage to the phosphotyrosine phosphatases and cell division cycle proteins Cdc25A, Cdc25B, and Cdc25C as well the tumor-suppressor p53. Cdc25A controls the G1/S and S-phase transition (prevents pRB dissociation through dephosphorylation of pRB proteins) while Cdc25B and Cdc25C control the G2/M transition (both upregulating Wee1 and Myt1 by phosphorylation, which together control Cdc2/CyclinB activity). Tumor supressor p53 protein activity links DNA damage to programmed cell death.

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Figure 1: Dynamic control of cell cycle events through cell signaling, checkpoints, nutrient availability and extracellular stress. (Click for larger version)​

The spindle assembly checkpoint is a molecular system that ensures accurate segregation of mitotic chromosomes and functions during the M-phase of cell division. The spindle checkpoint depends on the activity of two systems.

  1. The 26S proteasome (APC/C-cdc20 complex) for the degradation of cyclin B.
  2. The anaphase promoting complex/cyclosome (APC/C-cdh1 complex) for the degradation of cyclins and securin

How are these for provocative sounding titles:
Voges D, Zwickl P, Baumeister W. The 26S proteasome: a molecular machine designed for controlled proteolysis. Annu Rev Biochem. 1999;68:1015-68.
Peters JM. The anaphase promoting complex/cyclosome: a machine designed to destroy. Nat Rev Mol Cell Biol. 2006 Sep;7(9):644-56.

Cyclin B is ubiquitinylated and degraded by the the 26S proteasome (APC/C-cdc20 complex) which in turn results in the activation of the APC/C-cdh1 complex. The APC/C-cdc20 complex is controlled by the mitotic checkpoint complex (MCC) which detects tubulin and kinetochore integrity. The APC/C-cdh1 complex mediates the degradation of securin resulting in chromosome segregation.
 
Cell division: Cross-talk between DNA replication, DNA repair, cell cycle signaling and programmed cell death pathways (continued)
There is a considerable amount of cross-talk between DNA repair mechanisms, programmed cell cycle signaling pathways, cell death pathways (autophagy, apoptosis, mitotic catastrophe etc.) and other cell stress signaling pathways. All these intricately interwoven pathways serve to ensure accurate cell division and removal of faulty cells from a population through programmed cell death. The problem comes when one of the checkpoints or programmed cell death pathways become corrupted and causes uncontrolled cell division in multicellular organisms. Cancer is one of the outcomes of abrogated cell death signaling and uncontrolled cell division. Programmed cell death is however not limited to multicellular organisms as bacteria also contain the necessary pathways to self destruct.

E.g.:
Engelberg-Kulka H, Amitai S, Kolodkin-Gal I, Hazan R. Bacterial programmed cell death and multicellular behavior in bacteria. PLoS Genet. 2006 Oct;2(10):e135.

Rice KC, Bayles KW. Molecular control of bacterial death and lysis. Microbiol Mol Biol Rev. 2008 Mar;72(1):85-109.

The DNA replication, DNA repair, cell cycle signaling and programmed cell death pathways all work together to ensure cell division is accurate and these processes are present in even the simplest self-replicating cells. :cool:
 
Here is a gene with a funny name with an awesome array of signaling capabilities:
Sonic-hedgehog

Also plays a role in brain development:
Tiny Cellular Antennae Trigger Neural Stem Cells
ale University scientists today reported evidence suggesting that the tiny cilia found on brain cells of mammals, thought to be vestiges of a primeval past, actually play a critical role in relaying molecular signals that spur creation of neurons in an area of the brain involved in mood, learning and memory.

The cilia found on brain cells of mammals until recently had been viewed as a mysterious remnant of a distant evolutionary past, when the tiny hair-like structures were used by single-celled organisms to navigate a primordial world.

“Many neuroscientists are shocked to learn that cells in the brain have cilia. Thus it was even more exciting to show that cilia have a key function in regulating the birth of new neurons in the brain,” said Matthew Sarkisian, post doctoral fellow in the department of neurobiology and co-first author on the study.

In the past decade, scientists have discovered primary cilia may have important functions in many animals. For instance, in 2000, Yale University scientists discovered defects in these cilia could lead to rare type of kidney disease. Researchers have been finding new functions for primary cilia ever since.

In the present study, researchers discovered that in mice, primary cilia act like antennae to receive and coordinate signals that spur creation of new brain cells. These cilia receive signals from a key protein required in development called “sonic hedgehog.” When the Yale team deleted genes needed to form primary cilia, they discovered that mice developed significant brain abnormalities including hydrocephalus. They also found that the absence of primary cilia on neural stem cells disrupted the ability of sonic hedgehog to signal neural stem cells to initiate creation of new neurons in the brain.

Furthermore, this group also observed cilia on dividing brain tumor cells. Postdoctoral fellow and co-first author Joshua Breunig said, “Considering sonic hedgehog is also heavily implicated in brain tumor formation, our study places the primary cilium at the crossroads of both regenerative neurobiology and neuro-oncology.”

An interesting take on the evolution of sonic-hedghog.
 
Proteins Have Controlled Motions, Researcher Shows
Iowa State University researcher Robert Jer****n believes that his research shows proteins have controlled motions.
Most biochemists traditionally believe proteins have many random, uncontrolled movements.

Research conducted by Jer****n, director of the L.H. Baker Center for Bioinformatics and Biological Statistics together with Guang Song, an assistant professor in computer science and graduate student Lei Yang, over a 10-year period shows that not only are protein motions more restricted, but also that these restricted, controlled motions are part of the function of the proteins.

The group's findings were recently published in the journal "Structure"

Using as an example a protein from HIV virus, Jer****n conducted his research using a simple model and tested to see how the proteins moved. The large number of reported structures show exactly the motions that are required for their function, and exactly the same motions as computed by Jer****n's model.

"This is one experimental case that is indicative, but there are many others," he said.

Jer****n believes this research is the first step to better understanding proteins and cell behaviors.

"There is the possibility of creating designer drugs with this newly discovered information," he said.

"These are models that conform to the point of view that the structures have been designed to exert very strong control of their motions," he said. "Those motions correspond closely to the motions needed for their function."

For instance, HIV virus protein structures that Jer****n studied did not move randomly, but actually opened and closed to allow access to other structures.

There is a binding site that must open to permit access to the protein and then close again to allow the protein to function, he said.

Because the protein structure opens and closes as part of it function, Jer****n believes that the motion is controlled and part of the function of the protein.

Jer****n's studies used the HIV virus, but he believes that the results are relevant to many other protein structures.
So much control, all the way down to protein motion. :) :cool:



Nature's awesome flying machine. The measly fly:
Flies In Danger Escape With Safety Dance
(Check out the videos :))
You may think you know how to swat a fly, but Michael Dickinson's work could teach you a thing or two.

Dickinson used superslow-motion video cameras to study how a fly avoids getting swatted. First, he and his graduate student Gwyneth Card coaxed the fly to stand on a glass prism anchored to the middle of a small moat. The prism let him see the fly from below and the side simultaneously.

Then, he moved a kind of mini fly swatter toward the fly and recorded how the fly reacted.

Dickinson says a fly will typically jump off the surface and then begin to fly away from the swatter. But the high-speed cameras revealed something amazing about what happened before the fly jumped.

"They perform an elegant little ballet with their legs," says Dickinson. "They move their legs around to reposition their bodies so that when they do jump, they will push themselves away from the looming threat."

That ballet appears to give them a critical edge in escaping the swatter.

Dickinson says what's remarkable about this body position is how fast it happens. In less than a 10th of a second, the fly has to perceive the threat using its eyes, determine what direction it's coming from, and then make the appropriate movement with its legs so it jumps in the right direction. And all this is accomplished by a brain that's the size of a poppy seed.

So what are the lessons for swatting flies?

"You shouldn't swat where you see them," says Dickinson. "You should anticipate that they're going to jump away from you. So you should extend your swat in the direction of the fly's anticipated motion."

Of course, that assumes you want to swat the fly. Dickinson rarely does.

"When you see a fly flitting around your hair, or your potato salad, you might see an annoyance," he says. "But in my lab you really see a marvelous machine, arguably the most sophisticated flying device on the planet."

Dickinson's research appears in the journal Current Biology.

The peer-reviewed article abstract:
Visually Mediated Motor Planning in the Escape Response of Drosophila
 
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Using Living Cells As Nanotechnology Factories
ScienceDaily (Oct. 8, 2008) — In the tiny realm of nanotechnology, scientists have used a wide variety of materials to build atomic scale structures. But just as in the construction business, nanotechnology researchers can often be limited by the amount of raw materials. Now, Biodesign Institute at Arizona State University researcher Hao Yan has avoided these pitfalls by using cells as factories to make DNA based nanostructures inside a living cell.

The results were published in the early online edition of the Proceedings of the National Academy of Sciences.

Yan specializes in a fast-growing field within nanotechnology -- commonly known as structural DNA nanotechnology -- that uses the basic chemical units of DNA, abbreviated as C, T, A, or G, to self-fold into a number of different building blocks that can further self-assemble into patterned structures.

"This is a good example of artificial nanostructures that can be replicated using the machineries in live cells"
said Yan. "Cells are really good at making copies of double stranded DNA and we have used the cell like a copier machine to produce many, many copies of complex DNA nanostructures."





Cells Coordinate Gene Activity With FM Bursts, Scientists Find

Proteins Have Controlled Motions, Researcher Shows[/URL][/B]
ScienceDaily (Oct. 2, 2008) — How a cell achieves the coordinated control of a number of genes at the same time, a process that's necessary for it to regulate its own behavior and development, has long puzzled scientists.
Michael Elowitz, an assistant professor of biology and applied physics at the California Institute of Technology (Caltech), along with Long Cai, a postdoctoral research scholar at Caltech, and graduate student Chiraj Dalal, have discovered a surprising answer. Just as human engineers control devices ranging from dimmer switches to retrorockets using pulsed -- or frequency modulated (FM) -- signals, cells tune the expression of groups of genes using discrete bursts of activation.

Elowitz, who is also a Bren Scholar and an investigator with the Howard Hughes Medical Institute, and his colleagues discovered this process by combining mathematical and computational modeling with experiments on individual living cells. The scientists looked specifically at the molecular changes within simple baker's yeast (Saccharomyces cerevisiae) cells after exposure to excess calcium, which increases in concentration in cells in response to stressful conditions such as high salt levels, alkaline pH, and cell wall damage.

The scientists tracked that response using a protein called Crz1 labeled with a green fluorescent tag. Crz1 is stimulated in response to high calcium levels and activates genes that help protect the cell. The glowing of the fluorescent marker allowed Elowitz and colleagues to visualize the movement of Crz1 as it travelled within the cell from the cytoplasm into the cell nucleus and out again into the cytoplasm. Using time-lapse microscopy, they created "movies" of that movement.



Most biochemists traditionally believe proteins have many random, uncontrolled movements.


Research conducted by Jer****n, director of the L.H. Baker Center for Bioinformatics and Biological Statistics together with Guang Song, an assistant professor in computer science and graduate student Lei Yang, over a 10-year period shows that not only are protein motions more restricted, but also that these restricted, controlled motions are part of the function of the proteins.

The group's findings were recently published in the journal "Structure"

Using as an example a protein from HIV virus, Jer****n conducted his research using a simple model and tested to see how the proteins moved. The large number of reported structures show exactly the motions that are required for their function, and exactly the same motions as computed by Jer****n's model.

"This is one experimental case that is indicative, but there are many others," he said.

Jer****n believes this research is the first step to better understanding proteins and cell behaviors.

"There is the possibility of creating designer drugs with this newly discovered information," he said.

"These are models that conform to the point of view that the structures have been designed to exert very strong control of their motions," he said. "Those motions correspond closely to the motions needed for their function."

For instance, HIV virus protein structures that Jer****n studied did not move randomly, but actually opened and closed to allow access to other structures.

There is a binding site that must open to permit access to the protein and then close again to allow the protein to function, he said.

Because the protein structure opens and closes as part of it function, Jer****n believes that the motion is controlled and part of the function of the protein.

Jer****n's studies used the HIV virus, but he believes that the results are relevant to many other protein structures.

So much control, all the way down to protein motion. :):cool:
 
I've never seen someone talk to themself, quite as much as you do :p
Was wondering - have you ever had a power outage while compiling these posts? I can't imagine you about to click "Submit" and Eskom fails you... :p
 
Here, it's not so hard:
Something related to the replisome and DNA repair:
DNA Repair: Structure Of The Mre11 Protein Bound To DNA
ScienceDaily (Oct. 2, 2008) — Repairing breaks in the two strands of the DNA double helix is critical for avoiding cancer. In humans and other organisms, a molecular machine called the MRN complex is responsible for finding and signaling double-strand breaks (DSBs), then launching the error-free method of DNA repair called homologous recombination.

PIC



Something related to the movement of cells:
Landmark Discovery Of 'Engine' That Drives Cell Movement
ScienceDaily (Oct. 7, 2008) — How a cell assembles its internal machinery required for cell movement has been revealed for the first time.
The researchers discovered a complex of three proteins that directly regulates the myosin network within a cell, thus generating traction force to propel the cell forward. (Myosin is the most common protein found in muscle cells, and is responsible for the elastic and contractile properties of muscle. A different form of myosin is involved in cell movement.)

This action of the tripartite protein complex may be likened to a spring in a toy motorcar – when the protein complex assembles and moves backwards within the cell, it resembles the wound up "engine" of the toy car that has been pulled backwards.


Subsequent disassembling of the protein complex and the resultant forward movement of the cell can be likened to the released spring which unleashes the earlier stored potential energy to propel the car forward.

Michael Sheetz, Ph.D., who is William R Kenan Jr Professor of Cell Biology at the Department of Biological Sciences, Columbia University, and also Distinguished Visiting Professor at the National University of Singapore, said, "This is an exciting paper because Leung's group has discovered an unexpected step in cell migration and contractility — a complex of three proteins including a form of myosin, that is responsible for assembling most of the other myosin components involved in motile processes. The assembly mechanism has been a major mystery and is critical in a variety of diseases from cardiovascular to aging. Now we have a new tool to understand the bases of these critical processes."

Of the three proteins MRCK, LRAP35a and MYO18A, MRCK was discovered by the GSK-IMCB group 10 years ago, while the other two had hitherto unknown functions. Dr. Leung of IMCB said, "The success of the work relies on the commitment and perseverance of the team. A major contributor, Dr. Ivan Tan, is a home-grown scientist who has been working on this project for many years and he has had several clues as to how the system functions for some time, but it was only recently that the jigsaw puzzle was put together. The system has the potential to unravel other as yet undiscovered mechanisms that coordinate the different 'engines' for proper cell migration."


Emphasis mine.
Hard work with spectacular results :cool:.
 
Robustness and back-up systems​
New Evidence On The Robustness Of Metabolic Networks
ScienceDaily (Sep. 8, 2008) — Biological systems are constantly evolving in ways that increase their fitness for survival amidst environmental fluctuations and internal errors. Now, in a study of cell metabolism, a Northwestern University research team has found new evidence that evolution has produced cell metabolisms that are especially well suited to handle potentially harmful changes like gene deletions and mutations.

You Can Be Replaced: Immune Cells Compensate For Defective DNA Repair Factor


Genetic instability can lead to multiple problems, including cell death and many forms of cancer. Therefore, it is absolutely critical for cells to have both the means to constantly survey genes for damage and the mechanisms to repair broken DNA. Currently, there are six well characterized classical non-homologous end-joining (C-NHEJ) factors that repair double strand breaks (DSBs) in mammalian cells.Lymphocytes, a type of immune cell, use a kind of genetic shuffling called variable, diversity, joining V(D)J recombination. This gene shuffling occurs during lymphocyte development and helps to produce diverse immune system cells that can recognize all sorts of different foreign substances, called antigens, that might pose a threat to the organism. Previous work in mice has shown that deficiency of C-NHEJ factors results in a severely compromised immune system, because of incomplete V(D)J recombination, along with increased sensitivity to cellular ionizing radiation (IR) and genomic instability.
Preadaptations are good for the future. :cool:
 
When under attack, plants can signal microbial friends for help
11:39 a.m., Oct. 17, 2008----Researchers at the University of Delaware have discovered that when the leaf of a plant is under attack by a pathogen, it can send out an S.O.S. to the roots for help, and the roots will respond by secreting an acid that brings beneficial bacteria to the rescue.
The finding quashes the misperception that plants are “sitting ducks”--at the mercy of passing pathogens--and sheds new light on a sophisticated signaling system inside plants that rivals the nervous system in humans and animals.

Seems like The Happening is not too far fetched... :eek:?
 
Saga Of the Swamp Thing #24 - Moore & Bissette

The green Biosphere proposes a culling......
Hehe, you sure do like dem comics :).


Newly discovered mechanics of a molecular machine that transports proteins.

Channel hopping: protein translocation through the SecA–SecY complex
Newly synthesized proteins are translocated across the eukaryotic endoplasmic reticulum membrane or the prokaryotic plasma membrane through an evolutionarily conserved protein conducting channel or translocon known as Sec61 in eukaryotes and SecY in prokaryotes. In bacteria, the SecA ATPase is thought to be the motor for translocation through the SecY channel. Two papers by Tom Rapoport and colleagues report the long-awaited structure of the SecA–SecY complex from bacteria. The structure, reveals major conformational changes between both partners and suggests that SecA uses a two-helix finger to push translocating proteins into SecY's cytoplasmic funnel. Crosslinking studies provide further experimental support for this mechanism. In a third paper, Osamu Nureki and colleagues present a crystal structure of SecY bound to an anti-SecY Fab fragment revealing a pre-open state of the channel. Together these three papers provide novel insights into the path taken by a translocating protein. In News and Views, Anastassios Economou takes stock of where this work leaves current knowledge of this 'astonishing cellular nanomachine'

Research articles:
Structure of a complex of the ATPase SecA and the protein-translocation channel
A role for the two-helix finger of the SecA ATPase in protein translocation
Conformational transition of Sec machinery inferred from bacterial SecYE structures
Over 30% of proteins are secreted across or integrated into membranes. Their newly synthesized forms contain either cleavable signal sequences or non-cleavable membrane anchor sequences, which direct them to the evolutionarily conserved Sec translocon (SecYEG in prokaryotes and Sec61, comprising alpha-, bold gamma- and bold beta-subunits, in eukaryotes). The translocon then functions as a protein-conducting channel1. These processes of protein localization occur either at or after translation. In bacteria, the SecA ATPase2, 3 drives post-translational translocation. The only high-resolution structure of a translocon available so far is that for SecYEbold beta from the archaeon Methanococcus jannaschii 4, which lacks SecA. Here we present the 3.2-Å-resolution crystal structure of the SecYE translocon from a SecA-containing organism, Thermus thermophilus. The structure, solved as a complex with an anti-SecY Fab fragment, revealed a 'pre-open' state of SecYE, in which several transmembrane helices are shifted, as compared to the previous SecYEbold beta structure4, to create a hydrophobic crack open to the cytoplasm. Fab and SecA bind to a common site at the tip of the cytoplasmic domain of SecY. Molecular dynamics and disulphide mapping analyses suggest that the pre-open state might represent a SecYE conformational transition that is inducible by SecA binding. Moreover, we identified a SecA–SecYE interface that comprises SecA residues originally buried inside the protein, indicating that both the channel and the motor components of the Sec machinery undergo cooperative conformational changes on formation of the functional complex.

Exquisite control of biomolecular processes with the aid of nanomachines all the way down to the simplest organisms :cool:.
 
Hehe, you sure do like dem comics :).

It's an Alan Moore comic.

Point being of course that sentient plant life has a long history in literature and film.

Tolkein's Ents, Old Man Willow, Moore's interpretation of Swamp Thing, In Dante's inferno people have been turned into trees. The plant from Little shop of Horrors and Morticia Adamms guard plants. Piers Anthony frequently uses a variety of trees.

The theme of plants using an avatar is even used in the Thief game series.
 
Yep, your comics and pop media knowledge is superior ;).

Ever wondered how an embryo develops?
Read up on the "fifth DNA molecule" or epigenetics. Read a little on genomic imprinting and X-inactivation. Also, totipotential cells and pluropotency.


During development a genetic program governs the developmental process. Primordial germ cells (PGC) are prevented from entering the somatic program (somatic differentiation) and are demethylated (genome-wide erasure of existing epigenetic modifications/remocal of a methyl group from cytosine). Then the gametes are imprinted (targeted DNA methylation/addition of methyl group to cytosine) during gametogenesis, only to be demethylated again after fertilization. Then during development, DNA is methylated again, causing totipotential cells to become pluripotent. These genomic reprogramming events are strictly controlled.

And now:
Scientists trace molecular origin of proportional development.

CINCINNATI – When it comes to embryo formation in the lowly fruit fly, a little molecular messiness actually leads to enhanced developmental precision, according to a study in the Oct. 14 Developmental Cell from Cincinnati Children's Hospital Medical Center.

While the fundamentals of this tiny bug's reproductive biology may seem insignificant, one day they could matter quite a bit to humans. That's because the study provides new information about how cells choose their own fates, especially in maintaining the size relationship and proportionality of body parts during embryonic development, said Jun Ma, Ph.D., a researcher in the divisions of Biomedical Informatics and Developmental Biology at Cincinnati Children's and the study's corresponding author.

"We used the fruit fly in our study to trace the molecular origin of where body proportionality comes from, directly affecting how we think about precision control mechanisms during development," Dr. Ma said. "This new information is a basic, but very important, step. Although humans are far more complex, this could one day help us understand how two different-sized babies – with different mothers providing varied environmental and genetic influences – are born alike, with properly sized heads and limbs."

Besides discovering a scientific platform that will advance studies into precise, or normal, development, Dr. Ma and colleagues hope their knowledge will facilitate research into abnormal development, like certain types of birth defects.

Although fruit flies have miniscule brains and dine on rotten fruit, genetically the species has quite a bit in common with humans – a concept known as evolutionary conservation. This relationship has long made the insect a model for studying body patterning in animals.

Dr. Ma's team probed how a gene transcription regulatory protein called Bicoid turns on another gene, known as Hunchback. Hunchback instructs the embryo's anterior to begin formation of proportional body parts in the fruit fly's head and thoracic regions. Hunchback is switched on in the anterior half of the embryo, where the level of Bicoid is high. In normal (wild-type) embryos, the process begins when Bicoid diffuses from the anterior toward the posterior end, a principal already established in existing research literature. Bicoid, which comes from the mother, then forms a gradient along this body axis.

Dr. Ma and his colleagues discovered the amount of Bicoid in early embryos depends on the size of the egg. Larger embryos in the study showed higher Bicoid levels in the anterior region, while smaller embryos showed lower levels. This relationship between embryo size and Bicoid amount helps Bicoid establish a gradient scaled precisely according to each embryo's length, which is necessary for Hunchback to respond precisely, they said.

One area of messiness in the system is that the precision levels of Bicoid and Hunchback are different. The research team reported that imaging analyses of 28 wild-type embryos showed even a precise Bicoid gradient still has positional errors that go beyond the boundaries set up by its target Hunchback. Dr. Ma's team suggests that Bicoid can self correct its positional errors through a coupling that develops between Bicoid's forming gradient and the protein's activation of target genes. The correction essentially fine tunes the mechanism to achieve further developmental precision.

Other studies have suggested Bicoid level differences among individual embryos play little or no role in the precision of fruit fly embryo development. Bicoid gradient, they say, is inherently so precise at switching on its target genes that it approaches the limits set by basic physical principles. While offering important new insights into how Bicoid establishes a precise gradient along the embryo's length, Dr. Ma said the previous research also begged the questions: What then makes the Bicoid gradient so precise, or is it really so precise?

"Instead of discounting the variability of the Bicoid gradient among different embryos, we found this noise to be an advantage of the system," said Dr. Ma, also a professor of pediatrics at the University of Cincinnati College of Medicine. "The amount of Bicoid going to small and large embryos all self corrects, so the system is built to be very robust and precise so different cells can be told to become part of the head, or part of something else, in a proportionate manner."

Besides conducting staining and imaging tests on normal wild-type embryos to test their hypothesis, Dr.Ma's team also studied Bicoid and Hunchback expression in embryos from genetically altered, mutant (staufen) female fruit flies. They found Bicoid could not form a precise and scaled gradient in embryos from these mutant females, which, they concluded, contributed to additional Hunchback variations and disproportionate development.

Internal control of developmental processes whereby cells "choose" their own fate. Precise and robust control in a "messy system". :cool:
 
Molecular factories:
Scientists Unwrap The Elements Of Life
ScienceDaily (Oct. 22, 2008) — Researchers at Newcastle University have taken a step forward in our understanding of how the fundamental building blocks of life are put together.

The researchers have shown that the way the metals attach is identical for a protein that binds manganese to one that binds copper. In both cases the metals bind inside protein barrels with the same type of metal-attractions.

Carrying out the work in a blue-green algae, a cyanobacterium, the team has been able to show that a protein requiring copper transports to the periplasm, the outer area of the cell, where it then folds around the available metal, which is copper.

Conversely, manganese but not copper atoms are found in the cytosol, in the middle of the cell. The team has demonstrated that a protein requiring manganese folds in the cytosol. The manganese protein is then transported to the periplasm having first trapped its manganese.

Once folded, the manganese site is buried, the metal trapped inside the protein, and so the manganese protein can subsequently co-exist with the copper protein because its' metal becomes impervious to replacement by metals further up the Irving-Williams series.

The work exemplifies a cell overcoming the metal binding preferences of proteins.

The new discipline of synthetic biology aims to engineer cells to carry out useful tasks, for example to generate valuable compounds. Because metals are the catalysts for so much of biology, knowing how to engineer a supply of the right metals to the right proteins will be important to the success of these ventures.
Mmmm, reverse engineering the efficiency of intracellular biomolecular machinery and making use of it to design and synthesize valuable compounds. Sounds like a good strategy.
 
The inner life of mesoorganisms
Some of the most ingenious ideas for designing microfluidic systems come from observing plants and animals. A study that quantifies the protein-driven helical flow of liquid in large plant cells, for instance, may well inspire micron-scale liquid mixers and sensors.

This brings us back to the issue of biomimetic strategies that borrow nature’s designs to engineer useful devices. Strategies to increase mass transport rates in microchannels, for example, will be essential for rapid sensing of extremely dilute systems [7]. In microfluidics, the “staggered herringbone mixer” [8] incorporates ridges along the walls to drive counter-rotating, helical flows to enhance mixing across the channel, while reducing dispersion along the channel. The mesoorganisms studied by van de Meent et al. illustrate a case where nature, faced with a similar problem, found a similar solution. Hundreds of millions of years later, in developing new microfluidic technologies, humans have found solutions that are not so far from those evolved in nature. Even though the methods for driving the flows are different (pressure-driven vs “cargo-driven,” and chaotic vs regular), the resulting double-helical flows share much in common.

While much of biophysics has been devoted to single-molecule and molecular-level studies, many mysteries remain on larger scales, at the cell level and above, where perceptive questions and keen physical insight reveal many surprises and useful insight into nature’s bag of tricks. van de Meent et al. nicely highlight the interesting and potentially important implications of cyclosis, and more generally the seemingly endless supply of fascinating physical processes at work in biological systems of all scales.

Once again borrowing from design motifs in cells to support our own design initiative :cool:.
 
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