Academic literature on the topic 'Phenotypic clumping'
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Journal articles on the topic "Phenotypic clumping"
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Moreno, Eduardo, Angela McGaughran, Christian Rödelsperger, Manuel Zimmer, and Ralf J. Sommer. "Oxygen-induced social behaviours in Pristionchus pacificus have a distinct evolutionary history and genetic regulation from Caenorhabditis elegans." Proceedings of the Royal Society B: Biological Sciences 283, no. 1825 (February 24, 2016): 20152263. http://dx.doi.org/10.1098/rspb.2015.2263.
Full textAbstract:
Wild isolates of the nematode Caenorhabditis elegans perform social behaviours, namely clumping and bordering, to avoid hyperoxia under laboratory conditions. In contrast, the laboratory reference strain N2 has acquired a solitary behaviour in the laboratory, related to a gain-of-function variant in the neuropeptide Y-like receptor NPR-1. Here, we study the evolution and natural variation of clumping and bordering behaviours in Pristionchus pacificus nematodes in a natural context, using strains collected from 22 to 2400 metres above sea level on La Réunion Island. Through the analysis of 106 wild isolates, we show that the majority of strains display a solitary behaviour similar to C. elegans N2, whereas social behaviours are predominantly seen in strains that inhabit high-altitude locations. We show experimentally that P. pacificus social strains perform clumping and bordering to avoid hyperoxic conditions in the laboratory, suggesting that social strains may have adapted to or evolved a preference for the lower relative oxygen levels available at high altitude in nature. In contrast to C. elegans , clumping and bordering in P. pacificus do not correlate with locomotive behaviours in response to changes in oxygen conditions. Furthermore, QTL analysis indicates clumping and bordering to represent complex quantitative traits. Thus, clumping and bordering behaviours represent an example of phenotypic convergence with a different evolutionary history and distinct genetic control in both nematode species.
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Franco, Antonietta, Caroline E. Walton, and Xiawei Dang. "Mitochondria Clumping vs. Mitochondria Fusion in CMT2A Diseases." Life 12, no. 12 (December 15, 2022): 2110. http://dx.doi.org/10.3390/life12122110.
Full textAbstract:
Phenotypic variations in Charcot-Marie-Tooth disease type 2A (CMT2A) result from the many mutations in the mitochondrial fusion protein, mitofusin 2 (MFN2). While the GTPase domain mutations of MFN2 lack the ability to hydrolyze GTP and complete mitochondrial fusion, the mechanism of dysfunction in HR1 domain mutations has yet to be explored. Using Mfn1/Mfn2 double null cells and Mfn2 knock out (KO) fibroblasts, we measured the ability of this variant protein to change conformations and hydrolyze GTP. We found that a mutation in the HR1 domain (M376A) of MFN2 results in conformational change dysfunction while maintaining GTPase ability. Prolonged exposure to mitofusin agonist MiM 111 reverses mitochondrial fusion dysfunction in the HR1 mutant through encouraging an open conformation, resulting in a potential therapeutic model in this variant. Herein, we describe a novel mechanism of dysfunction in MFN2 variants through exploring domain-specific mitochondrial characteristics leading to CMT2A.
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Ayers, J. R., H. W. Leipold, and G. A. Padgett. "Lesions in Brangus Cattle with Chediak-Higashi Syndrome." Veterinary Pathology 25, no. 6 (November 1988): 432–36. http://dx.doi.org/10.1177/030098588802500605.
Full textAbstract:
Hair, peripheral blood leukocytes, and other tissues from two related Brangus calves with phenotypic characteristics of Chediak-Higashi syndrome were examined by light and electron microscopy. Enlarged, pleomorphic, cytoplasmic granules, morphologically compatible with lysosomes, were seen in several neutrophils, many eosinophils, renal tubular epithelial cells, and Kupffer cells. Hair shafts of the calves showed irregular distribution and clumping of melanin granules. Severe infection and a possible hemorrhagic tendency were recognized. These Brangus calves represent the third breed of cattle affected with this genetic disease.
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GONANO, M., I. HEIN, P. ZANGERL, A. RAMMELMAYR, and M. WAGNER. "Phenotypic and molecular characterization ofStaphylococcus aureusstrains of veterinary, dairy and human origin." Epidemiology and Infection 137, no. 5 (October 23, 2008): 688–99. http://dx.doi.org/10.1017/s0950268808001453.
Full textAbstract:
SUMMARYAustrian veterinary (n=91), dairy (n=86), and human strains (n=48) ofStaphylococcus aureuswere tested for various phenotypic properties including clumping factor, egg-yolk reaction, production of thermonuclease and susceptibility to 14 antibiotics. In addition the expression of enterotoxins (A–E), and the presence of enterotoxin genesseatosejandtstwas determined. Significant differences in antimicrobial susceptibility were found with 84·6% of veterinary, 57·0% of dairy, and 20·8% of human strains susceptible to all antibiotics tested (P<0·0005). More human strains produced enterotoxins (41·7%) than veterinary (9·9%) and dairy strains (12·6%) while 40·7% and 38·5% of veterinary, 47·7% and 52·3% of dairy, and 77·1% and 87·5% of human strains werese- andtst-positive, respectively. AFLP analysis revealed nine clusters with over- or under-representation of strains with specific characteristics. Strains clustered according to origin (veterinary, dairy, and human) and/or presence of toxin genes and antimicrobial resistance.
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Bhaduri, Saumya, and James L. Smith. "Virulence Plasmid (pYV)-Associated Expression of Phenotypic Virulent Determinants in PathogenicYersiniaSpecies: A Convenient Method for Monitoring the Presence of pYV under Culture Conditions and Its Application for Isolation/Detection ofYersinia pestisin Food." Journal of Pathogens 2011 (2011): 1–9. http://dx.doi.org/10.4061/2011/727313.
Full textAbstract:
InYersinia pestis,Y. pseudotuberculosis, andY. enterocolitica, phenotypic expression of virulence plasmid (pYV: 70-kb)-associated genetic determinants may include low-calcium response (Lcr, pinpoint colony, size = 0.36 mm), colony morphology (size = 1.13 mm), crystal violet (CV) binding (dark-violet colony), Congo Red (CR) uptake (red pinpoint colony, size = 0.36 mm), autoagglutination (AA = cells agglutinate), and hydrophobicity (HP = clumping of cells).Y. pseudotuberculosisis chromosomally closely related toY. pestis;whereas,Y. enterocoliticais chromosomally more distantly related toY. pestisandY. pseudotuberculosis. All three species demonstrate Lcr, CV binding, and CR uptake. The colony morphology/size, AA, and HP characteristics are expressed in bothY. pseudotuberculosisandY. enterocoliticabut not inY. pestis. Congo red uptake inY. pestiswas demonstrated only on calcium-deficient CR magnesium oxalate tryptic soy agar (CR-MOX), whereas this phenotype was expressed on both CR-MOX and low-calcium agarose media inY. pseudotuberculosisandY. enterocolitica. These phenotypes were detectable at 37°C within 24 h inY. enterocoliticaandY. pseudotuberculosisbut did not appear until 48 h inY. pestisdue to its slower growth rate at 37°C. The pYV is unstable (i.e., easily lost under a variety of culture conditions) in all three species but is more unstable inY. pestis. The specific CR uptake byY. pestisin CR-MOX and the delayed time interval to express Lcr and CR uptake provide a means to differentiateY. pestisfromY. enterocoliticaandY. pseudotuberculosis. These differences in pYV expression inY. pestiscan be used for its isolation and detection in food.
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Ramm, Susanne, Robert Vary, Twishi Gulati, Jennii Luu, Karla J. Cowley, Michael S. Janes, Nicholas Radio, and Kaylene J. Simpson. "High-Throughput Live and Fixed Cell Imaging Method to Screen Matrigel-Embedded Organoids." Organoids 2, no. 1 (December 24, 2022): 1–19. http://dx.doi.org/10.3390/organoids2010001.
Full textAbstract:
Technical advances in microscopy and automation have enabled image-based phenotypic screening of spheroids and organoids to become increasingly high throughput and high content at the same time. In particular, matrix-embedded 3D structures can recapitulate many aspects of parent (e.g., patient) tissues. Live-cell imaging of growing structures allows tremendous insight into population heterogeneity during drug treatment. However, screening for targeted markers and more detailed morphological analyses typically require fixation of 3D structures, and standard formaldehyde (FA) incubation conditions can dissolve collagen-based extracellular matrices such as Matrigel. The dislocation and clumping of the spheroids make image-based segmentation very difficult and the tracking of structures from the live cell stage to their fixed cell location virtually impossible. In this method, we present a fixation and staining protocol that is gentle enough to maintain 3D structures exactly in their live-cell location and does not alter their morphology. This opens up analytical strategies that connect the spheroid’s growth kinetics and heterogeneity of treatment responses with the more targeted fixed cell stains. Furthermore, we optimized the automated seeding and imaging of spheroids so that screening and phenotypic characterization can be performed in high-throughput at either low or high magnification and yield the same result, independent of the microscope used.
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Orjih, C. I., A. Ajayi, F. O. Alao, A. I. Adeleye, and S. I. Smith. "Characterization of biofilm formation in clinical urinary isolates of Staphylococcus aureus from five hospitals in Lagos State, Nigeria." African Journal of Clinical and Experimental Microbiology 22, no. 2 (April 7, 2021): 164–69. http://dx.doi.org/10.4314/ajcem.v22i2.8.
Full textAbstract:
Background: Biofilm formation by pathogens is of great clinical importance as it mediates persistence and resistance to antibiotics, hence posing difficulty in treatment and management of diseases. The aim of this study was to evaluate the biofilm forming potential of Staphylococcus aureus isolated from urine samples of females with urinary tract infection and to detect the presence of clumping factor (clfA) and intracellular adhesion (icaA) encoding genes.Methodology: A total of 50 S. aureus were obtained from urine samples of women in five hospitals in Lagos State, Nigeria. Isolates were confirmed by standard biochemical and novobiocin susceptibility tests. The isolates were screened for biofilm formation using three methods; Congo-red agar (CRA), tube, and tissue culture plate (TCP) methods. Detection of clfA and icaA genes was done by PCR.Results: The Congo red agar method showed that 39 (78%) of the isolates were biofilm producers while 11 (22%) were non-biofilm producers. However, the tube method indicated that 12 (24%) were strong biofilm producers, 26 (52%) were moderate biofilm producers, and 12 (24%) were non-biofilm producers. The standard TCP assay showed that strong biofilm producers (OD > 0.240) were 13 (26%), moderate biofilm producers were 22 (44%), and weak or non-biofilm producers (OD < 0.120) were 15 (30%). The tube method showed a good correlation with the TCP method for strong biofilm production. Ten (20%) isolates possessed clfA gene and 31 (62%)possessed icaA gene.Conclusion: The ability of S. aureus to form biofilm is a key risk factor that can increase morbidity and mortality from infections they cause. Hence, rapid and sensitive phenotypic methods can be used in screening for biofilm formation thereby providing data that can guide therapy and control of the pathogen.
Keywords: Staphylococcus aureus, Biofilm, Clumping factor, Intracellular adhesion
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Ericksen, Bryan. "Quantification of polysaccharides fixed to Gram stained slides using lactophenol cotton blue and digital image processing." F1000Research 4 (May 15, 2017): 1. http://dx.doi.org/10.12688/f1000research.5779.3.
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Dark blue rings and circles emerged when the non-specific polysaccharide stain lactophenol cotton blue was added to Gram stained slides. The dark blue staining is attributable to the presence of capsular polysaccharides and bacterial slime associated with clumps of Gram-negative bacteria. Since all bacterial cells are glycosylated and concentrate polysaccharides from the media, the majority of cells stain light blue. The contrast between dark and light staining is sufficient to enable a digital image processing thresholding technique to be quantitative with little background noise. Prior to the addition of lactophenol cotton blue, the Gram-stained slides appeared unremarkable, lacking ubiquitous clumps or stained polysaccharides. Adding lactophenol cotton blue to Gram stained slides is a quick and inexpensive way to screen cell cultures for bacterial slime, clumps and biofilms that are invisible using the Gram stain alone. The presence of cell clumping provides a possible explanation of the presence of persisters and paradoxical points observed in Virtual Colony Count antimicrobial assays, and suggests a phenotypic resistance mechanism to antimicrobial peptides involving capsular polysaccharides.
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Ericksen, Bryan. "Quantification of polysaccharides fixed to Gram stained slides using lactophenol cotton blue and digital image processing." F1000Research 4 (July 13, 2017): 1. http://dx.doi.org/10.12688/f1000research.5779.4.
Full textAbstract:
Dark blue rings and circles emerged when the non-specific polysaccharide stain lactophenol cotton blue was added to Gram stained slides. The dark blue staining is attributable to the presence of capsular polysaccharides and bacterial slime associated with clumps of Gram-negative bacteria. Since all bacterial cells are glycosylated and concentrate polysaccharides from the media, the majority of cells stain light blue. The contrast between dark and light staining is sufficient to enable a digital image processing thresholding technique to be quantitative with little background noise. Prior to the addition of lactophenol cotton blue, the Gram-stained slides appeared unremarkable, lacking ubiquitous clumps or stained polysaccharides. Adding lactophenol cotton blue to Gram stained slides is a quick and inexpensive way to screen cell cultures for bacterial slime, clumps and biofilms that are invisible using the Gram stain alone. The presence of cell clumping provides a possible explanation of the presence of persisters and paradoxical points observed in Virtual Colony Count antimicrobial assays, and suggests a phenotypic resistance mechanism to antimicrobial peptides involving capsular polysaccharides.
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Asante, Jonathan, Akebe L. K. Abia, Daniel Anokwah, Bakoena A. Hetsa, Dorcas O. Fatoba, Linda A. Bester, and Daniel G. Amoako. "Phenotypic and Genomic Insights into Biofilm Formation in Antibiotic-Resistant Clinical Coagulase-Negative Staphylococcus Species from South Africa." Genes 14, no. 1 (December 29, 2022): 104. http://dx.doi.org/10.3390/genes14010104.
Full textAbstract:
The work aims to investigate biofilm formation and biofilm/adhesion-encoding genes in coagulase-negative staphylococci (CoNS) species recovered from blood culture isolates. Eighty-nine clinical CoNS were confirmed using the VITEK 2 system, and antibiotic susceptibility testing of isolates was conducted using the Kirby-Bauer disk diffusion method against a panel of 20 antibiotics. Isolates were qualitatively screened using the Congo red agar medium. Quantitative assays were performed on microtiter plates, where the absorbances of the solubilised biofilms were recorded as optical densities and quantified. In all, 12.4% of the isolates were strong biofilm formers, 68.5% had moderate biofilm capacity, and 17.9% showed weak capacity. A subset of 18 isolates, mainly methicillin-resistant S. epidermidis, were investigated for adherence-related genes using whole-genome sequencing and bioinformatics analysis. The highest antibiotic resistance rates for strongly adherent isolates were observed against penicillin (100%) and cefoxitin (81.8%), but the isolates showed no resistance to linezolid (0.0%) and tigecycline (0.0%). The icaABC genes involved in biofilm formation were detected in 50% of the screened isolates. Other adherence-related genes, including autolysin gene atl (88.8%), elastin binding protein gene ebp (94.4%), cell wall-associated fibronectin-binding protein gene ebh (66.7%), clumping factor A gene clfA (5.5%), and pili gene ebpC (22.2%) were also found. The insertion sequence IS256, involved in biofilm formation, was found in 10/18 (55.5%) screened isolates. We demonstrate a high prevalence of biofilm-forming coagulase-negative staphylococci associated with various resistance phenotypes and a substantial agreement between the possession of biofilm-associated genes and the biofilm phenotype.
Dissertations / Theses on the topic "Phenotypic clumping"
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Onyambu, Frank Gekara. "Study of Platelet-mediated clumping adhesion phenotypes in Plasmodium falciparum malaria." Thesis, University of Oxford, 2015. http://ora.ox.ac.uk/objects/uuid:2bc489a9-121e-41ab-8830-1cb07e5b01f2.
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Platelet-mediated clumping of Plasmodium falciparum-infected erythrocytes (IEs) is a common property of field isolates associated with severe disease (Pain, Ferguson et al. 2001). Platelet receptors CD36 (Pain, Ferguson et al. 2001), P-Selectin (Wassmer, Taylor et al. 2008) and gC1qR (Biswas, Hafiz et al. 2007) mediate clumping. To characterize the molecular specificities of the clumping phenotype, I cloned clumping parasite line IT/C10 by limiting dilution. I characterized var gene expression in the IT/C10 clones using generic primers for the DBL tag region (Bull, Berriman et al. 2005). Clumping assays were conducted in the presence of specific reagents to delineate host factors hypothesized to contribute to development of the clumping phenotype. Finally, I conducted a clinical study with isolates from children with malaria in Kilifi, Kenya. This study shows that in parasite line IT/C10, platelet-mediated clumping is associated with Itvar30 suggesting a prominent role for the PfEMP-1 encoded by this var gene in development of platelet-mediated clumping. For IT/C10 parasites, platelet activation appears to be involved in platelet-mediated clumping. Platelet P-Selectin appears to mediate clumping using lectin-dependent interactions. To further elucidate the mechanisms that mediate clumping by host platelets, I have used a panel of platelet antagonists to delineate specific platelet activation pathways. Our results show that platelet activation plays an important role in platelet-mediated clumping. Finally, in this study, platelet-mediated clumping was associated with parasitaemia, but not with disease severity.
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Bangal, Priti Pandurang. "Understanding Rules of Assembly and Species Interactions in Mixed-species Bird Flocks." Thesis, 2019. https://etd.iisc.ac.in/handle/2005/4432.
Full textAbstract:
In mixed-species bird flocks (flocks hereafter), participants vary in their degree of similarity
with each other. Flock participants can gain group size (supplementary) benefits by choosing
similar flock partners, or complementary benefits from dissimilar partners. The nature of
benefits, therefore varies based on overall similarity in the flock. Earlier research has shown
that flocks world over tend to be phenotypically clumped and that intraspecifically gregarious
species are important benefit providers. In this thesis, I examine changing patterns of
associations and species importance with respect to group size in mixed-species bird flocks.
In my first chapter, I examine the relationship between flock size and phenotypic clumping. I
find that small flocks are more phenotypically clumped than expected by chance but as flocks
become larger, the phenotypic variation does not differ from what’s expected by chance. At a
global scale, I find that, flocks in regions with lower average flock size are more
phenotypically clumped. In the second chapter, I examine the importance of intra-specifically
gregarious species. I find that flocks with less than or equal to two gregarious species have
lower richness of non-gregarious species than expected by chance. I also study traits of
intraspecifically gregarious species that are linked to functional importance and find that
individual behavioural traits are not directly correlated to species importance. In the third
chapter, I construct emergent networks of flock participant species based on flock cooccurrence. I find that a few species are structurally important in flocks of all sizes, while a
few are important only in networks of large flocks. I also find that flock components that are
unconnected in smaller flock networks, merge in large flock networks. Overall, I find that
species similarity and presence of important species is crucial in smaller flocks whereas large
flocks are heterogenous groups that resemble random phenotypic assemblages of flocking
birds