scholarly journals Signatures of rapid evolution in urban and rural transcriptomes of white-footed mice (Peromyscus leucopus) in the New York metropolitan area

2013 ◽  
Author(s):  
Stephen E Harris ◽  
Jason Munshi-South ◽  
Craig Obergfell ◽  
Rachel O'Neill
Keyword(s):  
New York ◽  
Candidate Genes ◽  
High Throughput Sequencing ◽  
Peromyscus Leucopus ◽  
Rapid Evolution ◽  
Urban Ecosystems ◽  
Urban Environments ◽  
Forest Fragments ◽  
Protein Coding ◽  
Biological Phenomena

Urbanization is a major cause of ecological degradation around the world, and human settlement in large cities is accelerating. New York City (NYC) is one of the oldest and most urbanized cities in North America, but still maintains 20% vegetation cover and substantial populations of some native wildlife. The white-footed mouse, Peromyscus leucopus, is a common resident of NYC’s forest fragments and an emerging model system for examining the evolutionary consequences of urbanization. In this study, we developed transcriptomic resources for urban P. leucopus to examine evolutionary changes in protein-coding regions for an exemplar ‘urban adapter’. We used Roche 454 GS FLX+ high throughput sequencing to derive transcriptomes from multiple tissues from individuals across both urban and rural populations. From these data, we identified 31,015 SNPs and several candidate genes potentially experiencing positive selection in urban populations of P. leucopus. These candidate genes are involved in xenobiotic metabolism, innate immune response, demethylation activity, and other important biological phenomena in novel urban environments. This study is one of the first to report candidate genes exhibiting signatures of directional selection in divergent urban ecosystems.

scholarly journals Signatures of rapid evolution in urban and rural transcriptomes of white-footed mice (Peromyscus leucopus) in the New York metropolitan area

2013 ◽  
Author(s):  
Stephen E Harris ◽  
Jason Munshi-South ◽  
Craig Obergfell ◽  
Rachel O'Neill
Keyword(s):  
New York ◽  
Candidate Genes ◽  
High Throughput Sequencing ◽  
Peromyscus Leucopus ◽  
Rapid Evolution ◽  
Urban Ecosystems ◽  
Urban Environments ◽  
Forest Fragments ◽  
Protein Coding ◽  
Biological Phenomena

Urbanization is a major cause of ecological degradation around the world, and human settlement in large cities is accelerating. New York City (NYC) is one of the oldest and most urbanized cities in North America, but still maintains 20% vegetation cover and substantial populations of some native wildlife. The white-footed mouse, Peromyscus leucopus, is a common resident of NYC’s forest fragments and an emerging model system for examining the evolutionary consequences of urbanization. In this study, we developed transcriptomic resources for urban P. leucopus to examine evolutionary changes in protein-coding regions for an exemplar ‘urban adapter’. We used Roche 454 GS FLX+ high throughput sequencing to derive transcriptomes from multiple tissues from individuals across both urban and rural populations. From these data, we identified 31,015 SNPs and several candidate genes potentially experiencing positive selection in urban populations of P. leucopus. These candidate genes are involved in xenobiotic metabolism, innate immune response, demethylation activity, and other important biological phenomena in novel urban environments. This study is the first to report candidate genes exhibiting signatures of directional selection in divergent urban ecosystems.

scholarly journals Signatures of rapid evolution in urban and rural transcriptomes of white-footed mice (Peromyscus leucopus) in the New York metropolitan area

2013 ◽  
Author(s):  
Stephen E Harris ◽  
Jason Munshi-South ◽  
Craig Obergfell ◽  
Rachel O'Neill
Keyword(s):  
New York ◽  
Candidate Genes ◽  
High Throughput Sequencing ◽  
Peromyscus Leucopus ◽  
Rapid Evolution ◽  
Urban Ecosystems ◽  
Urban Environments ◽  
Forest Fragments ◽  
Protein Coding ◽  
Biological Phenomena

Urbanization is a major cause of ecological degradation around the world, and human settlement in large cities is accelerating. New York City (NYC) is one of the oldest and most urbanized cities in North America, but still maintains 20% vegetation cover and substantial populations of some native wildlife. The white-footed mouse, Peromyscus leucopus, is a common resident of NYC’s forest fragments and an emerging model system for examining the evolutionary consequences of urbanization. In this study, we developed transcriptomic resources for urban P. leucopus to examine evolutionary changes in protein-coding regions for an exemplar ‘urban adapter’. We used Roche 454 GS FLX+ high throughput sequencing to derive transcriptomes from multiple tissues from individuals across both urban and rural populations. From these data, we identified 31,015 SNPs and several candidate genes potentially experiencing positive selection in urban populations of P. leucopus. These candidate genes are involved in xenobiotic metabolism, innate immune response, demethylation activity, and other important biological phenomena in novel urban environments. This study is one of the first to report candidate genes exhibiting signatures of directional selection in divergent urban ecosystems.

scholarly journals Signatures of positive selection and local adaptation to urbanization in white-footed mice (Peromyscus leucopus)

2016 ◽  
Author(s):  
Stephen E. Harris ◽  
Jason Munshi-South
Keyword(s):  
New York ◽  
Candidate Genes ◽  
Demographic History ◽  
Peromyscus Leucopus ◽  
Null Model ◽  
Natural Ecosystems ◽  
Isolated Populations ◽  
Urban Populations ◽  
Landscape Genomics ◽  
Outlier Loci

ABSTRACTUrbanization significantly alters natural ecosystems and has accelerated globally. Urban wildlife populations are often highly fragmented by human infrastructure, and isolated populations may adapt in response to local urban pressures. However, relatively few studies have identified genomic signatures of adaptation in urban animals. We used a landscape genomics approach to examine signatures of selection in urban populations of white-footed mice (Peromyscus leucopus) in New York City. We analyzed 154,770 SNPs identified from transcriptome data from 48 P. leucopus individuals from three urban and three rural populations, and used outlier tests to identify evidence of urban adaptation. We accounted for demography by simulating a neutral SNP dataset under an inferred demographic history as a null model for outlier analysis. We also tested whether candidate genes were associated with environmental variables related to urbanization. In total, we detected 381 outlier loci and after stringent filtering, identified and annotated 19 candidate loci. Many of the candidate genes were involved in metabolic processes, and have well-established roles in metabolizing lipids and carbohydrates. Our results indicate that white-footed mice in NYC are adapting at the biomolecular level to local selective pressures in urban habitats. Annotation of outlier loci suggest selection is acting on metabolic pathways in urban populations, likely related to novel diets in cities that differ from diets in less disturbed areas.

scholarly journals Characteristics and Outcomes Among Hospitalized COVID-19-Positive Patients in a Nonurban Environment

2021 ◽  
Author(s):  
Robert P Lennon ◽  
Theodore J Demetriou ◽  
M Fahad Khalid ◽  
Lauren Jodi Van Scoy ◽  
Erin L Miller ◽  
...  
Keyword(s):  
New York ◽  
Medical Center ◽  
Academic Medical Center ◽  
Military Medicine ◽  
Case Series ◽  
Outcome Data ◽  
Urban Environments ◽  
Urban Setting ◽  
Published Data ◽  
Retrospective Case

ABSTRACT Introduction Virtually all hospitalized coronavirus disease-2019 (COVID-19) outcome data come from urban environments. The extent to which these findings are generalizable to other settings is unknown. Coronavirus disease-2019 data from large, urban settings may be particularly difficult to apply in military medicine, where practice environments are often semi-urban, rural, or austere. The purpose of this study is compare presenting characteristics and outcomes of U.S. patients with COVID-19 in a nonurban setting to similar patients in an urban setting. Materials and Methods This is a retrospective case series of adults with laboratory-confirmed COVID-19 infection who were admitted to Hershey Medical Center (HMC), a 548-bed tertiary academic medical center in central Pennsylvania serving semi-urban and rural populations, from March 23, 2020, to April 20, 2020 (the first month of COVID-19 admissions at HMC). Patients and outcomes of this cohort were compared to published data on a cohort of similar patients from the New York City (NYC) area. Results The cohorts had similar age, gender, comorbidities, need for intensive care or mechanical ventilation, and most vital sign and laboratory studies. The NYC’s cohort had shorter hospital stays (4.1 versus 7.2 days, P < .001) but more African American patients (23% versus 12%, P = .02) and higher prevalence of abnormal alanine (>60U/L; 39.0% versus 5.9%, P < .001) and aspartate (>40U/L; 58.4% versus 42.4%, P = .012) aminotransferase, oxygen saturation <90% (20.4% versus 7.2%, P = .004), and mortality (21% versus 1.4%, P < .001). Conclusions Hospitalists in nonurban environments would be prudent to use caution when considering the generalizability of results from dissimilar regions. Further investigation is needed to explore the possibility of reproducible causative systemic elements that may help improve COVID-19-related outcomes. Broader reports of these relationships across many settings will offer military medical planners greater ability to consider outcomes most relevant to their unique settings when considering COVID-19 planning.

scholarly journals Chloroplast genome variation and phylogenetic relationships of Atractylodes species

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Yiheng Wang ◽  
Sheng Wang ◽  
Yanlei Liu ◽  
Qingjun Yuan ◽  
Jiahui Sun ◽  
...  
Keyword(s):  
Chloroplast Genome ◽  
High Throughput Sequencing ◽  
Phylogenetic Analyses ◽  
Herbal Medicines ◽  
Structural Genomic ◽  
Protein Coding ◽  
Chloroplast Genomes ◽  
Original Plant ◽  
Morphological Differences ◽  
Rna Genes

Abstract Background Atractylodes DC is the basic original plant of the widely used herbal medicines “Baizhu” and “Cangzhu” and an endemic genus in East Asia. Species within the genus have minor morphological differences, and the universal DNA barcodes cannot clearly distinguish the systemic relationship or identify the species of the genus. In order to solve these question, we sequenced the chloroplast genomes of all species of Atractylodes using high-throughput sequencing. Results The results indicate that the chloroplast genome of Atractylodes has a typical quadripartite structure and ranges from 152,294 bp (A. carlinoides) to 153,261 bp (A. macrocephala) in size. The genome of all species contains 113 genes, including 79 protein-coding genes, 30 transfer RNA genes and four ribosomal RNA genes. Four hotspots, rpl22-rps19-rpl2, psbM-trnD, trnR-trnT(GGU), and trnT(UGU)-trnL, and a total of 42–47 simple sequence repeats (SSR) were identified as the most promising potentially variable makers for species delimitation and population genetic studies. Phylogenetic analyses of the whole chloroplast genomes indicate that Atractylodes is a clade within the tribe Cynareae; Atractylodes species form a monophyly that clearly reflects the relationship within the genus. Conclusions Our study included investigations of the sequences and structural genomic variations, phylogenetics and mutation dynamics of Atractylodes chloroplast genomes and will facilitate future studies in population genetics, taxonomy and species identification.

Screening and survival analysis of melanoma immunodrug response-related genes and the function of magnetic nanoparticles in gene extraction

2021 ◽  
Vol 11 (8) ◽  
pp. 1306-1312
Author(s):  
Li Song ◽  
Ningchao Du ◽  
Haitao Luo ◽  
Furong Li
Keyword(s):  
Survival Analysis ◽  
Magnetic Nanoparticles ◽  
Drug Response ◽  
High Throughput Sequencing ◽  
Cox Proportional Hazards ◽  
Sequencing Data ◽  
Protein Coding ◽  
Non Coding Rna ◽  
Long Non Coding Rna ◽  
Rna Genes

This study aimed to identify the association of protein coding and long non coding RNA genes with immunotherapy response in melanoma. Based on RNA sequencing data of melanoma specimens, the expression levels of protein coding and long non coding RNA genes were calculated using the Kallisto RNA-seq quantification method, and differently expressed genes were detected using the DESeq2 method. Cox proportional hazards regression was used to evaluate the effects of gene expression on survival. According to the clinical data of 14 patients with drug response and 11 patients without drug response, 18 protein coding genes and 14 long non coding RNAs showed differential expressions (multiple of difference > 2 and P < 0.01 after correction), among which the coding genes of differential expression were significantly enriched through the process of cell adhesion (P < 0.01). The results of survival analysis showed that 18 coding genes and 14 long non coding RNA genes had significant effects on patient survival (P < 0.01). In this study, magnetic nanoparticles can be used to extract genomic DNA and total RNA due to their paramagnetism and biocompatibility, then transcriptome high-throughput sequencing was performed. The method has the advantages of removing dangerous reagents such as phenol and chloroform, replacing inorganic coating such as silica with organic oil, and shortening reaction time. Protein coding and long non coding RNA genes as well as magnetic nanoparticles may serve as potential cancer immune biomarker targets for developing future oncological treatments.

One Vanderbilt: Unprecedented Project Delivery Through Integrated Innovation

2019 ◽  
Author(s):  
Andrew Cleary ◽  
Edward M. DePaola ◽  
Christopher R. Horch
Keyword(s):  
New York ◽  
Structural Steel ◽  
Fast Track ◽  
Urban Environments ◽  
Advanced Technology ◽  
Parametric Modelling ◽  
Under Construction ◽  
Construction Loads ◽  
Design Schedule ◽  
Construction Documents

<p>One Vanderbilt Avenue, currently under construction in midtown Manhattan, will be one of the tallest buildings in New York. By collaborating with the construction teams in the early stages of the design, the foundations and the superstructure were able to proceed well in advance of a typical project. For example, the structural steel was erected to the 6th floor, was fabricated to the 32nd Floor, and the shop drawings were checked up to the 45th floor on the day that the 100% Construction Documents were issued.</p><p>The structural steel frame was designed so that its core columns only carried 12 levels of framing and construction loads during the tower’s erection. A concrete shear wall system followed the steel framing, permitting the steel erection to proceed without regard to the concrete operations. When complete, the project will stand 1,401 feet tall and contain 26,000 tons of structural steel, and 93,000 cubic yards of concrete.</p><p>The presentation focuses on the challenges and technological requirements for vertical construction in dense urban environments. It explains the amount of detail, thought, and knowledge of construction that must happen earlier in the design process and the participants will appreciate how the fast‐track process can be applied to complex architectural, mechanical and structural designs.</p><p>It describes the integration of design team parametric modelling with the construction process early in the design schedule. Fast‐track projects with complex designs like One Vanderbilt can be successfully completed by understanding and integrating an IPD process, even with competing objectives. The presentation discusses the challenges and technological requirements for vertical construction in dense urban environments, including the importance of direct links to mass transportation.</p><p>This type of team structure is the future of the industry, and One Vanderbilt is the first of its kind to illustrate how innovative design ambitions are being realized through the use of increasingly refined and advanced technology.</p>

scholarly journals Public space: an exhibition of photography and video

2021 ◽  
Author(s):  
Martin Franchi
Keyword(s):  
New York ◽  
Public Space ◽  
General Public ◽  
Private Property ◽  
Urban Environments ◽  
First Century ◽  
The Public ◽  
Unrestricted Access ◽  
Private Corporations ◽  
The Public Sphere

Public Space is a photographic and video project examining the relationship between the public sphere and private corporations. The project explores various sites throughout Toronto and New York that are on private property but have been built with the intention of allowing the general public to have unrestricted access to these areas. These spaces are referred to as Privately Owned Public Space or “POPS”. The goal of the project is to question and document, through photographic and video practice, these spaces within the urban environment and to challenge others to consider whether these spaces are effective in achieving their intended use and if they are truly accessible to the general public. Loss of the public space is an ongoing issue that faces cities and developers often receive concessions to bylaw zoning requirements in exchange for incorporating POPS. This thesis project is a personal exploration of how these spaces are changing the urban environments of North American cities in the twenty first century.

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