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Journal articles on the topic 'Clone composition'
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Cottrell, Matthew T., and David L. Kirchman. "Community Composition of Marine Bacterioplankton Determined by 16S rRNA Gene Clone Libraries and Fluorescence In Situ Hybridization." Applied and Environmental Microbiology 66, no. 12 (December 1, 2000): 5116–22. http://dx.doi.org/10.1128/aem.66.12.5116-5122.2000.
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ABSTRACT We determined the compositions of bacterioplankton communities in surface waters of coastal California using clone libraries of 16S rRNA genes and fluorescence in situ hybridization (FISH) in order to compare the community structures inferred from these two culture-independent approaches. The compositions of two clone libraries were quite similar to those of clone libraries of marine bacterioplankton examined by previous studies. Clones from γ-proteobacteria comprised ca. 28% of the libraries, while approximately 55% of the clones came from α-proteobacteria, which dominated the clone libraries. TheCytophaga-Flavobacter group and three others each comprised 10% or fewer of the clone libraries. The community composition determined by FISH differed substantially from the composition implied by the clone libraries. The Cytophaga-Flavobacter group dominated 8 of the 11 communities assayed by FISH, including the two communities assayed using clone libraries. On average only 10% of DAPI (4′,6′-diamidino-2-phenylindole)-stained bacteria were detected by FISH with a probe for α-proteobacteria, but 30% of DAPI-stained bacteria appeared to be in the Cytophaga-Flavobacter group as determined by FISH. α-Proteobacteria were greatly overrepresented in clone libraries compared to their relative abundance determined by FISH, while the Cytophaga-Flavobacter group was underrepresented in clone libraries. Our data show that theCytophaga-Flavobacter group can be a numerically dominant component of coastal marine bacterioplankton communities.
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Bano, Nasreen, and James T. Hollibaugh. "Phylogenetic Composition of Bacterioplankton Assemblages from the Arctic Ocean." Applied and Environmental Microbiology 68, no. 2 (February 2002): 505–18. http://dx.doi.org/10.1128/aem.68.2.505-518.2002.
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ABSTRACT We analyzed the phylogenetic composition of bacterioplankton assemblages in 11 Arctic Ocean samples collected over three seasons (winter-spring 1995, summer 1996, and summer-fall 1997) by sequencing cloned fragments of 16S rRNA genes. The sequencing effort was directed by denaturing gradient gel electrophoresis (DGGE) screening of samples and the clone libraries. Sequences of 88 clones fell into seven major lineages of the domain Bacteria: α (36%)-, γ (32%)-, δ (14%)-, and ε (1%)-Proteobacteria; Cytophaga-Flexibacter-Bacteroides spp. (9%); Verrucomicrobium spp. (6%); and green nonsulfur bacteria (2%). A total of 34% of the cloned sequences (excluding clones in the SAR11 and Roseobacter groups) had sequence similarities that were <94% compared to previously reported sequences, indicating the presence of novel sequences. DGGE fingerprints of the selected samples showed that most of the bands were common to all samples in all three seasons. However, additional bands representing sequences related to Cytophaga and Polaribacter species were found in samples collected during the summer and fall. Of the clones in a library generated from one sample collected in spring of 1995, 50% were the same and were most closely affiliated (99% similarity) with Alteromonas macleodii, while 50% of the clones in another sample were most closely affiliated (90 to 96% similarity) with Oceanospirillum sp. The majority of the cloned sequences were most closely related to uncultured, environmental sequences. Prominent among these were members of the SAR11 group. Differences between mixed-layer and halocline samples were apparent in DGGE fingerprints and clone libraries. Sequences related to α-Proteobacteria (dominated by SAR11) were abundant (52%) in samples from the mixed layer, while sequences related to γ-proteobacteria were more abundant (44%) in halocline samples. Two bands corresponding to sequences related to SAR307 (common in deep water) and the high-G+C gram-positive bacteria were characteristic of the halocline samples.
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Yoncheva, Tatyana, and Zdravko Nakov. "Comparative Technological Characteristic of the Aligote 61-6 and Aligote N 10 Clones, Cultivated in the Soil and Climatic Conditions of the Region of Pleven." Acta Horticulturae et Regiotecturae 23, no. 1 (May 1, 2020): 25–30. http://dx.doi.org/10.2478/ahr-2020-0007.
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AbstractIn the period 2011–2013 a technological characteristic of the Ukrainian clone Aligote 61-6 was made at the Institute of Viticulture and Enology – Pleven. The Bulgarian candidate-clone Aligote N 10 was used for control. During the grapes ripening, the dynamics of sugar accumulation was monitored. Upon technological maturity the indicators of the yields were accounted and mechanical analysis was performed. The chemical composition of the must, the obtained wines and their organoleptic qualities were analyzed. In its mechanical composition, Aligote 61-6 was typically wine one and it did not differ significantly in the texture and structure of the cluster and berry from the control. The theoretical yield of both clones was high. They exhibited good sugar accumulation and similar acid content. Grapes from the control had better technological indicators for obtaining wines of optimal chemical composition and quality. In the 2011 and 2013 vintages, the control wines exceeded those of the Ukrainian clone in terms of sugar-free extract content. The experimental wines Aligote N 10 had higher titratable acidity compared to the Ukrainian clone. The difference in the phenolic substances ratio and the colour intensity in the samples from both clones were insignificant. The control wines were superior in their organoleptic qualities to those of the Ukrainian clone.
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Peirano-Bolelli, Pierina, Florencia Heller-Fuenzalida, Italo F. Cuneo, Álvaro Peña-Neira, and Alejandro Cáceres-Mella. "Changes in the Composition of Flavonols and Organic Acids during Ripening for Three cv. Sauvignon Blanc Clones Grown in a Cool-Climate Valley." Agronomy 12, no. 6 (June 2, 2022): 1357. http://dx.doi.org/10.3390/agronomy12061357.
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The influence of the geographical location and clone type on the contents of flavonols and organic acids of Sauvignon blanc grapes over the ripening process was investigated. The assay was carried out on three commercial clones of cv. Sauvignon blanc (Clone 242, Clone 107, and Clone 1-Davis) grown in two zones (referred to as low and high zones) in Casablanca Valley, Chile. The low zone is closer to the Pacific Ocean (i.e., 20 km away) than the high zone (which is 37 km away). Clear differences in the contents of total phenols, flavonols and organic acids of the grapes were observed during ripening. All the clones grown in the low zone exhibited a higher titratable acidity than those grown in the high zone. An analysis of the flavonol contents of the grape skins showed differences among clones associated with the geographical zone of cultivation. There was no difference in the tartaric acid concentration among clone types; however, a higher tartaric acid concentration was found in clones grown in the low zone than those grown in the high zone for all clone types. Similar results were found for the malic acid concentration. A discriminant analysis showed that the chemical analysis for the contents of total phenols, flavonols and organic acids influenced the classification based on the clone type. The results showed that grapes of different qualities can be grown in two geographical subunits into the larger area of Casablanca Valley.
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Grossnickle, Steven C., and Shihe Fan. "Genetic variation in summer gas exchange patterns of interior spruce (Picea glauca (Moench) Voss times Picea engelmannii Parry ex Engelm.)." Canadian Journal of Forest Research 28, no. 6 (June 1, 1998): 831–40. http://dx.doi.org/10.1139/x98-053.
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Interior spruce (Picea glauca (Moench) Voss x Picea engelmannii Parry ex Engelm.) somatic seedlings from a range of clones were measured for gas exchange processes in relation to summer atmospheric parameters. Carbon isotope composition ( delta 13C) of needles was compared with gas exchange parameters and intrinsic water use efficiency (WUEi). Needle conductance (gwv) decreased as vapour pressure deficit (VPD) increased. Clone T703 had the lowest gwv level across all VPD conditions, with clones G351, N366, and W460 having significantly greater gwv than clone T703 at VPD levels <2.0 kPa. Response of net photosynthesis (Pn) to photosynthetically active radiation (PAR) for all clones showed Pn to increase to PAR levels of around 1000 µmol ·m-2 ·s-1 and then, Pn rates were stable at higher PAR levels. Clones N366 and W460 had significantly greater Pn than clone T703 at all PAR levels. All clones showed Pn to decline as VPD increased, with clone W460 having the highest predicted Pn level across all VPD conditions and significantly greater Pn than clone T703. Higher WUEi was related to an increase in delta 13C, with clone T703 having the highest WUEi and delta 13C, followed by clone W460. Changes in delta 13C, for all clones, indicated a stronger relationship with gwv than with Pn.
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NATALINO OLIVEIRA, FLÁVIA, JORGE LUIZ COLODETTE, FERNANDO PALHA LEITE, and FERNANDO JOSÉ BORGES GOMES. "Effects of localized environment on eucalyptus clone chemical composition." September 2016 15, no. 9 (October 1, 2016): 599–605. http://dx.doi.org/10.32964/tj15.9.599.
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Eucalyptus wood is becoming the most important feedstock for bleached kraft pulp production, particularly in South America. However, pulp manufacturers have observed that some eucalyptus clones are resistant to wind action and others are not. Those lacking wind resistance are prone to breaking, which results in productivity losses. This study aims to investigate a correlation between the chemical composition of eucalyptus clones and their resistance to wind action. We found differences among the wind-resistant and non-wind-resistant clones, but that the fragility of trees studied for wind resistance does not correlate to the chemical composition of the wood. Four notable differences were observed. First, clones grown at lower altitudes differed from clones grown at higher altitudes in their acetyl, insoluble lignin, and extractives contents, and in their syringyl/guaiacyl (S/G) ratios. However, we found no relationship among these components and wind susceptibility. Second, soluble lignin content increased with the increase of wind resistance in the high altitude clones. Third, the low altitude clones showed slightly lower xylan content (12.4%) and higher lignin content (29.6%) than the others. Finally, the insoluble lignin content, total acetyl groups, extractives, ash contents, and S/G ratios of the clones were influenced by the region where they were grown.
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Bentzer, B. G., G. S. Foster, and A. R. Hellberg. "Impact of clone mixture composition on stability of 7th-year mean height in a series of Norway spruce clone tests." Canadian Journal of Forest Research 20, no. 6 (June 1, 1990): 757–63. http://dx.doi.org/10.1139/x90-100.
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Four mixtures of Norway spruce (Piceaabies (L.) Karst.), each containing 56 clones, were analysed for height at age 7 years at six locations in southern Sweden. The number of clones in each mixture was subsequently reduced in a stepwise manner from 56 to 40, 30, 20, 10, and finally, 5 clones. The reduction process was conducted in three ways: (i) random deletion, (ii) deletion based on height growth, and (iii) deletion based on clone stability. No difference among the means of clone mixtures could be found for 20–56 clones for any elimination procedure tested, and no mixture × location interaction existed despite the number of clones in the mixture or the elimination process used. Location effects were consistently significant, independent of the number of clones in each mixture. Also, replication effects were significant in all cases but one. Random elimination of clones resulted in weak differences between mixture means when 10 and 5 clones were included. Deletion of clones based on lack of stability or inferior height growth only slightly changed the variation pattern compared with when all 56 clones were present in each mixture. Relative height growth performance of clone mixtures with as few as 5 clones appeared to be stable within the region of Sweden that was represented by the trials.
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Reynolds, Andrew G., Margaret Cliff, Douglas A. Wardle, and Marjorie King. "Evaluation of Winegrapes in British Columbia: `Chardonnay' and `Pinot noir' Clones." HortTechnology 14, no. 4 (January 2004): 594–602. http://dx.doi.org/10.21273/horttech.14.4.0594.
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Eighty-five cultivars, selections and clones from European winegrape (Vitis spp.) breeding and selection programs were evaluated between 1993 and 1995 in a randomized complete-block experiment. These included Vitis vinifera clones from France as well as Freiburg, Geisenheim, and Weinsberg, Germany. Small yield and fruit composition differences were found amongst the 'Chardonnay' clones. The standard Prosser clone produced wines with highest earthy aroma and acidity and with lowest perfumy aroma, body and finish; Dijon clones 76 and 96 were most perfumy and least vegetal. `Pinot noir' clones also differed somewhat in terms of yield and fruit composition; `Samtröt', `Gamay Beaujolais', and clone Q1342-01 were amongst the most highly colored clones. These clones also tended to have the most intense berry and currant aromas as well as berry, cherry, and currant flavors. These aforementioned clones appear to be highly adaptable to viticultural regions where low heat units during fruit maturation presently limit industry growth.
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Moulin, Jordão Cabral, Daniel de Souza Ribeiro, Graziela Baptista Vidaurre, Lucas Braga Mulin, and Silvino Intra Moreira. "Effect of drought stress on the formation and lignification of eucalyptus wood cells." IAWA Journal 43, no. 3 (June 16, 2022): 263–75. http://dx.doi.org/10.1163/22941932-bja10092.
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Summary Environmental adaptation and cell differentiation processes are factors that influence the anatomical elements of wood. The objective of this study was to investigate the effect of water deficit on lignin composition in anatomical elements and on the characteristics of vessel-neighboring cells. Six-year-old clones of Eucalyptus urophylla and Eucalyptus grandis × Eucalyptus camaldulensis from wet and dry regions were used. All regions received a rainfall exclusion treatment. Cell wall width, cell wall thickness, and form factor of fibers close to and far from vessels were measured. In the same cells, lignin was measured in the middle lamella and vessels by a fluorescence technique. The vessel differentiation process affected cell wall thickness and lignin composition in neighboring cells. Lignin composition was increased in vessels compared to fibers or vasicentric tracheids. Middle lamella lignin was not affected by vessel differentiation or water deficit in either eucalyptus clone. E. grandis × E. camaldulensis is originally from a dry climate region and, therefore, did not suffer alterations in lignin when subjected to water stress conditions; however, this clone exhibited a higher number of vasicentric tracheids. E. urophylla is originally from a humid climate region and, when subjected to water deficit, showed increased wood lignin composition, which seems to be a strategy for better use of water resources. Alterations in lignin composition of vessel, vasicentric tracheid, and fiber cell walls resulting from exposure to water deficit conditions vary according to eucalyptus species.
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Weber, Sabine, Stephan Stubner, and Ralf Conrad. "Bacterial Populations Colonizing and Degrading Rice Straw in Anoxic Paddy Soil." Applied and Environmental Microbiology 67, no. 3 (March 1, 2001): 1318–27. http://dx.doi.org/10.1128/aem.67.3.1318-1327.2001.
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ABSTRACT Rice straw is a major substrate for the production of methane, a greenhouse gas, in flooded rice fields. The bacterial community degrading rice straw under anoxic conditions was investigated with molecular methods. Rice straw was incubated in paddy soil anaerobically for 71 days. Denaturing gradient gel electrophoresis (DGGE) of the amplified bacterial 16S rRNA genes showed that the composition of the bacterial community changed during the first 15 days but then was stable until the end of incubation. Fifteen DGGE bands with different signal intensities were excised, cloned, and sequenced. In addition, DNA was extracted from straw incubated for 1 and 29 days and the bacterial 16S rRNA genes were amplified and cloned. From these clone libraries 16 clones with different electrophoretic mobilities on a DGGE gel were sequenced. From a total of 31 clones, 20 belonged to different phylogenetic clusters of the clostridia, i.e., clostridial clusters I (14 clones), III (1 clone), IV (1 clone), and XIVa (4 clones). One clone fell also within the clostridia but could not be affiliated to one of the clostridial clusters. Ten clones grouped closely with the genera Bacillus (3 clones), Nitrosospira (1 clone), Fluoribacter (1 clones), andAcidobacterium (2 clones) and with clone sequences previously obtained from rice field soil (3 clones). The relative abundances of various phylogenetic groups in the rice straw-colonizing community were determined by fluorescence in situ hybridization (FISH). Bacteria were detached from the incubated rice straw with an efficiency of about 80 to 90%, as determined by dot blot hybridization of 16S rRNA in extract and residue. The number of active (i.e., a sufficient number of ribosomes) Bacteria detected with a general eubacterial probe (Eub338) after 8 days of incubation was 61% of the total cell counts. This percentage decreased to 17% after 29 days of incubation. Most (55%) of the active cells on day 8 belonged to the genus Clostridium, mainly to clostridial clusters I (24%), III (6%), and XIVa (24%). An additional 5% belonged to theCytophaga-Flavobacterium cluster of theCytophaga-Flavobacterium-Bacteroides phylum, 4% belonged to the α, β, and γ Proteobacteria, and 1.3% belonged to the Bacillus subbranch of the gram-positive bacteria with a low G+C content. The results show that the bacterial community colonizing and decomposing rice straw developed during the first 15 days of incubation and was dominated by members of different clostridial clusters, especially clusters I, III, and XIVa.
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Denecke, Klaus. "Partial clones." Asian-European Journal of Mathematics 13, no. 08 (May 28, 2020): 2050161. http://dx.doi.org/10.1142/s1793557120501612.
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A set [Formula: see text] of operations defined on a nonempty set [Formula: see text] is said to be a clone if [Formula: see text] is closed under composition of operations and contains all projection mappings. The concept of a clone belongs to the algebraic main concepts and has important applications in Computer Science. A clone can also be regarded as a many-sorted algebra where the sorts are the [Formula: see text]-ary operations defined on set [Formula: see text] for all natural numbers [Formula: see text] and the operations are the so-called superposition operations [Formula: see text] for natural numbers [Formula: see text] and the projection operations as nullary operations. Clones generalize monoids of transformations defined on set [Formula: see text] and satisfy three clone axioms. The most important axiom is the superassociative law, a generalization of the associative law. If the superposition operations are partial, i.e. not everywhere defined, instead of the many-sorted clone algebra, one obtains partial many-sorted algebras, the partial clones. Linear terms, linear tree languages or linear formulas form partial clones. In this paper, we give a survey on partial clones and their properties.
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Nogales, Balbina, Edward R. B. Moore, Enrique Llobet-Brossa, Ramon Rossello-Mora, Rudolf Amann, and Kenneth N. Timmis. "Combined Use of 16S Ribosomal DNA and 16S rRNA To Study the Bacterial Community of Polychlorinated Biphenyl-Polluted Soil." Applied and Environmental Microbiology 67, no. 4 (April 1, 2001): 1874–84. http://dx.doi.org/10.1128/aem.67.4.1874-1884.2001.
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ABSTRACT The bacterial diversity assessed from clone libraries prepared from rRNA (two libraries) and ribosomal DNA (rDNA) (one library) from polychlorinated biphenyl (PCB)-polluted soil has been analyzed. A good correspondence of the community composition found in the two types of library was observed. Nearly 29% of the cloned sequences in the rDNA library were identical to sequences in the rRNA libraries. More than 60% of the total cloned sequence types analyzed were grouped in phylogenetic groups (a clone group with sequence similarity higher than 97% [98% for Burkholderia andPseudomonas-type clones]) represented in both types of libraries. Some of those phylogenetic groups, mostly represented by a single (or pair) of cloned sequence type(s), were observed in only one of the types of library. An important difference between the libraries was the lack of clones representative of the Actinobacteriain the rDNA library. The PCB-polluted soil exhibited a high bacterial diversity which included representatives of two novel lineages. The apparent abundance of bacteria affiliated to the beta-subclass of theProteobacteria, and to the genus Burkholderiain particular, was confirmed by fluorescence in situ hybridization analysis. The possible influence on apparent diversity of low template concentrations was assessed by dilution of the RNA template prior to amplification by reverse transcription-PCR. Although differences in the composition of the two rRNA libraries obtained from high and low RNA concentrations were observed, the main components of the bacterial community were represented in both libraries, and therefore their detection was not compromised by the lower concentrations of template used in this study.
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Lan, Chuan-Ching, and Donald R. Love. "Molecular Characterisation of Bacterial Community Structure along the Intestinal Tract of Zebrafish (Danio rerio): A Pilot Study." ISRN Microbiology 2012 (February 14, 2012): 1–10. http://dx.doi.org/10.5402/2012/590385.
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The bacterial composition along the intestinal tract of Danio rerio was investigated by cultivation-independent analysis of the 16S rRNA gene. Clone libraries were constructed for three compartments of the intestinal tract of individual fish. 566 individual clones were differentiated by amplified 16S rRNA gene restriction analysis (ARDRA), and clone representatives from each operational taxonomic unit (OTU) were sequenced. As reported in other studies, we found that Proteobacteria was the most prominent phylum among clone libraries from different fish. Data generated from this pilot study indicated some compositional differences in bacterial communities. Two dominant classes, Gammaproteobacteria and Bacilli, displayed different levels of abundance in different compartments; Gammaproteobacteria increased along the intestinal tract, while Bacilli decreased its abundance along the proximal-distal axis. Less obvious spatial patterns were observed for other classes. In general, bacterial diversity in the intestinal bulb was greater than that in the posterior intestine. Interindividual differences in bacterial diversity and composition were also noted in this study.
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Jelinski, D. E., and L. J. Fisher. "Spatial variability in the nutrient composition of Populus tremuloides: clone-to-clone differences and implications for cervids." Oecologia 88, no. 1 (1991): 116–24. http://dx.doi.org/10.1007/bf00328411.
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Pimenta, Alexandre, Maíra Fasciotti, Thays Monteiro, and Kássio Lima. "Chemical Composition of Pyroligneous Acid Obtained from Eucalyptus GG100 Clone." Molecules 23, no. 2 (February 15, 2018): 426. http://dx.doi.org/10.3390/molecules23020426.
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Murphy, Robert, Jinzhong Fu, Ilya Darevsky, and Ross MacCulloch. "Clonal variation in the Caucasian rock lizard Lacerta armeniaca and its origin." Amphibia-Reptilia 21, no. 1 (2000): 83–89. http://dx.doi.org/10.1163/156853800507291.
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AbstractClonal variation in Lacerta armeniaca was investigated using allozyme electrophoresis and morphology. Among the 35 allozyme loci examined, three were variable, which divided L. armeniaca into four clones. One rare clone of L. armeniaca made up the majority of two populations. This contrasts to rare clones in other parthenogenetic Caucasian rock lizards which typically consist of only one or two individuals. Another rare clone, which showed a striking colouration difference, had different allelic composition at two loci. Although mutation is a possible explanation of the origin of the clonal variation, the alternative, multiple origin, is equally likely.
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Budeus, Bettina, Stefanie Schweigle de Reynoso, Martina Przekopowitz, Daniel Hoffmann, Marc Seifert, and Ralf Küppers. "Complexity of the human memory B-cell compartment is determined by the versatility of clonal diversification in germinal centers." Proceedings of the National Academy of Sciences 112, no. 38 (August 31, 2015): E5281—E5289. http://dx.doi.org/10.1073/pnas.1511270112.
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Our knowledge about the clonal composition and intraclonal diversity of the human memory B-cell compartment and the relationship between memory B-cell subsets is still limited, although these are central issues for our understanding of adaptive immunity. We performed a deep sequencing analysis of rearranged immunoglobulin (Ig) heavy chain genes from biological replicates, covering more than 100,000 memory B lymphocytes from two healthy adults. We reveal a highly similar B-cell receptor repertoire among the four main human IgM+ and IgG+ memory B-cell subsets. Strikingly, in both donors, 45% of sequences could be assigned to expanded clones, demonstrating that the human memory B-cell compartment is characterized by many, often very large, B-cell clones. Twenty percent of the clones consisted of class switched and IgM+(IgD+) members, a feature that correlated significantly with clone size. Hence, we provide strong evidence that the vast majority of Ig mutated B cells—including IgM+IgD+CD27+ B cells—are post-germinal center (GC) memory B cells. Clone members showed high intraclonal sequence diversity and high intraclonal versatility in Ig class and IgG subclass composition, with particular patterns of memory B-cell clone generation in GC reactions. In conclusion, GC produce amazingly large, complex, and diverse memory B-cell clones, equipping the human immune system with a versatile and highly diverse compartment of IgM+(IgD+) and class-switched memory B cells.
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Timke, Markus, Ngoc Quynh Wang-Lieu, Karlheinz Altendorf, and André Lipski. "Community Structure and Diversity of Biofilms from a Beer Bottling Plant as Revealed Using 16S rRNA Gene Clone Libraries." Applied and Environmental Microbiology 71, no. 10 (October 2005): 6446–52. http://dx.doi.org/10.1128/aem.71.10.6446-6452.2005.
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ABSTRACT The microbial composition of biofilms from a beer bottling plant was analyzed by a cultivation independent analysis of the 16S rRNA genes. Clone libraries were differentiated by amplified 16S rRNA gene restriction analysis and representative clones from each group were sequenced. The diversity of the clone libraries was comparable with the diversity found for environmental samples. No evidences for the presence of strictly anaerobic taxa or important beer spoilers were found, indicating that biofilms developed for more than 6 months at the plant formed no appropriate habitat for those microorganisms. The genus Methylobacterium was one of the dominating groups of the clone libraries. The size of this population was assessed by fluorescence in situ hybridization and fatty acid analysis. In addition, considerable numbers of clones were assigned to uncultivated organisms.
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Schlager, Theresa A., J. Owen Hendley, Alison L. Bell, and Thomas S. Whittam. "Clonal Diversity of Escherichia coli Colonizing Stools and Urinary Tracts of Young Girls." Infection and Immunity 70, no. 3 (March 2002): 1225–29. http://dx.doi.org/10.1128/iai.70.3.1225-1229.2002.
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ABSTRACT Intestinal carriage of Escherichia coli in prepubertal girls without a history of urinary tract infection was examined by collecting weekly stools and periurethral and urine samples over 3 to 4 weeks of study. Dominant and minor clones were defined by grouping 28 E. coli isolates into clonal types. Multiple enteric clones of E. coli, which changed week to week, were found in the 13 girls during the study (median, 3 clones/girl; range, 1 to 16 clones/girl). Dominance of an enteric clone did not predict persistence in the stool. In only 10 (34%) of the 29 episodes in which a dominant clone present in one weekly sample could have been detected the following week did it persist as the dominant clone in the next weekly sample. In 5 (17%) of the 29 episodes, a dominant clone found in one weekly sample was classified as a minor clone the next week. Both dominant and minor clones were observed to colonize the urinary tract. However, when colonization of the periurethra or bladder urine occurred, it was brief and often did not reflect the dominant stool flora from the same week. In fact, in only 40% of episodes was a clone that was detected either on the periurethra or in the urine also recovered from the stool the same week. Our findings suggest that the intestinal flora of healthy girls is multiclonal with frequent fluctuations in composition.
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Purnamaningsih, R., D. Sukmadjaja, S. Suhesti, and S. Rahayu. "In vitro propagation of six selected sugarcane mutant clones through leaf explants." IOP Conference Series: Earth and Environmental Science 883, no. 1 (October 1, 2021): 012075. http://dx.doi.org/10.1088/1755-1315/883/1/012075.
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Abstract Six mutant clones of sugarcane with high productivity have been produced through tissue culture techniques combined with mutations using gamma-ray irradiation and Ethyl Methane Sulfonate. The six mutant clones have been tested for stability in the field. They are proven to have high productivity and yields, so that they are very potential to be developed as superior varieties. To support the planting material sufficiency of these clones, an efficient propagation method was needed. Media formulations with different physical properties and composition of growth regulators were tested to obtain high seedling propagation rates. The media formulation for callus induction was Murashige dan Skoog (MS) + 3 mg/l 2,4-D + 3 g/l casein hydrolysate + 3% sucrose and for shoot regeneration was MS + 0,5 mg/l BA + 0,1 mg/l IBA + 100 mg/l PVP and 2% sucrose. Shoot proliferation was carried out on MS liquid (1, ½) + (0.3; 0.5 mg/l) BA + 0.1 mg/l IBA + 1 mg/l Kinetin + (0; 0.5 mg/l) GA3+ sucrose 2%. The results showed that callus induction, callus regeneration, and shoot proliferation of sugarcane mutant clones were influenced by the genotype and medium composition. The fastest callus induction was obtained from the MSP-4 clone (5.82 days), and the longest was MSB-7 (8.82 days). The largest callus diameter was obtained from MSB-6 clone on MS medium containing 1 mg/l BA, 100 mg/l PVP, and 2% sucrose. The highest number of shoots was obtained from the MSB-6 clone, while the least number of shoots conducted from the MSB-8 clone. The MSB-8 clones were more difficult to regenerate compared to the others. The best media formulation for shoot proliferation was ½ MS containing 0.5 mg/l BA, 1 mg/l Kinetin, and 0.1 mg/l IBA, while the best formulation for rooting was ½ MS.
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Samitsu, Y., and K. Hosaka. "Molecular marker analysis of 24- and 25-chromosome plants obtained from Solanum tuberosum L. subsp. andigena (2n = 4x = 48) pollinated with a Solanum phureja haploid inducer." Genome 45, no. 3 (June 1, 2002): 577–83. http://dx.doi.org/10.1139/g02-019.
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Clones with 24 or 25 chromosomes were obtained by pollinating an Andean cultivated tetraploid potato (Solanum tuberosum subsp. andigena clone 94H94, 2n = 4x = 48) with the Solanum phureja haploid-inducer clone 1.22. Their genetic composition was analyzed in an RAPD assay using 135 decamer primers and in an RFLP assay using 45 single-copy DNA probes. In total, 22 RAPD and 20 RFLP markers were found to be specific to S. phureja. None of these markers were found in the 24- and 25-chromosome clones. RFLP genotypes for the 45 RFLP loci were further determined for each clone. Genotypes of the 24-chromosome clones were characterized using two alleles randomly selected from four alleles of the parental tetraploid clone for almost all RFLP loci. Five 25-chromosome clones had extra alleles for all of the RFLP loci of chromosomes 4, 8, 10, 11, and 12, respectively, suggesting primary trisomy for one of these chromosomes. Clones with genotypes showing double reduction were also identified. Therefore, the obtained clones likely originated from random samples of female gametes, and hence are euhaploids or aneuhaploids of S. tuberosum subsp. andigena, strongly supporting parthenogenesis to be a primary mechanism for haploid induction in potato.Key words: Solanum tuberosum subsp. andigena, RFLP, RAPD, haploid, trisomic.
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Polanía-Hincapié, Paola Andrea, Juan Carlos Suárez, Héctor Eduardo Hernández, Vivian Yorlady Ramón-Triana, Liceth N. Cuéllar-Álvarez, and Fernando Casanoves. "Influence of Fermentation Time on the Chemical and Functional Composition of Different Cocoa Clones from Southern Colombia." Fermentation 9, no. 11 (November 16, 2023): 982. http://dx.doi.org/10.3390/fermentation9110982.
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Cocoa bean quality depends mainly on genetic material, edaphoclimatic factors and post-harvest processes such as fermentation. The impact of the fermentation process on the chemical and functional composition of different cocoa clones grown in southern Colombia was analyzed. A factorial design with repeated measures over time was used to analyze the effect of clone and fermentation time on chemical characteristics (bromatology, phenolic compounds and antioxidant activity). The bromatological characteristics showed significant differences between clones and fermentation time. Clones EET-8 and CCN-51 showed higher contents of acidity (0.51%), fat (63.61%), protein (12.85%) and carbohydrates (1.63 mg g−1). Moisture, acidity and sucrose increased their values between day 4 and day 6 of fermentation (p < 0.05). Phenolic compounds and antioxidant activity had significant differences between clones, where clones CCN-51 and ICS-95 had high contents of phenols (64.56 mg g−1), flavonoids (3.30 mg g−1) and DPPH reducing capacity (325.55 µmol g−1). In this sense, we consider the FSV-41 clone as the major grain quality index based on the results of chemical composition at the bromatological level, antioxidant activity and phenolic compounds.
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Haddad, L., and I. G. Rosenberg. "Finite Clones Containing All Permutations." Canadian Journal of Mathematics 46, no. 5 (October 1, 1994): 951–70. http://dx.doi.org/10.4153/cjm-1994-054-1.
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AbstractLet A be a finite set with |A| > 2. We describe all clones on A containing the set SA of all permutations of A among its unary operations. (A clone on A is a composition closed set of finitary operations on A containing all projections). With a few exceptions such a clone C is either essentially unary or cellular i.e. there exists a monoid M of self-maps of A containing SA such that either C = (= all essentially unary operations agreeing with some f ∊ M) or C = ∪ Гh where 1 < h ≤ |A| and Гh consists of all finitary operations on A taking at most h values. The exceptions are subclones of Burle's clone or of its variant (provided |A| is even).
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Pereira, Bárbara Luísa Corradi, Aylson Costa Oliveira, Ana Márcia Macedo Ladeira Carvalho, Angélica de Cássia Oliveira Carneiro, Larissa Carvalho Santos, and Benedito Rocha Vital. "Quality of Wood and Charcoal fromEucalyptusClones for Ironmaster Use." International Journal of Forestry Research 2012 (2012): 1–8. http://dx.doi.org/10.1155/2012/523025.
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Considering the wide variety of species and clones ofEucalyptuscultivated in Brazil, it is necessary to search for new information on wood properties, so that the selection of genetically superior material may be successful. The present study aimed to determine the properties of wood and charcoal from different clones ofEucalyptusspp. Six clones at the age of 7.5 years were evaluated and the samples were from a clonal, located in the city of Lassance, Minas Gerais, Brazil. Basic density, chemical composition, and higher heating value were determined. Carbonizations in a laboratory kiln were done and the levels of volatile matter, ash, and fixed carbon, higher heating value, and bulk density of the charcoal produced were determined. Evaluated genetic materials showed differences in their properties. According to research results, several properties of wood should be considered together for the selection of clones for charcoal production. However, basic density and chemical composition of wood, especially high contents of lignin and low contents of extractives, are the properties that had more influence on charcoal yield and its quality. Concerning charcoal production for steelmaking, clone 6 stood out and, conversely, clone 4 showed inferior properties to those of others.
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Liu, Alex, Severine Cathelin, Yitong Yang, Farzaneh Aboualizadeh, Amina Abow, Gurbaksh Basi, Lance Li, et al. "Single-Cell Proteogenomic Analysis of Clonal Evolution in Patient-Derived Xenograft Models of AML Treated with IDH Inhibitors." Blood 144, Supplement 1 (November 5, 2024): 4995. https://doi.org/10.1182/blood-2024-211634.
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The clonal architecture of acute myeloid leukemia (AML) can be highly complex and heterogeneous. This genetic diversity complicates the treatment of AML, as different clones may respond variably to therapies, contributing to treatment resistance and disease relapse. Understanding the mechanisms and implications of clonal evolution in AML is crucial for developing more effective treatment strategies that can target the diverse cellular populations. The generation of patient-derived xenograft (PDX) models has revolutionized the study of AML. One of the main uses of PDX models is to study how a leukemic sample might respond to different therapies. Here, we used single-cell DNA sequencing (scDNA-seq) and surface protein profiling to monitor the clonal evolution and differentiation of an isocitrate dehydrogenase 1 (IDH1)-mutated leukemic sample in response to ivosidenib (IVO), a mutant IDH1 inhibitor, either as monotherapy or in combination with venetoclax (VEN) or azacitidine (AZA). Single-cell mutation analysis of the engrafted cell population showed that the initial evolutionary path was linear characterized by the sequential acquisition of DNMT3AR882H (clone 1), WT1R467W (clone 2), IDH1R132H (clone 3), NPM1Trp288Cysfs*12 (clone 4), FLT3-ITD (clone 5), and WT1R439C (clone 6) mutations. Three subclones branched off at the end of this linear path with each acquiring either a TET2Q1548del (clone 7), DNMT3AD531del (clone 8), or KITH40QfsTer6 (clone 9) mutation. The overall clonal composition of the input primary sample and sample from vehicle-treated animals were largely similar. To quantify the differences in therapeutic response between clones, we developed a hierarchical multinomial Bayesian model that estimated the fold change in absolute cell numbers for each clone compared with vehicle treatment. This analysis revealed that both single-agent VEN and IVO+VEN were generally more effective in targeting earlier-stage clones (clones 3-5) than later-stage clones (clones 6-9). In contrast, single-agent AZA and IVO+AZA were effective in eliminating clone 6 as well as earlier-stage clones. Notably, the combination of IVO+AZA was effective in reducing all the clones by approximately the same magnitude, including clones 7 and 8 which demonstrated lower sensitivity to AZA monotherapy. Given that the WT1R439C mutation, acquired in clone 6, distinguished early-stage from late-stage clones, these findings suggest that WT1 mutations might contribute to IVO and VEN resistance and that the addition of AZA can overcome this mechanism of resistance. Consistent with these findings, the combination of IVO+AZA strongly upregulated the expression of the myeloid markers CD11b, CD14, and CD15 to a greater extent than with either single agent. These findings provide evidence that AZA and IVO could synergize to overcome the differentiation block in IDH1-mutated AML cells, reflecting the superior clinical efficacy of this regimen over single-agent IVO. To broaden the applicability of PDX models to study the competition between genetic clones that co-exist infrequently in an individual sample, we generated mixed PDX (mPDX) models by co-engrafting two or more leukemic samples in the same animal and used scDNA-seq to deconvolute the clonal composition and sample origin of the engrafted cells. As proof-of-principle, we generated an IDH1R132H/IDH2R140Q mPDX to model isoform switching in both directions by treating the animals with either IVO or enasidenib (ENA), a mutant IDH2 inhibitor. We observed the expected differentiation response and depletion of IDH1-mutated or IDH2-mutated clones by IVO or ENA treatment as single agents, respectively. Further studies are underway to demonstrate whether dual mutant IDH1 and IDH2 inhibition (IVO+ENA) will circumvent resistance driven by isoform switching. In summary, we demonstrate the utility of applying single-cell proteogenomic analysis in traditional and mixed PDX models to gain crucial insights into mechanisms of resistance and potential strategies to overcome it.
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Börner, F., L. Haddad, and R. Pöschel. "Minimal partial clones." Bulletin of the Australian Mathematical Society 44, no. 3 (December 1991): 405–15. http://dx.doi.org/10.1017/s0004972700029919.
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Let A be a finite set. A partial clone on A is a composition closed set of operations containing all projections. It is well known that the partial clones on A, ordered by inclusion, form a lattice. We show that the minimal partial clones on A are:(a) minimal clones of full operations or(b) generated by partial projections defined on a totally reflexive and totally symmetric domain.
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Qian, Xu, Fangyuan Jia, Jian Cai, Ying Shi, Changqing Duan, and Yibin Lan. "Characterization and Evolution of Volatile Compounds of Cabernet Sauvignon Wines from Two Different Clones during Oak Barrel Aging." Foods 11, no. 1 (December 29, 2021): 74. http://dx.doi.org/10.3390/foods11010074.
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Xinjiang is a major wine-making region in China, but its hot climate in summer and intense sun exposure negatively affect the aroma quality of Cabernet Sauvignon wine. The aim of this study was to characterize and differentiate the volatile composition of Cabernet Sauvignon wines from two clones (169 and 191) in Xinjiang, and to study their aromatic profile evolution during 12-month oak barrel aging period. Results showed that before aging, clone 169 wine contained higher concentrations of several alcohols and ethyl esters, while acetate esters and furanic compounds were higher in clone 191 wine. After aging, levels of many terpenes, norisoprenoids, volatile phenols and phenolic aldehydes were significantly higher in clone 169 wine than 191 wine. Aroma series analysis revealed that clone 169 wine exhibited higher floral and roasty aromas after aging, while clone 191 wine had stronger chemical aroma. Principal component analysis indicated that aging process played a primary role in the alteration of volatile profile in these wines. Clone played a secondary role and oak barrel had a tertiary contribution to the variation. The present work indicates that clone 169 is a better choice for producing high-quality aged Cabernet Sauvignon wine with intense and elegant aroma in Xinjiang.
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Triches, Willian dos Santos, Daniel Pazzini Eckhardt, Elisandra Nunes da Silva, Marcos Gabbardo, Fabio Clasen Chaves, Jessica Fernanda Hoffmann, Giovana Paula Zandoná, and Cesar Valmor Rombaldi. "Physico-chemical characterization of wines produced by different rootstock and Vitis vinifera cv. Tannat clones in vineyards of subtropical climate region." SEPTEMBER 2020, no. 14(9):2020 (September 20, 2020): 1506–18. http://dx.doi.org/10.21475/ajcs.20.14.09.p2644.
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Tannat wine trees are well characterized in Uruguay and the French region of Madiran for their high colour and phenolic concentrations. In addition to the cultivar, the rootstock, clone and region of production can influence the phenolic concentrations of wines. In this context, this study evaluated the rootstocks 'SO4' (Vitis berlandieri x Vitis riparia), 'Gravesac' ('161-49C' x '3309C') and '3309C' (Vitis riparia x Vitis rupestris) grafted with Tannat cultivar clones ('Californian', '944', '717', '398' and '794') to assess the physicochemical, phenolic and sensorial composition of the wine produced in the Campanha Gaúcha (RS) region, Southern Brazil, in a subtropical climate region. A vineyard planted in 2007 was used in this study (for 3 years during 2015, 2016 and 2017). The wine composition and the sensorial profile were evaluated as dependent variables. This study showed that the rootstocks and the Tannat clones did not influence the dependent variables evaluated and that the genetic materials and their combinations presented high oenological potential, providing wines with high alcohol content, colour and phenolic compound concentrations. This study suggests the diversification of rootstocks and clones as a way of increasing genetic variability, avoiding the cultivation of a single rootstock and clone.
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Ajijah, Nur, and Rr Sri Hartati. "PRIMARY AND SECONDARY SOMATIC EMBRYOGENESIS OF CACAO: THE EFFECT OF EXPLANT TYPES AND PLANT GROWTH REGULATORS." Indonesian Journal of Agricultural Science 20, no. 2 (January 17, 2020): 69. http://dx.doi.org/10.21082/ijas.v20n2.2019.p69-76.
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<p class="abstrakinggris">The success of cacao somatic embryogenesis is affected by many factors, including the basal salt medium, the genotype, the explant type, and the concentration and composition of plant growth regulators (PGRs). The study aimed to evaluate the effects of PGRs composition on the primary somatic embryo (PSE) response and the effect of explant type and PGRs composition used in inducing PSE on the secondary somatic embryogenesis (SSE) response. PSEs were induced from basal petal and staminoid explants of MCC 01 and MCC 02 clones on DKW medium containing 2,4-D 2 mg l<sup>-1 </sup>+ kinetin 0.5 mg l<sup>-1</sup> or 2,4-D 2 mg l<sup>-1</sup> + kinetin 0.125 – 0.250 mg l<sup>-1</sup> + thidiazuron (TDZ) 2.5 – 5 µg l<sup>-1</sup> or 2,4-D 2 mg l<sup>-1</sup> + TDZ 10 µg l<sup>-1</sup>. Genotype, explant type, and PGR composition dependently affected PSE response. The best PSE response was obtained from staminoid explant of MCC 02 clone on medium containing 2,4-D 2 mg l<sup>-1</sup> + kinetin 0.5 mg l<sup>-1</sup> (20%, 9 embryos). The explant type and PGR composition used in inducing PSEs affect the SSE response. The highest SSE response of MCC 01 clone was obtained from petal explant with medium containing 2,4-D 2 mg l<sup>-1</sup> + kinetin 0.5 mg l<sup>-1</sup>. The formation of SSEs could increase the multiplication rate of MCC 01 clone by 7 times.</p>
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Korenblum, Elisa, Diogo Bastos Souza, Monica Penna, and Lucy Seldin. "Molecular Analysis of the Bacterial Communities in Crude Oil Samples from Two Brazilian Offshore Petroleum Platforms." International Journal of Microbiology 2012 (2012): 1–8. http://dx.doi.org/10.1155/2012/156537.
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Crude oil samples with high- and low-water content from two offshore platforms (PA and PB) in Campos Basin, Brazil, were assessed for bacterial communities by 16S rRNA gene-based clone libraries. RDP Classifier was used to analyze a total of 156 clones within four libraries obtained from two platforms. The clone sequences were mainly affiliated withGammaproteobacteria(78.2% of the total clones); however, clones associated withBetaproteobacteria(10.9%),Alphaproteobacteria(9%), and Firmicutes (1.9%) were also identified.Pseudomonadaceaewas the most common family affiliated with these clone sequences. The sequences were further analyzed by MOTHUR, yielding 81 operational taxonomic units (OTUs) grouped at 97% stringency. Richness estimators also calculated by MOTHUR indicated that oil samples with high-water content were the most diverse. Comparison of bacterial communities present in these four samples using LIBSHUFF and Principal Component Analysis (PCA) indicated that the water content significantly influenced the community structure only of crude oil obtained from PA. Differences between PA and PB libraries were observed, suggesting the importance of the oil field as a driver of community composition in this habitat.
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Burin, Vívian Maria, Aparecido Lima da Silva, Luciane Isabel Malinovski, Jean Pierre Rosier, Leila Denise Falcão, and Marilde Teresinha Bordignon-Luiz. "Characterization and multivariate classification of grapes and wines of two Cabernet Sauvignon clones." Pesquisa Agropecuária Brasileira 46, no. 5 (May 2011): 474–81. http://dx.doi.org/10.1590/s0100-204x2011000500004.
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The objective of this work was to assess and characterize two clones, 169 and 685, of Cabernet Sauvignon grapes and to evaluate the wine produced from these grapes. The experiment was carried out in São Joaquim, SC, Brazil, during the 2009 harvest season. During grape ripening, the evolution of physical-chemical properties, phenolic compounds, organic acids, and anthocyanins was evaluated. During grape harvest, yield components were determined for each clone. Individual and total phenolics, individual and total anthocyanins, and antioxidant activity were evaluated for wine. The clones were also assessed regarding the duration of their phenological cycle. During ripening, the evolution of phenolic compounds and of physical-chemical parameters was similar for both clones; however, during harvest, significant differences were observed regarding yield, number of bunches per plant and berries per bunch, leaf area, and organic acid, polyphenol, and anthocyanin content. The wines produced from these clones showed significant differences regarding chemical composition. The clones showed similar phenological cycle and responses to bioclimatic parameters. Principal component analysis shows that clone 685 is strongly correlated with color characteristics, mainly monomeric anthocyanins, while clone 169 is correlated with individual phenolic compounds.
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Schierack, Peter, Antje R�mer, J�rg Jores, Heike Kaspar, Sebastian Guenther, Matthias Filter, J�rgen Eichberg, and Lothar H. Wieler. "Isolation and Characterization of Intestinal Escherichia coli Clones from Wild Boars in Germany." Applied and Environmental Microbiology 75, no. 3 (December 5, 2008): 695–702. http://dx.doi.org/10.1128/aem.01650-08.
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ABSTRACT Our understanding of the composition of Escherichia coli populations in wild boars is very limited. In order to obtain insight into the E. coli microflora of wild boars, we studied E. coli isolates from the jejunums, ileums, and colons of 21 wild boars hunted in five geographic locations in Germany. Ten isolates per section were subjected to clonal determination using pulsed-field gel electrophoresis. One representative isolate per clone was further investigated for virulence traits, phylogenetic affiliation, and antimicrobial susceptibility. Macrorestriction analysis of 620 isolates revealed a range of clone diversity among the sections and animals, with up to 9 and 16 different clones per section and animal, respectively. Most of the clones for a given animal were shared between two adjacent intestinal sections. The overall highest clonal diversity was observed within the colon. While the astA gene was present in a large number of clones, other virulence genes and hemolytic ability were detected only sporadically. Clones of all four ECOR groups dominated the intestinal sections. Phylogenetic analysis and the occurrence of virulence genes correlated with the isolation frequencies for clones. All E. coli clones from wild boars were susceptible to all antimicrobial agents tested. In conclusion, though several parameters (including an animal-specific and highly diverse E. coli clone composition, the simultaneous occurrence of single clones in two adjacent intestinal sections of a given animal, and a higher E. coli diversity in the large intestine than in the small intestine) of E. coli populations of wild boars were similar to those of previously described E. coli populations of conventionally reared domestic pigs, our data also indicate possible differences, as seen for the E. coli diversity in the large intestine, the occurrence of certain virulence genes and phylogenetic groups, and antimicrobial susceptibilities.
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Carulli, J. P., D. E. Krane, D. L. Hartl, and H. Ochman. "Compositional heterogeneity and patterns of molecular evolution in the Drosophila genome." Genetics 134, no. 3 (July 1, 1993): 837–45. http://dx.doi.org/10.1093/genetics/134.3.837.
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Abstract The rates and patterns of molecular evolution in many eukaryotic organisms have been shown to be influenced by the compartmentalization of their genomes into fractions of distinct base composition and mutational properties. We have examined the Drosophila genome to explore relationships between the nucleotide content of large chromosomal segments and the base composition and rate of evolution of genes within those segments. Direct determination of the G + C contents of yeast artificial chromosome clones containing inserts of Drosophila melanogaster DNA ranging from 140-340 kb revealed significant heterogeneity in base composition. The G + C content of the large segments studied ranged from 36.9% G + C for a clone containing the hunchback locus in polytene region 85, to 50.9% G + C for a clone that includes the rosy region in polytene region 87. Unlike other organisms, however, there was no significant correlation between the base composition of large chromosomal regions and the base composition at fourfold degenerate nucleotide sites of genes encompassed within those regions. Despite the situation seen in mammals, there was also no significant association between base composition and rate of nucleotide substitution. These results suggest that nucleotide sequence evolution in Drosophila differs from that of many vertebrates and does not reflect distinct mutational biases, as a function of base composition, in different genomic regions. Significant negative correlations between codon-usage bias and rates of synonymous site divergence, however, provide strong support for an argument that selection among alternative codons may be a major contributor to variability in evolutionary rates within Drosophila genomes.
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Meyer, Matthias, Kristin Morgenstern, Dávid Heilig, Bálint Heil, Gábor Kovács, Christoph Leibing, and Doris Krabel. "Biomass Allocation and Root Characteristics of Early-Stage Poplars (Populus spp.) for Assessing Their Water-Deficit Response During SRC Establishment." BioEnergy Research 14, no. 2 (April 17, 2021): 385–98. http://dx.doi.org/10.1007/s12155-021-10264-6.
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AbstractEarly above- and belowground biomass fractionation, root diameter composition and allocation of cumulated fine root length per total leaf area of Populus clones have been measured for a pre-assessment of the risk for plantation establishment during spring drought conditions. Four clones of Populus × euramericana, and one P. nigra × P. maximowiczii clone (cv. Max 3), were planted in sandy mix substrate and were exposed to one normal and one deficit watering regime over 65-day greenhouse experiments conducted during early summer. The P. × euramericana hybrids showed plasticity of their root biomass fractions. Although clone Max 3 was among the productive clones, even under deficit watering, it was not able to respond plastically to deficit watering. It showed no increase in the root biomass fraction and no increase in the ratio of cumulated fine root length per total leaf area. Therefore, the clone Max 3 should not be planted under high risk for spring drought. Planting the investigated P. × euramericana clones under water deficit likely involves a lower risk, but clone differences within this group must be considered. It can be concluded that the water deficit response of biomass allocation to roots and of the ratio of fine root length per unit leaf area is suitable traits to improve drought risk assessments that are based on yield response of poplar clones to drought. Percent plant loss data and the yield at the end of the first SRC rotation will be suitable to verify the present greenhouse assessment.
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Liu, Hongxing, Ping Zhu, Chunrong Tong, Yanli Zhao, Peng Cai, Juan Zhu, Fang Wang, et al. "Clonal Evolution of BCR-ABL1 Kinase Domain Mutation In Tyrosine Kinase Inhibitor Treatment Patient." Blood 116, no. 21 (November 19, 2010): 597. http://dx.doi.org/10.1182/blood.v116.21.597.597.
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Abstract Abstract 597 Resistance against tyrosine kinase inhibitors (TKI) has been an important issue in treatment for chronic myeloid leukemia (CML) and Ph-positive acute lymphoblastic leukemia (ALL), and it mainly result from BCR-ABL1 kinase domain mutation. Many studies have focused on the issue, however, characteristics of origin and evolution of BCR-ABL1 mutant clones remains unclear. In this study, we analyzed BCR-ABL1 mutations within the kinase domain for 189 bone marrow or peripheral blood samples, which were collected from 151 cases of CML or Ph-positive ALL. All samples were taken prior to and in the process of TKI treatment, followed by nested PCR and sequencing. Partial of the samples were cloned and sequenced to determine the composition and proportion of mutant clones. Quantification of BCR-ABL1 fusion gene expression was performed according to Europe Against Cancer Program protocol. We reported here that (i) Totally 43 patients harbored 27 BCR-ABL1 mutations, consisting of 24 point mutations, two frameshift mutations (1086_1087delAG/D363fsX380 and 1330delG/D444fsX452) and one in-frame insertion mutation (1073-1074insAAA/357-358insK); (ii) Both deletion mutations only occurred transiently with very low level of BCR-ABL1 expression (0.020% and 0.013% respectively), whereas the insertion mutation was detected in a nearly 100% of mutant clone with completely resistant against the Imatinib; (iii) One G250E and one L370Q mutant clones were detected in 4.1% (2/49) of the patients with BCR-ABL1 expression at low level (0.55% and 0.16% respectively) prior to TKI therapy. Following TKI treatment, resistant mutations were detected in 75.4% (43/57) of patients who presented drug resistance clinically; (iv) Coexistence of multiple mutations in a single clone or temporal evolution of different mutation clones were found in 6 patients, 4 of whom underwent reduction of drug dosage. One clone carrying E355G and T315I mutations simultaneously was detected in patient No.1, and proportion of the double mutant clone increased following incidence of TKI resistance. Two different clones carrying G250E and M351T respectively were detected in Patient No.2. The proportion of M351T clone with less resistance decreased, and the proportion of G250E clone with moderate resistance went up during Imatinib therapy. A similar phenomenon was seen in Patient No.6 carrying the mutation of Q252H and T315I. Two different clones carrying E275D and D444fsX452 respectively were detected at low proportion (11.3% and 15.1% respectively) and low BCR-ABL1 expression 0.013% in Patient No.3, and surprisingly, the two clones disappeared and a T315I clone emerged and became dominant a month after with CML progressed toward the blast crisis; (v) Three different TKI-resistant clones, Y253H, F359V and F486S, were simultaneously detected with a high BCR-ABL1 expression (142%) in a Ph positive ALL (Patient No.4), who is in follow-up presently; (vi)Two different clones carrying G250E and T315I respectively were detected in Patient No.5. The proportion of G250E clone with moderate resistance decreased, whereas frequency of the T315I clone with highly resistance increased following Imatinib and Dasatinib administration. This patient received allo-geneic bone marrow transplantation (BMT) due to TKI resistance, and thereafter the D363fsX380 mutation without kinase activity was transiently detected with very low level of BCR-ABL1 expression, and Dasatinib sensitivity was restored; (vii) Clone and sequencing also find that mutant clones were randomly occurred with low percentage even in pre TKI treatment samples and K562 cell line. These mutations could be common or uncommon resistant mutations, and also can be synonymous mutations or even loss of kinase activity mutations. Taken together, our data indicate that (i) Origin of mutant clones may be random in samples with and without TKI treatment; (ii) The mutation clones always have lower kinase activity than wild type clone, thus it can not evolution into the major clone in the absence of TKI; (iii) The TKI-resistant clone may acquire proliferating advantage, and evolve into the dominant clone under the pressure of TKI; and (iv) We further propose that temporary interruption of TKI and switching to non-selective therapy can be a valid therapeutic option for anti-resistant strategy. Disclosures: No relevant conflicts of interest to declare.
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Barroso, Gabriela Madureira, Alisson José Eufrásio De Carvalho, Isabela Goulart Custódio, Juliano Miari Correa, Tayna Sousa Duque, Daniel Valadão Silva, Bruno Caio Chaves Fernandes, Lucrécia Pacheco Batista, and José Barbosa Dos Santos. "Sensitivity of Eucalyptus Clones to Herbicides Associated with Foliar Fertilizers." Forests 13, no. 9 (September 15, 2022): 1490. http://dx.doi.org/10.3390/f13091490.
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Postemergence application of herbicides can cause phytotoxicity problems in eucalyptus seedlings. Foliar fertilization can improve seedling development and mitigate the effects of herbicides on eucalyptus. Thus, the objective of this work was to evaluate the sensitivity of eucalyptus clones subjected to herbicides applied postemergence and associated with the application of foliar fertilizer. For this, a field experiment was carried out with the application of the products indaziflam, clomazone, glyphosate + S-metolachlor, sulfentrazone, and diuron + sulfentrazone, plus the application of an additional foliar fertilizer (composition in g/L of 78, 13, 40.3, 1.17, 0.78, 16.9, 13, 14.3, 0.52, and 29.9, respectively, for C, N, S, B, Co, Fe, Cu, Mn, Mo, and Zn). Height, stem diameter, shoot dry mass, chlorophyll content, and visual intoxication were the analyzed variables. The herbicides indaziflam and glyphosate + S-metolachlor were the most harmful to the tested eucalyptus clones, interfering with the growth variables. Among the evaluated clones, Clone AEC 144 had more significant changes in the analyzed variables in treatments with herbicides and foliar fertilizer application. The eucalyptus seedlings were generally more sensitive to indaziflam and glyphosate + S-metolachlor herbicides. Foliar fertilization reduced the intoxication caused by indaziflam in Clone AEC 056. The fertilizer intensified treatment symptoms with clomazone and diuron + sulfentrazone in Clone AEC 144 and with sulfentrazone and diuron + sulfentrazone in Clone AEC 2034.
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Fotirić Akšić, Gašić, Dabić Zagorac, Sredojević, Tosti, Natić, and Meland. "Chemical Fingerprint of ‘Oblačinska’ Sour Cherry (Prunus cerasus L.) Pollen." Biomolecules 9, no. 9 (August 21, 2019): 391. http://dx.doi.org/10.3390/biom9090391.
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The aim of this research was to analyze sugars and phenolics of pollen obtained from 15 different ‘Oblačinska’ sour cherry clones and to assess the chemical fingerprint of this cultivar. Carbohydrate analysis was done using high-performance anion-exchange chromatography (HPAEC) with pulsed amperometric detection (PAD), while polyphenols were analyzed by ultra-high-performance liquid chromatography–diode array detector–tandem mass spectrometry (UHPLC-DAD MS/MS) system. Glucose was the most abundant sugar, followed by fructose and sucrose. Some samples had high level of stress sugars, especially trehalose. Rutin was predominantly polyphenol in a quantity up to 181.12 mg/kg (clone III/9), with chlorogenic acid (up to 59.93 mg/kg in clone III/9) and p-coumaric acid (up to 53.99 mg/kg in clone VIII/1) coming after. According to the principal component analysis (PCA), fructose, maltose, maltotriose, sorbitol, and trehalose were the most important sugars in separating pollen samples. PCA showed splitting off clones VIII/1, IV/8, III/9, and V/P according to the quantity of phenolics and dissimilar profiles. Large differences in chemical composition of studied ‘Oblačinska sour cherry’ clone pollen were shown, proving that it is not a cultivar, but population. Finally, due to the highest level of phenolics, clones IV/8, XV/3, and VIII/1 could be singled out as a promising one for producing functional food and/or in medicinal treatments.
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Sang, Yaru, Xiangyang Kang, and Pingdong Zhang. "Effect of Initial Planting Density on the Moisture Content and Chemical Composition of the Triploid Chinese White Poplar (Populus× tomentosa Carrière) Plantation." Forests 13, no. 9 (September 15, 2022): 1494. http://dx.doi.org/10.3390/f13091494.
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The triploid Chinese white poplar (Populus × tomentosa Carrière) features desirable growth traits and wood properties, making it the preferred species in the pulp and paper industries and the sawn timber industry. In this study, we characterized the effects of initial planting densities on the moisture content (MC) and four chemical components (benzene-alcohol (BA), holocellulose (HC), alpha-cellulose (AC), and klason lignin (KL)) of the triploid Chinese white poplar. In this study, 11-year-old Chinese white poplars with three triploid clones (S86, B331, and B301) and one diploid clone (1316) that were planted using seven levels of planting densities (2490, 1665, 1110, 832, 624, 499 and 416 trees/hm2) were examined in the Huabei Great Plain in China. The MC was observed to initially decrease and then subsequently increase with decreasing planting density, and exhibited significant differences under different initial planting densities (0.001 < p < 0.01). In terms of the chemical composition, the BA content of the triploid hybrid clones presented with much higher phenotypic variation (CVp = 17.11%–32.45%) at each planting density compared to either the MC (CVp = 3.73%–11.21%) or the other three chemical composition variations (CVp = 1.16%–11.46%). Substantial differences were observed in the chemical composition of the triploid hybrid clones (p < 0.05), while no differences were found in the chemical composition within the initial planting density categories. The correlation between the chemical composition of wood (BA, HC, AC, and KL) and growth traits was generally weak. These results demonstrate that compared with the MC, the chemical composition of the triploid Chinese white poplar was primarily controlled by its own genetic background and was almost unaffected by the initial planting density. Thus, it is important to select a suitable clone and initial planting density to ensure the full growth of these trees and to improve the quality of pulping in the construction of pulp timber forests.
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Salka, Ivette, Vladimíra Moulisová, Michal Koblížek, Günter Jost, Klaus Jürgens, and Matthias Labrenz. "Abundance, Depth Distribution, and Composition of Aerobic Bacteriochlorophyll a-Producing Bacteria in Four Basins of the Central Baltic Sea." Applied and Environmental Microbiology 74, no. 14 (May 23, 2008): 4398–404. http://dx.doi.org/10.1128/aem.02447-07.
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ABSTRACT The abundance, vertical distribution, and diversity of aerobic anoxygenic phototrophic bacteria (AAP) were studied at four basins of the Baltic Sea. AAP were enumerated by infrared epifluorescence microscopy, and their diversity was analyzed by using pufM gene clone libraries. In addition, numbers of CFU containing the pufM gene were determined, and representative strains were isolated. Both approaches indicated that AAP reached maximal abundance in the euphotic zone. Maximal AAP abundance was 2.5 × 105 cells ml−1 (11% of total prokaryotes) or 1.0 × 103 CFU ml−1 (9 to 10% of total CFU). Environmental pufM clone sequences were grouped into 11 operational taxonomic units phylogenetically related to cultivated members of the Alpha-, Beta-, and Gammaproteobacteria. In spite of varying pufM compositions, five clones were present in all libraries. Of these, Jannaschia-related clones were always found in relative abundances representing 25 to 30% of the total AAP clones. The abundances of the other clones varied. Clones potentially affiliated with typical freshwater Betaproteobacteria sequences were present at three Baltic Sea stations, whereas clones grouping with Loktanella represented 40% of the total cell numbers in the Gotland Basin. For three alphaproteobacterial clones, probable pufM phylogenetic relationships were supported by 16S rRNA gene analyses of Baltic AAP isolates, which showed nearly identical pufM sequences. Our data indicate that the studied AAP assemblages represented a mixture of marine and freshwater taxa, thus characterizing the Baltic Sea as a “melting pot” of abundant, polyphyletic aerobic photoheterotrophic bacteria.
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Schellenberg, John, Matthew G. Links, Janet E. Hill, Tim J. Dumonceaux, Geoffrey A. Peters, Shaun Tyler, T. Blake Ball, Alberto Severini, and Francis A. Plummer. "Pyrosequencing of the Chaperonin-60 Universal Target as a Tool for Determining Microbial Community Composition." Applied and Environmental Microbiology 75, no. 9 (March 6, 2009): 2889–98. http://dx.doi.org/10.1128/aem.01640-08.
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ABSTRACT We compared dideoxy sequencing of cloned chaperonin-60 universal target (cpn60 UT) amplicons to pyrosequencing of amplicons derived from vaginal microbial communities. In samples pooled from a number of individuals, the pyrosequencing method produced a data set that included virtually all of the sequences that were found within the clone library and revealed an additional level of taxonomic richness. However, the relative abundances of the sequences were different in the two datasets. These observations were expanded and confirmed by the analysis of paired clone library and pyrosequencing datasets from vaginal swabs taken from four individuals. Both for individuals with a normal vaginal microbiota and for those with bacterial vaginosis, the pyrosequencing method revealed a large number of low-abundance taxa that were missed by the clone library approach. In addition, we showed that the pyrosequencing method generates a reproducible profile of microbial community structure in replicate amplifications from the same community. We also compared the taxonomic composition of a vaginal microbial community determined by pyrosequencing of 16S rRNA amplicons to that obtained using cpn60 universal primers. We found that the profiles generated by the two molecular targets were highly similar, with slight differences in the proportional representation of the taxa detected. However, the number of operational taxonomic units was significantly higher in the cpn60 data set, suggesting that the protein-encoding gene provides improved species resolution over the 16S rRNA target. These observations demonstrate that pyrosequencing of cpn60 UT amplicons provides a robust, reliable method for deep sequencing of microbial communities.
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Prat, Loreto, Claudia Botti, and David Palzkill. "Rooting of jojoba cuttings: the effect of clone, substrate composition and temperature." Industrial Crops and Products 9, no. 1 (November 1998): 47–52. http://dx.doi.org/10.1016/s0926-6690(98)00013-2.
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Dedysh, Svetlana N., Timofei A. Pankratov, Svetlana E. Belova, Irina S. Kulichevskaya, and Werner Liesack. "Phylogenetic Analysis and In Situ Identification of Bacteria Community Composition in an Acidic Sphagnum Peat Bog." Applied and Environmental Microbiology 72, no. 3 (March 2006): 2110–17. http://dx.doi.org/10.1128/aem.72.3.2110-2117.2006.
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ABSTRACT The Bacteria community composition in an acidic Sphagnum peat bog (pH 3.9 to 4.5) was characterized by a combination of 16S rRNA gene clone library analysis, rRNA-targeted fluorescence in situ hybridization (FISH), and cultivation. Among 84 environmental 16S rRNA gene clones, a set of only 16 cloned sequences was closely related (≥95% similarity) to taxonomically described organisms. Main groups of clones were affiliated with the Acidobacteria (24 clones), Alphaproteobacteria (20), Verrucomicrobia (13), Actinobacteria (8), Deltaproteobacteria (4), Chloroflexi (3), and Planctomycetes (3). The proportion of cells that hybridized with oligonucleotide probes specific for members of the domains Bacteria (EUB338-mix) and Archaea (ARCH915 and ARC344) accounted for only 12 to 22% of the total cell counts. Up to 24% of the EUB338-positive cells could be assigned by FISH to specific bacterial phyla. Alphaproteobacteria and Planctomycetes were the most numerous bacterial groups (up to 1.3 × 107 and 1.1 × 107 cells g−1 peat, respectively). In contrast to conventional plating techniques, a novel biofilm-mediated enrichment approach allowed us to isolate some representatives of predominant Bacteria groups, such as Acidobacteria and Planctomycetes. This novel strategy has great potential to enable the isolation of a significant proportion of the peat bog bacterial diversity.
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Ewart, AJW, R. Gawel, SP Thistlewood, and MG McCarthy. "Evaluation of must composition and wine quality of six clones of Vitis vinifera cv. Sauvignon Blanc." Australian Journal of Experimental Agriculture 33, no. 7 (1993): 945. http://dx.doi.org/10.1071/ea9930945.
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The evaluation of 6 clonal selections of Sauvignon blanc grapes grown at McLaren Vale in South Australia identified 2 significantly (P<0.05) higher yielding clones, F4V6 and F14V9. F4V6 and F14V9 had significantly lower total soluble solids TTS) in the years where all clones were harvested together. In 1 year, F4V6 and F14V9 were harvested 9 days later than the remaining clones. Their TSS values were not significantly different, The titratable acidities of F4V6 and F14V9 were lower due to lower tartrate and malate levels. The pH of F4V6 was higher than that of any other clone at a similar maturity level. (Clones F4V6 and F14V9 had greater yields per vine in all 3 years.
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Maleckar, J. R., and L. A. Sherman. "The composition of the T cell receptor repertoire in nude mice." Journal of Immunology 138, no. 11 (June 1, 1987): 3873–76. http://dx.doi.org/10.4049/jimmunol.138.11.3873.
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Abstract Previous results from several laboratories have demonstrated the presence of functional T lymphocytes in congenitally athymic (nude) mice. The present study represents an analysis of the T cell receptor repertoire exhibited by such cells. Clones of H-2Kb-specific cytotoxic T lymphocytes (CTL) were generated under primary limiting dilution conditions by using spleen cells from nude mice. These clones were analyzed on a panel of Kb mutant target cells to assess the receptor specificity of each clone. Unlike thymic bearing mice the CTL repertoires of which are exceedingly diverse, it was found that in most cases the vast majority of clones from each individual exhibited the same reactivity pattern. The particular pattern varied from individual to individual. Clones from three animals that exhibited this phenomenon were additionally analyzed by using a monoclonal antibody that can detect the utilization of the gene products of the V beta 8 family. In one animal all clones were V beta 8 positive, whereas in the others, all clones were negative. We conclude that the T cell receptor repertoire in nude mice is extremely limited and represents in vivo expansion of a relatively small number of functional precursors.
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Öztürk, Z. Emel. "Consistency of scoring rules: a reinvestigation of composition-consistency." International Journal of Game Theory 49, no. 3 (January 31, 2020): 801–31. http://dx.doi.org/10.1007/s00182-020-00711-7.
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Abstract We consider a collective choice problem in which the number of alternatives and the number of voters vary. Two fundamental axioms of consistency in such a setting, reinforcement and composition-consistency, are incompatible. We first observe that the latter implies four conditions each of which can be formulated as a consistency axiom on its own right. We find that two of these conditions are compatible with reinforcement. In fact, one of these, called composition-consistency with respect to non-clone winners, turns out to characterize a class of scoring rules which contains the Plurality rule. When combined with a requirement of monotonicity, composition-consistency with respect to non-clone winners uniquely characterizes the Plurality rule. A second implication of composition-consistency leads to a class of scoring rules that always select a Plurality winner when combined with monotonicity.
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Zhang, Minglu, Sunny Jiang, Dian Tanuwidjaja, Nikolay Voutchkov, Eric M. V. Hoek, and Baoli Cai. "Composition and Variability of Biofouling Organisms in Seawater Reverse Osmosis Desalination Plants." Applied and Environmental Microbiology 77, no. 13 (May 6, 2011): 4390–98. http://dx.doi.org/10.1128/aem.00122-11.
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ABSTRACTSeawater reverse osmosis (SWRO) membrane biofouling remains a common challenge in the desalination industry, but the marine bacterial community that causes membrane fouling is poorly understood. Microbial communities at different stages of treatment processes (intake, cartridge filtration, and SWRO) of a desalination pilot plant were examined by both culture-based and culture-independent approaches. Bacterial isolates were identified to match the generaShewanella,Alteromonas,Vibrio, andCellulophagabased on 16S rRNA gene sequencing analysis. The 16S rRNA gene clone library of the SWRO membrane biofilm showed that a filamentous bacterium,Leucothrix mucor, which belongs to the gammaproteobacteria, accounted for nearly 30% of the clone library, while the rest of the microorganisms (61.2% of the total clones) were related to the alphaproteobacteria. 16S rRNA gene terminal restriction fragment length polymorphism (T-RFLP) analysis indicated that bacteria colonizing the SWRO membrane represented a subportion of microbes in the source seawater; however, they were quite different from those colonizing the cartridge filter. The examination of five SWRO membranes from desalination plants located in different parts of the world showed that although the bacterial communities from the membranes were not identical to each other, some dominant bacteria were commonly observed. In contrast, bacterial communities in source seawater were significantly different based on location and season. Microbial profiles from 14 cartridge filters collected from different plants also revealed spatial trends.
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Yulfa, Denny, Reni Mayerni, and Yusniwati Yusniwati. "Kualitas Kimia Serat beberapa Klon Rami Asal Sumatera Barat." Agrotechnology Research Journal 3, no. 2 (December 30, 2019): 115. http://dx.doi.org/10.20961/agrotechresj.v3i2.34761.
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<p>Flax/jute is natural fiber plants that that produce fiber from the bark. Ramie fiber has a better quality than the others natural fiber, so it can meet fiber the increase needs cultivar with the best chemical composition of fiber. The aim of this study was to detect the chemical composition of fiber in several clones of ramie from West Sumatera. The study was conducted on December 2018 at the Laboratory of Technology Agriculture Product Andalas University for analyzed the content of chemical composition (water, ash, holocellulose, cellulose, hemicellulose, and lignin). The result of this study showed that the highest level of water content, ash, hemicellulose, and lignin were found in Situjuah clones those are 40.43, 6.74, 14.39, and 9.98% respectively. Whereas for the highest level of holocellulose and cellulose contents were in Ramindo 1 clone those were 70.23 and 58.46% respectively.</p>
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Kondratovičs, Toms, Mārtiņš Zeps, Diāna Rupeika, Pauls Zeltiņš, Arnis Gailis, and Roberts Matisons. "Morphological and Physiological Responses of Hybrid Aspen (Populus tremuloides Michx. × Populus tremula L.) Clones to Light In Vitro." Plants 11, no. 20 (October 12, 2022): 2692. http://dx.doi.org/10.3390/plants11202692.
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Micropropagation of fast-growing tree genotypes such as the hybrid aspen (Populus tremuloides Michx. × Populus tremula L.) is increasing. The efficiency of micropropagation depends on the luminaires, hence luminescent electric diodes (LED), which emit light of a narrow spectrum, are gaining popularity. Mostly, different LEDs are combined to increase the photosynthetic efficiency. However, light also acts as an environmental signal, which triggers specific responses in plants, which are genotype specific, and regarding hybrid aspen, are likely affected by heterosis. In this study, morphological and physiological responses of clones of hybrid aspen with contrasting field performance to the spectral composition of illumination were studied in vitro. Among the 15 variables measured, area of leaves and concentration and ratio of chlorophyll a and b explained most of the variance (58.6%), thereby linking a specific combination of traits to productivity. These traits and their responses to light were affected by heterosis, as indicated by the clone-treatment interaction, particularly for the clone’s moderate productivity. The top-performing clones were little sensitive to illumination due to efficient photosystems. Nevertheless, illumination with wider spectral composition had generally positive effects on plantlet performance. Accordingly, clone-specific illumination protocols and luminaries capable of it are advantageous for the efficiency of micropropagation of hybrid aspen.
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Damavandi, Ojan Khatib, and David K. Lubensky. "Statistics of noisy growth with mechanical feedback in elastic tissues." Proceedings of the National Academy of Sciences 116, no. 12 (February 28, 2019): 5350–55. http://dx.doi.org/10.1073/pnas.1816100116.
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Tissue growth is a fundamental aspect of development and is intrinsically noisy. Stochasticity has important implications for morphogenesis, precise control of organ size, and regulation of tissue composition and heterogeneity. However, the basic statistical properties of growing tissues, particularly when growth induces mechanical stresses that can in turn affect growth rates, have received little attention. Here, we study the noisy growth of elastic sheets subject to mechanical feedback. Considering both isotropic and anisotropic growth, we find that the density–density correlation function shows power law scaling. We also consider the dynamics of marked, neutral clones of cells. We find that the areas (but not the shapes) of two clones are always statistically independent, even when they are adjacent. For anisotropic growth, we show that clone size variance scales like the average area squared and that the mode amplitudes characterizing clone shape show a slow1/ndecay, where n is the mode index. This is in stark contrast to the isotropic case, where relative variations in clone size and shape vanish at long times. The high variability in clone statistics observed in anisotropic growth is due to the presence of two soft modes—growth modes that generate no stress. Our results lay the groundwork for more in-depth explorations of the properties of noisy tissue growth in specific biological contexts.
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Gelsomino, Roberto, Marc Vancanneyt, Timothy M. Cogan, and Jean Swings. "Effect of Raw-Milk Cheese Consumption on the Enterococcal Flora of Human Feces." Applied and Environmental Microbiology 69, no. 1 (January 2003): 312–19. http://dx.doi.org/10.1128/aem.69.1.312-319.2003.
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ABSTRACT Enterococci are one of the major facultative anaerobic bacterial groups that reside in the human gastrointestinal tract. In the present study, the composition of the enterococcal fecal flora in three healthy humans was analyzed before, during, and after the daily consumption of ∼125 g of a raw-milk Cheddar-type cheese containing 3.2 × 104 enterococci/g of cheese. Enterococcal counts ranged between 1.4 × 102 and 2.5 × 108 CFU/g of feces and differed from subject to subject and from week to week. The cheese contained mainly Enterococcus casseliflavus and a small population of Enterococcus faecalis. Clonal relationships were determined by pulsed-field gel electrophoresis. Before and after consumption of the cheese, samples from humans contained mainly Enterococcus faecium, with some of the clones being resident. During consumption of the cheese, one particular transient clone of E. faecalis, clone Fs2, which was present in small numbers in the cheese, largely dominated the feces. Two clones of E. casseliflavus from the cheese were also found in the feces of one of the subjects during cheese consumption. These results suggest that a clone need not be present in a food in high numbers to establish itself in the intestine.