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Phytophthora root rot in the NY Times: Building a Better Christmas Tree (2012)

Phytophthora root rot in the NY Times: Building a Better Christmas Tree (2012) | WWWBiology | Scoop.it

Researchers are trying to develop a Christmas tree that will hold onto its needles from Thanksgiving to New Year’s — not a small thing in a $1 billion industry.

 

From Lab to Living Room - A typical tree can take from 8 to 12 years to go from seed cone to Christmas tree stand.

 

The largest Christmas tree operations harvest almost a million trees a year, transporting them by helicopter.

 

A small operation like Bell’s Christmas Tree Farm might raise fewer than 30,000 trees.

 

Before a seedling arrives at a small farm, it may have been germinated by a large forestry company and transplanted several times at a third nursery.

 

The quest for a better tree has led growers to look beyond favorites like blue spruce (below) to less common varieties, like Turkish, Korean and Canaan firs.

 

Organic Christmas tree farms are rare. Growers typically use pesticides to control blights like Phytophthora root rot and Swiss needle cast.


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From decisions to disorders: how neuroscience is changing what we know about ourselves

From decisions to disorders: how neuroscience is changing what we know about ourselves | WWWBiology | Scoop.it

People have wanted to understand our motivations, thoughts and behaviors since the ancient Greeks inscribed “know thyself” on the Temple of Apollo at Delphi. And understanding the brain’s place in health and disease is one of this century’s greatest challenges – take Alzheimer’s, dementia and depression for example.


There are many exciting contributions from neuroscience that have given insight into our thoughts and actions. Three neuroscientists have just been awarded the 2014 Nobel Prize for their discoveries of cells that act as a positioning system in the brain – in other words, the mechanism that allows us to navigate spaces using spatial information and memory at a cellular level.


There are many exciting contributions from neuroscience that have given insight into our thoughts and actions. For example, the neural basis of how we make fast and slow decisions and decision-making under conditions of uncertainty. There is also an understanding how the brain is affected by stress and how these stresses might switch our brains into habit mode, for example operating on “automatic pilot” and forgetting to carry out planned tasks, or the opposite goal-directed system, which would see you going out of your usual routine, for example, popping into a different supermarket to get special ingredients for a recipe.


Disruption in the balance between the two is evident in neuro-psychiatric disorders, such as obsessive compulsive disorder, and recent evidence suggests that lower grey matter volumes in the brain can bias towards habit formation. Neuroscience is also demonstrating commonalities in disorders of compulsivity, methamphetamine abuse and obese subjects with eating disorders.


Neuroscience can challenge previously accepted views. For example, major abnormalities in dopamine function were thought the main cause of adult attention deficit hyperactivity disorder (ADHD). However, recent work suggests that the main cause of the disorder may instead be associated with structural differences in grey matter in the brain.


What neuroscience has made evidently clear is that changes in the brain cause changes in your thinking and actions, but the relationship is two-way. Environmental stressors, including psychological and substance abuse, can also change the brain. We also now know our brains continue developing into late adolescence or early young adulthood, it is not surprising that these environmental influences are particularly potent in a number of disorders during childhood and adolescence including autism.



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Oceans experiencing largest sea level rise in 6,000 years, study says

Oceans experiencing largest sea level rise in 6,000 years, study says | WWWBiology | Scoop.it

There are two main forces that can drive sea levels higher. One is something called thermal expansion, which involves the expansion of ocean water as it warms. The other is an influx of additional water, ushered into the sea by melting ice sheets and glaciers. Scientists have long concluded that sea levels are rising. Just look at Miami. Or the Maldives. They’ve also discerned that major ice sheets are melting at a faster clip than previously understood.

 

What has been less clear, however, is whether the development is recent or not. Over the last several thousands of years, has the ocean risen and fallen and risen again? A new study, just published in PNAS, suggests that the ocean has been surprisingly static since 4,000 B.C..

 

But that changed 150 years ago. Reconstructing 35,000 years of sea fluctuations, the study, which researchers say is the most comprehensive of its kind, found that the oceans are experiencing greater sea rise than at any time over the last 6,000 years. “What we see in the tide gauges, we don’t see in the past record, so there’s something going on today that’s wasn’t going on before,” lead author Kurt Lambeck, a professor at Australian National University, told the Australia Broadcasting Corporation. “I think that is clearly the impact of rising temperatures.”

 

How much has the sea risen over the past century and a half? A lot. And it’s surging faster than ever. “There is robust evidence that sea levels have risen as a result of climate change,” Australian government research has found. “Over the last century, global average sea level rose by 1.7 mm [0.067 inches] per year, in recent years (between 1993 and 2010), this rate has increased to 3.2 mm [0.126 inches] per year.” In all, the sea has risen roughly 20 centimeters since the start of the 20th century. “The rate of sea level rise over the last century is unusually high in the context of the last 2,000 years,” the Australian report added.


But it’s not just the last 2,000 years. It’s the last 6,000 years, according to this recent study. And now, the rising sea levels over the last 100 years, is “beyond dispute,” Lambeck explained.


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NERONYC's curator insight, October 19, 6:04 PM

Preserve our invironment

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What Happens After Someone Survives Ebola?

What Happens After Someone Survives Ebola? | WWWBiology | Scoop.it

While most of the recent coverage of the ongoing Ebola outbreak has focused on rising death tolls and a few infected U.S. citizens, other segments of the population have passed mostly unnoticed from the harsh glare of the media spotlight: Survivors, and those who are seemingly immune to Ebola.


People who survive Ebola can lead normal lives post-recovery, though occasionally they can suffer inflammatory conditions of the joints afterwards, according to CBS. Recovery times can vary, and so can the amount of time it takes for the virus to clear out of the system.


The World Health Organization found that the virus can reside in semen for up to seven weeks after recovery. Survivors are generally assumed to be immune to the particular strain they are infected by, and are able to help tend to others infected with the same strain. What isn't clear is whether or not a person is immune to other strains of Ebola, or if their immunity will last.


As with most viral infections, patients who recover from Ebola end up with Ebola-fighting antibodies in their blood, making their blood a valuable (if controversial) treatment option for others who catch the infection. Kent Brantly, one of the most recognizable Ebola survivors, has donated more than a gallon of his blood to other patients. The plasma of his blood, which contains the antibodies, is separated out from the red blood cells, creating what’s known as a convalescent serum, which can then be given to a patient as a transfusion. The hope is that the antibodies in the serum will boost the patient’s immune response, attacking the virus, and allowing the body to recover.


But this treatment method, like all Ebola treatment methods, is far from ideal. To start with, scientists aren't even sure if it works. In addition, the serum can only be donated to people with a compatible blood type to the donor, and it’s unclear how long the immunity would last. Adding to the confusion, there are several different strains of Ebola, and there’s no guarantee that once someone has recovered from one strain of Ebola they are immune to others.


When Nancy Writebol, one of the survivors of Ebola who was whisked back to Atlanta soon after contracting the virus, was asked by Science Magazine if she would consider going back, she said: “I’ve done some reading on that and talked to doctors at Emory about that. My doctors at Emory are not sure how long immunity would last. It’s not been studied. I’ve read that even if a survivor was willing and able to help with the care for Ebola patients, because there are so many strains of Ebola, it would still be very wise and necessary to operate in PPEs and not just assume you’re immune.”


People who survived the disease are of particular interest to researchers, such as those working on the ZMapp drug, who hope that they can synthesize antibodies in the hopes of creating a cure.


But even less understood than the survivors are the people who were infected with Ebola but never developed any symptoms. After outbreaks in Uganda in the late 1990’s, scientists tested the blood of several people who were in close contact with Ebola patients, and found a number of them had markers in their blood indicating they carried the disease, but they were totally asymptomatic—they managed to completely avoid the horrifying symptoms of the disease.


In a letter in the Lancet this week, researchers look into the existence of these asymptomatic patients, and hope that identifying people who are naturally immune could help contain the outbreak as scientists work on developing a treatment. A 2010 study published by the French research organization IRD found that as much as 15.3 percent of Gabon's population could be immune to Ebola.


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Invasive plant wins competition against its native cousin

Invasive plant wins competition against its native cousin | WWWBiology | Scoop.it
Because of its aggressive behavior and its harmful effects, the invasive prairie plant Lespedeza cuneata has been added to several noxious weed lists.

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New Phytologist: Special Issue: Plants interacting with other organisms (October 2014)

New Phytologist: Special Issue: Plants interacting with other organisms (October 2014) | WWWBiology | Scoop.it

Editorial

 

Plant interactions with other organisms: molecules, ecology and evolution

 

Commentary

 

Different shades of JAZ during plant growth and defense

 

Nutrient supply differentially alters the dynamics of co-infecting phytoviruses

 

Letters

 

From shade avoidance responses to plant performance at vegetation level: using virtual plant modelling as a tool
F. J. Bongers, J. B. Evers, N. P. R. Anten & R. Pierik

 

Review

 

Magical mystery tour: MLO proteins in plant immunity and beyond
J. Acevedo-Garcia, S. Kusch & R. Panstruga

 

The squeeze cell hypothesis for the activation of jasmonate synthesis in response to wounding

E. E. Farmer, D. Gasperini & I. F. Acosta

 

Lipochitooligosaccharide recognition: an ancient story
Y. Liang, K. Tóth, Y. Cao, K. Tanaka, C. Espinoza & G. Stacey

 

Herbivore-induced plant volatiles: targets, perception and unanswered questions
M. Heil

 

There’s no place like home? An exploration of the mechanisms behind plant litter–decomposer affinity in terrestrial ecosystems
A. T. Austin, L. Vivanco, A. González-Arzac & L. I. Pérez

 

Insect herbivore-associated organisms affect plant responses to herbivory
F. Zhu, E. H. Poelman & M. Dicke

 

When mutualism goes bad: density- dependent impacts of introduced bees on plant reproduction
M. A. Aizen, C. L. Morales, D. P. Vázquez, L. A. Garibaldi, A. Sáez & L. D. Harder

 

Insect and pathogen attack and resistance in maize and its wild ancestors, the teosintes
E. S. de Lange, D. Balmer, B. Mauch-Mani & T. C. J. Turlings

 

Full papers

 

Linking phytochrome to plant immunity: low red : far-red ratios increase Arabidopsis susceptibility to Botrytis cinerea by reducing the biosynthesis of indolic glucosinolates and camalexin
M. D. Cargnel, P. V. Demkura & C. L. Ballaré

 

To grow or defend? Low red : far-red ratios reduce jasmonate sensitivity in Arabidopsis seedlings by promoting DELLA degradation and increasing JAZ10 stability
M. Leone, M. M. Keller, I. Cerrudo & C. L. Ballaré

 

β-Glucosidase BGLU42 is a MYB72-dependent key regulator of rhizobacteria-induced systemic resistance and modulates iron deficiency responses in Arabidopsis roots
C. Zamioudis, J. Hanson & C. M. J. Pieterse

 

Deciphering the language of plant communication: volatile chemotypes of sagebrush
R. Karban, W. C. Wetzel, K. Shiojiri, S. Ishizaki, S. R. Ramirez & J. D. Blande

 

The context dependence of beneficiary feedback effects on benefactors in plant facilitation
C. Schöb, R. M. Callaway, F. Anthelme, R. W. Brooker, L. A. Cavieres, Z. Kikvidze, C. J. Lortie, R. Michalet, F. I. Pugnaire, S. Xiao, B. H. Cranston, M-C. García, N. R. Hupp, L. D. Llambí, E. Lingua, A. M. Reid, L. Zhao & B. J. Butterfield

 

Herbivore-mediated material fluxes in a northern deciduous forest under elevated carbon dioxide and ozone concentrations
T. D. Meehan, J. J. Couture, A. E. Bennett & R. L. Lindroth

 

Are plant–soil feedback responses explained by plant traits?
C. Baxendale, K. H. Orwin, F. Poly, T. Pommier & R. D. Bardgett

 

Environmental nutrient supply alters prevalence and weakens competitive interactions among coinfecting viruses
C. Lacroix, E. W. Seabloom & E. T. Borer


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Nature Communications: Long-distance endosome trafficking drives fungal effector production during plant infection (2014)

Nature Communications: Long-distance endosome trafficking drives fungal effector production during plant infection (2014) | WWWBiology | Scoop.it

To cause plant disease, pathogenic fungi can secrete effector proteins into plant cells to suppress plant immunity and facilitate fungal infection. Most fungal pathogens infect plants using very long strand-like cells, called hyphae, that secrete effectors from their tips into host tissue. How fungi undergo long-distance cell signalling to regulate effector production during infection is not known. Here we show that long-distance retrograde motility of early endosomes (EEs) is necessary to trigger transcription of effector-encoding genes during plant infection by the pathogenic fungus Ustilago maydis. We demonstrate that motor-dependent retrograde EE motility is necessary for regulation of effector production and secretion during host cell invasion. We further show that retrograde signalling involves the mitogen-activated kinase Crk1 that travels on EEs and participates in control of effector production. Fungal pathogens therefore undergo long-range signalling to orchestrate host invasion.


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Malaria parasites found to hide out in the bone marrow

Malaria parasites found to hide out in the bone marrow | WWWBiology | Scoop.it

Malaria is an infectious disease which claims the lives of more children worldwide than any other; it is caused by parasitic micro-organisms, plasmodiums. These parasites are transmitted to their hosts via mosquito bites, where they induce a range of symptoms, including vomiting, fever, headaches, and, in severe cases, death. Incidence of malaria is prevalent in poverty stricken areas around the equator, with an estimated 207 million cases in 2012.  The most life threatening form of the disease is caused by Plasmodium falciparum. 


Within humans, P. falciparum undergoes two distinct stages, asexual replication, and differentiation into what are called gametocytes. Asexual replication occurs within red blood cells, with pathological symptoms arising from the inevitable red blood cell rupturing. Released parasites generally invade additional red blood cells for subsequent rounds of asexual replication; however, a small subset of parasites instead differentiate into the male and female forms that are refered to as gametocytes. Once taken up by a female Anopheles mosquito, these gametocytes are able to undergo sexual replication. Thus, the differentiation of P. falciparum into gametocytes represents an attractive target for intervention strategies. However, within the blood only mature gametocytes are found, and until recently, relatively little was known about immature gametocyte sequestration within tissues.

 

A recent study carried out a systematic organ survey of children who died from malaria, successfully identifying sites of immature gametocyte accumulation using a combination of immunohistochemical labelling, and quantitative reverse transcription polymerase chain reaction (qRT-PCR). The study provides strong evidence that gametocyte development occurs within the haematopoietic system present in the bone marrow, where they may form and develop within red blood cell precursors. Furthermore, binding interactions with red blood cell precursors seem to support the retention of developing gametocytes within the bone marrow’s extravascular space, where they are able to avoid immune detection until they are mature enough to be released back into the blood. The observation of gametocytes adopting a specialised niche within the haematopoietic system of the bone marrow is supported by anindependent study, which earlier this year used qRT-PCR to demonstrate that the bone marrow of infected children is enriched for immature gametocytes.

 

The recently characterised locations and mechanisms of gametocyte sequestration within the bone marrow, provide novel targets through which malaria transmission could be blocked, advancing both prevention and treatment efforts.


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Next-Gen Glaucoma Treatments: Microfluidic Implant And Smart Phone App Monitoring

Next-Gen Glaucoma Treatments: Microfluidic Implant And Smart Phone App Monitoring | WWWBiology | Scoop.it

Stanford Professor of Bioengineering and Applied Physics, Stephen Quake, and Head of the Ophthalmic Science and Engineering Lab at Bar Ilan University Dr. Yossi Mandell teamed up to create a state-of-the-art intraocular implant that will change glaucoma treatment by making intraocular pressure readings frequent, easy and convenient.

 

Made to fit inside a commonly used intraocular lens prosthetic, and implanted through simple surgery such as for cataracts which many glaucoma patients already receive, the device measures the pressure of the fluid within the eye.  A smart phone app or a wearable device such as Google Glass allows the wearer to take “snapshots” of the device that reports back the pressure.

 

The lens device holds a tiny tube, capped at one end and opened on the other, filled with gas. As the fluid pressure pushes against the gas, a marked scale permits reading of the intraocular pressure.  The implant does not interfere with vision, as proven in an Air Force-approved vision test, and in one reported study the implant was responsible for changes to treatment for glaucoma in nearly 80 percent of the wearers.

 

Nearly 2.2 million Americans battle the eye disease glaucoma.  Patients endure weekly visits to the ophthalmologist to have the disease monitored and treated. The disease is characterized by increasing pressure inside the eye, which results in a continuous loss of a specific type of retinal cell accompanied by degradation of the optic nerve fiber.  The mechanism that links pressure to damage is not clear but there is correlation between the intensity of pressure readings and level of damage.


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Why female biology matters

Why female biology matters | WWWBiology | Scoop.it
Female biology is neither magic nor mysterious. It doesn't make those in possession of it nurturing, or caring, or motherly. It doesn't mean we ought to bear children, nor does it mean we can alway...
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EZH2: An emerging role in melanoma... [Pigment Cell Melanoma Res. 2014] - PubMed - NCBI

PubMed comprises more than 23 million citations for biomedical literature from MEDLINE, life science journals, and online books. Citations may include links to full-text content from PubMed Central and publisher web sites.
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Not only in DNA's hands: Epigenetics has large say in blood formation

Not only in DNA's hands: Epigenetics has large say in blood formation | WWWBiology | Scoop.it
Blood stem cells have the potential to turn into any type of blood cell, whether it be the oxygen-carrying red blood cells, or the many types of white blood cells of the immune system that help fight infection. How exactly is the fate of these stem cells regulated? Preliminary findings from research ...

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Highly drug resistant, virulent strain of Pseudomonas aeruginosa arises in Ohio

Highly drug resistant, virulent strain of Pseudomonas aeruginosa arises in Ohio | WWWBiology | Scoop.it
A team of clinician researchers has discovered a highly virulent, multidrug resistant form of the pathogen, Pseudomonas aeruginosa, in patient samples in Ohio. Their investigation suggests that the particular genetic element involved, which is still rare in the United States, has been spreading heretofore ...

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Venom gets good buzz as potential cancer-fighter

Venom gets good buzz as potential cancer-fighter | WWWBiology | Scoop.it
Bee, snake or scorpion venom could form the basis of a new generation of cancer-fighting drugs, scientists will report here today. They have devised a method for targeting venom proteins specifically to malignant cells while sparing healthy ones, which reduces or eliminates side effects that the toxins ...

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Rats! NYC rats infected with at least 18 new viruses, but no bubonic plague bacteria found

Rats! NYC rats infected with at least 18 new viruses, but no bubonic plague bacteria found | WWWBiology | Scoop.it

Rats: some people enjoy their company as pets, to many others, they are virulent pests that helped the spread of the bubonic plague ("black death") in Medieval Europe. For New Yorkers, they are just one of many interesting local daily sights on the subway tracks and platforms. I can tell you from experience (source: I live in New York City) that they often seem healthier and in better spirits than many of the humans that call this fair city home. Yet it turns out some of them are carrying a surprising number of previously undocumented viruses, according to the results of a study of the Big Apple's rodents published today in the journal mBio and reported by The New York Times.

 

Specifically, scientists captured 133 rats from traps set in five locations around New York City, euthanized them, then took genetic samples of the bacteria and viral specimens found in their tissues and excretions (saliva, feces, etc). The scientists found lots of viruses, not surprisingly. But while many of the bacteria detected were expected — including e. coli and salmonella — the scientists also found at 18 completely new viruses. None of these new viruses have been found in humans, at least not yet, but two of them are structurally similar to Hepatitis C, which does occur in people and raises the risk of liver scarring and cancer. While there's no immediate cause for alarm, the scientists note that that the spread of these new viruses from rats to humans could theoretically already be occurring and is possible in the future, and are advocating for more comprehensive disease monitoring in humans. Something to think about the next time you're waiting for the downtown F train.


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New technique allows scientists to identify populations of rare mesenchymal stem cells in bone marrow

New technique allows scientists to identify populations of rare mesenchymal stem cells in bone marrow | WWWBiology | Scoop.it

Deep within the bone marrow resides a type of cells known as mesenchymal stem cells (MSCs). These immature cells can differentiate into cells that produce bone, cartilage, fat, or muscle — a trait that scientists have tried to exploit for tissue repair.


In a new study that should make it easier to develop such stem-cell-based therapies, a team of researchers from MIT and the Singapore-MIT Alliance in Research and Technology (SMART) has identified three physical characteristics of MSCs that can distinguish them from other immature cells found in the bone marrow. Based on this information, they plan to create devices that could rapidly isolate MSCs, making it easier to generate enough stem cells to treat patients.


Until now, there has been no good way to separate MSCs from bone marrow cells that have already begun to differentiate into other cell types, but share the same molecules on the cell surface. This may be one reason why research results vary among labs, and why stem-cell treatments now in clinical trials are not as effective as they could be, says Krystyn Van Vliet, an MIT associate professor of materials science and engineering and biological engineering and a senior author of the paper, which appears in theProceedings of the National Academy of Sciences this week.


“Some of the cells that you’re putting in and calling stem cells are producing a beneficial therapeutic outcome, but many of the cells that you’re putting in are not,” Van Vliet says. “Our approach provides a way to purify or highly enrich for the stem cells in that population. You can now find the needles in the haystack and use them for human therapy.”


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Madagascar's bark spider (Caerostris darwini) makes up to 82 feet large orb nets, 10 x stronger than Kevlar

Madagascar's bark spider (Caerostris darwini) makes up to 82 feet large orb nets, 10 x stronger than Kevlar | WWWBiology | Scoop.it

The web of the Darwin's bark spider (Caerostris darwini), can span some square feet (2.8 square meters) and is attached to each riverbank by anchor threads as long as 82 feet (25 meters).


Scientists have found the toughest material made by life yet — the silk of a spider whose giant webs span rivers, streams and even lakes. Spider silks were already the toughest known biomaterials, able to absorb massive amounts of energy before breaking. However, researchers have now revealed the Darwin's bark spider (Caerostris darwini) has the toughest silk ever seen — more than twice as tough as any previously described silk, and more than 10 times stronger than Kevlar.


Although scientists have investigated silks from 20-to-30 species of spiders before, most of these were chosen haphazardly — for instance, from researchers' backyards. There are over 40,000 species of spiders and each spider can produce up to seven different kinds of silk. Thus, more than 99.99 percent of spider silks are yet to be explored.


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PLOS Pathogens: The Secreted Peptide PIP1 Amplifies Immunity through Receptor-Like Kinase 7 (2014)

PLOS Pathogens: The Secreted Peptide PIP1 Amplifies Immunity through Receptor-Like Kinase 7 (2014) | WWWBiology | Scoop.it

In plants, innate immune responses are initiated by plasma membrane-located pattern recognition receptors (PRRs) upon recognition of elicitors, including exogenous pathogen-associated molecular patterns (PAMPs) and endogenous damage-associated molecular patterns (DAMPs). Arabidopsis thaliana produces more than 1000 secreted peptide candidates, but it has yet to be established whether any of these act as elicitors. Here we identified an A. thaliana gene family encoding precursors of PAMP-induced secreted peptides (prePIPs) through an in-silicoapproach. The expression of some members of the family, including prePIP1 and prePIP2, is induced by a variety of pathogens and elicitors. Subcellular localization and proteolytic processing analyses demonstrated that the prePIP1 product is secreted into extracellular spaces where it is cleaved at the C-terminus. Overexpression of prePIP1 and prePIP2, or exogenous application of PIP1 and PIP2 synthetic peptides corresponding to the C-terminal conserved regions in prePIP1 and prePIP2, enhanced immune responses and pathogen resistance in A. thaliana. Genetic and biochemical analyses suggested that the receptor-like kinase 7 (RLK7) functions as a receptor of PIP1. Once perceived by RLK7, PIP1 initiates overlapping and distinct immune signaling responses together with the DAMP PEP1. PIP1 and PEP1 cooperate in amplifying the immune responses triggered by the PAMP flagellin. Collectively, these studies provide significant insights into immune modulation by Arabidopsis endogenous secreted peptides.


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PLOS Pathogens: Adaptive Prediction As a Strategy in Microbial Infections (2014)

PLOS Pathogens: Adaptive Prediction As a Strategy in Microbial Infections (2014) | WWWBiology | Scoop.it

Microorganisms need to sense and respond to constantly changing microenvironments, and adapt their transcriptome, proteome, and metabolism accordingly to survive [1]. However, microbes sometimes react in a way which does not make immediate biological sense in light of the current environment—for example, by up-regulating an iron acquisition system in times of metal abundance. The reason for this seemingly nonsensical behavior can lie in the microbe's ability to predict a coming change in conditions by cues from the current environment. If the microbe (pre-)adapts accordingly, it will increase its fitness and chances of survival under subsequent selection pressures—a concept known as adaptive prediction.


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Estimating the fatality of the 2014 West African Ebola Outbreak

Estimating the fatality of the 2014 West African Ebola Outbreak | WWWBiology | Scoop.it

Case fatality rate" - or CFR - is a term that's been tossed around a lot lately in the context of the 2014 West African Ebola outbreak… But what does it really mean?

 

The CFR – which is calculated by dividing the number of deaths that have occurred due to a certain condition by the total number of cases – is actually a measure of risk. For infectious disease, CFR is a very important epidemiological measure to estimate because it tells us the probability of dying after infection. If estimated properly in the middle of an outbreak, it can even help us examine the efficacy of interventions as they take place.

 

Because different outbreaks of the same disease can demonstrate different CFRs, there’s usually a range of possible CFRs for a given disease. In the past, outbreaks caused by Zaire ebolavirus have demonstrated a mean end-of-outbreak CFR of 80% . But based off of the WHO's most recent report, it seems that only about 53% of reported Ebola cases thus far have ended in death since the 2014 outbreak began.

 

However, if we want to be particular, that 53% isn't really a CFR; it's actually the proportion of fatal cases - or PFC. This is a critical distinction. Because the outbreak in West Africa is still ongoing, we can't calculate end-of-outbreak CFR yet. We don’t know how many people will die from Ebola in the weeks ahead or how many total cases will ultimately accumulate by the end of the outbreak. So, for the time being, we have to make do with the PFC, which is essentially the number of deaths thus far divided by the number of cases to date.

 

When the WHO releases a report on the current situation in West Africa, it tells us two things: the number of people who've died and the number of reported cases at some specified point in time. For instance, in the most recent report, the WHO cited 4293 total cases and 2296 deaths as of September 8th. Dividing 2296 by 4293 gives us our previously stated PFC of 53%.

 

At first glance, it might seem then that only 53% of Ebola cases have been dying during this outbreak - a good deal less than the 80% we've seen prior... But what it really means is that only 53% of Ebola cases have died as of September 8th. We have no way of knowing whether all the people who were still hospitalized as of September 8th will survive the disease. Because of this, mid-outbreak PFC - as we've defined it thus far - doesn't tell us much about the likelihood of dying.

 

Despite Ebola’s frightening reputation, not all Ebola fatalities happen quickly. Without a little fine-tuning, PFC doesn't account for the lag between when a case is reported and when a case dies - approximately 16 days for this outbreak [3]. What this means is that the 2296 deaths reported as of September 8th were all likely reported as cases by August 23rd. Adjusting PFC for this lag-time gives us a much better approximation of CFR well before the outbreak ends.

 

Below is a chart that shows both unadjusted and lag-adjusted PFC over time for Ebola in West Africa [5]. The lag-adjusted PFC - about 80-85% - is significantly higher than the unadjusted PFC but is consistent with recent fatality estimates by Médecins Sans Frontières.


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Scientists reset human stem cells to earliest developmental state equivalent to 7-9 days old embryo

Scientists reset human stem cells to earliest developmental state equivalent to 7-9 days old embryo | WWWBiology | Scoop.it

Scientists have successfully ‘reset’ human pluripotent stem cells to the earliest developmental state – equivalent to cells found in an embryo before it implants in the womb (7-9 days old). These ‘pristine’ stem cells may mark the true starting point for human development, but have until now been impossible to replicate in the lab. fThe discovery, published in Cell, will lead to a better understanding of human development and could in future allow the production of safe and more reproducible starting materials for a wide range of applications including cell therapies.

Human pluripotent stem cells, which have the potential to become any of the cells and tissues in the body, can be made in the lab either from cells extracted from a very early stage embryo or from adult cells that have been induced into a pluripotent state.

However, scientists have struggled to generate human pluripotent stem cells that are truly pristine (also known as naïve). Instead, researchers have only been able to derive cells which have advanced slightly further down the developmental pathway. These bear some of the early hallmarks of differentiation into distinct cell types – they’re not a truly ‘blank slate’. This may explain why existing human pluripotent stem cell lines often exhibit a bias towards producing certain tissue types in the laboratory.

Now researchers led by the Wellcome Trust-Medical Research Council (MRC) Cambridge Stem Cell Institute at the University of Cambridge, have managed to induce a ground state by rewiring the genetic circuitry in human embryonic and induced pluripotent stem cells. Their ‘reset cells’ share many of the characteristics of authentic naïve embryonic stem cells isolated from mice, suggesting that they represent the earliest stage of development.

“Capturing embryonic stem cells is like stopping the developmental clock at the precise moment before they begin to turn into distinct cells and tissues,” explains Professor Austin Smith, Director of the Stem Cell Institute, who co-authored the paper. “Scientists have perfected a reliable way of doing this with mouse cells, but human cells have proved more difficult to arrest and show subtle differences between the individual cells. It’s as if the developmental clock has not stopped at the same time and some cells are a few minutes ahead of others.”

The process of generating stem cells in the lab is much easier to control in mouse cells, which can be frozen in a state of naïve pluripotency using a protein called LIF. Human cells are not as responsive to LIF, so they must be controlled in a different way that involves switching key genes on and off. For this reason scientists have been unable to generate human pluripotent cells that are as primitive or as consistent as mouse embryonic stem cells.

The researchers overcame this problem by introducing two genes – NANOG and KLF2 – causing the network of genes that control the cell to reboot and induce the naïve pluripotent state. Importantly, the introduced genes only need to be present for a short time. Then, like other stem cells, reset cells can self-renew indefinitely to produce large numbers, are stable and can differentiate into other cell types, including nerve and heart cells.

By studying the reset cells, scientists will be able to learn more about how normal embryo development progresses and also how it can go wrong, leading to miscarriage and developmental disorders. The naïve state of the reset stem cells may also make it easier and more reliable to grow and manipulate them in the laboratory and may allow them to serve as a blank canvas for creating specialised cells and tissues for use in regenerative medicine.

Professor Smith adds: “Our findings suggest that it is possible to rewind the clock to achieve true ground state pluripotency in human cells. These cells may represent the real starting point for formation of tissues in the human embryo. We hope that in time they will allow us to unlock the fundamental biology of early development, which is impossible to study directly in people.” - See more at: http://www.cam.ac.uk/research/news/scientists-reset-human-stem-cells-to-earliest-developmental-state#sthash.4gxh2MI9.dpuf


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Japanese woman is first recipient of next-generation stem cells

Japanese woman is first recipient of next-generation stem cells | WWWBiology | Scoop.it

A Japanese woman in her 70s is the world's first recipient of cells derived from induced pluripotent stem cells, a technology that has created great expectations since it could offer the same advantages as embryo-derived cells but without some of the controversial aspects and safety concerns.


In a two-hour procedure, a team of three eye specialists lead by Yasuo Kurimoto of the Kobe City Medical Center General Hospital, transplanted a 1.3 by 3.0 millimeter sheet of retinal pigment epithelium cells into an eye of the Hyogo prefecture resident, who suffers from age-related macular degeneration.

 

The procedure took place at the Institute of Biomedical Research and Innovation Hospital, next to the RIKEN Center for Developmental Biology (CDB) where ophthalmologist Masayo Takahashi had developed and tested the epithelium sheets. She derived them from the patient's skin cells, after producing induced pluripotent stem (iPS) cells and then getting them to differentiate into retinal cells. Afterwards, the patient experienced no effusive bleeding or other serious problems, RIKEN has reported.


The patient “took on all the risk that go with the treatment as well as the surgery”, Kurimoto said in a statement released by RIKEN. “I have deep respect for bravery she showed in resolving to go through with it.”

He hit a somber note in thanking Yoshiki Sasai, a CDB researcher who recenty committed suicide. “This project could not have existed without the late Yoshiki Sasai’s research, which led the way to differentiating retinal tissue from stem cells.”

 

Kurimoto also thanked Shinya Yamanaka, a stem-cell scientist at Kyoto University “without whose discovery of iPS cells, this clinical research would not be possible.” Yamanaka shared the 2012 Nobel Prize in Physiology or Medicine for that work.


Kurimoto performed the procedure a mere four days after a health-ministry committee gave Takahashi clearance for the human trials (see 'Next-generation stem cells cleared for human trial').



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No fly zone: Darwin's finches self-fumigate (with a little help)

No fly zone: Darwin's finches self-fumigate (with a little help) | WWWBiology | Scoop.it
When a bird species is threatened by nest parasites, you might think the logical next step is to fumigate – unsurprisingly, though, physically spraying nests (as you might spray an infested house) is disruptive… (Interesting emerging method in conservation...
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World’s Largest Dam Removal Unleashes U.S. River After Century of Electric Production

World’s Largest Dam Removal Unleashes U.S. River After Century of Electric Production | WWWBiology | Scoop.it
The last section of dam is being blasted from the Elwha River on Washington's Olympic Peninsula on Tuesday.

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Ebola vaccine trials set to begin in September

Ebola vaccine trials set to begin in September | WWWBiology | Scoop.it
(HealthDay)—Officials at the World Health Organization said that the first round of clinical trials of a potential Ebola vaccine made by drug maker GlaxoSmithKline could begin next month.

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Flowering plants revolutionised life on Earth

Flowering plants revolutionised life on Earth | WWWBiology | Scoop.it
New evidence from liverworts and beetles shows how the rise of flowering plants 100 million years ago created ideal conditions for a boom in terrestrial life.

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