Hydrogen powers important nitrogen-transforming bacteria

Nitrite-oxidizing bacteria are key players in the natural nitrogen cycle on Earth and in biological wastewater treatment plants. For decades, these specialist bacteria were thought to depend on nitrite as their source of energy. An international team of scientists led by Holger Daims, a microbiologist at the University of Vienna, has now shown that nitrite-oxidizing bacteria can use hydrogen as an alternative source of energy. The oxidation of hydrogen with oxygen enables their growth independent of nitrite and a lifestyle outside the nitrogen cycle. The study is published in the current issue of the journal Science.

Nitrogen, an essential chemical element for life, is transformed into its different chemical forms in numerous steps of the global nitrogen cycle. Nitrite-oxidizing bacteria are important players in nitrogen cycling since they convert the toxic nitrite to the less harmful nitrate. "Humans exploit this process in biological wastewater treatment. Moreover, the formed nitrate is a substrate for other important microbial processes and a source of nitrogen for many plants" explains Hanna Koch, first author of the study and Ph.D. student at the Department of Microbiology and Ecosystem Science of the University of Vienna. Since the description of the first nitrite-oxidizing bacteria in the 19th century, scientists have assumed that the survival of these microorganisms would depend on nitrite as their source of energy. Therefore, the presence of nitrite-oxidizing bacteria in the environment and in wastewater treatment plants has commonly been associated with the nitrogen cycle.

Nitrospira: Nitrite oxidizers with surprising features

The environmentally most widespread nitrite oxidizers belong to the genus Nitrospira. These bacteria occur in the most different habitats such as soil, rivers, lakes and oceans, and even in hot springs. In addition, Nitrospira are the key nitrite-oxidizing bacteria in wastewater treatment plants. A team of scientists from Austria, Denmark, Germany, and France has now revealed surprising facts about these microorganisms. "The genome analysis of a Nitrospira species indicated that this bacterium might use hydrogen as an alternative source of energy" says Holger Daims from the Department of Microbiology and Ecosystem Science of the University of Vienna. The potential of Nitrospira to use hydrogen was then studied in detail.

NanoSIMS at the University of Vienna for high-resolution single-cell analyses

The hydrogen-dependent growth of Nitrospira could be visualized in individual bacterial cells by using the high-resolution secondary ion mass spectrometer, also called "NanoSIMS," at the University of Vienna. Under high vacuum conditions like in space, this method shoots small particles out of single bacterial cells for subsequent identification by mass spectrometry. "This exciting approach is feasible at very few research institutions worldwide," says Daims about this high-tech equipment. The scientists could show that Nitrospira cells, which use hydrogen as the source of energy, incorporate carbon dioxide into their biomass. This metabolic activity is linked to cell proliferation and was important evidence that the Nitrospira bacteria indeed use hydrogen for growth. These newly discovered features raise numerous questions about the lifestyle of the "free-living" close relatives of this Nitrospira species in the environment and wastewater treatment plants.

New insights into the ecology of nitrite oxidizers

"The oxidation of hydrogen not only enables Nitrospira to colonize unexpected habitats, but also sustains their activity when nitrite is not available" explains Hanna Koch. Holger Daims adds: "This discovery was a great surprise to us. In the next step, we will explore how extensively environmental nitrite oxidizers use hydrogen as an energy source. Our goal is to better understand the ecology of these important bacteria and their significance for the global cycles of nitrogen and carbon."

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The above story is based on materials provided by University of Vienna . Note: Materials may be edited for content and length.

Homosexuality and evolution [Pharyngula]

I made the mistake of reading some of the comments on those last youtube videos. There were some good ones, but they were also laced with the usual grunting assholes complaining about gays and “trannies” and quoting the Bible and making racist remarks about Africans. Let us pass over those contemptible arguments; there’s no dealing with them rationally. Spit and move on.

But there’s another flavor of argument that annoys me to no end: people who cite science and evolution to support their ignorant misconceptions about human nature. I want to address two, one anti-gay and the other pro-gay, both wrong.

First, there is the reductionist who knows a tiny bit about selection.

interesting point of view, but no. Evolution is all about competition. If you dont produce offspring, you take yourself out of the running. They may help the larger group, but that is more along the lines of the group exploiting a weakness. Their genes do not pass on. In the evolutionary crucible, thats a game over. It doesn’t matter what disease you cure, what philosophy you teach, biologically, you lose. Now, again, in modern society, things are more complex. There are more qualities to a life than how many mini-me’s you can make, but for the purposes of biology, it ends there.

If evolution is all about competition, how come reproduction in sexual species requires cooperation between two individuals to occur? Have you ever noticed that reproduction isn’t actually literally replication? You take your complement of 20,000 pairs of genes, and you throw half of them away, splice the remainder into different combinations, and then you merge those with the similarly mangled set of genes from another person, and you produce a unique individual. Not a clone of either of you — someone completely different.

That should tell you right away that you aren’t the focal point of evolution. You are a test platform for a battery of genes, genes that are shared with other members of your community. Evolution sees the propagation of a pool of genes that tends to produce successful individuals; look up inclusive fitness sometime. You share genes and combinations of genes with your siblings, your cousins, and more distant relatives — there’s more than one way for your population to propagate itself than for every individual to maximize the number of offspring they produce.

I also have to laugh every time some oblivious multicellular animal announces that evolution is all about competition, and that all that matters is how many progeny you produce. Do you realize that your existence is entirely a product of cooperation? Your parents were made up of trillions of cells, almost all of them dedicated to specialized, non-reproductive functions, all in support of a tiny minority of cells that can produce gametes. And of all those gametes, only two combined to make you — the great lumbering mass of agglomerated metazoan cells that were your parents then dedicated themselves to cooperatively nurturing the little zygote that was you (and which was not genetically identical to either) into a roughly similar lumbering mass.

Further, if that’s too abstract for you, consider this: you’d most likely be dead right now if scientists hadn’t collaborated to make vaccines against childhood diseases, if doctors and family hadn’t worked to keep you healthy and educated. Imagine all those carpenters who built your house and plumbers who put in the pipes and electricians who wired it up; imagine the vast combines that work to deliver fuel for heating and food for eating. Everything that you think is important about you was created by cooperation.

If you think otherwise, go masturbate into a mud puddle and hope that some of your offspring can make it without any assistance.

Here’s the pro-gay argument based on evolution. It’s just as annoying.

from a view strictly based in the ideas of natural evolution, i always assumed “homosexuality” was as old as the species… and that it was evolution’s way of both keeping the growth of the species in check (since humans are one of the few species that have sex for pleasure) and ensuring orphaned younglings have a chance at receiving care, guidence, and protection in their formative years. mind you this is just a personal theory based on the nature of nature…

Do not anthropomorphize evolution. Evolution is not an entity that plans and manages populations, it is not a nanny that cares about youngsters — if they are orphaned, one evolutionary outcome is for them to die, another is for survivors to support them, and all that matters is whether the population persists. In particular, evolution isn’t concerned with keeping populations in check — it’s simply a ratchet that permits populations to strive, and eventually and inevitably they hit physical and biological limitations, or pressure from some other growing population, and then physics happens.

Nothing personal. Evolution doesn’t play favorites. It can’t: it’s just the outcome of chance and physical laws interacting in particular environments.

Here’s my perspective on evolution and homosexuality.

Humans are complex organisms whose development is plastic and strongly dependent on environmental influences. There is selection pressure for the population reproduce, which we social beings accomplish with a significant subset of individuals providing sufficient progeny to replenish the population each generation, and with a similarly significant subset of the population working cooperatively to provide a supportive environment.

Evolution doesn’t care. All that matters is that the population thrives into the next generation, and that requires that individuals cooperate. Evolution is not a micromanager, either; we acquire random variations purely by chance, some work, some don’t, and in general, there are so many competing factors driving our survival that selection cannot possibly fine-tune emergent properties of behavior to such a degree that biology can specify exactly who you will bump genitals with. We are dealing with general tendencies expressed to varying degrees in individuals within a population.

If there is one biological imperative for humans, it is this: love one another. Build communities. Cooperate. Help each other in adversity. Successful populations will express these behaviors to a greater degree.

There are also biases towards favoring sexual interactions with members of a different sex, but that’s a secondary priority. Even if sexual preference were non-existent and totally random, women would pair up with men half the time, which would be more than sufficient to propagate our species, especially if the other half are working cooperatively to build safe homes and stable food supplies and provide loving educational environments.

From my biological perspective, the negative behavior that affects the survival of the species isn’t homosexuality, but anything that disrupts the cooperative bonds of community and foments hate — homophobia in humans is the destructive behavior that selection should work against. But keep in mind that if God has lousy aim, evolution is even worse…so we should also encourage behaviors that discourage attitudes that work against our survival.

Surprising discovery: HIV hides in gut, evading eradication

Researchers at UC Davis have made some surprising discoveries about the body's initial responses to HIV infection. Studying simian immunodeficiency virus (SIV), the team found that specialized cells in the intestine called Paneth cells are early responders to viral invasion and are the source of gut inflammation by producing a cytokine called interleukin-1 beta (IL-1β).

Though aimed at the presence of virus, IL-1β causes breakdown of the gut epithelium that provides a barrier to protect the body against pathogens. Importantly, this occurs prior to the wide spread viral infection and immune cell killing. But in an interesting twist, a beneficial bacterium, Lactobacillus plantarum, helps mitigate the virus-induced inflammatory response and protects gut epithelial barrier. The study was published in the journal PLoS Pathogens.

One of the biggest obstacles to complete viral eradication and immune recovery is the stable HIV reservoir in the gut. There is very little information about the early viral invasion and the establishment of the gut reservoir.

"We want to understand what enables the virus to invade the gut, cause inflammation and kill the immune cells," said Satya Dandekar, lead author of the study and chair of the Department of Medical Microbiology and Immunology at UC Davis.

"Our study has identified Paneth cells as initial virus sensors in the gut that may induce early gut inflammation, cause tissue damage and help spread the viral infection. Our findings provide potential targets and new biomarkers for intervening or blocking early spread of viral infection," she said.

In the study, the researchers detected a very small number of SIV infected cells in the gut within initial 2.5 days of viral infection; however, the inflammatory response to the virus was playing havoc with the gut lining. IL-1β was reducing the production of tight-junction proteins, which are crucial to making the intestinal barrier impermeable to pathogens. As a result, the normally cohesive barrier was breaking down.

Digging deeper, the researchers found the inflammatory response through IL-1β production was initiated in Paneth cells, which are known to protect the intestinal stem cells to replenish the epithelial lining. This is the first report of Paneth cell sensing of SIV infection and IL-1β production that links to gut epithelial damage during early viral invasion. In turn, the epithelial breakdown underscores that there's more to the immune response than immune cells.

"The epithelium is more than a physical barrier," said first author Lauren Hirao. "It's providing support to immune cells in their defense against viruses and bacteria."

The researchers found that addition of a specific probiotic strain, Lactobacillus plantarum, to the gut reversed the damage by rapidly reducing IL-1β, resolving inflammation, and accelerating repair within hours. The study points to interesting possibilities of harnessing synergistic host-microbe interactions to intervene early viral spread and gut inflammation and to mitigate intestinal complications associated with HIV infection.

"Understanding the players in the immune response will be important to develop new therapies," said Hirao. "Seeing how these events play out can help us find the most opportune moments to intervene."

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The above story is based on materials provided by University of California - Davis Health System . Note: Materials may be edited for content and length.