Mosaic Composition Research Articles

Partial trisomy 8 mosaicism not detected by cultured amniotic-fluid cells

ObjectivePrenatal detection of trisomy 8 mosaicism can be misleading and remains challenging in genetic counseling. Identifying cases of partial or complete trisomy 8 mosaicism will highlight the pitfalls of conventional karyotyping in prenatal amniocentesis for partial or complete trisomy 8 mosaicism. Case reportThe patient was born uneventfully at term to a healthy 34-year-old mother. Analysis of the amniotic fluid (AF) cells showed a normal male karyotype. At birth, the newborn presented dysmorphic features, including asymmetric mandibles and ears, anteverted nostrils with a relatively long philtrum, retrognathia, and a clenched hand on the left side. Imaging studies revealed agenesis of the corpus callosum with bilateral colpocephaly, a common arterial trunk bifurcating into the left subclavian and carotid arteries, and bilateral pelviectasis. Cytogenetic analysis of the blood revealed mosaicism of partial trisomy 8: 47,XY,+del(8) (q21.3) [8]/46,XY [12]. Array comparative genomic hybridization (array-CGH) revealed 82.9 Mb duplications at chromosome 8p23.3-8q21.3 with dosage variations. Interphase fluorescence in situ hybridization analysis of urine sediments and buccal smears were compatible with mosaic compositions. A small colony of AF cells was found to have partial trisomy 8 in repeated analysis. ConclusionConventional karyotyping through amniocentesis has limitations particularly in detecting rare trisomy mosaicism if trisomic cells show growth disadvantage. Array-CGH using uncultured cells may be of help in providing more information on genetic dosage variations in such cases.

Untangling the hybrid nature of modern pig genomes: a mosaic derived from biogeographically distinct and highly divergent Sus scrofa populations.

The merging of populations after an extended period of isolation and divergence is a common phenomenon, in natural settings as well as due to human interference. Individuals with such hybrid origins contain genomes that essentially form a mosaic of different histories and demographies. Pigs are an excellent model species to study hybridization because European and Asian wild boars diverged ~1.2 Mya, and pigs were domesticated independently in Europe and Asia. During the Industrial Revolution in England, pigs were imported from China to improve the local pigs. This study utilizes the latest genomics tools to identify the origin of haplotypes in European domesticated pigs that are descendant from Asian and European populations. Our results reveal fine-scale haplotype structure representing different ancient demographic events, as well as a mosaic composition of those distinct histories due to recently introgressed haplotypes in the pig genome. As a consequence, nucleotide diversity in the genome of European domesticated pigs is higher when at least one haplotype of Asian origin is present, and haplotype length correlates negatively with recombination frequency and nucleotide diversity. Another consequence is that the inference of past effective population size is influenced by the background of the haplotypes in an individual, but we demonstrate that by careful sorting based on the origin of haplotypes, both distinct demographic histories can be reconstructed. Future detailed mapping of the genomic distribution of variation will enable a targeted approach to increase genetic diversity of captive and wild populations, thus facilitating conservation efforts in the near future.

Cryopreservation of glucose-6-phosphate dehydrogenase activity inside red blood cells: developing a specimen repository in support of development and evaluation of glucose-6-phosphate dehydrogenase deficiency tests

BackgroundGlucose-6-phosphate dehydrogenase (G6PD) deficiency is a common human enzyme deficiency. It is characterized by abnormally low levels of G6PD activity. Individuals with G6PD deficiency are at risk of undergoing acute haemolysis when exposed to 8‒aminoquinoline-based drugs, such as primaquine. For this reason it is imperative to identify individuals with G6PD deficiency prior to administering these anti-malarial drugs. There is a need for the development and evaluation of point-of-care G6PD deficiency screening tests suitable for areas of the developing world where malarial treatments are frequently administered. The development and evaluation of new G6PD tests will be greatly assisted with the availability of specimen repositories.MethodsCryopreservation of erythrocytes was evaluated as a means to preserve G6PD activity. Blood specimens from 31 patients including ten specimens with normal G6PD activity, three with intermediate activity, and 18 with deficient activity were cryopreserved for up to six months.ResultsGood correlation in G6PD activity between fresh and cryopreserved specimens (R2 = 0.95). The cryopreserved specimens show an overall small drop in mean G6PD activity of 0.23 U/g Hb (P=0.23). Cytochemical staining showed that intracellular G6PD activity distribution within the red blood cell populations is preserved during cryopreservation. Furthermore, the mosaic composition of red blood cells in heterozygous women is also preserved for six months or more. The fluorescent spot and the BinaxNOW qualitative tests for G6PD deficiency also showed high concordance in G6PD status determination between cryopreserved specimens and fresh specimens.ConclusionsA methodology for establishing a specimen panel for evaluation of G6PD tests is described. The approach is similar to that used in several malaria research facilities for the cryopreservation of parasites in clinical specimens and axenic cultures. Specimens stored in this manner will aid both the development and evaluation of current and emerging G6PD tests. The availability of G6PD tests is a critical bottleneck to broader access to drugs that confer radical cure of Plasmodium vivax, a requirement for elimination of malaria.

Alien invasive neophytes of the Southeastern part of the Pannonian Plain

Abstract Floristic diversity in the Pannonian Plain is the result of mosaic habitat composition, characterized by steppes, saline meadows, and lowland forests along major rivers. In the last few centuries, the flora has become enriched by species introduced by human activities, such as colonization and industrialization. Presently it consists of nearly 1800 species. As a result of 30 years of field research as well as herbarium and literature searches, a list of invasive alien neophytes has been compiled and is presented here. The list includes 152 species, classified as either naturalized, casual, or unknown. One of the species is listed in Red Book of Serbian Flora. Eighty species are naturalized, and 61 are casual species. The majority of the introduced flora originates from North America (66) and the Old World (43). Most alien invasive species of the Southeastern part of the Pannonian Plain, were introduced accidentally by seed material or deliberately by nursery saplings. The annual and perennial herbaceous plants, which flower in the summer and summer-autumn periods, are represented in the greatest numbers. The alien flora was further analyzed with respect to taxonomy, life forms, pollination, and seed dispersal mode. The greatest number of alien species appears in anthropogenic and semi-natural habitats (59). In natural habitats, 45 invasive taxa were recorded, representing a conservation threat to biodiversity.

Defining vegetation age class distributions for multispecies conservation in fire-prone landscapes

The generation of heterogeneous fire mosaics is commonly advocated as a strategy for biodiversity conservation in flammable ecosystems, but it is usually unclear how mosaic properties link to biodiversity outcomes. Here we define a formal relationship between these elements and outline a method for determining the composition of fire mosaics defined by vegetation age classes that maximise species diversity. The method involves 1. quantifying species abundance in each of several previously defined vegetation age classes, and 2. using optimisation to determine the age class distribution that maximises species diversity. We applied the method to 135 species from four taxa in a southeastern Australian heathy woodland. In addition, we quantified the degree to which each taxa could act as a surrogate for others, and assessed how our chosen diversity metric changed with departures from the optimal distribution. Optimal age class distributions differed among taxa, and surrogacy relationships between most groups were poor. Departure from the optimal distribution resulted in an estimated decline in species diversity, a measure that may be used to quantify the biodiversity cost of alternative management strategies. Our measure of departure, relative entropy, was a strong predictor of diversity decline for some taxa but not for others. In cases where predictive capacity was strong, the rate of decline differed among groups. In flammable ecosystems our method can help determine fire management strategies empirically linked to a landscape-scale conservation objective.

Influence of Land Mosaic Composition and Structure on Patchy Populations: The Case of the Water Vole (Arvicola sapidus) in Mediterranean Farmland

The ability of patchy populations to persist in human-dominated landscapes is often assessed using focal patch approaches, in which the local occurrence or abundance of a species is related to the properties of individual patches and the surrounding landscape context. However, useful additional insights could probably be gained through broader, mosaic-level approaches, whereby whole land mosaics with contrasting patch-network and matrix characteristics are the units of investigation. In this study we addressed this issue, analysing how the southern water vole (Arvicola sapidus) responds to variables describing patch-network and matrix properties within replicated Mediterranean farmland mosaics, across a gradient of agricultural intensification. Patch-network characteristics had a dominant effect, with the total amount of habitat positively influencing both the occurrence of water voles and the proportion of area occupied in land mosaics. The proportions of patches and area occupied by the species were positively influenced by mean patch size, and negatively so by patch isolation. Matrix effects were weak, although there was a tendency for a higher proportion of occupied patches in more intensive, irrigated agricultural landscapes, particularly during the dry season. In terms of conservation, results suggest that water voles may be able to cope well with, or even be favoured by, the on-going expansion of irrigated agriculture in Mediterranean dry-lands, provided that a number of patches of wet herbaceous vegetation are maintained within the farmland mosaic. Overall, our study suggests that the mosaic-level approach may provide a useful framework to understand the responses of patchy populations to land use change.

Plastid-localized amino acid biosynthetic pathways of Plantae are predominantly composed of non-cyanobacterial enzymes.

Studies of photosynthetic eukaryotes have revealed that the evolution of plastids from cyanobacteria involved the recruitment of non-cyanobacterial proteins. Our phylogenetic survey of >100 Arabidopsis nuclear-encoded plastid enzymes involved in amino acid biosynthesis identified only 21 unambiguous cyanobacterial-derived proteins. Some of the several non-cyanobacterial plastid enzymes have a shared phylogenetic origin in the three Plantae lineages. We hypothesize that during the evolution of plastids some enzymes encoded in the host nuclear genome were mistargeted into the plastid. Then, the activity of those foreign enzymes was sustained by both the plastid metabolites and interactions with the native cyanobacterial enzymes. Some of the novel enzymatic activities were favored by selective compartmentation of additional complementary enzymes. The mosaic phylogenetic composition of the plastid amino acid biosynthetic pathways and the reduced number of plastid-encoded proteins of non-cyanobacterial origin suggest that enzyme recruitment underlies the recompartmentation of metabolic routes during the evolution of plastids.

Mosaic-Level Inference of the Impact of Land Cover Changes in Agricultural Landscapes on Biodiversity: A Case-Study with a Threatened Grassland Bird

Changes in land use/land cover are a major driver of biodiversity change in the Mediterranean region. Understanding how animal populations respond to these landscape changes often requires using landscape mosaics as the unit of investigation, but few previous studies have measured both response and explanatory variables at the land mosaic level. Here, we used a “whole-landscape” approach to assess the influence of regional variation in the land cover composition of 81 farmland mosaics (mean area of 2900 ha) on the population density of a threatened bird, the little bustard (Tetrax tetrax), in southern Portugal. Results showed that ca. 50% of the regional variability in the density of little bustards could be explained by three variables summarising the land cover composition and diversity in the studied mosaics. Little bustard breeding males attained higher population density in land mosaics with a low land cover diversity, with less forests, and dominated by grasslands. Land mosaic composition gradients showed that agricultural intensification was not reflected in a loss of land cover diversity, as in many other regions of Europe. On the contrary, it led to the introduction of new land cover types in homogenous farmland, which increased land cover diversity but reduced overall landscape suitability for the species. Based on these results, the impact of recent land cover changes in Europe on the little bustard populations is evaluated.

An ORFan No More: The Bacteriophage T4 39.2 Gene Product, NwgI, Modulates GroEL Chaperone Function

Bacteriophages are the most abundant biological entities in our biosphere, characterized by their hyperplasticity, mosaic composition, and the many unknown functions (ORFans) encoded by their immense genetic repertoire. These genes are potentially maintained by the bacteriophage to allow efficient propagation on hosts encountered in nature. To test this hypothesis, we devised a selection to identify bacteriophage-encoded gene(s) that modulate the host Escherichia coli GroEL/GroES chaperone machine, which is essential for the folding of certain host and bacteriophage proteins. As a result, we identified the bacteriophage RB69 gene 39.2, of previously unknown function and showed that homologs of 39.2 in bacteriophages T4, RB43, and RB49 similarly modulate GroEL/GroES.Production of wild-type bacteriophage T4 Gp39.2, a 58-amino-acid protein, (a) enables diverse bacteriophages to plaque on the otherwise nonpermissive groES or groEL mutant hosts in an allele-specific manner, (b) suppresses the temperature-sensitive phenotype of both groES and groEL mutants, (c) suppresses the defective UV-induced PolV function (UmuCD) of the groEL44 mutant, and (d) is lethal to the host when overproduced. Finally, as proof of principle that Gp39.2 is essential for bacteriophage growth on certain bacterial hosts, we constructed a T4 39.2 deletion strain and showed that, unlike the isogenic wild-type parent, it is incapable of propagating on certain groEL mutant hosts. We propose a model of how Gp39.2 modulates GroES/GroEL function.

Formation of Hyperspectral Near-Infrared Images from Artworks

ABSTRACTIn this paper, a novel hyperspectral image acquisition system able to obtain a set of narrowband images (~2,25 nm of bandwidth) and the related composition of monochrome images in the near-infrared is described. The aim of this system is to discriminate the materials by their optical spectral response in the range of 900-1700 nm. This system has been developed in the framework of a collaborative project that includes the improvement of the automatic composition of reflectographic mosaics in order to study the underdrawing of large formats big artworks in real-time. The main features of this project are detailed in this paper. Furthermore, a few enlightening results of the hyperspectral system and new lines of research are shown.

Restricted diffusion of OXPHOS complexes in dynamic mitochondria delays their exchange between cristae and engenders a transitory mosaic distribution

Mitochondria are involved in cellular energy supply, signaling and apoptosis. Their ability to fuse and divide provides functional and morphological flexibility and is a key feature in mitochondrial quality maintenance. To study the impact of mitochondrial fusion/fission on the reorganization of inner membrane proteins, oxidative phosphorylation (OXPHOS) complexes in mitochondria of different HeLa cells were tagged with fluorescent proteins (GFP and DsRed-HA), and cells were fused by polyethylene glycol treatment. Redistribution of the tagged OXPHOS complexes was then followed by means of immunoelectron microscopy, two color super-resolution fluorescence microscopy and single molecule tracking. In contrast to outer membrane and matrix proteins, which mix quickly and homogeneously upon mitochondrial fusion, the mixing of inner membrane proteins was decelerated. Our data suggest that the composition of cristae is preserved during fusion of mitochondria and that cristae with mixed OXPHOS complexes are only slowly and successively formed by restricted diffusion of inner membrane proteins into existing cristae. The resulting transitory mosaic composition of the inner mitochondrial membrane illuminates mitochondrial heterogeneity and potentially is linked to local differences in function and membrane potential.

Real-time image composition of bladder mosaics in fluorescence endoscopy

Today, photodynamic diagnostics is commonly used in endoscopic intervention of the urinary bladder. Excited by a narrow band illumination, fluorescence markers enhance the visual contrast between b...

Cellular automata and integrodifferential equation models for cell renewal in mosaic tissues.

Mosaic tissues are composed of two or more genetically distinct cell types. They occur naturally, and are also a useful experimental method for exploring tissue growth and maintenance. By marking the different cell types, one can study the patterns formed by proliferation, renewal and migration. Here, we present mathematical modelling suggesting that small changes in the type of interaction that cells have with their local cellular environment can lead to very different outcomes for the composition of mosaics. In cell renewal, proliferation of each cell type may depend linearly or nonlinearly on the local proportion of cells of that type, and these two possibilities produce very different patterns. We study two variations of a cellular automaton model based on simple rules for renewal. We then propose an integrodifferential equation model, and again consider two different forms of cellular interaction. The results of the continuous and cellular automata models are qualitatively the same, and we observe that changes in local environment interaction affect the dynamics for both. Furthermore, we demonstrate that the models reproduce some of the patterns seen in actual mosaic tissues. In particular, our results suggest that the differing patterns seen in organ parenchymas may be driven purely by the process of cell replacement under different interaction scenarios.

Complex Mosaic Composition of Near Full-Length Genomes of Two NED (NIH-ENVA-DOD) Subtype Panel HIV Type 1 Strains, BCF-Dioum and BCF-Kita, Originating from the Democratic Republic of Congo (DRC)

Sequence characterization of the near full-length genomes of HIV-1 isolates BCF-Dioum and BCF-Kita, originating from the Democratic Republic of Congo (DRC), was continued. These NED panel isolates, contributed by F. Brun-Vezinet (ENVA-France), were first identified as subtypes G and H, respectively. Our earlier analyses of portions of their pol genes showed that both were likely to be intersubtype recombinants of different composition. This study analyzed the remainder of each genome, confirming them to be complex recombinants. The BCF-Dioum genome resembles CRF06_cpx strains found in West Africa, composed of subtypes A/G/J/K. The BCF-Kita genome is a unique complex recombinant A-F-G-H-K-U strain. These data support previous observations of the complexity of strains originating from the DRC. BCF-Dioum may be a suitable strain for standards and reagents since it matches a defined circulating recombinant form. Studies and reagents made from BCF-Kita should take into account its complex genome.

Assessing conservation status on coastal dunes: A multiscale approach

Coastal dune systems are particularly fragile and threatened environments, which, however, provide fundamental ecosystem services to nearby urban areas acting for example as protective buffers against erosion. Correctly assessing their conservation status is a priority in order to manage them adequately and to plan urban development in coastal regions. In this paper we propose a practical multiscale method for the assessment of the conservation status of sandy coastal environment. The proposed method is articulated in two stages, one focusing on the landscape and the other on the plant community level. In the first phase mosaic structure and composition of the coastal landscape are analyzed using a series of indicators: natural coastal surface, richness of land cover typologies, landscape diversity and eveness, number and average size of habitat patches, and mean shape index. At a detailed scale, floristic, vegetational and structural aspects of the dune plant communities are analyzed along the main environmental gradient by measuring: spatial connectivity and richness of boundaries, species diversity, eveness and chorological index. In this work we apply and test the method in an experimental area on the Tyrrhenian coast of Italy (Latium region), comparing the conservation status of two study sites.

Genetic diversity of the Leptospiral immunoglobulin-like (Lig) genes in pathogenic Leptospira spp.

Recent serologic, immunoprotection, and pathogenesis studies identified the Lig proteins as key virulence determinants in interactions of leptospiral pathogens with the mammalian host. We examined the sequence variation and recombination patterns of ligA, ligB, and ligC among 10 pathogenic strains from five Leptospira species. All strains were found to have intact ligB genes and genetic drift accounting for most of the ligB genetic diversity observed. The ligA gene was found exclusively in L. interrogans and L. kirschneri strains, and was created from ligB by a two-step partial gene duplication process. The aminoterminal domain of LigB and the LigA paralog were essentially identical (98.5±0.8% mean identity) in strains with both genes. Like ligB, ligC gene variation also followed phylogenetic patterns, suggesting an early gene duplication event. However, ligC is a pseudogene in several strains, suggesting that LigC is not essential for virulence. Two ligB genes and one ligC gene had mosaic compositions and evidence for recombination events between related Leptospira species was also found for some ligA genes. In conclusion, the results presented here indicate that Lig diversity has important ramifications for the selection of Lig polypeptides for use in diagnosis and as vaccine candidates. This sequence information will aid the identification of highly conserved regions within the Lig proteins and improve upon the performance characteristics of the Lig proteins in diagnostic assays and in subunit vaccine formulations with the potential to confer heterologous protection.

Near Full-Length Genome Characterization of an HIV Type 1 CRF25_cpx Strain from Cameroon

Recombinant forms of HIV-1 contribute significantly to the ongoing epidemic. In the present study, we characterized the near full-length genome of one candidate HIV-1 CRF25_cpx strain originating in Cameroon, 06CM-BA-040. Viral RNA was extracted from plasma, and the genome was obtained using RT-PCR amplification to generate 10 overlapping fragments. Bootscanning, recombination breakpoint analysis, and phylogenetic trees confirmed that 06CM-BA-040 had a genomic structure consistent with two available CRF25_cpx reference sequences. The CRF25_cpx mosaic composition consisted of nine segments derived from subtypes A and G as well as unclassified (U) regions. Subtype G and CRF25_cpx clusters diverged from each other with long branch lengths but were distinct from other known subtypes with high bootstrap support (94%). The epidemiological significance of CRF25_cpx strains is unknown; however, the availability of additional genomic sequences will improve our understanding of the overall genetic diversity within this recombinant form of HIV-1.

The 185/333 Gene Family Is a Rapidly Diversifying Host-Defense Gene Cluster in the Purple Sea Urchin Strongylocentrotus purpuratus

The genome of the purple sea urchin contains numerous large gene families with putative immunological functions. One gene family, known as 185/333, is characterized by extraordinary molecular diversity resulting from single nucleotide polymorphisms and the presence or the absence of 27 large blocks of sequences known as elements. The mosaic composition of elements, known as element patterns, that is present within the members of this gene family is encoded entirely in the second of two exons. Many of the elements correspond to one of six types of repeats that are present throughout the genes. The sequence diversity and variation in element patterns led us to investigate the evolution of the 185/333 gene family. The work presented here suggests that the element patterns are the result of both recombination and duplication and/or deletion of intragenic repeats. Each element is composed of a limited number of similar but distinct sequences, and their distribution among the 185/333 genes suggests frequent recombination within this gene family. Phylogenetic analyses of five 185/333 elements and two regions of the intron were performed using two tests: incongruence length difference and incongruence permutation. Results indicated that each pair of sequence segments was incongruent, suggesting that recombination occurs frequently along the length of the genes, including both the intron and the second exon, and that recombination is not restricted to intact elements. Paradoxically, the high level of similarity among the elements indicated that the 185/333 genes appear to be the result of a recent diversification. These results add to the growing body of evidence suggesting that invertebrate immune systems are not simple and static, but are dynamic and highly complex, and may employ group-specific mechanisms for diversification.

Continuous Crossover(s) Events of HIV-1 CRF01_AE and B Subtype Strains in Malaysia: Evidence of Rapid and Extensive HIV-1 Evolution in the Region

The Asian HIV epidemic appears to be complex, characterized by the prevalence of multiple subtypes and circulating recombinant forms with gradual replacement of pure HIV-1 subtypes in several geographical regions. The main objectives of the present study are to identify and analyse the full-length viral genomes of three unique recombinant forms (URFs); the HIV-1 isolates 07MYKLD47, 07MYKLD48 and 07MYKLD49 from Malaysia. Long-range polymerase chain reaction (PCR) amplification of seven overlapping reading frames was used to derive near full-length HIV-1 genomes. Detailed phylogenetic and bootscanning analyses were performed to determine phylogenetic associations and subtypic assignments. We further confirmed the mosaic composition of these CRF01_AE/B inter-subtype recombinant forms, which are composed of B-subtype fragment(s) in the backbone of CRF01_AE. Both 07MYKLD47 and 07MYKLD48 have an insertion of B subtype (880 bp and 532 bp) in the gag-pol and gp41-env gene regions, respectively. Whereas the isolate 07MYKLD49 has three B-subtype fragments inserted in different gene region along the genome; one each in the gag-pol (1862 bp) and pol-vif (1935 bp) regions, and a short B-subtype insertion (541 bp) in the 5' LTR-gag region. This highlights the public health relevance of newly emerging second generation HIV-1 recombinant forms and their dispersal, along with their rapid and continuous evolution in the region.

Exploring arboreal ant community composition and co‐occurrence patterns in plantations of oil palm Elaeis guineensis in Borneo and Peninsular Malaysia

The oil palm, Elaeis guineensis, is a native of West Africa and is now extensively grown in south‐east Asia. In 2005, the crop covered four million ha of Malaysia. We examined the arboreal ant fauna in two oil palm plantations that had been farmed with integrated pest management practices for at least 10 yr. Having cut and examined palm fronds from 595 and 503 palms in Borneo and Peninsular Malaysia respectively, we studied diversity in ant assemblages, analysed composition of ant mosaics by stepwise use of null‐models, and explored the influence of exotic vs native species on community structure. Altogether we sampled 52 species of canopy ants, of which 23 species were shared between Borneo and Peninsular Malaysia. Seventeen species in Borneo and 24 species in Peninsular Malaysia accounted for 95% of all species occurrences (SOCs). Fortysix percent of all SOCs belonged to 12 tramp ant species with pan‐tropical distributions. Forty percent of all SOCs were exotic ants. Six dominant species were found in Borneo, five in the Peninsula. The three most abundant species, Anoplolepis gracilipes, Oecophylla smaragdina and Technomyrmex albipes were dominant in both sites. Three dominants were invasive species that were found on more palms than the native group. Dominant tramp species coexisted with non‐dominants more often and tolerated more species of non‐dominant ants than native dominants. Null model analyses indicated that species were arranged in mosaics at both the Peninsular Malaysia and Borneo sites. Dominant species showed much less co‐occurrence than expected by chance, pointing towards species segregation (even in presence of introduced, invasive species). Similar results were obtained for all species. Non‐dominant ants were either positively associated with their dominants, or co‐occurred randomly in the presence of dominant species. In contrast, ant assemblages on palms without dominants showed species segregation.