A Morphological and Genetic Study of Taxonomy and Evolutionary Divergence in Xanthisma Gracile and Xanthisma Spinulosum

Discerning the basis of phenotypic and genotypic differences within and between taxa is crucial for understanding the evolution of species, subspecies or varieties and races. In this dissertation, I have presented three studies, which use morphological characters and genetic Amplified Fragment Length Polymorphisms (AFLPs) to differentiate cytotypes, populations and species of the genus Xanthisma. The first study is aimed at clarifying the species status of Haplopappus ravenii, which has been considered to be a separate species by some taxonomists and a race of Xanthisma gracile by other researchers. Considering the morphological species concept and the genotypic cluster definition of a species, there was insufficient distinction in either dataset to support these taxa as distinct species. It was found that H. ravenii is more appropriately classified as a a cytotype or a race of X. gracile. In the second study, the genetic structure of X. gracile was quantified across populations occupying distinct habitat types (desert, grasslands, and pinyon juniper woodlands) in order to test the hypothesis of local adaptation and to determine the potential for intraspecific divergence. Samples from desert habitats showed higher genetic divergence than samples in the other two habitats. This study is indicative of local adaptation of populations and that changes in climate and habitat play a very important role in the genetic differentiation of plant systems. The third study evaluated the taxonomy of Xanthisma spinulosum and three of its subspecies that co-occur in Arizona. Herbarium specimens representative of the three subspecies were used to test for significant morphological and genetic divergence that would support their recognition. The morphological characters originally utilized by taxonomists who named these taxa were not significantly different among the three taxa. This finding was further supported by the molecular data, suggesting the presence of one contiguous species. This dissertation aims at stressing the importance of taxonomic status and understanding the role that environment can play on shaping differentiation between taxa

Patterns of Genetic Divergence Across Geographically Variable Populations of \u3ci\u3eXanthisma gracile\u3c/i\u3e (Asteraceae)

Premise of research. Numerous biotic and abiotic factors can contribute to local selection and lead to geographic structure and genetic divergence between populations. The southwestern United States contains many distinctive plant communities, ranging from woodlands to desert scrub, that are shaped by species adapting to local variation in elevation, precipitation, seasonality, and soils. Given this variation, species occurring across diverse habitats are expected to harbor high genetic diversity and exhibit significant genetic differences associated with environmental variation. Methodology. Here, we studied the genetic divergence of populations of Xanthisma gracile (Asteraceae) across Arizona using amplified fragment length polymorphisms and evaluated associations between genetic structure, geographic distance between populations, and variation in climatic factors. This species occurs in desert grasslands at low altitudes as well as in open pine forests at intermediate altitudes and exhibits phenotypic variation in plant height, leaf shape and pubescence, and floral traits. Pivotal results. We detected significant genetic structure across populations and found that a population from arid central Arizona is much more genetically distant than samples from northern and southern Arizona that occur in more mesic habitats. We also detected evidence for selection on numerous loci associated with variation in temperature and precipitation. Conclusions. Major changes have occurred across the Southwest since the Last Glacial Maximum, and genetic divergence in X. gracile across Arizona likely reflects selection for survival in climatically diverse habitats

Small-Scale Population Connectivity and Genetic Structure in Canada Thistle \u3ci\u3e(Cirsium arvense)\u3c/i\u3e

Premise of research. Population connectivity, the exchange of genes among geographically separated subpopulations, is thought to be a key process for the maintenance of genetic diversity and the survival of invasive species in newly colonized areas. Plant populations\u27 degree of genetic connectivity, which occurs via pollen and seed dispersal, leads to different degrees of genetic admixture and genetic structure. Environmental barriers and differential selection pressures that are variable across time and space tend to alter genetic structure within and among populations via restriction or facilitation of gene flow. Canada thistle, an invasive species of the United States and Canada, is well known for production of high numbers of seeds, asexual reproduction, and wide environmental tolerance. These factors may influence its success as an invader by facilitating population persistence. Methodology. In this study we evaluated genetic connectivity of 12 Canada thistle populations across a 75-km area using 10 microsatellite loci, estimated the spatial scale of genetic exchange between populations, and tested for an association between genetic structure and variation in landscape characteristics. Pivotal results. All loci were highly polymorphic within populations, and populations were significantly differentiated from one another ( FST = 0.21 , p = 0.001), but environmental, geographic, and climatic factors were found to have little explanatory power for the observed genetic structure. Bayesian clustering analysis suggested the presence of two distinct genetic groups and admixture in several populations. Conclusions. We conclude that, for this species, genetic admixture and co-occurrence of genetically distinct types may play an important role in rapid adjustment to diverse environments and persistence of populations across the landscape

Internet of Things in Health Care Using Fog Computing

Internet of Things has seeded in many areas of humanoid lifestyle, of which the health care is the most crucial area on which the focus is to be induced. This paper will describe the use of smartphones as a sensor to keep the track of the health of the patients. Considering the various disadvantages of using cloud computing, this paper will be talking about the use of fog computing for faster analysis of data. Fog Computing will emphasize on three types of patients and those would include the ones who are critically Injured or just generally hospitalized or the ones who might in future need occasional monitoring since they were discharged depending upon their current health status

Phylogenomic classification and the evolution of Clonal complex 5 methicillin-resistant Staphylococcus aureus in the Western Hemisphere

Clonal complex 5 methicillin-resistant Staphylococcus aureus (CC5-MRSA) includes multiple prevalent clones that cause hospital-associated infections in the Western Hemisphere. Here, we present a phylogenomic study of these MRSA to reveal their phylogeny, spatial and temporal population structure, and the evolution of selected traits. We studied 598 genome sequences, including 409 newly generated sequences, from 11 countries in Central, North, and South America, and references from Asia and Europe. An early-branching CC5-Basal clade is well-dispersed geographically, is methicillin-susceptible and MRSA predominantly of ST5-IV such as the USA800 clone, and includes separate subclades for avian and porcine strains. In the early 1970s and early 1960s, respectively, two clades appeared that subsequently underwent major expansions in the Western Hemisphere: a CC5-I clade in South America and a CC5-II clade largely in Central and North America. The CC5-I clade includes the ST5-I Chilean/Cordobes clone, and the ST228-I South German clone as an early offshoot, but is distinct from other ST5-I clones from Europe that nest within CC5-Basal. The CC5-II clade includes divergent strains of the ST5-II USA100 clone, various other clones, and most known vancomycin-resistant strains of S. aureus, but is distinct from ST5-II strain N315 from Japan that nests within CC5-Basal. The recombination rate of CC5 was much lower than has been reported for other S. aureus genetic backgrounds, which indicates that recurrence of vancomycin resistance in CC5 is not likely due to an enhanced promiscuity. An increased number of antibiotic resistances and decreased number of toxins with distance from the CC5 tree root were observed. Of note, the expansions of the CC5-I and CC5-II clades in the Western Hemisphere were preceded by convergent gains of resistance to fluoroquinolone, macrolide, and lincosamide antibiotics, and convergent losses of the staphylococcal enterotoxin p (sep) gene from the immune evasion gene cluster of phage ΦSa3. Unique losses of surface proteins were also noted for these two clades. In summary, our study has determined the relationships of different clades and clones of CC5 and has revealed genomic changes for increased antibiotic resistance and decreased virulence associated with the expansions of these MRSA in the Western Hemisphere.Fil: Challagundla, Lavanya. University of Mississippi; Estados UnidosFil: Reyes, Jinnethe. Universidad El Bosque; ColombiaFil: Rafiqullah, Iftekhar. University of Mississippi; Estados UnidosFil: Sordelli, Daniel Oscar. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Houssay. Instituto de Investigaciones en Microbiología y Parasitología Médica. Universidad de Buenos Aires. Facultad de Medicina. Instituto de Investigaciones en Microbiología y Parasitología Médica; ArgentinaFil: Echaniz-Aviles, Gabriela. Instituto Nacional de Salud Pùblica; MéxicoFil: Velazquez-Meza, Maria E.. Instituto Nacional de Salud Pública; MéxicoFil: Castillo-Ramírez, Santiago. Universidad Nacional Autónoma de México; MéxicoFil: Fittipaldi, Nahuel. University of Toronto; Canadá. Public Health Ontario Laboratory; CanadáFil: Feldgarden, Michael. National Institutes of Health; Estados UnidosFil: Chapman, Sinéad B.. Broad Institute of MIT and Harvard; Estados UnidosFil: Calderwood, Michael S.. Dartmouth–Hitchcock Medical Center; Estados UnidosFil: Carvajal, Lina P.. Universidad El Bosque; ColombiaFil: Rincon, Sandra. Universidad El Bosque; ColombiaFil: Blake, Hanson. University of Texas; Estados UnidosFil: Planet, Paul J.. University of Pennsylvania; Estados UnidosFil: Arias, Cesar A.. Universidad El Bosque; Colombia. University of Texas; Estados UnidosFil: Diaz, Lorena. Universidad El Bosque; ColombiaFil: Robinson, D. Ashley. University of Mississippi; Estados Unido

Range expansion and the origin of USA300 north american epidemic methicillin-resistant Staphylococcus aureus

The USA300 North American epidemic (USA300-NAE) clone of methicillin-resistant Staphylococcus aureus has caused a wave of severe skin and soft tissue infections in the United States since it emerged in the early 2000s, but its geographic origin is obscure. Here we use the population genomic signatures expected from the serial founder effects of a geographic range expansion to infer the origin of USA300-NAE and identify polymorphisms associated with its spread. Genome sequences from 357 isolates from 22 U.S. states and territories and seven other countries are compared. We observe two significant signatures of range expansion, including decreases in genetic diversity and increases in derived allele frequency with geographic distance from the Pennsylvania region. These signatures account for approximately half of the core nucleotide variation of this clone, occur genome wide, and are robust to heterogeneity in temporal sampling of isolates, human population density, and recombination detection methods. The potential for positive selection of a gyrA fluoroquinolone resistance allele and several intergenic regions, along with a 2.4 times higher recombination rate in a resistant subclade, is noted. These results are the first to show a pattern of genetic variation that is consistent with a range expansion of an epidemic bacterial clone, and they highlight a rarely considered but potentially common mechanism by which genetic drift may profoundly influence bacterial genetic variation. IMPORTANCE The process of geographic spread of an origin population by a series of smaller populations can result in distinctive patterns of genetic variation. We detect these patterns for the first time with an epidemic bacterial clone and use them to uncover the clone’s geographic origin and variants associated with its spread. We study the USA300 clone of methicillin-resistant Staphylococcus aureus, which was first noticed in the early 2000s and subsequently became the leading cause of skin and soft tissue infections in the United States. The eastern United States is the most likely origin of epidemic USA300. Relatively few variants, which include an antibiotic resistance mutation, have persisted during this clone’s spread. Our study suggests that an early chapter in the genetic history of this epidemic bacterial clone was greatly influenced by random subsampling of isolates during the clone’s geographic spread

Pre-detection history of extensively drug-resistant tuberculosis in KwaZulu-Natal, South Africa

Antimicrobial-resistant (AMR) infections pose a major threat to global public health. Similar to other AMR pathogens, both historical and ongoing drug-resistant tuberculosis (TB) epidemics are characterized by transmission of a limited number of predominant Mycobacterium tuberculosis (Mtb) strains. Understanding how these predominant strains achieve sustained transmission, particularly during the critical period before they are detected via clinical or public health surveillance, can inform strategies for prevention and containment. In this study, we employ whole-genome sequence (WGS) data from TB clinical isolates collected in KwaZulu-Natal, South Africa to examine the pre-detection history of a successful strain of extensively drug-resistant (XDR) TB known as LAM4/KZN, first identified in a widely reported cluster of cases in 2005. We identify marked expansion of this strain concurrent with the onset of the generalized HIV epidemic 12 y prior to 2005, localize its geographic origin to a location in northeastern KwaZulu-Natal ∼400 km away from the site of the 2005 outbreak, and use protein structural modeling to propose a mechanism for how strain-specific rpoB mutations offset fitness costs associated with rifampin resistance in LAM4/KZN. Our findings highlight the importance of HIV coinfection, high preexisting rates of drug-resistant TB, human migration, and pathoadaptive evolution in the emergence and dispersal of this critical public health threat. We propose that integrating wholegenome sequencing into routine public health surveillance can enable the early detection and local containment of AMR pathogens before they achieve widespread dispersal.The National Institute of Allergy and Infectious Disease and National Institutes of Health.https://www.pnas.orgpm2020Medical Microbiolog

Lunatic Fringe and p53 Cooperatively Suppress Mesenchymal Stem-Like Breast Cancer

Claudin-low breast cancer (CLBC) is a poor prognosis molecular subtype showing stemness and mesenchymal features. We previously discovered that deletion of a Notch signaling modulator, Lunatic Fringe (Lfng), in the mouse mammary gland induced a subset of tumors resembling CLBC. Here we report that deletion of one copy of p53 on this background not only accelerated mammary tumor development but also led to a complete penetrance of the mesenchymal stem-like phenotype. All mammary tumors examined in the Lfng/p53 compound mutant mice displayed a mesenchymal/spindloid pathology. These tumors showed high level expressions of epithelial-to-mesenchymal transition (EMT) markers including Vimentin, Twist, and PDGFRα, a gene known to be enriched in CLBC. Prior to tumor onset, Lfng/p53 mutant mammary glands exhibited increased levels of Vimentin and E-cadherin, but decreased expressions of cytokeratin 14 and cytokeratin 8, accompanied by elevated basal cell proliferation and an expanded mammary stem cell-enriched population. Lfng/p53 mutant glands displayed increased accumulation of Notch3 intracellular fragment, up-regulation of Hes5 and down-regulation of Hes1. Analysis in human breast cancer datasets found the lowest HES1 and second lowest LFNG expressions in CLBC among molecular subtypes, and low level of LFNG is associated with poor survival. Immunostaining of human breast cancer tissue array found correlation between survival and LFNG immunoreactivity. Finally, patients carrying TP53 mutations express lower LFNG than patients with wild type TP53. Taken together, these data revealed genetic interaction between Lfng and p53 in mammary tumorigenesis, established a new mouse model resembling CLBC, and may suggest targeting strategy for this disease

Pre-detection history of extensively drug-resistant tuberculosis in KwaZulu-Natal, South Africa

Antimicrobial-resistant (AMR) infections pose a major threat to global public health. Similar to other AMR pathogens, both historical and ongoing drug-resistant tuberculosis (TB) epidemics are characterized by transmission of a limited number of predominant Mycobacterium tuberculosis (Mtb) strains. Understanding how these predominant strains achieve sustained transmission, particularly during the critical period before they are detected via clinical or public health surveillance, can inform strategies for prevention and containment. In this study, we employ whole-genome sequence (WGS) data from TB clinical isolates collected in KwaZulu-Natal, South Africa to examine the pre-detection history of a successful strain of extensively drug-resistant (XDR) TB known as LAM4/KZN, first identified in a widely reported cluster of cases in 2005. We identify marked expansion of this strain concurrent with the onset of the generalized HIV epidemic 12 y prior to 2005, localize its geographic origin to a location in northeastern KwaZulu-Natal ∼400 km away from the site of the 2005 outbreak, and use protein structural modeling to propose a mechanism for how strain-specific rpoB mutations offset fitness costs associated with rifampin resistance in LAM4/KZN. Our findings highlight the importance of HIV coinfection, high preexisting rates of drug-resistant TB, human migration, and pathoadaptive evolution in the emergence and dispersal of this critical public health threat. We propose that integrating wholegenome sequencing into routine public health surveillance can enable the early detection and local containment of AMR pathogens before they achieve widespread dispersal.The National Institute of Allergy and Infectious Disease and National Institutes of Health.https://www.pnas.orgpm2020Medical Microbiolog