Tag Archives: Life Science

Making Embryonic Stem Cells

photo of Junying Yu, an assistant scientist with the University of Wisconsin-Madison by Bryce Richter, 2007.

Holy Grail of stem cell research within reach by Mark Johnson

It was time to test the 14 genes she had selected as the best candidates to reprogram a cell.

Using viruses to deliver the genes, she inserted all 14 at once into human cells. On the morning of July 1, 2006, Yu arrived at the lab and examined the culture dishes. Her eyes focused on a few colonies, each resembling a crowded city viewed from space. They looked like embryonic stem cells.
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Cells must pass certain tests. They must multiply for weeks while remaining in their delicate, primitive state. When they are allowed to develop, they must turn into all the other cell types.

Bad things happen. Cells develop too soon. Cells die. There is no “aha!” moment, Thomson has said, only stress. He looked at the colonies and suppressed any excitement. He told Yu, essentially: OK, well get back to me in a couple of weeks.
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In the fall of 2006, Yu was preparing to whittle down her list of genes when she fell ill. The pain in her gut was awful. She struggled to eat. Her doctor thought it was a stomach flu. Instead, in late October, Yu’s appendix burst. She was laid up for a month. When she returned to the lab, the problem with the culture medium struck again.

Not until January 2007 was she able to begin narrowing the list of genes. She spent several months testing subsets of them, finally arriving at four. Two, Oct4 and Sox2, were “Yamanaka factors,” the name given to the genes the Japanese scientist had used to reprogram mouse cells. Two, Nanog and Lin28, were not.

Using a virus to deliver the four genes, she reprogrammed a line of fetal cells, then repeated the experiments with more mature cells. Although the process was inefficient, succeeding with only a small fraction of cells, it did work.

Dr. Junying Yu, an American trained scientist who entered the US as a foreign student from China. Which is somewhat ironic given the movement of USA based stem cell researches to China. Great article showing the process of scientific inquiry.

Social Amoeba

Amoebic Morality by Carol Otte

At first their behavior might seem odd; to gather together in the face of starvation surely ought to end in cannibalism or death. Not so, for they are capable of an extraordinary and rare transformation. The amoebas set aside their lives as individuals and join ranks to form a new multicellular entity. Not all the amoebas will survive this cooperative venture, however. Some will sacrifice themselves to help the rest find a new life elsewhere.

These astonishing creatures are Dictyostelium discoideum, and they are a member of the slime mold family. They are also known as social amoebas. Aside from the novelty value of an organism that alternates between unicellular and multicellular existence, D. discoideum is highly useful in several areas of research. Among other things, this organism offers a stellar opportunity to study cell communication, cell differentiation, and the evolution of altruism.

In response to the cAMP distress call, up to one hundred thousand of the amoebas assemble. They first form a tower, which eventually topples over into an oblong blob about two millimeters long. The identical amoebas within this pseudoplasmodium– or slug– begin to differentiate and take on specialized roles.

Another cool example of how life has evolved novel solutions to perpetuate genes.

Dolphins Using Tools to Hunt

photo of a dolphin with a sponge it uses to hunt

Photograph of dolphin with a sponge it uses to hunt, courtesy of Ewa Krzyszczyk, PLoS, high resolution.

Cool open access research from PLoS One, Why Do Dolphins Carry Sponges?

Tool use is rare in wild animals, but of widespread interest because of its relationship to animal cognition, social learning and culture. Despite such attention, quantifying the costs and benefits of tool use has been difficult, largely because if tool use occurs, all population members typically exhibit the behavior. In Shark Bay, Australia, only a subset of the bottlenose dolphin population uses marine sponges as tools, providing an opportunity to assess both proximate and ultimate costs and benefits and document patterns of transmission.

We compared sponge-carrying (sponger) females to non-sponge-carrying (non-sponger) females and show that spongers were more solitary, spent more time in deep water channel habitats, dived for longer durations, and devoted more time to foraging than non-spongers; and, even with these potential proximate costs, calving success of sponger females was not significantly different from non-spongers. We also show a clear female-bias in the ontogeny of sponging. With a solitary lifestyle, specialization, and high foraging demands, spongers used tools more than any non-human animal. We suggest that the ecological, social, and developmental mechanisms involved likely (1) help explain the high intrapopulation variation in female behaviour, (2) indicate tradeoffs (e.g., time allocation) between ecological and social factors and, (3) constrain the spread of this innovation to primarily vertical transmission.

The dolphins use the sponge to push along the ocean floor and disturb fish, that are hidden. Once the fish start swimming away the dolphin abandons the sponge and catches and eats the fish. Then the dolphin goes back and gets the sponge and continues.

One Sneeze, 150 Colds for Commuters

One sneeze, 150 colds for commuters

An analysis of the germs unleashed from a single commuter’s sneeze showed that within minutes they are being passed on via escalator handrails or seats on trains and underground carriages. At the busiest stations, one sneeze not smothered by a tissue or handkerchief will provide enough germs to infect another 150 commuters.
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A single sneeze expels 100,000 droplets of germs into the air at 90mph. Individual droplets get transferred to handles, rails and other areas frequently held or touched. Up to 10 per cent of all commuters will come into contact with an area infected by that one sneeze, Dr Henderson calculated.
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Researchers asked 1,300 workers about their health and found 99 per cent of commuters suffered at least one cold last winter. In contrast, just 58 per cent of those who work from home and 88 per cent of those who walk to work regularly caught a cold last winter.

It is amazing (or maybe not but I find it amazing) how well cold viruses have evolved to have us sneeze and send out personal virus jet packs to spread them all over and let them infect others. It is sad how impolite some people are as they go around potentially infecting hundreds of other people. Partially their ignorance of basic science may also be to blame for their behavior. It is too bad others have to suffer due to their bad manners and ignorance.

Dealth of Artic Plankton a Warning on Warming

Death bloom of plankton a warning on warming by David Perlman

Vanishing Arctic sea ice brought on by climate change is causing the crucially important microscopic marine plants called phytoplankton to bloom explosively and die away as never before, a phenomenon that is likely to create havoc among migratory creatures that rely on the ocean for food, Stanford scientists have found.
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Phytoplankton throughout the world’s oceans is the crucial nutrient at the base of the food web on which all marine life depends; when it’s plentiful, life thrives and when it’s gone, marine life is impossible.
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“It’s a complex system,” Arrigo said in an interview, “but as the changes in ice cover throw the timing of phytoplankton abundance off, then the birds and animals whose brains have long been programmed to migrate north at specific times of the year will have missed the boat if there’s no nourishment for them when they get there.”

Every spring and summer, phytoplankton in the Arctic blooms richly in explosive pulses, nourished by nitrogen and phosphorous in the seawater, and when those chemicals are consumed, the blooms end, Arrigo said.

Genes Counter a Bacterial Attack

Gene against bacterial attack unravelled

Humans have an innate defence system against deadly bacteria. However, how the step from gene to anti-bacterial effect occurs in the body is not yet known. To date, B. Pseudomallei, a bacterium suitable for bioweapons, had managed to elude medics. It can remain hidden in the human body for many years without being detected by the immune system. The bacteria can suddenly become activated and spread throughout the body, resulting in the patient dying from blood poisoning. AMC physician Joost Wiersinga and the Laboratory for Experimental Internal Medicine discovered which gene-protein combination renders the lethal bacteria B. pseudomallei harmless.

Wiersinga focussed on the so-called Toll-like receptors. These are the proteins that initiate the fight against pathogens. There are currently ten known Toll-like receptors which are located on the outside of immune cells, our body’s defence system. The toll-like receptors jointly function as a 10-figure alarm code. Upon coming into contact with the immune cell each bacterium enters its own Toll code. For known pathogens this sets off an alarm in the immune system and the defence mechanism is activated. Yet B. pseudomallei fools the system by entering the code of a harmless bacterium. As a result the body’s defence system remains on standby.

Yet some people are resistant: they become infected but not ill. Wiersinga found a genetic cause for this resistance. He discovered which toll receptor can fend off B. pseudomallei. He did this by rearing mice DNA in which the gene for Toll2 production was switched on and off. ‘The group where the gene for Toll2 was switched off, survived the bacterial infection’, says Wiersinga. ‘The other receptor that we investigated, Toll4, had no effect – even though for the past ten years medics had regarded this as the most important receptor.’ The ultimate aim of this study is to develop a vaccine.

PLoS paper: MyD88 Dependent Signaling Contributes to Protective Host Defense against Burkholderia pseudomallei

Marine Plankton From 100 Million Years Ago Found in Amber

photo of foraminifer in amber

Marine microorganisms have been found in amber dating from the middle of the Cretaceous period. The fossils were collected in Charente, in France. This completely unexpected discovery will deepen our understanding of these lost marine species as well as providing precious data about the coastal environment of Western France during the Cretaceous. This work was carried out by researchers at the GÃ©osciences Rennes laboratory, together with researchers from the PalÃ©obiodiversitÃ© et PalÃ©oenvironnement laboratory in Paris and the Centre de GÃ©ochimie de la Surface in Strasbourg.

Amber is a fossil resin with a reputation for preserving even the most minute details of insects and other terrestrial arthropods (spiders, scorpions, mites) that lived in resiniferous trees. The forest-based provenance of amber in theory makes it impossible for marine animals to be trapped in the resin. Nonetheless, researchers from the GÃ©osciences Rennes laboratory have discovered various inclusions of marine plankton in amber from the Mid-Cretaceous (100 to 98 million years ago). These micro-organisms are found in just a few pieces of amber among the thousands that have been studied, but show a remarkable diversity: unicellular algae, mainly diatoms found in large numbers, traces of animal plankton, such as radiolaria and a foraminifer, spiny skeletons of sponges and of echinoderms.

Foraminifera (the photo shows one in Amber) are amoeboid protists with reticulating pseudopods, fine strands of cytoplasm that branch and merge to form a dynamic net.[1] They typically produce a test, or shell, which can have either one or multiple chambers, some becoming quite elaborate in structure.[2] These shells are made of calcium carbonate (CaCO3) or agglutinated sediment particles. About 275,000 species are recognized, both living and fossil.[citation needed] They are usually less than 1 mm in size.”

Carried out together with researchers at the MusÃ©um national d’histoire naturelle, the study of diatoms pushed back by 10 to 30 million years the known date for the appearance of certain marine forms of this type of algae. This new information, taken together with recent data on molecular phylogeny, marks a huge advance in our understanding of the complex evolutionary history of diatoms.

The presence of these marine organisms in the amber is an ecological paradox. How did these marine species become stuck and then trapped in the conifers’ resin? The most likely scenario is that the forest producing the amber was very close to the coast, potentially shrouded by plankton-bearing mist or flooded by sea water during storms.

The preservation of marine organisms in amber is an exceptional asset, allowing us to deepen our understanding of these lost species and to have a clear idea about the coastal environment of Western France during the Cretaceous.

press release

Yogurts Used to Combat Superbugs

Yoghurts used to combat superbugs

Dieticians at Addenbrooke’s have said evidence suggested the yoghurt might cut the risk of contracting C.diff. Caroline Heyes, dietetic services manager at Addenbrooke’s hospital, said: “Probiotic yoghurts may play a role in preventing C.difficile infection so we have been running a pilot on three of the care of the elderly wards for six months.
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“We can’t say for sure how much of that benefit is down to the yoghurt and how much they are down to a whole range of infection control procedures that the hospital has in place such as the deep cleaning programme, the bare-below-the-elbow programme, and the increased isolation procedures,” Ms Heyes said.

Bacteria and Efficient Food Digestion

Gut Bacteria May Cause And Fight Disease, Obesity

“We’re all sterile until we’re born,” says Glenn Gibson, a microbiologist at the University of Reading in Britain. “We haven’t got anything in us right up until the time we come into this big, bad, dirty world.”

But as soon as we pass out of the birth canal, when we are fetched by a doctor’s hands, placed in a hospital crib, put on our mother’s breast, when we drag a thumb across a blanket and stick that thumb in our mouths, when we swallow our first soft food, we are invaded by all sorts of bacteria. Once inside, they multiply – until the bacteria inside us outnumber our human cells.
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University of Chicago immunologist Alexander Chervonsky, with collaborators from Yale University, recently reported that doses of the right stomach bacteria can stop the development of type 1 diabetes in lab mice. “By changing who is living in our guts, we can prevent type 1 diabetes,” he told The Wall Street Journal.

The bottom line: We now have two sets of genes to think about – the ones we got from our parents and the ones of organisms living inside us. Our parents’ genes we can’t change, but the other set? Now that is one of the newest and most exciting fields in cell biology.

Follow link with related podcast: Gut bacteria may cause and fight, disease, obesity. This whole area of the ecosystem within us and our health I find fascinating. And I fall for confirmation bias on things like becoming inefficient at converting food to energy as a way reduce obesity.

You could have two people sitting down to a bowl of cheerios, they could each eat the same number of cheerios but because of a difference in their gut bacteria one will get more calories than the other.

They then gave an example of the difference being 95 calories versus 99 calories. Hardly seems huge but it would add up. Still that is a less amazing difference than I was expecting.

Vampire Moth Discovered

Entomologist Jennifer Zaspel at the University of Florida in Gainesville said the discovery suggests the moth population could be on an “evolutionary trajectory” away from other C. thalictri populations.

In January, she will compare the Russian population’s DNA to that of other populations and other species to confirm her suspicions. “Based on geography, based on behavior, and based on a phenotypic variation we saw in the wing pattern, we can speculate that this represents something different, something new,” Zaspel said.
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Only male moths exhibit blood feeding, she noted, raising the possibility that as in some species of butterflies and other moths, the Russian moths do it to pass on salt to females during copulation.

“There is no evidence it prolongs the life of the male, or anything like that,” she said. “So we suspect that it is probably going to the female.” The sexual gift, she said, would provide a nutritional boost to young larvae that feed on leaf-rich, but sodium-poor, diets.