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News Article | November 16, 2016
Site: phys.org

"Our results suggest that ATM keypads integrate microbes from different sources, including the human microbiome, foods, and potentially novel environmental organisms adapted to air or surfaces," said senior study author Jane M. Carlton, PhD, director of the Center for Genomics and Systems Biology, and professor of biology, at New York University. "DNA obtained from ATM keypads may therefore provide a record of both human behavior and environmental sources of microbes." During the study - part of a larger effort to study microbes across New York City—the investigators in June and July 2014 took swabs of keypads from 66 ATM machines in eight neighborhoods over three New York boroughs: Manhattan, Queens and Brooklyn. Four of the machines were located outdoors. Then, in the lab, they studied samples with 16S amplicon sequencing, used to identify and compare bacteria; and 18S amplicon sequencing, used to identify parasites, fungi and protists (other microscopic organisms).The most abundant bacteria found across most samples were normal human skin microbes from the Actinobacteria, Bacteroides, Firmicutes, and Proteobacteria families. Overall, the bacteria samples had low diversity and showed no obvious clustering by geography. In the 18S sequencing, investigators found some fungi and low levels of protists. The most common identified sources of microbes on the keypads were household surfaces such as televisions, restrooms, kitchens and pillows. Researchers found microbes from bony fish and mollusks, and from chicken on some neighborhood ATMs, suggesting that residual DNA from a meal may remain on a person's hands and be transferred to the ATM keypad upon use. ATM keypads located in laundromats and stores had the highest number of biomarkers, with the most prominent being Lactobacillales (lactic acid bacteria), which is usually found in decomposing plants or milk products. In samples from Manhattan, researchers observed the biomarker Xeromyces bisporus, a foodborne mold associated with spoiled baked goods. "It seems plausible that this fungus may have been transferred from people who have recently handled baked goods, particularly in a commuter-heavy area such as Midtown Manhattan where there are many nearby convenience stores and cafés selling this type of food product to business workers," Carlton said. Researchers found no significant difference in the keypads from ATMs located outdoors versus indoors. Since each ATM keypad in New York City is most likely utilized by hundreds of people each day (and may come into contact with air, water, and microbes from different urban surfaces), the microbial communities obtained in this study may represent an "average" community that is effectively pooled from vastly different sources, said study coauthor Maria Gloria Dominguez-Bello, PhD, an associate professor in New York University School of Medicine's Human Microbiome Program. The relative lack of diversity among locations could result from periodic cleaning of the machines, which would wipe out some of the microbes, as well as usage of ATMs by tourists, commuters from other locations, etc., the researchers said. Next, they'll study microbes in the city's cats, dogs, mice, pigeons and cockroaches.


News Article | November 16, 2016
Site: www.sciencedaily.com

Automated teller machine keypads in New York City hold microbes from human skin, household surfaces, or traces of food, a study by researchers at New York University has found. The work shows that ATMs can provide a repository to offer a picture of a city's DNA. "Our results suggest that ATM keypads integrate microbes from different sources, including the human microbiome, foods, and potentially novel environmental organisms adapted to air or surfaces," explains senior study author Jane Carlton, director of the Center for Genomics and Systems Biology and professor of biology at NYU. "DNA obtained from ATM keypads may therefore provide a record of both human behavior and environmental sources of microbes." During the study -- published this week in mSphere, an open access journal from the American Society for Microbiology -- the scientists in June and July 2014 took swabs of keypads from 66 ATM machines in eight neighborhoods over three New York boroughs: Manhattan, Queens, and Brooklyn. The research team's sequencing methods revealed an array of human skin microbes. Specifically, the most common identified sources of microbes on the keypads were household surfaces such as televisions, restrooms, kitchens and pillows. Researchers also found microbes from bony fish, mollusks, and chicken in different New York City neighborhoods, suggesting that residual DNA from a meal may remain on a person's hands and be transferred to the ATM keypad upon use while also pointing to a link between geography and specific microbes. ATM keypads located in laundromats and stores had the highest number of biomarkers with the most prominent being Lactobacillales (lactic acid bacteria), which is usually found in decomposing plants or milk products. In samples from Manhattan, researchers observed the biomarker Xeromyces bisporus, which is associated with spoiled baked goods. Researchers found no significant difference in the keypads from ATMs located outdoors versus indoors. Since each ATM keypad in New York City is most likely utilized by hundreds of people each day (and may come into contact with air, water, and microbes from different urban surfaces), the microbial communities obtained in this study may represent an "average" community that is effectively pooled from vastly different sources, notes study co-author Maria Gloria Dominguez-Bello, an associate professor in NYU School of Medicine's Human Microbiome Program. Overall, the samples had low diversity and showed no obvious clustering by geography. The relative lack of diversity among locations could result from periodic cleaning of the machines, which would wipe out some of the microbes, as well as usage of ATMs by tourists, commuters from other locations, the researchers said.


News Article | November 16, 2016
Site: www.eurekalert.org

Automated teller machine keypads in New York City hold microbes from human skin, household surfaces, or traces of food, a study by researchers at New York University has found. The work shows that ATMs can provide a repository to offer a picture of a city's DNA. "Our results suggest that ATM keypads integrate microbes from different sources, including the human microbiome, foods, and potentially novel environmental organisms adapted to air or surfaces," explains senior study author Jane Carlton, director of the Center for Genomics and Systems Biology and professor of biology at NYU. "DNA obtained from ATM keypads may therefore provide a record of both human behavior and environmental sources of microbes." During the study--published this week in mSphere, an open access journal from the American Society for Microbiology--the scientists in June and July 2014 took swabs of keypads from 66 ATM machines in eight neighborhoods over three New York boroughs: Manhattan, Queens, and Brooklyn. The research team's sequencing methods revealed an array of human skin microbes. Specifically, the most common identified sources of microbes on the keypads were household surfaces such as televisions, restrooms, kitchens and pillows. Researchers also found microbes from bony fish, mollusks, and chicken in different New York City neighborhoods, suggesting that residual DNA from a meal may remain on a person's hands and be transferred to the ATM keypad upon use while also pointing to a link between geography and specific microbes. ATM keypads located in laundromats and stores had the highest number of biomarkers with the most prominent being Lactobacillales (lactic acid bacteria), which is usually found in decomposing plants or milk products. In samples from Manhattan, researchers observed the biomarker Xeromyces bisporus, which is associated with spoiled baked goods. Researchers found no significant difference in the keypads from ATMs located outdoors versus indoors. Since each ATM keypad in New York City is most likely utilized by hundreds of people each day (and may come into contact with air, water, and microbes from different urban surfaces), the microbial communities obtained in this study may represent an "average" community that is effectively pooled from vastly different sources, notes study co-author Maria Gloria Dominguez-Bello, an associate professor in NYU School of Medicine's Human Microbiome Program. Overall, the samples had low diversity and showed no obvious clustering by geography. The relative lack of diversity among locations could result from periodic cleaning of the machines, which would wipe out some of the microbes, as well as usage of ATMs by tourists, commuters from other locations, the researchers said. The work was partially funded by a New York University Grand Challenge project called "Microbes, Sewage, Health and Disease: Mapping the New York City Metagenome." The paper's first author was Holly Bik, a postdoctoral researcher in NYU's Center for Genomics and Systems Biology at the time of the study and now an assistant professor at the University of California at Riverside. The study's other authors included: Julia Maritz, a doctoral candidate in NYU's Department of Biology; Albert Luong, a student at NYU School of Medicine; and Hakdong Shin, a postdoctoral fellow at NYU School of Medicine. The research, linked to a larger effort to study microbes across New York City, was supported, in part, by the Sloan Foundation.


News Article | November 16, 2016
Site: www.eurekalert.org

WASHINGTON, DC - November 16, 2016 - Automated teller machine keypads in New York City have plenty of microbes but they're mostly from normal human skin, household surfaces or traces of food, according to a study published this week in mSphere, an open access journal from the American Society for Microbiology. "Our results suggest that ATM keypads integrate microbes from different sources, including the human microbiome, foods, and potentially novel environmental organisms adapted to air or surfaces," said senior study author Jane M. Carlton, PhD, director of the Center for Genomics and Systems Biology, and professor of biology, at New York University. "DNA obtained from ATM keypads may therefore provide a record of both human behavior and environmental sources of microbes." During the study - part of a larger effort to study microbes across New York City -- the investigators in June and July 2014 took swabs of keypads from 66 ATM machines in eight neighborhoods over three New York boroughs: Manhattan, Queens and Brooklyn. Four of the machines were located outdoors. Then, in the lab, they studied samples with 16S amplicon sequencing, used to identify and compare bacteria; and 18S amplicon sequencing, used to identify parasites, fungi and protists (other microscopic organisms).The most abundant bacteria found across most samples were normal human skin microbes from the Actinobacteria, Bacteroides, Firmicutes, and Proteobacteria families. Overall, the bacteria samples had low diversity and showed no obvious clustering by geography. In the 18S sequencing, investigators found some fungi and low levels of protists. The most common identified sources of microbes on the keypads were household surfaces such as televisions, restrooms, kitchens and pillows. Researchers found microbes from bony fish and mollusks, and from chicken on some neighborhood ATMs, suggesting that residual DNA from a meal may remain on a person's hands and be transferred to the ATM keypad upon use. ATM keypads located in laundromats and stores had the highest number of biomarkers, with the most prominent being Lactobacillales (lactic acid bacteria), which is usually found in decomposing plants or milk products. In samples from Manhattan, researchers observed the biomarker Xeromyces bisporus, a foodborne mold associated with spoiled baked goods. "It seems plausible that this fungus may have been transferred from people who have recently handled baked goods, particularly in a commuter-heavy area such as Midtown Manhattan where there are many nearby convenience stores and cafés selling this type of food product to business workers," Carlton said. Researchers found no significant difference in the keypads from ATMs located outdoors versus indoors. Since each ATM keypad in New York City is most likely utilized by hundreds of people each day (and may come into contact with air, water, and microbes from different urban surfaces), the microbial communities obtained in this study may represent an "average" community that is effectively pooled from vastly different sources, said study coauthor Maria Gloria Dominguez-Bello, PhD, an associate professor in New York University School of Medicine's Human Microbiome Program. The relative lack of diversity among locations could result from periodic cleaning of the machines, which would wipe out some of the microbes, as well as usage of ATMs by tourists, commuters from other locations, etc., the researchers said. Next, they'll study microbes in the city's cats, dogs, mice, pigeons and cockroaches. The work was partially funded by a New York University Grand Challenge project called "Microbes, Sewage, Health and Disease: Mapping the New York City Metagenome." The American Society for Microbiology is the largest single life science society, composed of over 47,000 scientists and health professionals. ASM's mission is to promote and advance the microbial sciences. ASM advances the microbial sciences through conferences, publications, certifications and educational opportunities. It enhances laboratory capacity around the globe through training and resources. It provides a network for scientists in academia, industry and clinical settings. Additionally, ASM promotes a deeper understanding of the microbial sciences to diverse audiences.


Lin W.-H.,Center for Genomics and Systems Biology | Kussell E.,Center for Genomics and Systems Biology | Kussell E.,New York University
Nucleic Acids Research | Year: 2012

Simple sequence repeats (SSRs) are indel mutational hotspots in genomes. In prokaryotes, SSR loci can cause phase variation, a microbial survival strategy that relies on stochastic, reversible on-off switching of gene activity. By analyzing multiple strains of 42 fully sequenced prokaryotic species, we measure the relative variability and density distribution of SSRs in coding regions. We demonstrate that repeat type strongly influences indel mutation rates, and that the most mutable types are most strongly avoided across genomes. We thoroughly characterize SSR density and variability as a function of N→C position along protein sequences. Using codon-shuffling algorithms that preserve amino acid sequence, we assess evolutionary pressures on SSRs. We find that coding sequences suppress repeats in the middle of proteins, and enrich repeats near termini, yielding U-shaped SSR density curves. We show that for many species this characteristic shape can be attributed to purely biophysical constraints of protein structure. In multiple cases, however, particularly in certain pathogenic bacteria, we observe over enrichment of SSRs near protein N-termini significantly beyond expectation based on structural constraints. This increases the probability that frameshifts result in non-functional proteins, revealing that these species may evolutionarily tune SSR positions in coding regions to facilitate phase variation. © 2011 The Author(s).


Meade J.C.,University of Mississippi Medical Center | Carlton J.M.,Center for Genomics and Systems Biology
Sexually Transmitted Infections | Year: 2013

Recent advances in genetic characterisation of Trichomonas vaginalis isolates show that the extensive clinical variability in trichomoniasis and its disease sequelae are matched by significant genetic diversity in the organism itself, suggesting a connection between the genetic identity of isolates and their clinical manifestations. Indeed, a high degree of genetic heterogeneity in T vaginalis isolates has been observed using multiple genotyping techniques. A unique twotype population structure that is both local and global in distribution has been identified, and there is evidence of recombination within each group, although sexual recombination between the groups appears to be constrained. There is conflicting evidence in these studies for correlations between T vaginalis genetic identity and clinical presentation, metronidazole susceptibility, and the presence of T vaginalis virus, underscoring the need for adoption of a common standard for genotyping the parasite. Moving forward, microsatellite genotyping and multilocus sequence typing are the most robust techniques for future investigations of T vaginalis genotype-phenotype associations.


Birnbaum K.D.,Center for Genomics and Systems Biology | Kussell E.,Center for Genomics and Systems Biology | Kussell E.,New York University
Nucleic Acids Research | Year: 2011

Global gene expression measurements are increasingly obtained as a function of cell type, spatial position within a tissue and other biologically meaningful coordinates. Such data should enable quantitative analysis of the cell-type specificity of gene expression, but such analyses can often be confounded by the presence of noise. We introduce a specificity measure Spec that quantifies the information in a gene's complete expression profile regarding any given cell type, and an uncertainty measure dSpec, which measures the effect of noise on specificity. Using global gene expression data from the mouse brain, plant root and human white blood cells, we show that Spec identifies genes with variable expression levels that are nonetheless highly specific of particular cell types. When samples from different individuals are used, dSpec measures genes' transcriptional plasticity in each cell type. Our approach is broadly applicable to mapped gene expression measurements in stem cell biology, developmental biology, cancer biology and biomarker identification. As an example of such applications, we show that Spec identifies a new class of biomarkers, which exhibit variable expression without compromising specificity. The approach provides a unifying theoretical framework for quantifying specificity in the presence of noise, which is widely applicable across diverse biological systems. © 2011 The Author(s).


Greenfield A.,New York University | Hafemeister C.,Center for Genomics and Systems Biology | Bonneau R.,New York University | Bonneau R.,Center for Genomics and Systems Biology | Bonneau R.,Courant Institute of Mathematical Sciences
Bioinformatics | Year: 2013

Inferring global regulatory networks (GRNs) from genome-wide data is a computational challenge central to the field of systems biology. Although the primary data currently used to infer GRNs consist of gene expression and proteomics measurements, there is a growing abundance of alternate data types that can reveal regulatory interactions, e.g. ChIP-Chip, literature-derived interactions, protein-protein interactions. GRN inference requires the development of integrative methods capable of using these alternate data as priors on the GRN structure. Each source of structure priors has its unique biases and inherent potential errors; thus, GRN methods using these data must be robust to noisy inputs. Results:We developed two methods for incorporating structure priors into GRN inference. Both methods [Modified Elastic Net (MEN) and Bayesian Best Subset Regression (BBSR)] extend the previously described Inferelator framework, enabling the use of prior information. We test our methods on one synthetic and two bacterial datasets, and show that both MEN and BBSR infer accurate GRNs even when the structure prior used has significant amounts of error (490%erroneous interactions). We find that BBSR outperforms MEN at inferring GRNs from expression data and noisy structure priors. © 2013 The Author.


Perry M.,New York University | Desplan C.,New York University | Desplan C.,Center for Genomics and Systems Biology
Science Signaling | Year: 2013

Signaling in development is not always on or off; often, distinct intensity and duration of signaling leads to distinct outcomes. This is true for receptor tyrosine kinase (RTK) signaling in many contexts, where negative feedback often plays a role. Although such negative feedback might reduce or even turn off signaling output over time, continued signaling is often maintained for proper cell fate specifi cation. In this issue, Sieglitz et al. identify a positive regulator of Rasmediated RTK signaling that they name Rau. Rau is necessary to achieve specifi c signaling intensity for the differentiation of photoreceptors and of glia that wrap axons in the developing Drosophila eye disc. Both the negative regulator Sprouty and Rau infl uence signaling through the guanosine triphosphatase Ras; specifi - cally, Rau forms a positive feedback loop important for counteracting the Sprouty negative feedback loop. © 2013 American Association for the Advancement of Science.


News Article | November 9, 2015
Site: phys.org

Now, researchers at NYU Abu Dhabi have developed a map of genetic changes across the genome of date palms. They have also established genetic differences between Middle Eastern and North African date palms, an important discovery that sheds light on that long elusive question. In a new paper published in Nature Communications, researchers at the Center for Genomics and Systems Biology at NYUAD have identified more than 7 million mutations or nucleotide polymorphisms that are found between date palm varieties. They have also identified genes that may be important in fruit ripening, fruit color and disease resistance in dates. The study also offers two possible explanations for the crop's origin. One suggests that contemporary date palms descend from two distinct domestication events—an early event in the Middle East, and a later one in North Africa. A second hypothesis proposes that date palms were first cultivated in the Middle East and later spread to North Africa, but somewhere along the way North African dates were crossed with a wild predecessor. The research is part of the 100 Dates! genome sequencing project led by Dorothy Schiff Professor of Genomics Michael Purugganan. The project's goal is to learn more about the traits and evolution of the date palm through analysis of the plant's genome. "The data on diversity in the genomes helps us to identify genes that may help develop better date palms," said Purugganan, who is also a professor of biology. "It also tells us how date palms evolve, and provides clues as to where date palms came from." Evidence from archeological digs suggest that the origin of domesticated dates is in the Gulf. Seeds have been found on Dalma Island, Abu Dhabi that are more than 7,000 years old. Cultivated dates seem to appear about 3,000 years later in North Africa, according to excavation of ancient sites. The team analyzed the genome of 62 varieties of date palm from 12 countries. Seventeen samples came from North Africa; 36 inhabit the Middle East; nine are native to South Asia. The work was a collaboration between NYUAD and UAE University, as well as other researchers in Dubai, Iraq, US, Syria, Tunisia, Pakistan and Qatar. The wild ancestor of the date palm is elusive, but identifying one would provide scientists with valuable information. Khaled Hazzouri, senior research scientist at NYUAD and lead author on the paper, entitled Whole genome re-sequencing of date palms yield insights into diversification of a fruit tree crop, says: "It is important to know the identity and geographic origin of the wild progenitor of a domesticated species because it will help us understand the evolutionary process underlying domestication and the nature of the genetic changes underlying domestication." Purugganan, Hazzouri, and the team also discovered a genetic mutation that causes the trees to produce either yellow or red fruit. Interestingly, the date palm shares this genetic mutation with its very distant cousin, the oil palm. These two plants are separated by approximately 60 million years of evolution, so it's surprising that genes in both species would code for the same trait. "This similarity tells us that evolution uses the same genes in different species to get the same result," Purugganan said. It's possible that information like this could be used by plant breeders to engineer date varieties that have particular traits. For example, since some varieties of date palms can live on water with high salinity, farmers who grow crops in arid terrain could plant date palm varieties suitable for that type of climate. The 100 Dates! project is still in its first phase, and there is considerable research yet to be done. The next phase will include obtaining more samples and mapping important genes, and future research will include collaborations with researchers at UAE University in Al Ain and the University of Baghdad.

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