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TWiM 69 Letters

Gian writes:

Beloved TWiMers,

Did you see this paper in PLoS Computational Biology? It's mind-blowing. U. Maryland researchers found evidence for Acinetobacter and Pseudomonas nucleic acid integrated into human chromosomes and mitochondria, possibly causing cancer in some cases.

Bacteria-Human Somatic Cell Lateral Gene Transfer Is Enriched in Cancer Samples


Big fan,

Bard College

Robin writes:

Liquid water without bacteria on earth:

Aqueous humour
Cerebrospinal fluid
Amniotic fluid

(No mention of exclusion of biological entities.)

Ergot on the forehead: close, but no cigars!


It is used medicinally for treatment of acute migraine attacks (sometimes in combination with caffeine).





Dihydroergotamine (/daɪˌhaɪdroʊ.ɜrˈɡɒtəmiːn/ dy-hy-droh-ur-got-ə-meen; brand names D.H.E. 45 and Migranal) is an ergot alkaloid used to treat migraines.


Spores "blow in".

Bacteria, if spore-formers, may do likewise.

Tinea versicolor/pityriasis versicolor:

Recent research has shown that the majority of Tinea versicolor is caused by the Malassezia globosa fungus, although Malassezia furfur is responsible for a small number of cases.


(Mostly a cosmetic problem.)

Microbiotum & microbiogenome?

Don writes:

Greetings and the usual well earned accolades. I have a few questions about the protective effect of "melanin" in the gut on the reticuloendothelial system. If melanin ?or its precursors are truly insoluable how was the bone marrow protected? Were the mice restrained during radiation to shadow the bone marrow by the gut laden with rooms, or is a melanin precursor responsible for the remarkable effect? To have fed refined melanin instead of the Trader Joe's fungii would answer a lot of questions. It is usually the failure of the bone marrow [reticuloendothelial system] that has killed those people with radiation poisoning, and a protectant would aid such mundane efforts as a manned Mars mission. Thanks again for your gift to science.

Don Kingsley Jr, MD

Marion writes:

the letter below posed the question how do prokaryotes perform chemiosmosis with only one membrane.

two membranes are not required for proton gradient-driven ATP synthesis. proton pumps in electron transport chains in the prokaryotic cell membrane concentrate protons inside the cell. this drives membrane-bound ATP synthase, producing ATP inside the cell. in fact, mitochondria are hypothesized to have been derived from endosymbiosis of the ancestors of purple sulfur bacteria.

A perquisite of teaching undergraduates.

original email:
Nick writes:
I teach high school AP Biology and Microbiology and have a question about ATP sythesis via oxidative phosphorylation in Gram-positive bacteria (and I guess archaens, too). In mitochondria, chloroplasts, and Gram-negative bacteria, it is possible to concentrate cations (hydrogen or sodium) in an enclosed space to drive ATP synthesis through chemiosmosis. I do not, however, understand how this is accomplished in Gram-positive bacteria and have been unable to find a satisfying answer on my own. Some things I found seem to indicate that the cell wall may trap hydrogen ions (I read something about secreted enzymes not gaining function until they made it all the way out of the capsule due to lower than optimal pH levels) or that aerobic respiration only occurs at high efficiency in the deepest layers of biofilms (something about protons concentrating when the attaching surface has a negative charge), which leads me to believe that Gram-positive bacteria are indeed pumping proton
s out into the surrounding extracellular fluid in the hope that they can be used before they diffuse away.

Greg writes:

Dear TWiM hosts,
The last few episodes have been great as usual. I wanted to comment on two things.

1. I feel that the term "microbiome" should refer to the set of microbes living in a given environment. It seems to me that there needs to be a term for this idea in any case. As for the set of genes or genomes present in a given sample, am I wrong in thinking that the word "metagenome" is adequate for this? Besides, what exactly do we mean when we add "-ome" to the end of a word? A genome is a set of genes (well, sort of). A proteome is a set of proteins. It seems logical that a microbiome should be a set of microbes. We have the added bonus that a microbiome can also be a biome. I don't know, but perhaps the word was even used in this sense before everyone started overzealously adding "-ome" words to our, um, word-ome.

2. The story from TWiM #67 about melanin-containing fungi living in environments with a lot of ionizing radiation was indeed fascinating, but I am inclined to feel skeptical about the idea that these fungi are actually deriving energy from that radiation. Is there any evidence that the fungi harness the energy of ionizing radiation? I am neither a microbiologist nor a nuclear physicist but my first guess would be that the fungi are merely unusually resistant to radiation - perhaps they are very good at repairing damage to their DNA. This resistance would allow them to thrive where other organisms can't, even while using conventional sources of food. Although I can't say I understand photosynthesis, my impression is that there is a good understanding of how the energy of visible light can be harvested by chemical means. The energy of visible photons must be a good match to the energy of a useful transition between states of a molecule. Of course, ionizing radiation also couples to chemical changes, since it can blow molecules apart, but is there any way to capture the energy when this happens? I haven't heard of anything like this. It is worth finding out, but as Carl Sagan said: "Extraordinary claims require extraordinary evidence."

I am a great fan of TWiV, TWiP, and TWiM. Keep up the great work!




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