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Posted by Megan on July 19th, 2017  ⟩  0 comments

Our increasing awareness of the human microbiome has promoted research on bacteria, fungi, pathogens and other microbes which coexist around and within our bodies. These unseen organisms influence our physiology and behavior. As methods and trajectories of such studies proliferate, scientists have expanded their perspectives to other species’ microbiomes.

Companion species – livestock providing sustenance and domesticated animals we cohabitate with – are of particular interest to researchers. One such species, cats, has validated the model of individualized microbiomes in non-human organisms. From this confirmation, we infer their distinctions originate in varied diet and environment, consequently affecting each cat’s health and behavior.

Recent science confirms that human interaction with cats has impacted their microbiome. Inversely, studies have proved companionship with cats can benefit the human microbiome. Scientists are exploring the relationship, comparing the everyday cat owner to their four-legged friend. Much of this research comes from an unlikely place – the household litterbox.



The "Kittybiome" Project and Feline Health 

A Kickstarter community project, aptly named “Kittybiome,” sought to uncover microbial subtleties concealed in the waste usually discarded by cat owners. Pioneered by researchers like Holly Ganz of UC Davis, Kittybiome engaged in “DNA sequencing technologies to explore” the microbiomes of cats, household and otherwise.

Donations were crowd-funded by largely cat owners interested in findings which would improve feline health knowledge. Donors sent samples of their cats’ feces and received their sequenced DNA in return. Alternatively, pledges were relegated to sequencing DNA from shelter cats and individuals from wild species of the felidae family, including leopards, pumas, lions and cheetahs.

They hypothesized unique colonies of bacteria impact feline health and behavior as they do in humans. Researchers anticipated a relationship between the concentration of strains and a cat’s individual characteristics: temperament, body condition, digestive patterns, indoor/outdoor living status and antibiotic exposure. Substances produced and consumed by the bacteria determines their interaction with the feline host and promote either favorable or disadvantaged health.

In the last two years, Kittybiome has been using advanced DNA sequencing techniques to determine concentrations of bacterial, fungal and other microbial populations in feline digestive systems. The process involves tactics similar to human microbiome testing. DNA is prepared to standard concentrations using PCR, purified, and then sequenced for bacterial identification. As with human microbe sequencing, ultra-high-throughput microbial community analysis is used. Kittybiome’s process features the specialized Illumina MiSeq platform to target specific DNA. Bacterial taxa are identified in a sample by their V4 hypervariable region, a portion of the 16S rRNA.

The resulting data confirms what researchers theorized. All cats display unique combinations of strains; individuals as close as housemates have varying microbial representation. Findings imply diet, breed and disease have reciprocal influences on hundreds of potential microbial phylotypes.

Kittybiome has also ratified research which diagnoses low microbial diversity as a contributor to feline digestive problems. Digestive systems with low concentrations of beneficial bacteria are more sensitive to the negative effects of stomach pathogens and antibiotic use. This month, an update to Kittybiome’s data provided the statistic that 10% cats in the U.S. and U.K. have such chronic digestive problems.

Medical progress has already resulted from Kittybiome’s data. A new treatment for feline diarrhea is being developed, microbiotic supplements which introduce and increase the presence of anti-inflammatory and digestion-promoting colonies. Trials with pets volunteered by their owners have resulted in improved microbiome representation. The study continues today with more donations – both funds and samples – promoting Kittybiome’s success as a scientific inquiry.



Health Implications for Humans

Understanding the cat microbiome doesn’t just improve the health of our pets. Past research reveals similar microbiome phylogeny and functional capacity between humans and companion species. Cats rely less on microbes for digestion than we do, but their microbiome is still an important component of general health. The presence or absence of certain strains determines wellbeing in cats and humans; both species are potential vectors for microbes passed to the other. Pet health is therefore relevant to owner health, implicit in the microbe exchange of cohabitation.

Microorganism presence is low in the “indoor microbiome” maintained by modern sanitation. At extreme levels, a hygienic environment can be disadvantageous. Underexposure to innocuous microbes can induce heightened immunological responses (i.e. allergies and asthma) – if certain strains are absent from the diet or environment, health can suffer from conditions like impaired digestion. Microbial groups are necessary for the development of functional immunological and digestive systems, so encountering harmless strains promotes long-term wellbeing.

The indoor microbiome is diversified by the presence of cats which carry different species of bacteria and fungi than humans do. Cats transfer new strains to the human environment, transporting them from outdoors and emitting species from their own dietary microbiome. Felines have been documented to incorporate 24 categories of bacterial species into our homes, indoor cats carrying less diversity.



Corroborating Research

Data has confirmed the theory of health benefits from exposure to our pets’ microbiomes. Multiple studies demonstrate companion species stimulating human immune systems during development. Infants living their first three months with pets had two times increased abundance of bacteria Ruminococcus – linked to reduced allergies – and Oscillospira – associated to decreased obesity risk. This result is consistent in subjects exposed to pets despite potential confounding factors like cesarean section, antibiotic prescriptions and breast-feeding variable between children.

Further inquiry in a 2013 survey showed infants who lived with companion species did not contract wheezy bronchitis by age two. A 16% reduction was observed in atopic characteristics with perpetual cohabitation. Pathology thus appears to be reduced by the immunological exchange with companion species.

Also recorded by the survey was an increased population of Bifidobacteria longum, complimented by lower occupation of Bifidobacteria breve. Bifidobacteria longum is important for the development of infant GIT microbiomes – results suggested that raised colonization “conferred protection” for the digestive system. Likewise, “Bifidobacterium breve heightened risk of crying and fussing during the first months of life of an infant,” so its comparatively low presence suggests profit for humans. The implication of these discoveries support the physiological gains of cat cohabitation.

Research is still being conducted to quantify the positive influence cat-vectored microbes have on other aspects of human health, digestion and mood. Future research will delve into active samples from the digestive system to visualize metabolic interactions and responsiveness. Relevant phylogeny may also be visualized in immunological systems of microbes from the nose and ears.

Science has led to an increasing appreciation for the invisible organisms of our environment. Now, we have seen the organisms we know and love – our pets – carry additional benefits for us in the form of such microbes. There is potential for future probiotic-like supplements derived from the microbiome of companion species. Until then, you can reward your furry family members with a treat for their contribution to your health. That’s a trick you can’t teach.



References

Deng, P., & Swanson, K. S. (2015). Gut microbiota of humans, dogs and cats: current knowledge and future opportunities and challenges. British Journal of Nutrition, 113(S1), S6-S17. Retrieved June 28, 2017.

Gitlin, J. M. (2017, March 16). My cats poop for science. Retrieved June 28, 2017, from https://arstechnica.com/science

Kittybiome. (2015-2017). Kittybiome: kitty microbiomes for cat health and biology. Retrieved June 28, 2017, from https://www.kickstarter.com/projects/catbiome

Schiffman, R. (2017, June 6). Are Pets the New Probiotic? Retrieved June 28, 2017, from https://www.nytimes.com/2017/06/06/well/family/are...

Whiteman, H. (2017, April 7). Pets alter infants' microbiota to lower risk of allergies, obesity. Retrieved June 28, 2017, from http://www.medicalnewstoday.com/articles

Nermes, M. (2013). Perinatal Pet Exposure, Faecal Microbiota, and Wheezy Bronchitis: Is There a Connection? ISRN Allergy, 2013. Retrieved June 28, 2017, from https://www.hindawi.com/journals/



            Megan Hardie
       GoldBio Staff Writer

Megan Hardie is an undergraduate student at The Ohio State
University’s Honors Arts and Sciences program. Her eclectic
interests have led to a rather unwieldly degree title: BS in
Anthropological Sciences and BA English Creative Writing,
Forensics Minor. She aspires to a PhD in Forensic Anthropology
and MA in English. In her career, she endeavors to apply the
qualities of literature to the scientific mode and vice versa,
integrating analysis with artistic expression.

Category Code:79101, 88241, 79102, 79105

Posted by Megan on July 6th, 2017  ⟩  0 comments

America’s inhabitation by humans is a discussion among archaeologists with new, compelling and contradictory data discovered each year. New methods of research and sources of information sometimes present more questions than answers, but a study has risen to clear some uncertainties – that of Shuká Káa. At first an inconclusive test subject, advanced procedures to amplify Shuká Káa’s ancient deoxyribose nucleic acid (aDNA) illuminated part of our centuries-obscured genomic history.

Ancient DNA

Genomic research potential expanded following the development of polymerase chain reaction (PCR) analysis for DNA. PCR maximizes whatever tiny source of genetic material is found, perhaps a single hair follicle. The method provides crucial data to bioarchaeology, the study of archaeological human remains. PCR’s laboratory function extends to ancient DNA studies on genome to pathology, population to individual such as Shuká Káa, an ancient hunter gatherer who proved to be an ancient genomic ancestor of Canada’s Pacific Northwest.



DNA as a Genomic Identifier

Discovered twenty years ago in a southeastern Alaskan cave, Shuká Káa was believed to be over 10 thousand years old. He had been exposed to the elements for long enough that archaeologists believed his mitochondrial DNA (mtDNA) would be a more reliable source of genomic data. Shuká Káa’s mtDNA was extracted and sequenced to determine his lineage among other ancient individuals (Kennewick Man and Anzick-1) as well as contemporary North Americans.

mtDNA is a separate sequence with hundreds of copies per cell. It consists of around 17,000 pairs to the 30 billion in nDNA. Mitochondria are inherited along the matrilineal line, so mtDNA carried by an individual imitates their biological mother’s. mtDNA has lower ID resolution, but it’s useful in degraded samples due to its longevity in destructive conditions.

Contained in mtDNA are SNPs along with areas known as hypervariable regions (HV1 and HV2) which have been observed as highly mutable. Single nucleotide polymorphism (SNPs) manifest variable DNA nucleotides at one loci. These portions of DNA don’t code for phenotypes, yet genetic studies treat them as alleles from which identity can be assessed.

Unfortunately, in the case of Shuká Káa, no direct haplogroup matches were found, and he was reburied in 2008 in the ceremonial tradition of indigenous groups. The mystery of his relation to contemporary tribes remained, but scientists had not exhausted their research on his identity.

DNA has a projected stability of up to one million years, but no samples are discovered under the conditions necessary for ideal preservation. DNA’s code is obscured by centuries of environmental degradation, so more work is necessary to extract it. In cases like Shuká Káa’s when the sequence is damaged, fractured or otherwise too miniscule to guarantee testing accuracy, portions of DNA are amplified by PCR.



PCR Methods with aDNA

Amplifying DNA is as essential in aDNA investigation as it is in biochemistry. “Ancient DNA” is a classification of nDNA and mtDNA without defined boundaries of age: all historical, archaeological or otherwise ancient specimens are relegated to this category.

Like the DNA used in forensic or biochemical tests, aDNA must be identified and isolated from cellular samples. This is more challenging in ancient remains like Shuká Káa’s due to varying levels of degradation. Archaeological human sources of DNA include bones, dentition and hair follicles. Such tissues are ideal for PCR because they take a longer period than soft tissue does to decay, so even heavily decomposed or mummified samples are viable for replication purposes.

Old samples are endangered by their extended exposure to unmediated environments. Basic decomposition, acidity, temperature fluctuations, moisture, bacteria, and even the contents of air will contribute to DNA degradation. If a sample isn’t adequately prepared, the integrity of sequencing tests are risked. Conclusive data is therefore achieved through DNA amplification by PCR. If enough aDNA can be salvaged, amplification begins until the number of replicates is conducive to sequencing.

There is a specific approach of PCR more precise and better suited for aDNA. Taq polymerase is the enzyme commonly employed for PCR replication, responsible for the attaching nucleotides to a template of DNA. Multiple displacement amplification (MDA) replaces Taq polymerase with ɸ29 DNA polymerase derived from the bacteriophage ɸ29. It amplifies DNA in a mechanism similar to the rolling circle method. The results have a lower rate of error and come in fractions averaging 10kb, larger than those produced in Taq-mediated PCR. Allelic dropout and preferential amplification have still been observed, so the method is not infallible, but it is an advantage for bioarchaeologists.

Shuká Káa’s aDNA was sequenced again in 2017 with PCR amplification and admixture analysis. This time, with methodology 10 years further matured, nDNA was sampled from the tissue of his molars. Only 6% of his genome was recovered due to advanced DNA damage. Even with a fraction of his genome, this new data reinitiated the search for Shuká Káa’s descendants.



Applying PCR to aDNA Studies

aDNA studies have a place in our contemporary culture. The early years of PCR were witness to the exhumation of a skeleton reported to be Auschwitz’s infamous “Angel of Death,” Dr. Josef Mengele. Highly degraded samples were taken from the femur, and microsatellite alleles were amplified. Comparison to Mengele’s son confirmed paternity and gave strong evidence to the skeleton’s identity. A 2014 PCR on mtDNA identified Aaron Kominski as iconic killer Jack the Ripper over a century after his infamous crimes occurred. Skepticism persists, because the research was conducted proceeding a nonfiction book entailing the results.

Bioarchaeology aDNA goes further than a couple of centuries. The field surveys archaeological remains to understand individual, population and environmental experiences through human history. Two focal aspects in the expertise include genomic and pathological studies of ancient people. Ancient human DNA research is lucrative to both trajectories; environmental interactions are revealed with the incorporation of aDNA from other organisms. PCR is an indispensable tool for bioarchaeologists to unlock the ancient world, and the key to such knowledge is in individuals like Shuká Káa.



HUMAN GENOME

Instead of having genomes from only contemporary individuals, ancient people have been rediscovered with PCR. Often, only fractions of a genome can be extracted. These can be amplified to give insights into an ancient person’s genetic attributes by examining specific loci for individualizing characteristics.

Whole genomic amplification (WGA) is another route which studies an individual’s comprehensive genome. This method produces a robust sample of genomic aDNA. PCR-based WGA methods use Taq polymerase to gather a range of the represented genome in 3kb fragments. The alternative isothermal method, MDA, binds random hexameters to denatured DNA strands using ɸ29 polymerase, producing up to 99% genome coverage.

Biological relatedness or biodistance, the focus of Shuká Káa’s case study, is analyzed via PCR-visualized genomic variation. Biodistance is defined in bioarchaeology as a measure of relatedness among groups divided by temporal and geographical factors. Genetic traits reflecting these differences are unveiled by aDNA surveys. Researchers infer from biodistance what kinship, social striations or genetic disorders differentiated the population. PCR employed for this purpose therefore assists in reviewing relatedness, intra-/inter-population relationships, population history and more.

Genomic population studies range from archaic hominins to post-colonization in the Americas. Here are just a few notable examples:

  • The Denisovan group of Siberia, human ancestors who contributed 4-6% of their genome to contemporary Melanesians, received 1.9 fold coverage from a single phalange and tooth. From these miniscule mtDNA samples, a model of population history and lineage identified Denisovan divergence from Neanderthals.
  • mtDNA from 24 Neolithic agriculturalists 7500 years old brought context to European ancestry. In analysis, researchers determined Neolithic farmers had a low genetic influence on modern female lineages of mtDNA in comparison to Paleolithic hunter-gatherers.
  • 50 individuals of a pre-Colombian Amerindian group on Norris Farms were analyzed with PCR methodology. Based on mtDNA, four lineages were determined, and the results indicated these were the major groups present during colonization.

Genomic projections can be individual but have been conducted on scales for entire species. The Human Genome Project benefited from PCR and electrophoresis testing. Another genome sequence was conducted for Neanderthals: three individuals provided 4 billion nucleotides, giving context to their gene flow and influence on modern human populations in Afro-Eurasia.

Research on Shuká Káa’s genome compared the new nDNA sequence to dental samples of indigenous groups and British Columbian individuals from 6075-1750 years ago. The results were surprising: his genome was closely associated to the British Columbian skeletons, and these were related to a number of indigenous Pacific Northwest groups in haplogroup D4h3a and A2. His mtDNA and nDNA consequently suggested kinship to the Tsimshian, Tlingit, Nisga’a, and Haida tribes. It was inferred Shuká Káa is a common ancestor and the region has genetic continuity for at least ten millennia.

Broader implications also surfaced. Shuká Káa was proven genetically dissimilar from the nearly 13,000 year old Montanan Anzick Child and Kennewick Man. This data implied that, at this period in the Americas, at least two genetically distinct lineages existed. Experts thus concluded that the initial inhabitation of the Americas is more complex than previously hypothesized.



HUMAN PATHOLOGY

Biological relatedness can also be interpreted from pathology, and PCR helps bioarchaeologists evaluate ancient disease identifiable in human remains. It recognizes known genetic characteristics for hereditary disorders and detects the relics of infectious disease. Disease inherited or contracted is visualized to understand frequency and impact. Those which still afflict contemporary populations like tuberculosis and syphilis have extra significance, because understanding their origins and past influence can aid in current experimentation.

Genetic disorders are easily located at their known loci. Infection is not so easily identified in archaeological circumstances. Certain diseases infest a population without leaving physiological impressions. Of these pathogens, though, some leave genetic indicators in those they’ve infected.

One aDNA experiment searched for the mycobacterium tuberculosis complex (MTBC) in 133 geographically and temporally spaced skeletal samples. Four quantitative PCR assays were conducted to locate ancient MTBC indicators at conserved regions of the complex. They targeted the rpoB gene and insertion elements IS6110 and IS1081 believed to be specific to MTBC complex indication. Seven samples were positively identified with probe technology.

Leprosy (Mycobacterium leprae) is a disease historically coexisting with tuberculosis. More common as an epidemic in ancient times, it’s characterized by long-term incubation and neurological complications. Leprosy was one of 92 pathogens featured in a study that parallel-screened archival samples of bone, dental pulp and mummified ancient tissue. Pathogenic strains were isolated in their genomic conservation sequences, and ancient M. leprae DNA was located in the predetermined sample. The efficiency of this screening technique was an added achievement to the amplification technique.

Some vectored plagues leave no skeletal signature due to their rapid killing power, but they can be detected in aDNA. Malaria epidemics (Plasmodium falciparum) and bubonic plagues (Yersinia pestis) have changed human immunology and impacted the genome of affected societies. Parasitic malaria DNA was found in ancient Roman samples using hybridization capture mtDNA of modern strains. Similar PCR results were produced with the Yersinia pestis specific plasminogen activator gene: “plague pit” remains in the Netherlands, England and France have revealed aDNA of the bubonic pathogen.



ENVIRONMENT

Other experiments focus on ancient species and environments which influenced our evolution. While not autonomous from human bodies, paleomicrobiology – studying the microbiome of ancient humans – is genetically explored through the analysis of dental calculus. One approach to the oral microbiome is amplicon sequencing the variable regions V1-V9 in the highly conserved bacterial 16S rRNA gene. This method, of course, requires amplification which can be achieved with the primer-based tactics of PCR. Scientists thus know more about the diet, behavior and microbes of ancient life.

Investigating domesticated species of ancient human agriculture is integral to chronicling the human condition. Archaegenomic examination uses DNA techniques previously developed for human study on botanical samples. The crop aDNA is sequenced, and short-term genome evolution is inferred to be caused by selective manipulated by humans in adaptation to drought. Such rapid change was documented in cotton from Africa, Brazil and Peru as well as barley in Qasr Ibrim, Egypt. aDNA therefore reveals historical behavior of humans interacting with domesticated species.

A final class of research involves what is known as “environmental” DNA (eDNA). Environmental samples are collected from water, ice and sediments. They contextualize biodiversity in a region for thousands of years; DNA from flora and fauna are also analyzed for transitions and extinctions. Some organismal DNA can be located in the sediment itself, as aDNA of extinct woolly mammoths and moa birds were found in Siberia and New Zealand. aDNA from organisms persists if the environmental matrix contains large organic molecules, particles or minerals to protect it from nuclease activity. Other aDNA is conserved through natural transformation when other cells integrate extracellular DNA into their genomes.



Future Research with PCR

The discoveries of aDNA, mtDNA, and PCR have coalesced to give us valuable insight into the past of our species, and it can be inferred that the benefits of this scientific industry will proliferate in the future. Sequencing the genome of Shuká Káa is only one example of our ever-advancing scientific endeavors. The subject of America’s first inhabitants has not yet been concluded, but we are nearing the answers which have evaded previous research.

Laboratories worldwide have become involved in the inspection of DNA far older than the science itself. Kits are dispensed to researchers interested in accessing the genome of damaged samples; the supplies for analysis include ladders for genotyping, PCR mix, primer mix, and positive control DNA. Using the same electrophoresis PCR as is conducted on known samples, aDNA researchers bring life back to material long dead and almost lost in the degrading circumstances of time.

New technology is being developed to make PCR more efficient: rapid ID, bead hybridization binding to SNPs, SNP scanning chip hybridization and SNP-STR parallel sequencing are just a few new resources rising in the field. Next Generation Sequencing (NGS) also offers promising results beyond the current projection of PCR. With the addition of newly developed technology, it’s inevitable that even more discoveries will be made from retrospectively studying our ancestors globally.

[Agarose LEDNA 1kb ladderDNA 100bp ladder]



References

Ahrai, S. M., Farajnia, S., Rahimi-Mianji, G., Saheb, S. M., & Nejati-Javaremi, A. (2010). Whole genome amplification: Use of advanced isothermal method. African Journal of Biotechnology, 9(54), 9248-9254.

Allaby, R. G. et al. (2015). Using archaeogenomic and computational approaches to unravel the history of local adaptation in crops. Philosophical Transactions of the Royal Society B: Biological Sciences, 370(1660), 20130377. Retrieved June 15, 2017, from https://www.ncbi.nlm.nih.gov/pubmed.

Alonso, Antonio et al. Real-time PCR designs to estimate nuclear and mitochondrial DNA copy number in forensic and ancient DNA studies. Forensic Science International, 139(2), 141-149. Retrieved June 14, 2017, from https://www.ncbi.nlm.nih.gov/pubmed.

Bos, K. I., Jäger, G., Schuenemann, V. J., Vågene, Å. J., Spyrou, M. A., Herbig, A., … Krause, J. (2015). Parallel detection of ancient pathogens via array-based DNA capture. Philosophical Transactions of the Royal Society B: Biological Sciences, 370(1660), 20130375. Retrieved June 15, 2017, from https://www.ncbi.nlm.nih.gov/pubmed.

Fan, H., & Chu, J.-Y. (2007). A Brief Review of Short Tandem Repeat Mutation. Genomics, Proteomics & Bioinformatics, 5(1), 7–14.

Haak, W. (2005). Ancient DNA from the first European farmers in 7500-year-old Neolithic sites. Science, 310(5750), 1016-1018. Retrieved June 15, 2017, from https://www.ncbi.nlm.nih.gov/pubmed.

Hagelberg, E., Hofreiter, M., & Keyser, C. (2015). Ancient DNA: the first three decades. Philosophical Transactions of the Royal Society B: Biological Sciences, 370(1660). Retrieved June 14, 2017, from https://www.ncbi.nlm.nih.gov/pubmed.

Harkins, K. M., Buikstra, J. E., Campbell, T., Bos, K. I., Johnson, E. D., Krause, J., & Stone, A. C. (2015). Screening ancient tuberculosis with qPCR: challenges and opportunities. Philosophical Transactions of the Royal Society B: Biological Sciences, 370(1660), 20130622. Retrieved June 15, 2017, from https://www.ncbi.nlm.nih.gov/pubmed.

Houck, M. M., & Siegel, J. A. (2010). Fundamentals of Forensic Science (2nd ed.). Cambridge, MA: Academic Press.

Jeffreys, A. J., Allen, M. J., Hagelberg, E., & Sonnberg, A. (1992). Identification of the skeletal remains of Josef Mengele by DNA analysis. Forensic Science International, 56(1), 65-76. Retrieved June 14, 2017, from https://www.ncbi.nlm.nih.gov/pubmed.

Larsen, C. S. (2015). Bioarchaeology: Interpreting Behavior from the Human Skeleton (2nd ed., Cambridge Studies in Biological and Evolutionary Anthropology). Cambridge: Cambridge University Press.

Lindo, J. (2017). Ancient individuals from the North American Northwest Coast reveal 10,000 years of regional genetic continuity. PNAS, 114(16), 4093-4098. Retrieved June 19, 2017, from http://www.pnas.org

Pedersen, M. W. et al. (2015). Ancient and modern environmental DNA. Philosophical Transactions of the Royal Society B: Biological Sciences, 370(1660), 20130383. Retrieved June 15, 2017, from https://www.ncbi.nlm.nih.gov/pubmed.

Reich, D et al. (2010). Genetic history of an archaic hominin group from Denisova Cave in Siberia. Nature, 468(7327), 1053-60. Retrieved June 15, 2017, from https://www.ncbi.nlm.nih.gov/pubmed.

Stone, A. C., & Stoneking, M. (1993). Ancient DNA from a pre-Columbian Amerindian population. American Journal of Physical Anthropology, 92(4), 463-71. Retrieved June 15, 2017, from https://www.ncbi.nlm.nih.gov/pubmed.

Warinner, C., Speller, C., & Collins, M. J. (2015). A new era in palaeomicrobiology: prospects for ancient dental calculus as a long-term record of the human oral microbiome. Philosophical Transactions of the Royal Society B: Biological Sciences, 370(1660), 20130376. Retrieved June 15, 2017, from https://www.ncbi.nlm.nih.gov/pubmed.



                 Megan Hardie
            GoldBio Staff Writer

Megan Hardie is an undergraduate student at The Ohio State
University’s Honors Arts and Sciences program. Her eclectic
interests have led to a rather unwieldly degree title: BS in
Anthropological Sciences and BA English Creative Writing,
Forensics Minor. She aspires to a PhD in Forensic Anthropology
and MA in English. In her career, she endeavors to apply the
qualities of literature to the scientific mode and vice versa,
integrating analysis with artistic expression.

Category Code:79101, 79102 88221

Posted by Megan on June 13th, 2017  ⟩  0 comments

The overuse of antibiotics has been debated in the biochemical and medical fields for decades, concern peaking in the last ten years as previously effective antibiotics prove increasingly obsolete against bacterial evolution. Opportunistic microbes can retaliate against our medicine faster with each generation; we produce innovative ways to combat them, but it’s a constant race for advancement.

This conflict has been deemed a crisis by experts and even the beginnings of an “antibiotics apocalypse.” Consequences go beyond an incurable case of Staphylococcus or E. coli – surgical procedures would become infinitely more life-threatening, and the danger of food shortages from infections in livestock would also pose complications. If allowed to continue their rampant evolution, our bacterial adversaries (as opposed to those who benefit us, like our microbiome) could make injuries as innocuous as papercuts potentially lethal.

In response to the bacterial uprising, the Infectious Diseases Society of America (IDSA) proposed in 2010 a “10 x ‘20” initiative that encouraged the scientific community to circumvent any such apocalyptic outcome. They stated that by 2020, it was in the best interests of the U.S. government and pharmaceutical sector to research and produce 10 new and effective antibiotics. Since the late 1980s, no such inventions had occurred.

To assess if research has taken the initiative to relieve our anxiety, we must first address what developments have transpired in the bacterial world following the mass-production of antibiotics. 



The Rise of an Antibacterial Apocalypse

Antibiotics can become outdated after their initial application in medicinal settings. Dispensed through prescription and over-the-counter purchases, they’re easily accessible and often depended on by those experiencing illnesses symptomatic of bacterial infection. Penicillin was the first weapon against such disease, but it eventually lost effectiveness against resistant strains of bacteria. Those strains then surpassed yet other classes of antibiotics. Contemporary statistics from the Center of Disease Control and Prevention report that tens of thousands die annually in the U.S. and Europe from such “resistant,” untreatable bacteria.

Higher grade antibiotics are used even more frequently in developing countries due to the cost of identifying diseases; to be certain a patient will survive, the most effective antibiotics are prescribed and thus lose their potency more rapidly. Strains of Staphylococcus aureus and E. coli bacteria associated with the waste of a hospital in India have shown upwards to complete resistance against over half a dozen antibiotics. In a laboratory setting, pathogens like E. coli have been isolated and studied in laboratory environments to reveal resistance to colistin and even MDR antibiotics like carbapenem. 

Antibiotic treatment was later introduced to food production and the veterinary profession. Contamination of the environment from waste products in these facilities contributes to the oversaturation of antibiotics in our surroundings, allowing bacteria to evolve under the rug through environmental selection. The speed of antibiotic futility increases steadily, but the expense of clinical trials, sluggish approval of new drugs and caution from pharmaceutical industries makes it harder for new antibiotics to become widely available.

Progress and New Discoveries

It’s obvious that the human race will benefit from an expansion of our antibiotic registry. So what progress has been made?

Recent input from Antibiotic Action and Sally Davies, England’s Chief Medical Officer, proved convincing to government officials in England. Developing strategies against bacterial resistance has become a major topic among the country’s government officials. Their Department of Health agreed to publish a five-year “Antimicrobial Resistance Strategy.” This plan promotes both the “responsible use of antibiotics” and “development of new diagnostics, therapeutics and antibiotics” for use in the medical field.

In the U.S. and globally, the IDSA has made further recommendations to its “10 x ‘20” goal. The association has sent advocacy letters to the World Health Organization, U.N., and the Trump administration at the end of 2016 and early 2017 urging continued support for antibiotic innovation programs. They likewise raised awareness to implement the Strategies to Address Antimicrobial Resistance (STAAR) Act, legislation similar to England’s Antimicrobial Resistance Strategy. The Food and Drug Administration and CDC, which has noted the appearance of “nightmare bacteria” in new strains, are also participating in campaigns for increased attention to this research.

Trial testing for new antibiotics is a growing feature of medical research. By March of this year, 41 antibiotics were undergoing clinical trials: two NDA submissions, 15 Phase 1 trials, 13 Phase 2, and 11 Phase 3. Many new substances are expected to act against resistant gram-negative ESKAPE pathogens and CDC "urgent threat" pathogens. None of these drugs are guaranteed to qualify beyond trials, but their inclusion in the research process is promising.

Experimentation in 2015 demonstrated persistent microbes being exterminated by teixobactin, isolated from an uncultured bacterium E. terrae. In the laboratory setting, teixobactin bound to conserved motifs of lipid II and III, inhibiting the synthesis of cell walls in bacteria and causing cell lysis. Teixobactin proved effective against pathogens already displaying drug-resistance. Results predict that it would take 30 years for bacteria to develop resistance against this class of antibiotics.

Boromycin – a boron-containing polyether macrolide antibiotic derived from Streptomyces antibioticusshowed similar results in 2016. Because of their lower rates of selectivity, ionophores like boromycin are used in veterinary medicine but not human treatments. Researchers claimed boromycin was “a potent, submicromolar inhibitor of mycobacterial growth with submicromolar bactericidal activity against growing and non-growing drug tolerant persister bacilli.” When injected into a sample of B. subtilis, it induced a collapse of the microbes’ potassium gradients. Results from tests with M. bovis demonstrated boromycin’s ability to hinder mycobacteria as well as gram-positive types. Its effect on membrane polarization also reduced ATP in the bacteria and caused cell lysis. Resistant mutations were not detected. These are all positive attributes to boromycin’s antibiotic resume, raising the possibility it could transition to human medicine.

Another research project displayed the benefits of alternative resources for extinguishing bacteria. February of this year, a speaker at the American Association for the Advancement of Science presented test results on the use of inorganic silver nanoparticles (AgNP) merged with an antibiotic, streptomycin. The experiment against E. coli microbes sought to determine if the addition of silver reduced resistance development. The results were encouraging: AgNP inhibited E. coli growth, and its partnering with streptomycin lengthened the suppression period of E. coli generation. This method is especially exciting, because lowering the concentration of antibiotics used in treatment would demote bacterial resistance mutation.

Future Projections

With the “10 x ‘20” goal unmet as of 2017, has the campaign for new antibiotics stagnated? No – with so many dedicated scientists and organizations funding the coordination of this research, it’s clear there has been and will be progress. Science does not operate on deadlines, and it cannot be known when the next breakthrough might surprise us from the petri dish of an unsuspecting graduate student.

Still, the questions remain: when will we discover new antibiotics, and why has it not happened yet?

There is danger in lagging behind bacterial advancement. A recent project at Harvard has shown the possible damage of antibiotic resistance if it is not reduced to a microscopic size: an estimated ten million could die in the next three decades if no progress is made against rising frequencies of resistant bacteria. Similar projections were made by Jim O’Neill, who predicted additional ten million casualties annually starting in 2050 if the post-antibiotic apocalypse occurred. O’Neill made suggestions to refrain from abusing current antibiotics by reducing use in agriculture and medicine. He also advocated educating the public on their responsibility to the movement through alternatives like routine vaccinations.

Bacteria do not procrastinate. To preserve the current state of global health, we must get an advantage over the pathogens present in our daily environment. It’s unrealistic to assume a breakthrough will occur autonomously – the scientific community is depended upon to produce it. Our knowledge and equip is ever-increasing in its capability to innovate against the biological threats of past centuries. The necessity of testing continues. Formulating new drugs in the next three years is crucial if we are to achieve or surpass the original "10 x '20" goal. This global affair takes the cooperation of labs, the scientific community, and contributors across the board to create a safety blanket for our generation and those to come. 

References

British Society for Antimicrobial Chemotherapy. (n.d.). Antimicrobial resistance poses 'catastrophic threat', says Chief Medical Officer. Retrieved June 07, 2017, from http://bsac.org.uk/antimicrobial-resistance-poses-...

Call, D. R., Matthews, L., Subbiah, M., & Liu, J. (2013). Do antibiotic residues in soils play a role in amplification and transmission of antibiotic resistant bacteria in cattle populations?. Frontiers in microbiology, 4(193).

Center for Disease Control and Prevention. (2017, April 10). Antibiotic Resistance Threats in the United States, 2013. Retrieved June 07, 2017, from https://www.cdc.gov/drugresistance/threat-report-2...

Divya, S., Jessen, G., Divya, L., Naz, A. R., Midhun, G., & Suriyanarayanan, S. (2016). Antibiotic Resistance Patterns of E. coli and Staphylococcus aureus Isolated from Hospital wastewater samples of Mysore, Karnataka, South India. Bulletin of Environmental and Scientific Research, 5(3-4).

Ling, Losee L. et al. (2015). A new antibiotic kills pathogens without detectable resistance. Nature, 517(455-459).

Moreira, W., Aziz, D. B., & Thomas, D. (2016). Boromycin Kills Mycobacterial Persisters without Detectable Resistance. Frontiers in Microbiology, 7, 199.

The PEW Charitable Trusts. (2016). [Antibiotics Currently in Clinical Development]. Retrieved June 07, 2017, from hhttp://www.pewtrusts.org/~/media/assets/2017/05/antibiotics-currently-in-clinical-development-03-2017.pdf?la=en

Pas, S. (2017, February 17). Reducing Antibiotic Resistance and MIC Using Silver Nanoparticles with Antibiotics. Lecture presented at AAAS 2017 Annual Meeting in Exhibit Hall (Hynes Convention Center), Boston.

Poirel, L., Kieffer, N., Liassine, N., Thanh, D., & Nordmann, P. (2016). Plasmid-mediated carbapenem and colistin resistance in a clinical isolate of Escherichia coli. Lancet Infect Dis, 16(281).

Smith, O. (2017, March 20). Antibiotic Apocalypse: Harvard reveals doomsday scenario that could kill 10 million a year. Retrieved June 07, 2017, from http://www.express.co.uk/news/world/781168/Harvard...

Thakuria, B., & Lahon, K. (2013). The Beta Lactam Antibiotics as an Empirical Therapy in a Developing Country: An Update on Their Current Status and Recommendations to Counter the Resistance against Them. Journal of Clinical and Diagnostic Research, 7(6), 1207-1214.

Yong, E. (2016, May 19). The Plan to Avert Our Post-Antibiotic Apocalypse. Retrieved June 07, 2017, from https://www.theatlantic.com/science/archive/2016/0...

(Antibiotic Fall from Grace; Development of New Antibiotics Countdown)


               Megan Hardie
         GoldBio Staff Writer     

Megan Hardie is an undergraduate student at The Ohio State
University’s Honors Arts and Sciences program. Her eclectic
interests have led to a rather unwieldly degree title: BS in
Anthropological Sciences and BA English Creative Writing,
Forensics Minor. She aspires to a PhD in Forensic Anthropology
and MA in English. In her career, she endeavors to apply the
qualities of literature to the scientific mode and vice versa,
integrating analysis with artistic expression.

 

Category Code:79102, 88221, 88241

Posted by Karen on June 5th, 2017  ⟩  0 comments

For over 30 years GoldBio has made it its mission to stand behind life science research because we believe that by promoting research and discovery, the world will change for the better.

Therefore, we are always looking to hear from you in order to better support your vision. Of course, telling us what’s important to you might not always be so easy, especially when you’re very busy, so GoldBio has created convenient places on its site to let your voice be heard. What are your needs? What are your goals? What can we do better? What are/aren’t we doing well? What ideas do you have? How has your experience with GoldBio been?

This article will very briefly take you through the possible ways you can leave feedback, share ideas and let us know what you think.



Thumbs Up/Thumbs Down Feature (Beta Mode):

On certain product pages you might see the thumbs up/thumbs down icons. If you have ordered the product from GoldBio, used it and want to share your thoughts with us, simply select the icon that best represents your experience. Your icon selection will be noted, and after you click, a set of fields will appear where you can leave more details.

Another convenient feature is that your feedback can be left anonymously, and no fields are required.



Search Results Page:

Our website’s search bar enables you to search our inventory based on product name, catalog number or CAS number. If you search and we have the item or have items related to your query, the search results page will list it out for you.

However, if your query led to no results, there is still a way to let us know what you are looking for. Your inquiry on the form shown below could prompt us to consider carrying the product of interest. 



Article Comments:

GoldBio publishes and shares articles geared toward life science research and life in the field. Like what you read? Don’t like what you read? Have suggestions on what to add to the story or want to suggest supplemental material? At the end of every article is a comment section for you to tell us more, ask questions and share your ideas.

Perhaps the article had tips for a certain process, and through your experience you have advice that might be useful to other readers. This is a great opportunity to share your knowledge, open a dialog and help inspire others.





Live Chat Feedback: 

Our live chat feature allows you to digitally connect to a GoldBio representative. This platform offers a convenient way to ask questions, request information, update us on an order – anything that is important to you. 

While the live chat is one way you can give us helpful feedback, the poll that follows it is a way to rate your overall experience during the session. It only takes seconds and is as easy to do as the picture below shows.



Social Media:

While it’s offsite, connecting with our social media channels is another way you can share thoughts, offer suggestions or keep in touch. Our primary channels include Facebook, Twitter, YouTube and LinkedIn.

        
         

Have suggestions, tips or ideas for the site? Let us know. Comment below. Or get in touch via live chat, social, email, phone or one of the platforms listed above. We appreciate hearing from you because you are what drives science forward.


    
              Karen Martin
GoldBio Marketing Coordinator


"To understand the universe is to understand math." My 8th grade
math teacher's quote meant nothing to me at the time. Then came
college, and the revelation that the adults in my past were right all
along. But since math feels less tangible, I fell for biology and have
found pure happiness behind my desk at GoldBio, learning, writing


Category Code: 88261

Posted by Rebecca on May 24th, 2017  ⟩  0 comments

TSE Certificates come packaged with products that could potentially have TSE risk, such as BSA (Bovine Serum Albumin), but many people don’t know what they mean or why they’re so important.

BSE/TSE Certificate of Compliance

If you’re shopping for bovine-derived reagents for your research, you’ve probably come across a mention about being ”TSE Compliant” quite a few times, but wondered what that meant or why it matters. I’ll discuss what it means to be TSE (Transmissible Spongiform Encephalopathy) compliant and why TSE certificates are so important.

TSE compliance certificates are a type of CEP (Certificate of Suitability to the European Pharmacopoeia). They are used to maximize safety when working with materials that could potentially be contaminated with TSE. Any material with a TSE CEP has been confirmed by the European Directorate for the Quality of Medicines to be suitably controlled by the relevant monographs established by the European Pharmacopoeia. What this means is that the substance is compliant with the standard measures used to minimize the risk of TSE contamination. These CEPs are recognized by members of the European Pharmacopoeia as well as institutions in other countries such as the FDA in the United States. Minimizing the risk of TSE contamination in products like GoldBio’s Bovine Serum Albumin is extremely important to human safety, but why?

TSEs are diseases caused by prions which lead to degeneration of the nervous system. Some examples of TSEs include Creutzfeldt-Jakob disease, scrapie in sheep and bovine spongiform encephalopathy (commonly referred to as mad cow disease). These illnesses have existed for quite a long time, with the first documentation of them occurring centuries ago.

In the 1980s, when the first TSE epidemic occurred, scientists began focusing more of their time and effort to understand these conditions. In the UK, it was discovered that cattle were being fed with a supplement containing dead sheep, supporting the theory that bovine spongiform encephalopathy arose due to ingestion of scrapie-infected sheep. Rules and regulations began to be put in place by the governing bodies in the UK and research of the topic continued to increase. By 1996, a link between the human form of mad cow disease, Creutzfeldt-Jakob disease, and BSE from ingestion of beef was found.

With the link between BSE and Creutzfeldt-Jakob being discovered, scientists confirmed that horizontal transmission of TSEs from animals to humans can occur. This is of great concern when working with certain animal-derived reagents in the lab because there is currently no cure or treatment for TSEs. With an incubation period of months to decades, the nervous system is highly affected at the time of prion disease diagnosis. Once symptoms become apparent, prognosis is not good—patients usually die within months to a few years.

Although the prevalence of TSEs is low globally, it is important to take precautions to ensure their spread is minimized. Many scientists work directly with products derived from bovine serum and this would be reason for concern if TSE compliance had not been developed.

It is important to remember, however, that many materials used in labs are synthetic or derived from animal tissues that do not pose a risk of contracting a prion disease so not all products will be TSE certified. It is important, however, to ensure TSE compliance when purchasing products like BSA, especially if purchasing from Europe or other countries where there is a higher risk of TSE contamination.

Next time you see a TSE Certificate when opening a new shipment of Bovine Serum Albumin from GoldBio, you can be glad to know that it is TSE CEP certified. Our BSA is protease and certified TSE CEP compliant, manufactured in the United States in a closed loop system from USDA-inspected, healthy animals.

References:

Prion Disease - History. (2010, February 1). Retrieved June 17, 2016, from http://prion.systemsbiology.net/page/PosterView/display/poster_id/1

Bovine Spongiform Encephalopathy. (2016, March 17). Retrieved June 17, 2016, from http://www.fda.gov/AnimalVeterinary/GuidanceComplianceEnforcement/ComplianceEnforcement/BovineSpongiformEncephalopathy/ucm2006517.htm

Section VIII-H: Prion Diseases. (n.d.). Retrieved June 17, 2016, from https://www.cdc.gov/biosafety/publications/bmbl5/bmbl5_sect_viii_h.pdf

Ramachandran, T. S., et. al. (2014, October 27). Prion-Related Diseases. Retrieved June 17, 2016, from http://emedicine.medscape.com/article/1168941-overview#a6


    
              Rebecca Talley
         GoldBio Staff Writer


Rebecca is a medical student at the University of Missouri.
She previously worked as a lab technician while studying
biology at Truman State University. As an aspiring
reproductive endocrinologist with an interest in global
health, Rebecca has traveled across Central America on
medical mission trips. With a passion for the life sciences,
she enjoys writing for GoldBio.

 

Category Code: 79104, 79107, 79108, 79109