scholarly journals Low Genetic Variation and No Detectable Population Structure in Aspergillus fumigatus Compared to Closely Related Neosartorya Species

2006 ◽  
Vol 5 (4) ◽  
pp. 650-657 ◽  
Author(s):  
Carla Rydholm ◽  
George Szakacs ◽  
François Lutzoni
Keyword(s):  
Genetic Variation ◽  
Aspergillus Fumigatus ◽  
Data Set ◽  
Neosartorya Fischeri ◽  
Natural Isolates ◽  
Immunosuppressed Patients ◽  
History Of ◽  
America South ◽  
Population Genetic Variation ◽  
Intensive Work

ABSTRACT Aspergillus fumigatus is an anamorphic euascomycete mold with a ubiquitous presence worldwide. Despite intensive work to understand its success as a pathogen infecting immunosuppressed patients, the population dynamics and recent evolutionary history of A. fumigatus remain understudied. We examined patterns of genetic variation at three intergenic loci for 70 natural isolates from Europe, North America, South America, Asia, Africa, and Australia. The same loci were used to analyze within-population genetic variation for 33 isolates obtained from five geographic locations. Neither data set detected evidence of population differentiation or found any association between the genetic and geographic distances among these isolates. No evidence for genetic differentiation within the two A. fumigatus mating types was detected. The genetic diversity of A. fumigatus, contrasted with that of its close teleomorphic relatives, Neosartorya fischeri and Neosartorya spinosa, is remarkably low.

Population Genetics ofCaenorhabditis elegans: The Paradox of Low Polymorphism in a Widespread Species

Genetics ◽  
2003 ◽  
Vol 163 (1) ◽  
pp. 147-157 ◽  
Author(s):  
Arjun Sivasundar ◽  
Jody Hey
Keyword(s):  
Genetic Variation ◽  
Microsatellite Loci ◽  
Population Expansion ◽  
Widespread Species ◽  
C Elegans ◽  
Model Research ◽  
The World ◽  
Natural Isolates ◽  
History Of ◽  
Low Levels

AbstractCaenorhabditis elegans has become one of the most widely used model research organisms, yet we have little information on evolutionary processes and recent evolutionary history of this widespread species. We examined patterns of variation at 20 microsatellite loci in a sample of 23 natural isolates of C. elegans from various parts of the world. One-half of the loci were monomorphic among all strains, and overall genetic variation at microsatellite loci was low, relative to most other species. Some population structure was detected, but there was no association between the genetic and geographic distances among different natural isolates. Thus, despite the nearly worldwide occurrence of C. elegans, little evidence was found for local adaptation in strains derived from different parts of the world. The low levels of genetic variation within and among populations suggest that recent colonization and population expansion might have occurred. However, the patterns of variation are not consistent with population expansion. A possible explanation for the observed patterns is the action of background selection to reduce polymorphism, coupled with ongoing gene flow among populations worldwide.

scholarly journals Population Structure of 93 Varieties of Rice ( Oryza Sativa L. subsp. Hsien Ting) in Qinba, China

2020 ◽  
Author(s):  
Yu Zhang ◽  
Ye wen Wang ◽  
Yue xing Wang ◽  
Shi mao Zheng ◽  
Wan ying Zhou ◽  
...  
Keyword(s):  
Population Structure ◽  
Genetic Variation ◽  
Agronomic Traits ◽  
Distance Matrix ◽  
Mantel Test ◽  
Rice Varieties ◽  
Genetic Distance Matrix ◽  
History Of ◽  
Variation Explained ◽  
Population Genetic Variation

Abstract BackgroundThe Qinba region is the transition region between indica and japonica varieties with a long history of indica varieties planting. 72,824 SNPs data based on GBS method, 48 pairs core primers of SSRs, and 15 agronomic traits were employed to explore the population structure of 93 rice varieties. The Mantel test was used to analyze the distance matrix generated using NlaIII-GBS only, MseI-GBS only, by combining NlaIII-GBS and MseI-GBS data and SSR.ResultIn this study, a total of 379 alleles were obtained using 48 pairs core primer of SSR, encompassing an average of 8.0 alleles per primer. The PPB and PIC was 88.65% and 0.77, respectively. Among these, RM278 possess the highest TNB and NPB, and the PPB in 29 pairs of SSR markers was 100%. RM176 showed the highest PIC. MAF was set to 0.05, and 39,872, 35,547 and 67,621 SNPs were obtained via NlaIII-GBS only, MseI-GBS only, and merged NlaIII-GBS and MseI-GBS data, respectively. The IBS genetic similarity coefficient average was 0.74. The results showed that the correlation between the genetic distance matrix based on NlaIII-GBS and MseI-GBS was the largest (R2=0.88), followed by NlaIII-GBS and SSR (R2=0.35), then by merged NlaIII-GBS and MseI-GBS data and SSR (R2=0.33), and the smallest by MseI-GBS and SSR (R2=0.27). The results showed that the 93 rice varieties could be clustered into two subgroups. Molecular variance analysis revealed that the genetic variation was 2% among populations and 98% within populations. Tajima’s D value was 1.66, and the FST between the two populations was 0.61, and the Nm was 0.16.ConclusionThe population genetic variation explained by SNP was larger than that explained by SSR. Through cluster analysis, the 93 samples were divided into 2 subgroups, with more than 97% of the samples clustered into one subgroup. The gene flow of 93 samples used in this study is larger than that of naturally self-pollinated crops, which may be caused by long-term breeding selection of indica varieties in the Qinba region. However, the genetic structure of the rice population is simple and lacked rare alleles.

scholarly journals Cancer immunotherapy in special challenging populations: recommendations of the Advisory Committee of Spanish Melanoma Group (GEM)

2021 ◽  
Vol 9 (3) ◽  
pp. e001664
Author(s):  
Maria Gonzalez-Cao ◽  
Teresa Puertolas ◽  
Mar Riveiro ◽  
Eva Muñoz-Couselo ◽  
Carolina Ortiz ◽  
...  
Keyword(s):  
Cancer Immunotherapy ◽  
Multidisciplinary Approach ◽  
Checkpoint Inhibitors ◽  
Solid Organ Transplantation ◽  
Latent Tuberculosis ◽  
Solid Organ ◽  
Chronic Infections ◽  
Immunosuppressed Patients ◽  
History Of ◽  
Evidence Based Guidelines

Cancer immunotherapy based on the use of antibodies targeting the so-called checkpoint inhibitors, such as programmed cell death-1 receptor, its ligand, or CTLA-4, has shown durable clinical benefit and survival improvement in melanoma and other tumors. However, there are some special situations that could be a challenge for clinical management. Persons with chronic infections, such as HIV-1 or viral hepatitis, latent tuberculosis, or a history of solid organ transplantation, could be candidates for cancer immunotherapy, but their management requires a multidisciplinary approach. The Spanish Melanoma Group (GEM) panel in collaboration with experts in virology and immunology from different centers in Spain reviewed the literature and developed evidence-based guidelines for cancer immunotherapy management in patients with chronic infections and immunosuppression. These are the first clinical guidelines for cancer immunotherapy treatment in special challenging populations. Cancer immunotherapy in chronically infected or immunosuppressed patients is feasible but needs a multidisciplinary approach in order to decrease the risk of complications related to the coexistent comorbidities.

scholarly journals Long-Term Experimental Evolution in Escherichia coli. VI. Environmental Constraints on Adaptation and Divergence

Genetics ◽  
1997 ◽  
Vol 146 (2) ◽  
pp. 471-479 ◽  
Author(s):  
Michael Travisano
Keyword(s):  
Escherichia Coli ◽  
Genetic Variation ◽  
Experimental Evolution ◽  
Population Genetic ◽  
Environmental Constraints ◽  
Asymmetric Pattern ◽  
Nutrient Environment ◽  
Mean Fitness ◽  
Population Genetic Variation

The effect of environment on adaptation and divergence was examined in two sets of populations of Escherichia coli selected for 1000 generations in either maltose- or glucose-limited media. Twelve replicate populations selected in maltose-limited medium improved in fitness in the selected environment, by an average of 22.5%. Statistically significant among-population genetic variation for fitness was observed during the course of the propagation, but this variation was small relative to the fitness improvement. Mean fitness in a novel nutrient environment, glucose-limited medium, improved to the same extent as in the selected environment, with no statistically significant among-population genetic variation. In contrast, 12 replicate populations previously selected for 1000 generations in glucose-limited medium showed no improvement, as a group, in fitness in maltose-limited medium and substantial genetic variation. This asymmetric pattern of correlated responses suggests that small changes in the environment can have profound effects on adaptation and divergence.

Economics of respiratory disease in dairy replacement heifers

2020 ◽  
Vol 21 (2) ◽  
pp. 143-148
Author(s):  
Michael W. Overton
Keyword(s):  
Respiratory Disease ◽  
Milk Production ◽  
Incident Case ◽  
Data Set ◽  
Dairy Heifers ◽  
The Usa ◽  
History Of ◽  
On Farm ◽  
The Impact ◽  
Selective Culling

AbstractBovine respiratory disease (BRD) is a frequent disease concern in dairy cattle and is most commonly diagnosed in young dairy heifers. The impact of BRD is highly variable, depending on the accuracy and completeness of detection, effectiveness of treatment, and on-farm culling practices. Consequences include decreased rate of weight gain, a higher culling risk either as heifers or as cows, delayed age at first service, delayed age at first calving, and in some cases, lower future milk production. In this data set of 104,100 dairy replacement heifers from across the USA, 36.6% had one or more cases diagnosed within the first 120 days of age with the highest risk of new cases occurring prior to weaning. Comparison of the raising cost for heifers with BRD and those without a recorded history of BRD resulted in an estimated cost per incident case occurring in the first 120 days of age of $252 or $282, depending upon whether anticipated future milk production differences were considered or not. Current market conditions contributed to a cost estimate that is significantly higher than previously published estimates, driven in part by the losses associated with selective culling of a subset of heifers that experienced BRD.

scholarly journals Reactivation of BK Polyomavirus in Urine Cytology Is Not Associated with Urothelial Cell Carcinoma

Viruses ◽  
2020 ◽  
Vol 12 (12) ◽  
pp. 1412
Author(s):  
Faisal Klufah ◽  
Ghalib Mobaraki ◽  
Axel zur Hausen ◽  
Iryna V. Samarska
Keyword(s):  
Cell Carcinoma ◽  
Urine Cytology ◽  
Urothelial Cell ◽  
The Other ◽  
Urothelial Cell Carcinoma ◽  
Tissue Samples ◽  
Bk Polyomavirus ◽  
Ffpe Tissues ◽  
Immunosuppressed Patients ◽  
History Of

BK polyomavirus (BKPyV) has been associated with some high-grade and special urothelial cell carcinoma (UCC) subtypes in immunosuppressed patients. Here, we evaluated the relationship of BKPyV-positive urine cytology specimens (UCS) with UCC. A large single-institution database was retrospectively searched for UCS positive for decoy cells, suggesting BKPyV infection. These were tested for the presence of BKPyV by PCR and immunohistochemistry (IHC) in urine sediments and formalin-fixed paraffin-embedded (FFPE) tissue samples of UCC. Decoy cells were reported in 30 patients out of the database with 22.867 UCS. Of these 30 patients, 16 (53.3%) had no history of UCC. Six patients out of these 16 had a history of transplantation, 4 had a history of severe chronic medical conditions, and 6 had no chronic disease. The other fourteen patients were diagnosed with either in situ or invasive UCC of the urinary bladder (14/30; 46.6%) prior to the detection of decoy cells in the urine. Nine of these UCC patients received intravesical treatment (BCG or mitomycin) after the first presentation with UCC. However, the clinical data on the treatment of the other five UCC patients was lacking. IHC identified BKPyV-positivity in the urine samples of non-UCC and UCC patients, while no BKPyV positivity was found in FFPE tissues of primary UCCs and metastases. In addition, BKPyV-PCR results revealed the presence of BKPyV DNA in the urine of the UCC cases, yet none in the UCC tissues itself. These data strongly indicate that BKPyV reactivation is not restricted to immunosuppression. It can be found in UCS of the immunocompetent patients and may be related to the intravesical BCG or mitomycin treatment of the UCC patients.

Characteristics and Care of U.S. Nursing Home Residents with a History of Chronic Mental Illness

2000 ◽  
Vol 19 (S2) ◽  
pp. 1-17 ◽  
Author(s):  
Charles D. Phillips ◽  
Kathleen M. Spry
Keyword(s):  
Nursing Home ◽  
Nursing Home Residents ◽  
Minimum Data Set ◽  
Chronic Mental Illness ◽  
Data Set ◽  
Minimum Data ◽  
Troubles Mentaux ◽  
History Of ◽  
Resident Assessment ◽  
Medicaments Psychotropes

RÉSUMÉTrès peu de recherches ont été effectuées sur les pensionnaires des maisons de soins ayant manifestés des troubles mentaux chroniques sans démence avant leur entrée en institution. Les données du Minimum Data Set for Nursing Home Resident Assessment and Care Screening (MDS) de 1993 ont été utilisées pouranalyser les différences dans les caractéristiques et les soins se rapportant à ce type de pensionnaires par rapport aux autres pensionnaires. Cette enquête portait sur 70 000 pensionnaires du Kansas, du Maine, du Mississippi et du Dakota du Sud. Les caractéristiques des pensionnaires qui éprouvaient ce type de troubles mentaux chroniques étaient plus fréquemment les suivantes: sexe masculin, 65 ans et plus, bénéficiaires de Medicaid, moins médicalement inaptes et niveau plus élevé de problèmes de comportements. Ces pensionnaires reçoivent aussi davantage de médicaments psychotropes et suivant une thérapie, la prévalence de la thérapie étant cependant moins éleveé. Les informations recueillies pourraient laisser croire que les soins accordés à ces pensionnaires ne sont pas des plus appropriés.

Genetic variation in allozymes of western larch

1986 ◽  
Vol 16 (5) ◽  
pp. 1013-1018 ◽  
Author(s):  
Lauren Fins ◽  
Lisa W. Seeb
Keyword(s):  
Genetic Variation ◽  
Genetic Drift ◽  
Fire History ◽  
Glacial History ◽  
Geographic Proximity ◽  
Electrophoretic Variation ◽  
Inland Empire ◽  
Genetic History ◽  
Expected Heterozygosity ◽  
History Of

Seed samples from 19 stands of Larixoccidentalis Nutt. were analyzed for electrophoretic variation at 23 loci. Because sample sizes consisted of only 9 or 10 trees per stand (18–20 alleles per locus per stand), samples were grouped by geographic proximity into four larger samples. For all measures of variation, this species scored lower than most, but within the range observed for other western conifers. Most of the variation was found within rather than between the population groups. The single southern sample appeared to be genetically distinct from the others. Although some variation was observed between individual stand samples in expected heterozygosity, the consistently low values for all samples suggest that genetic drift has played a major role in the genetic history of the species in the Inland Empire, both through its glacial history in postulated refugia and through fire history in recent times.

scholarly journals The complete mitochondrial genome of the intertidal spider (Desis jiaxiangi) provides novel insights into the adaptive evolution of the mitogenome and the evolution of spiders

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Fan Li ◽  
Yunyun Lv ◽  
Zhengyong Wen ◽  
Chao Bian ◽  
Xinhui Zhang ◽  
...  
Keyword(s):  
Positive Selection ◽  
Adaptive Evolution ◽  
Physiological Activity ◽  
Complete Mitochondrial Genome ◽  
Dynamic Environment ◽  
Data Set ◽  
History Of ◽  
Complete Mitogenome ◽  
Selection Signal ◽  
Positive Selection Signal

Abstract Background Although almost all extant spider species live in terrestrial environments, a few species live fully submerged in freshwater or seawater. The intertidal spiders (genus Desis) built silk nests within coral crevices can survive submerged in high tides. The diving bell spider, Argyroneta aquatica, resides in a similar dynamic environment but exclusively in freshwater. Given the pivotal role played by mitochondria in supplying most energy for physiological activity via oxidative phosphorylation and the environment, herein we sequenced the complete mitogenome of Desis jiaxiangi to investigate the adaptive evolution of the aquatic spider mitogenomes and the evolution of spiders. Results We assembled a complete mitogenome of the intertidal spider Desis jiaxiangi and performed comparative mitochondrial analyses of data set comprising of Desis jiaxiangi and other 45 previously published spider mitogenome sequences, including that of Argyroneta aquatica. We found a unique transposition of trnL2 and trnN genes in Desis jiaxiangi. Our robust phylogenetic topology clearly deciphered the evolutionary relationships between Desis jiaxiangi and Argyroneta aquatica as well as other spiders. We dated the divergence of Desis jiaxiangi and Argyroneta aquatica to the late Cretaceous at ~ 98 Ma. Our selection analyses detected a positive selection signal in the nd4 gene of the aquatic branch comprising both Desis jiaxiangi and Argyroneta aquatica. Surprisingly, Pirata subpiraticus, Hypochilus thorelli, and Argyroneta aquatica each had a higher Ka/Ks value in the 13 PCGs dataset among 46 taxa with complete mitogenomes, and these three species also showed positive selection signal in the nd6 gene. Conclusions Our finding of the unique transposition of trnL2 and trnN genes indicates that these genes may have experienced rearrangements in the history of intertidal spider evolution. The positive selection signals in the nd4 and nd6 genes might enable a better understanding of the spider metabolic adaptations in relation to different environments. Our construction of a novel mitogenome for the intertidal spider thus sheds light on the evolutionary history of spiders and their mitogenomes.

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