congratulations alli weis on her paper published in genome announcements!

Draft Genome Sequences of Campylobacter jejuni Strains That Cause Abortion in Livestock

Allison M. Weis,a,b Kristin A. Clothier,c Bihua C. Huang,a,b Nguyet Kong,a,b Bart C. Weimera,b
School of Veterinary Medicine, UC Davis, Davis, California, USAa; 100K Pathogen Genome Project, UC Davis, Davis, California, USAb; California Animal Health and Food Safety, Davis, California, USAc

Campylobacter jejuni is an intestinal bacterium that can cause abortion in livestock. This publication announces the public re- lease of 15 Campylobacter jejuni genome sequences from isolates linked to abortion in livestock. These isolates are part of the 100K Pathogen Genome Project and are from clinical cases at the University of California (UC) Davis.

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Being thankful!

Contributed by Robin Jones

It’s that time of year again, a time that starts with Thanksgiving and usually ends up after the new year.  We sit, we ponder, we find the things we are thankful for.  We share those thoughts with friends and family, we post on Facebook or send out a tweet. While there are many people who can take up pages filled with all of the things they are thankful for, for some it is a struggle to find even the most minute thing to be grateful for. They feel the burdens of life crushing in on them and wonder if there really is anything worth mentioning.

Over the Thanksgiving holiday I read an article by David G. Allan, CNN entitled, The year of living thankfully.  In his article David writes, “You may not have everything you want or even need, but that probably leaves buckets — nay, container ships — full of tangible and conceptual items for which to be grateful. Things can always be better, but they can always be worse. It often depends on how you look at that proverbial glass of water.

To get in better touch with gratefulness, all you have to do is find easy ways to count blessings more often than, say, over an annual turkey dinner. Keep them boiling on the front burner of your mind, and you increase your appreciation of life.”

 His article is filled with wonderful suggestions on how we can approach life finding the blessings and joy rather than focusing on the negative.  In today’s world when there is so much happening that can draw our attention to the negative, I suggest giving this article a read and challenge yourself to  think of how we can change our perspective to see the positive.  When people start to see the positive in their lives it bleeds out on to those they come in contact with.  Wouldn’t it be lovely to meet a friend for coffee and discuss how your bucket is overflowing rather than how angry all the minutia in life makes us?

 I wish each of you a happy holiday season, but more importantly I wish you each a life filled with joy and gratitude.

 To read David G. Allan’s article

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When fiber starved, friendly gut microbes go bad

Contributed by Azarene Foutouhi

A recent study conducted at the University of Michigan has shown that a low fiber diet results in a higher incidence of infections of the gut due to increased access to the cell wall by pathogenic bacteria. Germ-free mice (lacking a microbiome) were given a transplant of Human gut microbes in order to study the impact of fiber on the stability of the microbiome and its impact on the health of the gut. When given a normal fiber-rich diet the colon of mice appear healthy with a thick protective layer of mucus covering the lining of the colon. However, when the transplanted mice were fed a diet lacking all fiber the normally thick mucosal layer appeared thin. The thinness of the mucus layer atop the colon’s cell wall was due to the proliferation of bacteria able to digest it. Therefore the fiber starvation of bacteria that normally contributed to a healthy gut resulted in increased access of pathogenic bacteria to cells of the colon. The ability to non-invasively treat or prevent digestive tract disorders by the maintenance of a fiber-rich diet has great potential, especially in individuals suffering from inflammatory symptoms.

 

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Zombie virus?

Contributed by Ning Chin

A must-do during Halloween is watching horror movies. I recently watched the Korean zombie movie “Train to Busan” and liked it a lot. In the movie, once you’re bitten by a zombie, you’re turned into a zombie in a few minutes—unless you’re one of the main characters. Within a few minutes of getting bitten by a zombie, your veins turn black and purple. Your iris and pupil turn white. And then you lost your humanity. After the movie, I had to think of reasons that zombie virus cannot be real so I can sleep at night.

The main reason that zombies are fearful is because it can spread very fast. In reality, the closest thing that can cause zombie-like symptoms are rabies. After getting bitten by a rabid animal, the person can show symptoms of rabies within one to three months. If zombie virus exists, the incubation period has to be way shorter. Shortest incubation time for virus to show symptom is from influenza with a minimum of 24 hours, which is still slower than the zombie virus. The whole movie is within the time of a one-hour train ride, so the max number of people infected with zombie virus is dependent on the amount of people the first zombie can bite in one-hour, which is probably max 60 people, if she can bite one person per minute. At this rate, it’s safe to assume that we can detect the situation in time to prevent further spread of the virus.

Since the whole movie in within the time range of a one-hour train ride, the movie didn’t show how long can the zombies “live” after being turned to zombie. When infected with rabies, once symptoms start showing, the patient only has a few days to live. If the zombie virus is similar, then implementing quarantine would be the best way to end this. As long as the zombies cannot infect more people, then the virus can die with the quarantined zombies. Though it’s also not clear in the movie what was the origin of the virus.

Regardless of what is the science behind zombie virus, human nature will never change. Do you choose to be selfish and protect yourself regardless of others’ safety? Or do you stick together and take risks to ensure that everybody live? Horror movies always reflect flaws in human nature. Monsters and ghosts are scary, but they’re imaginative. However, these are choices that people make in real life. There’s no right answer, but it leaves us something to think about.

 

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The genetic difference of predatory bacteria

Contributed by Poyin Chen

In the spirit of Halloween, the blog post today will be on the genetic difference of predatory bacteria.

Vampirococcus is a predatory bacteria found in lakes in Spain and feeds on Chromatium, a purple sulfur bacteria. As the name suggests, Vampirococcus gets its food by sucking out the insides of its prey (Figure 1). Unfortunately, Vampirococcus has never before been grown in culture. As a consequence, we have no information on the genetic makeup of this organism. (1)

Many other predatory bacteria do exist and have been isolated in pure culture, allowing for genome sequencing and comparative analysis against non-predatory bacteria. When compared against non-predators, predatory bacteria were found to encode more genes for mevalonate metabolism, adhesion and signaling, and essential metabolite scavenging. In contrast, non-predators had more genes dedicated toward DOXP metabolism, amino acid biosynthesis, and riboflavin biosynthesis. Additionally, predatory bacteria were found to encode significantly more proteases, the majority of which are involved in protein and membrane degradation (2).

The pronounced differences in gene function abundances between predatory and non-predatory bacteria indicate that predatory bacteria are able to co-opt metabolites found in the prey cytosol and incorporate these metabolites into their own, incomplete metabolic processes. This is observed in the predatory preference for mevalonate metabolism from Glycolysis while non-predators favor the alternate pathway (DOXP) stemming from Glycolysis (Figure 2) (2).

Knowing what we know about bacterial vampires, one begins to wonder if, like their bacterial counterparts, human vampires need to drink our blood to harvest components such as white blood cells to keep themselves disease free. The more you know…

Figure 1

Image source: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC323246/pdf/pnas00311-0181.pdf

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Figure 2

Image source: http://www.genome.jp/kegg/pathway.html

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References:

  1. Guerrero R, Pedros-Alio C, Esteve I, Mas J, Chase D, Margulis L. 1986. Predatory prokaryotes: predation and primary consumption evolved in bacteria. Proc Natl Acad Sci U S A 83:2138-2142.
  2. Pasternak Z, Pietrokovski S, Rotem O, Gophna U, Lurie-Weinberger MN, Jurkevitch E. 2013. By their genes ye shall know them: genomic signatures of predatory bacteria. ISME J 7:756-769.
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Recognizing World Polio Day

Contributed by Narine Arabyan

October 24th is recognized as World Polio Day. Poliomyelitis (polio) is highly infectious virus that affects young children. This virus is spread from person to person through the faecal-oral route or through contaminated water or food. The virus then resides and multiplies in the intestines, invades the nervous system by destroying nerve cells in the spinal cord causing muscle wasting and paralysis. There is no cure for polio; however it can only be prevented by immunization. In 1988, 350,000 cases of polio were recorded worldwide according to World Health Organization (WHO). This same year WHO initiated global efforts to eradicate polio and relied heavily on the oral polio vaccine containing weakened forms of strains of polio viruses developed by Albert Sabin and Mikhail Chumakov. Since 1988, polio cases have been reduced by 99.9%. Polio was eliminated in the Americas by 1994. This is all thanks to polio vaccination; however, polio has not been completely eradicated yet. In 2016, still a total of 27 cases of polio were recorded in Afghanistan, Pakistan and Nigeria. 27 total cases of polio seems very few, however the road to eradication is not easy.

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Cholera in Haiti

Contributed by Alli Weis

Back in 2010 there was a devastating earthquake in Haiti. In response, to help Haiti with the struggles, a team of UN Nepalese peacekeepers arrived. The peacekeepers set up camp in the rural Center Department of Haiti, about 61 miles outside of the capitol, Port-au-Prince and many people became sick with Cholera in the region directly surrounding the camp. Within a year, by March 2011, 4,672 Haitian people had died from Cholera. After investigation it seems as though sewage from the UN camp was seeping into a nearby river, the Arbitonite River, infecting the downstream water sources. Cholera had not been seen in Haiti for over 150 years and was therefore not considered a major health concern for the island people prior to the earthquake and the arrival of aid workers.

Cholera is caused by the bacterium Vibrio cholerae and causes severe watery diarrhea that can lead to dehydration and death. Cholera is spread via the fecal oral route, by drinking contaminated water and eating contaminated food containing V. cholera. Every year there are between 3-5 million cases of Cholera worldwide and about 100,000 deaths, according to the US CDC. It seems likely that the UN peacekeepers were sick with Cholera before entering Haiti and were the cause of the epidemic in Haiti, which by now has killed at least 10,000 people. To further the evidence, genotyping of the Cholera strain revealed that various samples collected from Haitian patients were serogroup O1, serotype Ogawa, which is a strain found in South Asia (CDC). Since this initial event in Haiti, the Dominican Republic has also

Only very recently, August of 2016, the UN accepted responsibility in the role after a journalist wrote a report showing not only bacterial linkages but also revealed that the UN tried to cover the story up. We are likely to hear much more about this story, as the investigations into the UN treatment of the situation are currently ongoing.

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Single-Cell Sequencing and The Illumina / Bio-Rad Single Cell Sequencing Solution

Contributed by Carol Huang

In mid-September, I attended Illumina user group meeting. The topic of single cell sequencing caught my attention for my recent experience on single cell RNA sequencing for a collaborator.

Next generation sequencing has provided high accuracy and in depth genetic information for a cell population, tissue and organs. Bulk cell RNA sequencing can identify a tissue, organism that drive a disease pathology and identify gene expression patterns at a macro level. While, there are numbers of cell types within a population of cells. Each cell type has a distinct lineage and function. The lineage and developmental stage of each cell determine how they respond to each other and to their environment. Most single-cell tissue sequencing were on cancer research. Single-cell sequencing also enables to identify cell types driving a particular pathology, understand composition of complex cell mixture and identify rare cell types.

In metagenomics studies, single-cell sequencing allows to identify low-abundant species that might missing in population sequencing. Single-cell sequencing can effectively characterize organisms hard to culture in vitro. Single-cell sequencing has improved detection and analysis of outbreaks, food-borne pathogens and microbial distribution in environment.

Current single-cell sequencing has time-consuming for cell isolation and cost-efficiency problem. BioRad has partnered with Illumina to solve this problem. Using BioRad Droplet Digital technology accommodate high-throughput single-cell isolation. Through ddSEQ Isolator single cells isolated and barcoded; coupled with Illumina’s reagent and Nextera library kit single cell libraries can be efficiently sequenced; after data can be analyzed and stored at BaseSpace. This system can isolate 10,000 cells per day and cost of all consumables, sequencer and software from Illuminar is $1 per cell. This solution will accelerate single-cell studies a great deal.

Ref: www.bio-rad.com/ddSEQ

www.illumina.com

 

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Exceptional employees: hard to find and easy ignore

 

Contributed by Bart Weimer, PhD

Since I have 4 students that are graduating and leaving the lab for their next adventure I’ve had many thoughts about finding new employees (students) and traits that my students might possess to make them exceptional. We even dedicated an entire lab meeting to the topic.

The concept of unicorn employees is interesting – where the skill set and contributions are so unique that they are rare and almost impossible to find. When you do find them how do you treat them and, as important, how do they treat others? As was suggested these traits come into focus for a number of areas to create your reputation: 1) knowledge of your field, 2) interpersonal skills, 3) collaborative capability, 4) ability to share and acknowledge credit, and others that impact your working relationships.

Recently, Inc. magazine published the 8 things that will get you fired (http://www.inc.com/jeff-haden/8-signs-an-employee-should-be-fired-that-never-appear-on-performance-evaluations.html) – if someone pays attention behavior and interpersonal skills. While science is focused on productivity via manuscripts there is also the need to bring focus on the ‘soft’ skills that enable people to work with others. There is an element of being a just a plain old good human being. Something that seems to be lost on many in science today.

This also applies to interviewing new students. Being a student also includes an element of being an employee. Bringing the lens of mentoring to this discussion puts a collaborative spin on bring these skills forward into the work force. It is critical that new students have the capacity to learn these skills to be successful in graduate school, but also their future career path. Knowledge of science is very important, but it is just as important as knowing how to behave and collaborate, especially in times of increased use of technology that brings barriers into place that inhibit mastering these skills.

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Mothers microbiome shapes her offspring’s immune system

Contributed by Nguyet Kong

The microbiome of a pregnant mouse can influence the development of her offspring’s immune system. A paper published in Science, the researchers describe the introduction of bacteria to the pregnant mice and the results of this experiment. It has been believed that the gut microbiome is developed during and after birth that leads to enhance immune system. This experiment show that the mice pups have benefited from the bacteria from the mother’s gut during pregnancy. The researchers have used a genetically engineered strain of E. coli that have a short life for the experiment, so they can introduce it to the mother’s gut microbiome, but die off before the pups are born and exposure to it. Also the researcher studied the pups after birth comparing to a control group and they found that minimal exposure did have impact, the pups have high level of immune cells. Thus, the researchers studied the DNA of the pups compare to the control group and found that differences in their transcriptional profiles. There was an increase in expression of genes that cause mucus and ion channel production in the gut, the researchers suggest was evidence of the mother’s microbiome had an impact on immune system development of the offspring. The researchers didn’t see evidence of the bacteria getting transfer from mother to pups by the placenta, but found bacterial metabolites from mother to pup by milk.

Gomez de Aguero et al. The maternal microbiota drives early postnatal innate immune development, Science (2016). DOI: 10.1126/science.aad2571

http://www.the-scientist.com/?articles.view/articleNo/45614/title/Mother-s-Microbiome-Shapes-Offspring-s-Immunity/

https://www.sciencedaily.com/releases/2016/03/160317150002.htm

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