Monday, July 15, 2019

BacterioFiles 391 - Slime Stores Sodium Sensibility

Physarum polycephalum on a log
By frankenstoen - flickr, CC BY 2.5
This episode: Slime molds can learn to get used to salt and hold on to that memory even after a period of dormancy!

Download Episode (8.9 MB, 9.7 minutes)

Show notes:
Microbe of the episode: Nocardia transvalensis

News item

Takeaways
Slime mold Physarum polycephalum has many surprisingly intelligent abilities, despite being only a single cell. Studying how these abilities work in the cell can teach us new ways that life can do things. The ability of interest here is habituation, or learning not to avoid a chemical that seems unpleasant to the cell but is not necessarily harmful, especially with a food reward.

The slime mold can become habituated to salt, in this case, learning to tolerate it enough to pass through a gradient of increasing concentration to get to some food as quickly as it crosses the same distance with no salt present. The scientists here learned that the cell takes up sodium into itself as it habituates, and holds onto both sodium and its memory through a period of hibernation.

Journal Paper:
Boussard A., Delescluse J., Pérez-Escudero A., Dussutour A. 2019. Memory inception and preservation in slime moulds: the quest for a common mechanism. Phil Trans R Soc B 374:20180368.

Post questions or comments here or email to bacteriofiles@gmail.com. Thanks for listening!

Subscribe: Apple Podcasts, RSS, Google Play. Support the show at Patreon, or check out the show at Twitter or Facebook.
Floor Fungi Fracture Phthalates

Monday, July 8, 2019

BacterioFiles 390 - Friendly Phages Find Foes

E. coli bacteria
This episode: Bacteria carry deadly phages and use them against rival strains!

Download Episode (9.4 MB, 10.2 minutes)

Show notes:
Microbe of the episode: Bifidobacterium bifidum

News item

Takeaways
Bacteria such as Escherichia coli live in environments such as the gut with many other types of microbes, and often develop communities of microbes cooperating and/or competing with each other for resources. But in order to cooperate or compete, bacteria must first be able to identify and discriminate between themselves and others. Sometimes microbes do this by exchanging membrane molecules, or secreting chemical signals that only partners can detect, or transferring plasmids or producing antimicrobial compounds that kill competitors.

In the current study, scientists discovered a strain of E. coli that carries around phages that help them distinguish other strains and compete with them. When this strain encounters another, the phages it carries attack and destroy cells of the other strain, while leaving the carrier strain mostly unharmed. This strategy is not without cost, though; the viral proteins take resources to produce, and when there's no competing strains around, the virus can attack its carrier to some extent.

Journal Paper:
Song S, Guo Y, Kim J-S, Wang X, Wood TK. 2019. Phages Mediate Bacterial Self-Recognition. Cell Reports 27:737-749.e4.

Other interesting stories:

Post questions or comments here or email to bacteriofiles@gmail.com. Thanks for listening!

Subscribe: Apple Podcasts, RSS, Google Play. Support the show at Patreon, or check out the show at Twitter or Facebook.
Floor Fungi Fracture Phthalates

Monday, July 1, 2019

BacterioFiles 389 - Prokaryotes Pacify Protein Problem

E. coli bacteria
This episode: Engineered bacteria could help people digest an essential nutrient when they can't digest it themselves!

Download Episode (8.5 MB, 9.3 minutes)

Show notes:
Microbe of the episode: Kadipiro virus

News item (paywall)

Science-Based Medicine blog article about phenylketonuria, Synlogic, and engineering bacteria to treat this disorder, with lots of good detail

Takeaways
Treating genetic disorders can be very difficult. Sometimes they can be managed, with lifestyle, diet, or medication, but cure has almost always been out of the picture. With a disorder such as phenylketonuria (PKU), for example, in which the body is unable to fully metabolize the amino acid phenylalanine, diet and medication may work to some extent.

In an effort to provide better options for PKU, scientists at Synlogic, Inc have created a strain of Escherichia coli that produces phenylalanine-degrading enzymes in the gut. The hope is that ingesting this bacterium could allow PKU patients to be less restrictive with their diet.

Journal Paper:
Isabella VM, Ha BN, Castillo MJ, Lubkowicz DJ, Rowe SE, Millet YA, Anderson CL, Li N, Fisher AB, West KA, Reeder PJ, Momin MM, Bergeron CG, Guilmain SE, Miller PF, Kurtz CB, Falb D. 2018. Development of a synthetic live bacterial therapeutic for the human metabolic disease phenylketonuria. Nat Biotechnol 36:857–864.

Other interesting stories:

Post questions or comments here or email to bacteriofiles@gmail.com. Thanks for listening!

Subscribe: Apple Podcasts, RSS, Google Play. Support the show at Patreon, or check out the show at Twitter or Facebook.
Floor Fungi Fracture Phthalates

Wednesday, June 26, 2019

Skipping a week

Sorry, no episode this week, due to vacations and busy-ness.

Sunday, June 16, 2019

BacterioFiles 388 - Floor Fungi Fracture Phthalates

This episode: Microbes in household dust help degrade potentially harmful plasticizer chemicals!

Thanks to Ashleigh Bope for her contribution!

Download Episode (6.7 MB, 7.3 minutes)

Show notes:
Microbe of the episode: Rosa rugosa leaf distortion virus

News item

Takeaways
Modern life and technology comes with modern challenges, including exposure to chemicals in building materials and such that humans didn't encounter much before the last few generations. Phthalate esters, found in PVC and other materials, can accumulate in homes and cause some problems, especially in children.

Modern life is also new to microbes, but they are very adaptable and versatile. In this study, microbes in household dust show some ability to break down the phthalates over time. Whether this activity is significant and beneficial to residents remains to be discovered.

Journal Paper:
Bope A, Haines SR, Hegarty B, Weschler CJ, Peccia J, Dannemiller KC. Degradation of phthalate esters in floor dust at elevated relative humidity. Environ Sci: Processes Impacts.

Other interesting stories:

Post questions or comments here or email to bacteriofiles@gmail.com. Thanks for listening!

Subscribe: Apple Podcasts, RSS, Google Play. Support the show at Patreon, or check out the show at Twitter or Facebook.
Floor Fungi Fracture Phthalates

Monday, June 10, 2019

BacterioFiles 387 - Carbonate Creators Combat Cracking

Sporosarcina pasteurii
By Ghosh et al. 2019. 
PLoS ONE 14(1):e0210339 
CC BY 4.0
This episode: Bacteria strengthen concrete while helping to prevent damage from road salts!

Download Episode (6.8 MB, 7.4 minutes)

Show notes:
Microbe of the episode: Azospirillum brasilense

News item

Takeaways
Winter is a bad time for concrete outside. Water seeps into cracks and freezes, causing bigger cracks that widen into potholes. Even the road salts used to keep water from freezing can react with compounds in the cement to break down the structure of the concrete.

This study looks to bacteria for a solution for protecting concrete from these reactions. Sporosarcina pasteurii, given the right nutrients, can take the harmful salt compounds and turn them into minerals that strengthen the concrete instead of weakening it.

Journal Paper:
Ksara M, Newkirk R, Langroodi SK, Althoey F, Sales CM, Schauer CL, Farnam Y. 2019. Microbial damage mitigation strategy in cementitious materials exposed to calcium chloride. Construction and Building Materials 195:1–9.

Other interesting stories:

Post questions or comments here or email to bacteriofiles@gmail.com. Thanks for listening!

Subscribe: Apple Podcasts, RSS, Google Play. Support the show at Patreon, or check out the show at Twitter or Facebook.

Monday, June 3, 2019

BacterioFiles 386 - Cupola Contaminant Cleaners

Pisa cupola painting
By JoJan, CC BY-SA 3.0
This episode: Bacteria help gently clean residue off artworks painted on stone!

Download Episode (5.6 MB, 6.1 minutes)

Show notes:
Microbe of the episode: Cellulophaga virus Cba171

Takeaways
More and more cleaning products these days contain an ingredient called "enzymes." These are proteins that break down contaminants biologically instead of just removing them chemically, in a targeted manner.

In a similar approach, this study explores applying bacteria directly to classic artwork painted directly on stone, to clean up residues on the surface. These bacteria can produce enzymes on site and degrade the contaminants while leaving the underlying paint intact.

Journal Paper:
Ranalli G, Zanardini E, Rampazzi L, Corti C, Andreotti A, Colombini MP, Bosch‐Roig P, Lustrato G, Giantomassi C, Zari D, Virilli P. 2019. Onsite advanced biocleaning system on historical wall paintings using new agar-gauze bacteria gel. J Appl Microbiol 126:1785–1796.

Other interesting stories:

Post questions or comments here or email to bacteriofiles@gmail.com. Thanks for listening!

Subscribe: Apple Podcasts, RSS, Google Play. Support the show at Patreon, or check out the show at Twitter or Facebook.

Monday, May 27, 2019

BacterioFiles 385 - Prokaryotes Protect Paper

Lysobacter enzymogenes 
attacking a fungal hypha
GFDL
This episode: Bacteria produce antifungal compounds that can protect paper from fungal deterioration!

Download Episode (6.8 MB, 7.4 minutes)

Show notes:
Microbe of the episode: Acetobacter aceti

Takeaways
Paper is a very useful information storage medium, but it is also somewhat delicious for microbes that can break it down as food, degrade the quality, and cause indelible stains and discoloration under the right conditions. Preventing this usually requires careful control, such as keeping humidity low, for storing paper for long periods.

In this study, scientists tested the ability of the bacterium Lysobacter enzymogenes to protect paper via the antifungal compounds it produces. This first required filtering out the pigments that the bacteria produced, to prevent them from discoloring the paper. Once a method for this filtering was in place, they found the bacterial culture supernatant could significantly reduce fungal growth on various kinds of paper, and protect the paper from staining and degradation.

Journal Paper:
Chen Z, Zou J, Chen B, Du L, Wang M. 2019. Protecting books from mold damage by decreasing paper bioreceptivity to fungal attack using de-coloured cell-free supernatant of Lysobacter enzymogenes C3. J Appl Microbiol 126:1772–1784.

Post questions or comments here or email to bacteriofiles@gmail.com. Thanks for listening!

Subscribe: Apple Podcasts, RSS, Google Play. Support the show at Patreon, or check out the show at Twitter or Facebook.

Monday, May 20, 2019

BacterioFiles 384 - Moss Materials Modify Microbiota

Moss with fungi
This episode: Contact with soil materials and moss causes significant, though short-term, changes in the skin microbiota!

Thanks to Dr. Mira Grönroos for her contribution!

Download Episode (7.1 MB, 7.75 minutes)

Show notes:
Microbe of the episode: Leonurus mosaic virus

Takeaways
Exposure to microbes throughout life is thought to help calibrate the immune system to some extent, reducing the risk of allergies and asthma without losing defense against pathogens. In this study, rubbing soil or packets of moss on the skin changed the composition of the skin microbiota temporarily, so this may be a way to help with this important type of exposure, but it is not yet known how to achieve optimal long-term effects.

Journal Paper:
Grönroos M, Parajuli A, Laitinen OH, Roslund MI, Vari HK, Hyöty H, Puhakka R, Sinkkonen A. 2019. Short-term direct contact with soil and plant materials leads to an immediate increase in diversity of skin microbiota. MicrobiologyOpen 8:e00645.

Other interesting stories:

Post questions or comments here or email to bacteriofiles@gmail.com. Thanks for listening!

Subscribe: Apple Podcasts, RSS, Google Play. Support the show at Patreon, or check out the show at Twitter or Facebook.

Monday, May 13, 2019

BacterioFiles 383 - Communities Carry Communicable Communities

Village in Fiji
By Merbabu~commonswiki
I'm back! This episode: Looking at how people in different villages share microbes!

Download Episode (6.5 MB, 7.0 minutes)

Show notes:
Microbe of the episode: Cristispira pectinis

Takeaways
Our microbiota, the communities of microbes living in and on our bodies, are incredibly diverse and varied. Each person's is different, and they can change drastically over time with changes in location, diet, lifestyle, and other factors.

Learning how our microbiota forms and changes and functions is important, because it can affect many aspects of health. In this study, villagers in the islands of Fiji share microbes with others in the same and other villages, but not always in patterns that might be expected.

Journal Paper:
Brito IL, Gurry T, Zhao S, Huang K, Young SK, Shea TP, Naisilisili W, Jenkins AP, Jupiter SD, Gevers D, Alm EJ. Transmission of human-associated microbiota along family and social networks. Nat Microbiol.

Other interesting stories:

Post questions or comments here or email to bacteriofiles@gmail.com. Thanks for listening!

Subscribe: Apple Podcasts, RSS, Google Play. Support the show at Patreon, or check out the show at Twitter or Facebook.

Monday, April 15, 2019

BacterioFiles 382 - Small Scavengers Suck Sizeable Cells

Rhodotorula prey yeast
By A doubt, CC BY-SA 3.0
This episode: Fungus-hunting amoebas have different strategies for detecting and preying on single-celled and filamentous fungi!

Also, a personal note: I'm going to be taking a few weeks off the podcast to be able to take full advantage of spring, but I'll be back as soon as the weather gets too hot.

Download Episode (7.5 MB, 8.2 minutes)

Show notes:
Microbe of the episode: Chondromyces catenulatus

Takeaways
Amoebas in the microbial world are like powerful predators, going around gobbling up whatever they find that's small enough, by a process called phagocytosis, in which they surround their prey with their cell membrane and engulf it. It's similar to macrophages or white blood cells as part of our immune system in our bodies.

The prey of amoebas includes bacteria, large viruses, and single-celled fungi called yeasts. In this study, scientists showed that some yeasts make great food sources for a certain kind of amoeba called Protostelium aurantium, while others either lack nutritional value or hide from the predators by covering up certain recognition molecules on their cell wall.

They found that the amoebas could also consume the spores of filamentous fungi, and could even attack the filaments, or hyphae. In this latter case, instead of engulfing the large filaments, they pierced the cells and extracted their contents, an approach named ruphocytosis, from the Greek for suck or slurp.

Journal Paper:
Radosa S, Ferling I, Sprague JL, Westermann M, Hillmann F. The different morphologies of yeast and filamentous fungi trigger distinct killing and feeding mechanisms in a fungivorous amoeba. Environ Microbiol.

Other interesting stories:

Post questions or comments here or email to bacteriofiles@gmail.com. Thanks for listening!

Subscribe: Apple Podcasts, RSS, Google Play. Support the show at Patreon, or check out the show at Twitter or Facebook.

Monday, April 8, 2019

BacterioFiles 381 - Chlorophyll Can Convey Cancer Characteristics

Tumor imaging by MSOT
By Peters et al. 2019,
Nat Commun 10:1191, CC BY 4.0
This episode: Pigmented bacteria can be used in a cancer imaging technique that combines light and sound!

Download Episode (8.9 MB, 9.75 minutes)

Show notes:
Microbe of the episode: Streptomyces bellus

Takeaways
Because "cancer" is a general term that describes many different forms of disease affecting different cells in different parts of the body, effective cancer treatment relies on understanding the location and physiology of the cancer in a given patient. New imaging technologies for diagnosis and analysis of cancer and for cancer research can be very valuable, especially if they don't require big investments of money and space.

One promising imaging technology is called multispectral optoacoustic imaging, or MSOT. This uses pulses of light to create vibrations as pigments in tissues absorb the light and undergo thermal expansion; these vibrations are then detected by ultrasound technology. This approach allows good resolution and depth of imaging without large equipment like MRI machines, but the best results require adding pigments into the body.

In this study, scientists showed that the photosynthetic pigments of purple non-sulfur bacteria can be useful in this optoacoustic imaging, providing a somewhat long-term, nontoxic approach. It proved especially interesting when they discovered that the wavelength spectrum changing over time was an indication of macrophage activity in the tumors.

Journal Paper:
Peters L, Weidenfeld I, Klemm U, Loeschcke A, Weihmann R, Jaeger K-E, Drepper T, Ntziachristos V, Stiel AC. 2019. Phototrophic purple bacteria as optoacoustic in vivo reporters of macrophage activity. Nat Commun 10:1191.

Other interesting stories:

Post questions or comments here or email to bacteriofiles@gmail.com. Thanks for listening!

Subscribe: Apple Podcasts, RSS, Google Play. Support the show at Patreon, or check out the show at Twitter or Facebook.

Monday, April 1, 2019

BacterioFiles 380 - Plant Promoter Produces Polymer

Herbaspirillum-like bacteria
in banana plants
Scientific Figure on
ResearchGate. CC BY-NC 4.0
This episode: A microbe that boosts plant growth needs to make storage polymers for both itself and the plant's sake!

Download Episode (7.1 MB, 7.75 minutes)

Show notes:
Microbe of the episode: Suid gammaherpesvirus 3

Takeaways
Bacteria that promote plant growth are fascinating and not too hard to find. Plants and microbes make good partners by each contributing something the other needs. Plants make sugars via photosynthesis that microbes can use as food, and microbes can gather nutrients that plants can't make, can drive off pathogens, and can contribute to plant growth in other ways.

However, plants aren't making sugars all the time, because the sun goes down every day. So what do partner microbes do at these times? In this study, a beneficial microbe Herbaspirillum seropedicae was found to produce a storage compound called polyhydroxyalkanoate, or PHA, that it could use to store food for times of scarcity. Mutants of this microbe that could not make the storage compound weren't very beneficial for their plant partners.

Journal Paper:
Alves LPS, Amaral FP do, Kim D, Bom MT, Gavídia MP, Teixeira CS, Holthman F, Pedrosa F de O, Souza EM de, Chubatsu LS, Müller-Santos M, Stacey G. 2019. Importance of Poly-3-Hydroxybutyrate Metabolism to the Ability of Herbaspirillum seropedicae To Promote Plant Growth. Appl Environ Microbiol 85:e02586-18.

Other interesting stories:

Post questions or comments here or email to bacteriofiles@gmail.com. Thanks for listening!

Subscribe: Apple Podcasts, RSS, Google Play. Support the show at Patreon, or check out the show at Twitter or Facebook.

Monday, March 25, 2019

BacterioFiles 379 - Photons Facilitate Faster Flourishing

This episode: Light increases the growth even of some bacteria that don't harvest its energy!

Download Episode (9.0 MB, 9.75 minutes)

Show notes:
Microbe of the episode: Methylococcus thermophilus

News item

Takeaways
Light from the sun is one of the fundamental sources of energy for life on this planet. Plants and other phototrophs—photosynthetic organisms that get their energy mainly from light—form the foundation of the food web, and organisms that feed on them or that feed on organisms that feed on them are all dependent on the ability to capture the sun's rays.

There are other ways to benefit directly from the sun's energy, besides photosynthesis—some microbes have enzymes that use light energy to repair damage to DNA (the same damage that is caused by ultraviolet light), and we use sunlight to synthesize vitamin D.

In this study, however, microbes are discovered to grow faster in the presence of light despite not being phototrophs or producing any light-harvesting proteins. The scientists discover some possible light-sensing proteins, though, that could regulate these microbes' behavior, allowing them to synchronize their growth cycles to phototroph partners in aquatic environments.

Journal Paper:
Maresca JA, Keffer JL, Hempel P, Polson SW, Shevchenko O, Bhavsar J, Powell D, Miller KJ, Singh A, Hahn MW. Light modulates the physiology of non-phototrophic Actinobacteria. J Bacteriol JB.00740-18.

Other interesting stories:

Post questions or comments here or email to bacteriofiles@gmail.com. Thanks for listening!

Subscribe: Apple Podcasts, RSS, Google Play. Support the show at Patreon, or check out the show at Twitter or Facebook.

Monday, March 18, 2019

BacterioFiles 378 - Medusa Makes Marble Microbes

Medusavirus
Yoshikawa et al. 2019 J Virol.
This episode: Newly discovered giant virus from a hot spring turns its amoeba hosts to stone!

Download Episode (6.7 MB, 7.3 minutes)

Show notes:
Microbe of the episode: Listeria virus P70

News item

Takeaways
Viruses come in endless different shapes, sizes, and genetic configurations. Even within the group called giant viruses there is a large amount of variety. Many of their genes are unknown, without homology to any other sequences we have acquired in other areas of life. There is great potential to learn interesting things from these viruses.

In this study, a new giant virus is discovered. Like many others, this infects amoebas, and causes them to transform from dynamic, shape-shifting cells into hard little cyst-like circles. This ability gave it the name Medusavirus. It's the first giant virus found in a relatively hot environment (a hot spring), and among other interesting features, it shows signs of multiple instances of gene transfer to and from its amoeba host.

Journal Paper:
Yoshikawa G, Blanc-Mathieu R, Song C, Kayama Y, Mochizuki T, Murata K, Ogata H, Takemura M. 2019. Medusavirus, a novel large DNA virus discovered from hot spring water. J Virol JVI.02130-18.

Other interesting stories:

Post questions or comments here or email to bacteriofiles@gmail.com. Thanks for listening!

Subscribe: Apple Podcasts, RSS, Google Play. Support the show at Patreon, or check out the show at Twitter or Facebook.

Monday, March 11, 2019

BacterioFiles 377 - Distributed Defense-Defeating Devices

This episode: Newly discovered CRISPR-inhibiting genes are found in many different bacterial groups!

Download Episode (8.0 MB, 8.8 minutes)

Show notes:
Microbe of the episode: Borrelia mazzottii

News item

Takeaways
The discovery of the microbial immune system, CRISPR-Cas, changed many things about the way we think of microbial ecology and interactions with microbe-infecting viruses. The CRISPR-Cas system can learn to detect new threats by capturing bits of their genetic sequences and using these to target the Cas proteins to chop up any such sequences that make it into the cytoplasm. This can greatly increase microbial survival in certain ecosystems in which viruses regularly kill a large percentage of the microbial population.

To overcome this defense, a virus has to adapt, either by acquiring mutations that change its sequence, thus escaping detection, or by acquiring anti-CRISPR proteins that shut down the microbial defense directly. These possibilities make the complex ecology even more interesting.

In this study, scientists develop a clever method for screening for new anti-CRISPR genes, and go searching for them in samples from various places (soil, animal guts, human gut). They find several new examples, which turn out to be found in many different kinds of species in many different environments.

Journal Paper:
Uribe RV, Helm E van der, Misiakou M-A, Lee S-W, Kol S, Sommer MOA. 2019. Discovery and Characterization of Cas9 Inhibitors Disseminated across Seven Bacterial Phyla. Cell Host & Microbe 25:233-241.e5.

Other interesting stories:

Post questions or comments here or email to bacteriofiles@gmail.com. Thanks for listening!

Subscribe: Apple Podcasts, RSS, Google Play. Support the show at Patreon, or check out the show at Twitter or Facebook.

Monday, March 4, 2019

BacterioFiles 376 - Pressurized Pollutant Pulls Products

Bacillus megaterium
By Osmoregulator, CCBY-SA 3.0
This episode: Supercritical carbon dioxide and bacteria that can grow in it make a great combination for biofuel production!

Download Episode (9.4 MB, 10.2 minutes)

Show notes:
Microbe of the episode: Flexibacter aggregans

Takeaways
Biofuels are an important part of humanity's move away from non-renewable resources. They have a higher energy density than batteries are yet able to achieve, giving them significant advantages for transportation purposes in which tapping into an electric grid isn't possible. Depending on the biofuel, they also have the advantage of existing infrastructure: we don't need to build a whole new system of charging or refueling stations, but can use the systems already in place.

However, biofuels as a collection of technologies still need some refinements. Yields for the more potentially sustainable approaches are low, and the lower the concentration of a soluble fuel, the more difficult it is to separate it from the non-fuel components of a fermentation. Microbial products also face the risk of contamination of a fermentation by unwanted organisms that use up the substrate without producing desirable products.

In this study, supercritical carbon dioxide is considered as a fix for both of these problems. The gas is pressurized to a point at which it is indistinguishable from liquid. A strain of Bacillus megaterium is specially selected as capable of growing and fermenting in this environment, while contaminants are inhibited. The solvent potential of supercritical carbon dioxide also serves as a way to extract the biofuel product—in this case, isobutanol—from the aqueous part of the culture medium. While it needs some development, this approach yields promising results.

Journal Paper:
Boock JT, Freedman AJE, Tompsett GA, Muse SK, Allen AJ, Jackson LA, Castro-Dominguez B, Timko MT, Prather KLJ, Thompson JR. 2019. Engineered microbial biofuel production and recovery under supercritical carbon dioxide. Nat Commun 10:587.

Other interesting stories:

Post questions or comments here or email to bacteriofiles@gmail.com. Thanks for listening!

Subscribe: Apple Podcasts, RSS, Google Play. Support the show at Patreon, or check out the show at Twitter or Facebook.

Monday, February 25, 2019

BacterioFiles 375 - Prepared Pathogen Preserves Perception

This episode: A cancer-killing virus could help increase success of treatment of a form of eye cancer in children!

Download Episode (8.0 MB, 8.7 minutes)

Show notes:
Microbe of the episode: Acanthamoeba polyphaga mimivirus

News item

Takeaways
Cancer obviously is a serious concern, and can be tricky to treat because there are endless varieties in all different places in the body, each of which can have its own expected progression, aggressiveness, and methods of treatment to take into account.

Even more serious is when the cancer is in very young children, as is often the case with a cancer of the eye called retinoblastoma. There are about 8000 cases of this disease per year, and when treatment is unsuccessful, it can lead to the loss of one or both eyes.

In this study, investigators looked into using a cancer-targeting, oncolytic virus to complement the normal treatment of chemotherapy. The virus for the most part remained localized to the eye where it should be, and targeted the cancer instead of healthy cells, and so seems promising. In the small trial with two patients included in this study, the virus didn't cause a complete recovery, but showed some modest promising results.

Journal Paper:
Pascual-Pasto G, Bazan-Peregrino M, Olaciregui NG, Restrepo-Perdomo CA, Mato-Berciano A, Ottaviani D, Weber K, Correa G, Paco S, Vila-Ubach M, Cuadrado-Vilanova M, Castillo-Ecija H, Botteri G, Garcia-Gerique L, Moreno-Gilabert H, Gimenez-Alejandre M, Alonso-Lopez P, Farrera-Sal M, Torres-Manjon S, Ramos-Lozano D, Moreno R, Aerts I, Doz F, Cassoux N, Chapeaublanc E, Torrebadell M, Roldan M, König A, Suñol M, Claverol J, Lavarino C, De TC, Fu L, Radvanyi F, Munier FL, Catalá-Mora J, Mora J, Alemany R, Cascalló M, Chantada GL, Carcaboso AM. 2019. Therapeutic targeting of the RB1 pathway in retinoblastoma with the oncolytic adenovirus VCN-01. Sci Transl Med 11:eaat9321.

Other interesting stories:

Post questions or comments here or email to bacteriofiles@gmail.com. Thanks for listening!

Subscribe: Apple Podcasts, RSS, Google Play. Support the show at Patreon, or check out the show at Twitter or Facebook.

Monday, February 18, 2019

BacterioFiles 374 - Microbes Muzzle Malicious Metal

Elemental arsenic
By Tomihahndorf
CC BY-SA 3.0
This episode: Mouse gut microbes, from mice or from human donors, can protect mice against arsenic toxicity!

Download Episode (6.3 MB, 6.9 minutes)

Show notes:
Microbe of the episode: Streptomyces griseus

News item

Takeaways
Our gut microbes benefit us in many ways, including nutritionally—by producing vitamins and helping to digest food—and by helping us in defense against pathogens and other immunological threats.

Many things we do can affect our gut microbes too, positively or negatively. What we eat, toxins we encounter, and other aspects of lifestyle can damage our microbial communities.

In this study, we see that the reverse could be true, that gut microbes, and specifically one called Faecalibacterium prausnitzii, can protect their host against toxins such as arsenic.

Journal Paper:
Coryell M, McAlpine M, Pinkham NV, McDermott TR, Walk ST. 2018. The gut microbiome is required for full protection against acute arsenic toxicity in mouse models. Nat Commun 9:5424.

Other interesting stories:

Post questions or comments here or email to bacteriofiles@gmail.com. Thanks for listening!

Subscribe: Apple Podcasts, RSS, Google Play. Support the show at Patreon, or check out the show at Twitter or Facebook.

Monday, February 11, 2019

BacterioFiles 373 - Plant Pilots Prevent Parching

Emmer wheat
This episode: Beneficial fungi found inside wild grain plants help wheat plants grow better with less water!

Download Episode (7.1 MB, 7.75 minutes)

Show notes:
Microbe of the episode: Beijerinckia indica

Takeaways
As we have microbial communities in our guts, on our skin, and in various other places in and on our bodies, plants also have beneficial microbial symbionts around their roots, on their leaf surfaces, and even inside their tissues. These microbes can be bacteria, fungi, or other, and can help plants gather nutrients, resist diseases or pests, and other things.

In this study, some fungi living in grain plants—called endophytes, or "inside plants"—can help wheat tolerate drought and grow better with less water. Studying this system could lead to breakthroughs in wheat farming, all thanks to microbes.

Journal Paper:
Llorens E, Sharon O, Camañes G, García‐Agustín P, Sharon A. Endophytes from wild cereals protect wheat plants from drought by alteration of physiological responses of the plants to water stress. Environ Microbiol.

Other interesting stories:

Post questions or comments here or email to bacteriofiles@gmail.com. Thanks for listening!

Subscribe: Apple Podcasts, RSS, Google Play. Support the show at Patreon, or check out the show at Twitter or Facebook.

Monday, February 4, 2019

BacterioFiles 372 - Roundworm Riders Repel Raiders

Nematode
By Bob Goldstein, UNC Chapel Hill
CC BY-SA 3.0
This episode: Bacteria that help nematodes prey on insects also help keep fungi from stealing their kills!

Download Episode (7.4 MB, 8.1 minutes)

Show notes:
Microbe of the episode: Artogeia rapae granulovirus

Takeaways
Soil is an incredibly complex ecosystem, with many different interactions constantly happening between plants, insects, bacteria, fungi, and other organisms, not to mention a large variety of shifting environmental conditions. All of these are competing with some and cooperating with others to try to survive and thrive the best they can.

One interesting interaction takes place between small roundworms in the soil, called nematodes, and bacteria they carry around that cause disease in insects. These nematodes prey on insects by injecting the bacteria into them, which kill and start digesting the insects. The nematodes then feed on the insects and the bacteria until the resources have been exhausted, and then move on to the next insect, taking some bacteria with them again.

In this study, the scientists wondered how these partners deal with competitors in the soil that might want to take advantage of their resources. They discover that the bacteria produce compounds that can repel and inhibit fungi that might otherwise steal their kills.

Journal Paper:
Shan S, Wang W, Song C, Wang M, Sun B, Li Y, Fu Y, Gu X, Ruan W, Rasmann S. The symbiotic bacteria Alcaligenes faecalis of the entomopathogenic nematodes Oscheius spp. exhibit potential biocontrol of plant- and entomopathogenic fungi. Microb Biotechnol.

Other interesting stories:

Post questions or comments here or email to bacteriofiles@gmail.com. Thanks for listening!

Subscribe: Apple Podcasts, RSS, Google Play. Support the show at Patreon, or check out the show at Twitter or Facebook.

Monday, January 28, 2019

BacterioFiles 371 - Cell Stalker Senses Signals

Vibrio cholerae
This episode: Phages eavesdrop on bacterial communications to attack at the perfect moment!

Thanks to Justin Silpe and Dr. Bonnie Bassler for their contributions!

Download Episode (11.1 MB, 12.2 minutes)

Show notes:
Microbe of the episode: Artichoke Aegean ringspot virus

News item

Takeaways
Even organisms as small as bacteria can, and often do, communicate with each other through a process called quorum sensing, in which each cell releases a small amount of a certain chemical into their surroundings. When the population is large enough that the concentration of this chemical builds up to a certain level, the cells in the population change their behavior. The specifics of this change depend on the species and the situation.

But since this chemical signal is released into the environment, anything around that can sense it can listen in on the communications of a bacterial population. In this study, Justin Silpe and Dr. Bonnie Bassler find a type of virus that uses such a chemical communication as a signal to come out of stasis and hijack a whole population of bacteria at once!

Journal Paper:
Silpe JE, Bassler BL. 2019. A Host-Produced Quorum-Sensing Autoinducer Controls a Phage Lysis-Lysogeny Decision. Cell 176:268-280.E13.

Other interesting stories:

Post questions or comments here or email to bacteriofiles@gmail.com. Thanks for listening!

Subscribe: Apple Podcasts, RSS, Google Play. Support the show at Patreon, or check out the show at Twitter or Facebook.

Monday, January 21, 2019

BacterioFiles 370 - Magnets Make Messenger More Moveable

Baculoviruses in occlusion body
This episode: Enhancing a virus with magnetic nanoparticles and CRISPR-Cas gene editing abilities makes it a good vector for genetic therapies!

Download Episode (11.2 MB, 12.25 minutes)

Show notes:
Microbe of the episode: Staphylococcus virus S253

News item

Takeaways
Gene delivery, getting genetic content for gene therapy to the correct tissues in an organism, has long been a very tricky problem. And genetic modification, making specific changes at a specific place in a genome, is also difficult.

Viruses can help with both delivery and modification, but they're often not specific and targeted enough to be effective, or even safe. Off-target effects could be harmful or even deadly, potentially resulting in cancer.

In this study, a virus is modified with nanotechnology in the form of tiny magnets to allow humans to target it to specific tissues, and given the ability to modify specific genes using the bacterial CRISPR-Cas system. These modifications potentially make this gene delivery system much more safe and effective.

Journal Paper:
Zhu H, Zhang L, Tong S, Lee CM, Deshmukh H, Bao G. 2018. Spatial control of in vivo CRISPR–Cas9 genome editing via nanomagnets. Nat Biomed Eng.

Other interesting stories:

Post questions or comments here or email to bacteriofiles@gmail.com. Thanks for listening!

Subscribe: Apple Podcasts, RSS, Google Play. Support the show at Patreon, or check out the show at Twitter or Facebook.

Monday, January 14, 2019

BacterioFiles 369 - Powering Purple Prokaryote Protonation

This episode: Purple phototrophic bacteria could use certain kinds of wastewater, along with electric current, to produce valuable products like hydrogen without much waste!

Thanks to Dr. Ioanna Vasiliadou for her contribution!

Download Episode (12.7 MB, 13.9 minutes)

Show notes:
Microbe of the episode: Streptomyces tendae

News item

Takeaways
Purple phototrophic bacteria can take light energy and use it to help power their metabolism. They're not dependent on it like plants, but can use light or other energy sources for their versatile metabolism.

This versatility makes them very interesting candidates for industrial biotechnology applications. These bacteria can take in various combinations of nutrients and produce a number of different valuable products, including protein-rich feed, bioplastics, and biofuels such as hydrogen gas.

Today's study shows they can also take up electrons directly to help make their biofuel production process even more environmentally sustainable.

Journal Paper:
Vasiliadou IA, Berná A, Manchon C, Melero JA, Martinez F, Esteve-Nuñez A, Puyol D. 2018. Biological and Bioelectrochemical Systems for Hydrogen Production and Carbon Fixation Using Purple Phototrophic Bacteria. Front Energy Res 6:107.

Other interesting stories:

Post questions or comments here or email to bacteriofiles@gmail.com. Thanks for listening!

Subscribe: Apple Podcasts, RSS, Google Play. Support the show at Patreon, or check out the show at Twitter or Facebook.

Monday, January 7, 2019

BacterioFiles 368 - Prokaryotes Promote Passing Parent Peculiarities

Drosophila fruit fly
By André Karwath, CC BY-SA 2.5
This episode: Fruit fly gut microbes can mediate non-genetic traits passed from parents to offspring!

Thanks to Dr. Per Stenberg for his contribution!

Download Episode (10.0 MB, 10.9 minutes)

Show notes:
Microbe of the episode: Bifidobacterium breve

News item

Takeaways
Heritability of traits is essential for evolution; if an ability can't be passed on from generation to generation, then natural selection can't act on it on a population-wide level.

An organism's genome is the source of most heritable traits, as DNA gets passed on to offspring, but a number of other ways of passing on traits have been discovered, in the field of epigenetics.

In this study, the gut microbes from fruit flies raised in one temperature could affect the gene expression of their offspring raised in a different temperature, compared to flies that had been kept at the latter temperature over both generations. While the effects on fly fitness or behavior are not yet known, these results suggest that gut microbes, transmitted from parents to offspring, could be another mechanism of heritability.

Journal Paper:
Zare A, Johansson A-M, Karlsson E, Delhomme N, Stenberg P. 2018. The gut microbiome participates in transgenerational inheritance of low-temperature responses in Drosophila melanogaster. FEBS Lett 592:4078–4086.

Other interesting stories:

Post questions or comments here or email to bacteriofiles@gmail.com. Thanks for listening!

Subscribe: Apple Podcasts, RSS, Google Play. Support the show at Patreon, or check out the show at Twitter or Facebook.