Microbiology (BIOL420)
Bugs in the News from the 2017 Microbiology Class
from Allison Y.;
This Op-Doc shares the story of Josiah Zayner, a former NASA scientist who suffered from IBS, diarrhea, gastrointestinal ulcers, and would need to "go to the bathroom every 20 minutes.” Having seen a good number of doctors without finding any solutions to his issues, Zayner realized that modern medicine had failed to give him the answers he needed. Unwilling to deal with chronic indigestion for the rest of his life, Zayner took matters into his own hands, proposing an extreme version of a fecal transplant. Typically, fecal transplants are done in a sterile, controlled hospital environment to treat patients infected with Clostridium difficile, which, if left untreated, can be fatal. Despite the high risk of unknowns in his pseudo-experiment (i.e. untested fecal matter can contain unforeseen parasites and pathogens; also risk for contracting hepatitis), Zayner was committed to the idea that he could recolonize his microbiome with that of another young, strong, healthy male. Once Zayner found himself a well-digesting candidate, he collected skin, oral, and fecal samples from that individual. On the first night of the transplant, Zayner drank a concoction of antibiotics to eradicate his indigenous bacteria. Then, for the next 72 hours, he ingested capsules that contained his donor's fecal matter and other biochemical components. Eight weeks after his experiment, Zayner not only said that most of his digestive issues had receded, but also had a lab perform genetic testing on the microbes in his stool. In comparing his results with the bacterial sequences of his donor’s stool, we learn that the bacteria which now inhabit Zayner’s gut are very identical to that of his donor.
https://www.nytimes.com/2017/04/11/opinion/gut-hack.html?mcubz=0
from Julia T.;
Tardigrades are found to be very closely related to nematodes and are classified as extremophiles. This study looked at the extent of their ability to undergo anhydrobiosis and the possible benefits that this ability could provide to humans. This was done by analyzing the genome of this critter, and found them to be related to nematodes and supported the traditional “tardigrade-arthropod link.” The tardigrade should be of interest to us, especially our class, because it could potentially change the extent to which we are able to distribute vaccinations across our world.
This part of the CNN article highlights the basic idea:
"Even then, the vaccine will have a shelf life, and we would have to guarantee keeping it cold all the time. Now imagine the same vaccine, coated in tardigrade desiccation proteins. Stored at room temperature and shipped by post, the vaccine would have a much extended shelf life, and would be ready to use whenever and wherever it was needed.”
CNN article about tardigrades.
http://www.cnn.com/2017/07/27/health/tardigrade-water-bear-survival-study/index.html
Research Article:
http://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.2002266
Bugs in the News: Cyanobacteria Blooms (Andrew S.)
Cyanobacteria, also known as blue-green algae, are believed to be among the oldest bacteria in the world. They are most famously known for their massive “blooms,” which are common in eutrophic bodies of water and can be toxic to humans and animals. One species in particular, Microcystis aeruginosa, is known to produce a hepatotoxin (liver toxin) that can be particularly harmful to humans. Cyanobacteria are oxygenic phototrophs, which means that they use light as a source of energy, and produce oxygen in the process. Their sheer abundance makes them a significant contributor to the global oxygen supply. One thing that makes them unique is that they can perform photosynthesis and respiration in the exact same compartment, often using the same electron carriers interchangeably. The light harvesting complex of cyanobacteria, the phycobillisome, is of particular interest in the discussion of bacterial morphology, because many filamentous cyanobacteria can alter the shape of the phycobillisome for optimal light energy absorption at various wavelengths depending on their position within the water column. This is called complimentary chromatic adaptation. Furthermore, in nutrient depleted conditions, they can engulf this apparatus entirely as a source of nitrogen and other much needed resources (Grossman et al., 1). Phycobillins (or phycocyannin), in addition to chlorophyll, are the main photosynthetic pigments responsible for light harvesting and photosynthesis in these bacteria. These remarkable bacteria are also capable of fixing nitrogen, which makes them particularly influential within the ecosystem.
Grossman, A. R., Schaefer, M. R., & Chiang, A. G. (1993, September 01). The phycobilisome, a light-harvesting complex responsive to environmental conditions.
Bugs in the News (Amanda S.)
Choanoflagellates are free-living or colonial eukaryotes that are considered to be the closest living relatives to animals. One type of choanoflagellate, Salpingoeca rosetta, recently came into the news for some unusual behavior. In the lab of Nicole King, a professor at UC Berkeley, this behavior was accidentally discovered when S. rosetta were observed in the presence of a marine bacterium, Vibrio fischeri. V. fischeri secretes a protein called EroS that causes S. rosetta to sexually reproduce. King's lab was able to demonstrate the reproduction through meiotic recombination as well as video of the cells fusing in groups called rosettes. This is significant because choanoflagellates typically demonstrate asexual reproduction.
This aphrodisiac-like behavior is induced by just a single EroS protein. Of further interest is that EroS is a chondroitin lyase whose substrate, chondroitin sulfate, was previously thought to be present only in animals. The explanation behind S. rosetta's behavior is that it actually produces chondroitin sulfate, which allows it to interact with bacteria containing EroS or other chondroitin lyases who can then induce mating in S. rosetta. In nature, bacteria may regulate mating behavior of S. rosetta, demonstrating that interactions between "simple" organisms are sometimes more complex than previously thought. Further studies could also increase understanding in the mechanism of evolution from single-celled organisms to humans over hundreds of millions of years.
END FIRST GROUPING (EXAM 1)
Bugs in the News – Gaby C.
Although often thought of as a lethal virus, the Zika virus is currently being looked into as a treatment for brain cancer, specifically, against glioblastoma stem cells. Recently, researchers discovered that the virus selectively infects and kills hard-to-treat cancerous cells in adult brains. The virus is initially diluted into a less lethal dosage and injected directly into a brain tumor during surgery. The researchers experimented on adult mice brains and found that the Zika injections shrank aggressive tumors while leaving other healthy brain cells unharmed. Given that this study is relatively new in medical research, it still poses a positive direction for possible cancer treatments in humans.
BBC News Health article: http://www.bbc.com/news/health-41146628
The Journal of Experimental Medicine article: http://jem.rupress.org/content/early/2017/09/05/jem.20171093
Bug in the news - Jingyi C.
News from New York Times: Gut Bacteria Fluctuate with the Seasons
https://www.nytimes.com/2017/08/24/science/gut-bacteria-hadza-diet-health.html
http://science.sciencemag.org/content/357/6353/802\
This paper was published on Science. Researchers went to Tanzania, where they studied a local community called Hadza. Hadza is the last remaining population in Africa that still live a hunter-gather style, which means, their activities are largely rely on their food resources. During the wet season (November to April), they forage for berry and consume honey. During the dry season (May to October) they hunt for animal and eat a lot of meat. Through the all year, they eat fiber rich plants and baobab(plant). Researchers collected 350 fecal samples in 12 months period, and from 188 recoded unique individuals’ samples, researchers found that the Hadza’s microbial community are cyclic and can be differentiated by seasons. For example, 70.2% of the Bacteroidetes would disappear in dry season, and 78.2% of Bacteroidetes would come back during the wet season. Therefore, researchers hypothesis that: seasonal dietary changes might lead to related changes in the functional capacity of the microbial community. Then researchers compared the microbiotas of Hadza with it of American. They found largely difference. The Hadza microbiotas show greater functional capacity of utilization of plant carbohydrates than the microbiotas of Americans, which relates to the fact that Hadza eat more plants than American do.
Bugs in the news from Ashley S.,
A study published in Science discovered a certain type of bacteria that contains an enzyme that can inhibit the chemotherapeutic drug gemcitabine in human pancreatic tumor cells. Essentially, the bacteria kept the drug from killing cancerous (and healthy) cells. Scientists isolated the gene that encoded for the enzyme that enabled the bacteria to do this as cytidine deaminase (CDD). This gene comes in two forms – a short and a long form. Only the bacteria with the long form of the CDD gene, mainly found in Gammaproeobacteria, could inactivate gemcitabine. Gammaproteobacteria are Gram-negative bacteria, and examples of other kinds of these bacteria include Salmonella spp. (enteritis and typhoid fever), Yersinia pestis (plague), Vibrio cholerae (cholera), Pseudomonas aeruginosa (lung infections in cystic fibrosis patients), and Escherichia coli (food poisoning). The specific Gammaproteobacteria in the study are usually found in pancreatic ductal adenocarcinoma (PDAC) cells, which means that the intratumor bacteria in these cells contributed to drug resistance. Important areas of research and further questions that this study sparked are whether bacteria are present in other cancers and the idea of treating cancer with a combined method of antibiotics and chemotherapy for maximum effect.
Excerpt: https://www.sciencedaily.com/releases/2017/09/170918100656.htm
Original: http://science.sciencemag.org/content/357/6356/1156.full
Bugs in the News, Kathryn M.
In class we have discussed how bacteria and other microbes are passed on from mothers to their infants during birth. Recently, it has been studied that mothers not only pass on bacteria, but also fungi to their infants during breastfeeding. Before this study fungi had been seen in the milk of cows, but never studied in human milk until now. Also women who suffered from breast infections or mastitis had fungi present in their breastmilk. However, this study has shown that healthy women also have fungi present in their breastmilk. A sample size of 65 mothers showed that 89% of the milk samples had trace amounts of fungi that were supplying the infants with nutrients with the most common genera of fungi being, Malassezia,Candida, and Saccharomyces. It is believed that these fungi, like bacteria, actually help the infant's microbiome and health. The authors hope that this study and example of fungi in breastmilk can help spur on more studies of how these fungi actually help the microbiome.
Article Title: "Multiple Approaches Detect the Presence of Fungi in Human Breastmilk Samples from Healthy Mothers"
Authors: Alba Boix-Amorós, Cecilia Martinez-Costa, Amparo Querol, Maria Carmen Collado, and Alex Mira
https://www.nature.com/articles/s41598-017-13270-x
Second Group Ending (EXAM 2)
Bugs in the News: Hannah C.
In Denmark, researchers analyzed the ratio of Prevotella and Bacteroides for their success as a weight loss enhancement. They found that those who were overweight were more likely to lose more weight when given a low fat, high fiber diet with a high ratio of the two gut microbes. This study looked at 62 overweight people given either a high fiber low fat diet or a normal Danish diet. The gut microbes were the most efficient in aiding weight loss (decrease in 10.9 pounds) when participants were given a specific diet rather than their normal danish diet (loss of 5.5 pounds). This finding is something that could be beneficial in the future when we know more about the gut microbiome because we could use these microbes as a supplement for those who at a higher health risk due to obesity.
End third grouping (EXAM 3)
Bugs in the News: Jessica G.
Traditionally, eggs have been decontaminated with compounds such as formaldehyde, which is toxic to humans. Pyrazines, a type of volatile organic compound, represent a less toxic alternative to egg decontamination. Volatile organic compounds (VOC's) are evaporated easily, which provides an added benefit as a disinfectant. Pyrazines are made by plants as a secondary metabolite but can also be produced by bacteria for industrial purposes (bacteria species not listed in the article). Pyrazines can then be applied to the surface of eggs to disinfect them. This study focused on a shift in the microbial community using LIVE/DEAD staining of microbes. The authors of this paper found that Micrococcus species in particular (which affect egg hatchability and viability) were decreased by pyrazines. The decontamination rate of pyrazines in this experiment was up to 99.6% (depending on the dose and method used), which is similar to the rates found with the more traditional formaldehyde.
Bugs in the News, Justin C.
Researchers at the Columbia University Medical Center used the CRISPR-Cas system to turn E.Coli into the world's smallest tape recorder. They accomplished this by modifying two plasmids. The first plasmid altered allowed the ability to create more copies of itself in response to external stimulus. The second plasmid modified was the recording plasmid, drives recorder and marks time utilizing CRISPR-Cas system. When there is no stimulus, the second plasmid inserts spacer sequences into the system. To analyze the bacteria, they use computational tools to analyze the CRISPR locus. This offers medical benefit by having a patient swallow the bacteria, and could be used to monitor and detect changes in the gastrointestinal system. The researchers found that the genetically modified bacteria could handle three
simultaneous signals and record for three days.
https://www.sciencedaily.com/releases/2017/11/171124084333.htm
Bugs in the News, Lauren A.
Fusobacterium nucleatum is a type of bacteria that has recently been found in colon cancer tumors. In a recent study, researchers discovered that the bacteria travel with the cancer as the cancer spreads through the body. For example, in individuals whose colon cancer has spread to their liver, the bacteria was not only found in the colon but it was also found in the liver cells. It is, however, unknown if the bacteria actually causes or spurs the growth of cancer but another thought is that the bacteria might have negative effects on the immune system’s response to cancer treatments which allows the tumors to grow more aggressively. The researchers treated the mice in the lab with an antibiotic, Metronidazole, that was successful in slowing the growth of the mice’s tumors. However, researchers are hesitant to advise cancer patients to begin taking the antibiotic because it kills other bacteria in addition to Fusobacterium nucleatum and the side effects or future implications are still unknown.
Bugs in the News, Emma A.
There has been a recent outbreak of mumps on SU’s campus with 41 confirmed cases and 78 probable cases. Mumps rubulavirus is an enveloped, icosahedral virus with negative-sense ssRNA that can be spread through respiratory secretions. The virus can be propagated prior to showing symptoms and up to 5 days into the prodromal period. There has been a resurgence of cases on college campus recently, which correlates with the deteriorated immunity that appears approximately 10 years after the second dose. This raised questions about the effectiveness of the MMR vaccine due to the fact that all infected individuals had received both shots in the series. The sole provider for the MMR vaccine, Merck&Co, is facing allegations concerning falsified records of vaccine efficacy. It’s theorized that since the vaccine’s release in 1967, the potency has significantly declined and that Merck&Co was aware of the waning effectiveness, but continued to produce the vaccine while fabricating data and conducting improper testing. They stick by their claim of the vaccine being 95% effective, while the CDC states that it is generally 88% effective while other sources estimate that the vaccine is 78% effective. A 3rd booster is recommended for groups at a higher risk of contracting mumps.
http://www.syracuse.com/health/index.ssf/2017/11/su_mumps_outbreak_whistleblowers_say_vaccine_ineffective.html
Bugs in the News, Gillian C.
https://www.sciencedaily.com/releases/2017/10/171005103458.htm
Summary:
The invading bacteria Bdellovibrio bacteriovorus is being investigated as a potential solution to antibiotic-resistant pathogenic bacteria. Bdellovibrio has been found to create "portholes" in the walls of host bacterium using D amino acids, enter through them, and seal the bacterium up from the inside. Bdellovibrio then essentially plasters the inside of the bacterium with D amino acids, so that they don't burst and the internal cell contents can be eaten without leaking to the outside, and the host bacterium doesn't collapse before its contents are eaten. Knowing this mechanism of the invading predatory bacteria could help design new ways to kill pathogens without releasing pathogenic material by bursting them.
Bugs in the News from Julian S.
The article I chose investigated why the 2016 to 2017 flu vaccine had limited effectiveness, providing only 43% of individuals immunity to H3N2 flu virus. The article traced the problem to the lack of a new antigenic site caused by a missense mutation changing the structure of antigens produced for the vaccine. The missense mutation caused the vaccine to loose the antigenic glycosylation in site B in its Hemagglutinin glycoproteins. Ultimately, this did not properly entrain the body to “recognize” the circulating H3N2 virus’s new antigenic sites leading to reduced effectiveness of the vaccine. Further research also showed, that once an individual was exposed to the other antigenic sites, which are located in the H3 head, the immune response to antigens that contain both site B glycosalation and h3 head antigen sites was reduced significantly. Basically, once immune system “learned” the less effective H3 antigenic site, it was much more difficult to spur it to recognize the site B glycosalation antigen site. Researchers argued in light of this event, that greater care must be taken to develop new systems to reduce egg or cell culture adaptive mutations.
Gillian C.
Here's the link to an article I found for my Bugs In The News spiel - https://www.sciencedaily.com/releases/2017/10/171005103458.htm
Summary:
The invading bacteria Bdellovibrio bacteriovorus is being investigated as a potential solution to antibiotic-resistant pathogenic bacteria. Bdellovibrio has been found to create "portholes" in the walls of host bacterium using D amino acids, enter through them, and seal the bacterium up from the inside. Bdellovibrio then essentially plasters the inside of the bacterium with D amino acids, so that they don't burst and the internal cell contents can be eaten without leaking to the outside, and the host bacterium doesn't collapse before its contents are eaten. Knowing this mechanism of the invading predatory bacteria could help design new ways to kill pathogens without releasing pathogenic material by bursting them.
Johnny B.
The study that I found looked at the correlation between the gut microbiome and neurodegenerative diseases such as Alzheimer’s and Parkinson’s. They found that certain microbes in the gut produce metabolites that can prevent protein misfolding in our cells, which is what generally leads to these diseases. They also found that in a rat model those with Parkinson’s had a specific inflammatory protein in the colon, suggesting that there may be a link between the gut and the disease. However, the most substantial fact was that when they injected primate’s stomachs with proteins associated with Parkinson’s the animals started to show signs of the disease in their brains greatly substantiating the connection between the disease and the gut microbiome.
Alexander S.
Mycobacterium is a genus of pathogen with a known connection to Tuberculosis, a disease responsible for approximately 1.7 million deaths per year. A study from the University of Notre Dame examined the ability of Mycobacterium within a host to produce what are known as Virulence Factors proteins, but only when the bacterium senses the presence of cargo transport machinery within the cell. The mycobacterium can sense the presence of the molecular transport machinery and will then proceed to collect Virulence Factor protein substrates and load them onto the cargo transport. Researchers disabled one of the proteins that makes up the transport machinery and noticed that the entire structure was disabled. The other proteins of the cargo transport were not found, and the transcription factor of the Mycobacterium that codes for the VF protein substrates was also missing. This indicated that the Mycobacterium was able to sense the lack of the molecular machinery, meaning that the VF protein would be unable to be transmitted out of the cell and throughout the host, so the Mycobacterium stopped collecting the substrates to build the VF proteins. This awareness of the pathogen is profound in that it has the capacity to sense external factors of the host, modifying its own gene expression to improve efficiency and the likelihood of survival.
Source:
New study finds mycobacteria can sense presence of proteins that cause disease
Victoria K.
A study done by researchers at MIT was looking at the effect of a high salt diet on healthy gut microbes and how this might relate to hypertension. One group of mice was fed a high salt diet for 14 days and the effects were hypertension, a higher Th17-cell count (a pro inflammatory T helper cell), and an absence of Lactobacillus murinus. The control group, not fed high amounts of salt, had normal values. After continuing the first group on a high salt diet, they fed them a probiotic containing Lactobacillus and the blood pressure decreased as well as the Th17 cell count. After these results, the researchers are interested in the role of probiotics, particularly Lactobacillus, in treatment of hypertension induced by high salt intake.