Modulation of macrophage phenotype and protein secretion via heparin-IL-4 functionalized supramolecular elastomers.

Hallmark of the in situ tissue engineering approach is the use of bioresorbable, synthetic, acellular scaffolds, which are designed to modulate the inflammatory response and actively trigger tissue regeneration by the body itself at the site of implantation. Much research is devoted to the design of synthetic materials modulating the polarization of macrophages, which are essential mediators of the early stages of the inflammatory response. Here, we present a novel method for the functionalization of elastomers based on synthetic peptide chemistry, supramolecular self-assembly, and immobilization of heparin and interleukin 4 (IL-4), which is known to skew the polarization of macrophages into the wound healing "M2" phenotype. Ureido-pyrimidinone (UPy)-modified chain extended polycaprolactone (CE-UPy-PCL) was mixed with a UPy-modified heparin binding peptide (UPy-HBP) to allow for immobilization of heparin, and further functionalization with IL-4 via its heparin binding domain. As a first proof of principle, CE-UPy-PCL and UPy-HBP were premixed in solution, dropcast and exposed to primary human monocyte-derived macrophages, in the presence or absence of IL-4-heparin functionalization. It was demonstrated that the supramolecular IL-4-heparin functionalization effectively promoted macrophage polarization into an anti-inflammatory phenotype, in terms of morphology, immunohistochemistry and cytokine secretion. Moreover, the supramolecular functionalization approach used was successfully translated to 3D electrospun scaffolds for in situ tissue engineering purposes, where UPy-HBP retention, and heparin and IL-4 attachment to the supramolecular scaffolds were proven over 7 days. Lastly, human monocyte-derived macrophages were cultured on 3D scaffolds, which, in case of IL-4-heparin functionalization, were proven to promote of an anti-inflammatory environment on protein level. This study presents a novel method in designing a versatile class of functionalized elastomers that effectively harness the anti-inflammatory behavior of macrophages in vitro, and as such, may be instrumental for the development of a new class of synthetic materials for in situ tissue engineering purposes. STATEMENT OF SIGNIFICANCE: Macrophages and their phenotypic and functional plasticity play a pivotal role in metabolic homeostasis and tissue repair. Based on this notion, bioactivated materials modulating macrophage polarization were extensively investigated in the past. Here, we designed immunomodulating, synthetic materials based on supramolecular immobilization of a heparin binding peptide, and further bioactivation with heparin and IL-4, an anti-inflammatory cytokine responsible for M2 activation and polarization. Human monocyte-derived macrophages cultured on heparin-IL-4 bioactivated materials displayed an elongated morphology and an anti-inflammatory phenotype, with downregulation of pro-inflammatory cytokines and promotion of anti-inflammatory cytokines over time. This study represents the first step in designing a novel class of synthetic, bioactivated materials that harness the regenerative behavior of host macrophages towards in situ tissue regeneration.

Hydrolytic and oxidative degradation of electrospun supramolecular biomaterials: In vitro degradation pathways.

The emerging field of in situ tissue engineering (TE) of load bearing tissues places high demands on the implanted scaffolds, as these scaffolds should provide mechanical stability immediately upon implantation. The new class of synthetic supramolecular biomaterial polymers, which contain non-covalent interactions between the polymer chains, thereby forming complex 3D structures by self assembly. Here, we have aimed to map the degradation characteristics of promising (supramolecular) materials, by using a combination of in vitro tests. The selected biomaterials were all polycaprolactones (PCLs), either conventional and unmodified PCL, or PCL with supramolecular hydrogen bonding moieties (either 2-ureido-[1H]-pyrimidin-4-one or bis-urea units) incorporated into the backbone. As these materials are elastomeric, they are suitable candidates for cardiovascular TE applications. Electrospun scaffold strips of these materials were incubated with solutions containing enzymes that catalyze hydrolysis, or solutions containing oxidative species. At several time points, chemical, morphological, and mechanical properties were investigated. It was demonstrated that conventional and supramolecular PCL-based polymers respond differently to enzyme-accelerated hydrolytic or oxidative degradation, depending on the morphological and chemical composition of the material. Conventional PCL is more prone to hydrolytic enzymatic degradation as compared to the investigated supramolecular materials, while, in contrast, the latter materials are more susceptible to oxidative degradation. Given the observed degradation pathways of the examined materials, we are able to tailor degradation characteristics by combining selected PCL backbones with additional supramolecular moieties. The presented combination of in vitro test methods can be employed to screen, limit, and select biomaterials for pre-clinical in vivo studies targeted to different clinical applications.

Designing sustainable sanitation in urban planning proposed for Changzhou, China.

China is undergoing rapid urbanization and economic development. This requires a new approach on spatial planning and environmental infrastructure. In the presented project an example of this approach is given for the city of Changzhou (China) where a new residential area (Qinglong district) will be developed for 100.000 inhabitants. Key issue within the formulation of sustainable sanitation concepts is the integration and management of water, waste and energy in such a way that they will become beneficial to the establishment of the envisaged green city. Starting point was the closing of material cycles focusing on possibilities to recover and reuse valuable resources and energy from "waste" produced in an urban setting. Four different scenarios focusing on water, nutrient and energy recovery were compared with the baseline wastewater management practice. Besides environmental benefits, the economical benefits of sustainable sanitation concepts are attractive, the break even point with the baseline scenario, is already after 5 years, provided that recovered resources will be sold for a marketable price. We believe that presented concepts are applicable for a wide range of new urban development initiatives in China and similar rapidly developing densely populated regions worldwide.

Norovirus in a Dutch tertiary care hospital (2002-2007): frequent nosocomial transmission and dominance of GIIb strains in young children.

We report a retrospective analysis of norovirus (NoV) infections occurring in patients of a tertiary care hospital during five winter seasons (2002/03 to 2006/07). Data were compared with national surveillance data and with corresponding data for rotavirus. Between July 2002 and June 2007, faecal specimens from 221 (9.0%) of 2458 hospital patients with diarrhoea tested positive for NoV. The incidence in children varied from 2.52 per 1000 admissions in 2004/05 (when testing began to be performed routinely) to 11.9 per 1000 admissions in 2006/07, while the incidence in adults remained stable (mean: 1.49 per 1000 admissions). Two genotypes predominated during the study period: GIIb strains occurred mainly in children below the age of two-and-a-half years [odds ratio (OR): 14.7; P<0.0001] whereas GII.4 strains affected all age groups. Compared with rotavirus infections, NoV infections in children were more often hospital-acquired (59% vs 39%, OR: 2.29; P<0.01). Among these cases we identified 22 clusters of NoV infection among inpatients. Twelve of 53 patients from whom follow-up samples were available demonstrated long-term virus shedding. We report a dynamic pattern of sporadic NoV infections in large hospitals, with frequent nosocomial transmission and with the predominance of GIIb-related strains in children. Effective prevention strategies are required to reduce the impact of sporadic NoV infection in vulnerable patients.

Anaerobic biodegradation of estrogens--hard to digest.

Although many publications are available on the fate of estrone (E1), 17beta-estradiol (E2) and 17alpha-ethynylestradiol (EE2) during aerobic wastewater treatment, little is published on their fate under strictly anaerobic conditions. Present research investigated the digestibility of E1 and EE2, using digested pig manure, granular UASB sludge, UASB-septic tank sludge and activated sludge as inocula. Besides, actual concentrations were measured in a UASB septic tank treating black water. Under anaerobic conditions E1 is reduced to E2 but the extent of this reduction depends on type of inoculum. No significant loss of the sum of E1 and E2 and of EE2 was observed. Adsorption was responsible for a 32-35% loss of E1 and E2 from the liquid phase in the UASB septic tank and the effluent still contained considerable concentrations of respectively 4.02 microg/l and 18.79 microg/l for E1 and E2 with a large fraction present in conjugated form. No EE2 was detected in the UASB effluent.

Fate of oestrogens during anaerobic blackwater treatment with micro-aerobic post-treatment.

The fate of oestrone (E1), 17beta-oestradiol (E2) and 17alpha-ethynyloestradiol (EE2) was investigated in a concentrated blackwater treatment system consisting of an UASB septic tank, with micro-aerobic post-treatment. In UASB septic tank effluent a (natural) total concentration of 4.02 microg/L E1 and 18.69 microg/L E2, comprising the sum of conjugated (>70% for E1 and >80% for E2) and unconjugated forms, was measured. During post-treatment the unconjugated oestrogens were removed to below 1 microg/L. A percentage of 77% of the measured unconjugated E1 and 82% of E2 was associated with particles >1.2 microm in the final effluent implying high sorption affinity of both compounds. When spiking the UASB septic tank effluent with E1, E2, EE2 and the sulphate conjugate of E2, removal in the micro-aerobic post-treatment was >99% for both E2 and EE2 and 83% for E1. The lower removal value for E1 was a result of (slow) deconjugation during the treatment, and in the final effluent still 40% of E1 and 99% of E2 was present in conjugated form. The latter was the result of incomplete deconjugation of the spiked E2(3S) in the post-treatment system.

Oestrogen removal from biological pretreated wastewater within decentralised sanitation and re-use concepts.

Two parallel researches were performed; one focused on the fate of oestrogens in the biological treatment systems within decentralised sanitation and re-use concepts (DESAR), the second related to the development of a suitable specific removal method. A new affinity membrane was developed using antibodies as specific binding sites for hormone removal. It was found that, especially in anaerobic treatment, the core technology in DESAR, the removal is insufficient and therefore an additional separation method is required. The affinity membrane with antibodies was found to be a suitable additional method, though in the current system it only removes one selected compound. Future research will focus on making this method more feasible in practise.

Variable selection pressures across lineages in Trichodesmium and related cyanobacteria based on the heterocyst differentiation protein gene hetR.

Due to the irreversible inhibition of nitrogenase by O2, N2 fixation is incompatible with the oxygenic photosynthesis of cyanobacteria. These organisms have therefore evolved various strategies for growing diazotrophically. One group of N2-fixing cyanobacteria has specialized cells, heterocysts, which contain the nitrogenase, lack the oxygenic photosystem II, and are virtually anoxic inside as the result of respiratory activity and a thick glycolipid cell wall. The hetR gene encodes a serine protease which is thought to be involved in the regulation of heterocyst development and in DNA binding. Although hetR is also present in many non-heterocystous N2-fixing cyanobacteria, its function in these organisms is unknown. In this study, hetR sequences of the N2-fixing, non-heterocystous cyanobacterium Trichodesmium spp. and related genera were examined for signatures of selection. In parsimony- or distance-based hetR phylogenies, the filamentous non-heterocystous cyanobacteria Symploca sp. and Leptolyngbya sp. were closest to Trichodesmium sp. However, accommodating molecular attributes of hetR such as nucleotide frequencies and rate heterogeneity in phylogenetic analyses suggested that many other genera could not be excluded as sister taxa of Trichodesmium. Maximum likelihood analysis of the dN/dS ratio (omega) showed that-irrespective of the use of Symploca, Leptolyngbya, or more distant taxa as an outgroup-the lineage between an outgroup and Trichodesmium (omega1=0.02-0.05) and a lineage leading to Trichodesmium erythraeum (omega1=0.02) were under much stronger purifying selection than the other lineages in Trichodesmium (omega0=0.13-0.32). Although the results from the maximum likelihood analyses are most trustworthy because of codon usage bias in Trichodesmium, the results from a simpler tree-based McDonald-Kreitman test were in general agreement. Due to their quite different assumptions, the combination of these two methods of analysis circumvents multiple testing which, in general, is problematic when using branch models. Although the causal selective forces underlying the substitution patterns in hetR have not yet been identified, these findings parallel the variety of physiological, molecular, and behavioral differences in cyanobacteria related to N2 fixation. The heterogeneity of selection pressures in Trichodesmium is more surprising, because multiple adaptation mechanisms have not been described in this genus.

Non-homogenized ITS regions in the parasitic nematode Cooperia oncophora.

Here, the validity of the assumption of concerted evolution of ribosomal regions in larval and adult Cooperia oncophora was assessed. In each of 4 individuals of this parasitic nematode, at least 78% of the sequences comprised different ITS variants. This implies that concerted evolution is not acting, which is corroborated by the scarcity of signatures of gene conversion and recombination. Mis-incorporation of nucleotides and illegitimate PCR-induced recombination turned out to be unlikely, and positions with substantial frequencies of alternative nucleotides corresponded to ambiguous positions in published ITS2 sequences of this and other Cooperia species based on direct sequencing. The ITS regions of each individual C. oncophora displayed a significant excess of unique mutations in agreement with expansion of the ribosomal gene family. Interesting corollaries of the inferred size changes of this gene family are genomic rearrangements that occur during larval development such as multiple rounds of endoduplication (in Rhabditidae), chromatin diminution (in Ascaris), and non-compensatory mutations on the secondary structure of the ITS2. It is yet unknown which process is important in trichostrongylids. Finally, although it can not be rigorously assessed in Cooperia, the ITS polymorphisms can readily be envisioned to affect phylogenetic reconstructions of closely related nematodes.

Demographic expansion of parasitic nematodes of livestock based on mitochondrial DNA regions that conflict with the infinite-sites model.

Mitochondrial ND4 sequences of populations of four species of parasitic nematodes of livestock were subjected to demographic analyses. Deviation from selective neutrality was detectable using the frequency spectrum of segregating sites and highly negative neutrality statistics. However, the mitochondrial data sets do not comply with the infinite-sites model that underlies these tests, and as a consequence, it was not established whether these features are solely a result of population expansion, or whether aspects of the molecular evolution of these mitochondrial regions are also involved. Coalescent analyses based on Fu's Fs neutrality test, which incorporated estimates of rate heterogeneity, the transition-transversion ratio and nucleotide bias, as well as analyses that are fairly robust to deviations from the infinite-sites model supported population expansion. Also analyses that do not depend on the infinite-sites model suggested historical population expansion of these nematodes. The very similar time since expansion, the absence of signatures of positive selection in ND4 and the logical association with human demography imply that selective sweeps of mitochondrial variants are less probable, and that expansion is the most likely scenario for the parasitic nematodes of livestock. The methods used to characterize the expansion have different assumptions and emphasize different aspects of expansions. The resulting restrictions on the interpretation of expansions are outlined.

Genetic structure of a population sample of apomictic dandelions.

In Northern Europe, dandelion populations consist solely of triploid or higher polyploid apomicts. Without a regular sexual cycle or lateral gene transmission, a clonal structure is expected for Taraxacum apomicts, although this was not found by compatibility analysis. In this study, we investigate whether this observation could be suported by performing independent tests based on data from hypervariable microsatellite markers as well as more conservative data based on allozymes and matrilinear cpDNA markers. In addition, population genetic methods were used to test departure from panmictic expectations, which is expected for clonal populations. Results indicated that many data sets, again, did not agree with expectations from clonal evolution because only small groups of genotypes exhibit no marker incompatibility. Population genetic analysis revealed that virtually all genotypes, but not individuals, agreed with random segregation and genotypic equilibria. Exceptions were genotypes with rare allozyme alleles or nearly identical microsatellite genotypes. Consequently, a population sample of apomictic dandelions essentially harbours genotypes that resulted from segregation and/or recombination and only a few genotypes that may have differentiated by somatic mutations.

A novel method for the isolation of gastro-intestinal nematode eggs that allows automated analysis of digital images of egg preparations and high throughput screening.

A simple and robust method for the isolation of gastro-intestinal nematode eggs from faeces is described that uses both salt- and sugar solutions for flotation. Application of this 'salt-sugar' isolation method to large numbers of faecal samples of adult dairy cows indicates a 3- or 4-fold reduction in the proportion of e.p.g.-negative cows relative to studies that used other techniques for egg isolation. The procedure detects more eggs than the Wisconsin flotation method in replicate samples and in spiked egg-free faeces. The number of recovered eggs in spiked faecal samples is linear over a range of egg concentrations, and the transparent faecal preparations that result from the protocol can be stored as digital images which can be used as input for an efficient automated egg-counting procedure. The increased rate of processing of faeces combined with the large reduction of the percentage of e.p.g.-negative cows allows more accurate analysis of large numbers of adult or resistant animals for studies of nematode parasitism.

Molecular phylogeny of Coelogyne (Epidendroideae; Orchidaceae) based on plastid RFLPS, matK, and nuclear ribosomal ITS sequences: evidence for polyphyly.

To evaluate the monophyly of Coelogyne (Epidendroideae; Orchidaceae) and reveal sectional relationships and relations to allied genera in subtribe Coelogyninae, we collected PCR (polymerase chain reaction) amplified restriction fragment length polymorphisms (RFLPs) from 11 plastid regions for 42 taxa (28 Coelogyne species and 14 representatives of other genera) and three outgroups from Bletiinae and Thuniinae. We also sequenced a large portion of the plastid trnK intron (mostly matK) and the nuclear ribosomal DNA internal transcribed spacers ITS1 and ITS2 (including the 5.8S gene). Separate phylogenetic analyses on each data set using maximum parsimony produced mainly congruent (except for the position of Panisea) but weakly supported clades. Parsimony analysis of the combined data clearly identified three main clades in Coelogyninae. Whereas Coelogyninae are monophyletic, Coelogyne is polyphyletic, with species falling into at least two well-supported clades. The utility of morphological characters used in previous classifications was explored by reconstructing character state evolution on one of the four molecular trees. Lip base and petal shape were homoplasious, whereas ovary indumentum and flower number were congruent with well-supported groups. The implications of our results for the classification of Coelogyne are discussed, and a reorganization of the genus by including Neogyna and Pholidota and removing several species is proposed.

The evolution of reproductive isolation in the ectomycorrhizal Hebeloma crustuliniforme aggregate (Basidiomycetes) in northwestern Europe: a phylogenetic approach.

To reconstruct the evolution of reproductive isolation in the ectomycorrhizal Hebeloma crustuliniforme aggregate (Basidiomycetes), phylogenetic relationships were determined between strains that belong to a clade consisting of nine intercompatibility groups (ICGs, biological species). Four of these nine ICGs are partially compatible and belong to the H. crustuliniforme aggregate. Different levels of partial compatibility have been found between these four ICGs. Between ICGs 3 and 4, 15% of the combinations were compatible. One strain was compatible with all isolates of both ICGs 3 and 4 and also with one isolate of ICG 2. Both a nuclear phylogeny, based on ribosomal IGS sequence data, and a mitochondrial phylogeny, based on a group-I intron located in the large subunit ribosomal RNA gene (LrRNA), were reconstructed. The level of incompatibility was compared with the phylogenetic history of individuals belonging to this clade. Different relationships were found between the level of compatibility and the relative age of the most recent common ancestor (MRCA) for different ICGs. On the one hand, the evolution of incompatibility between ICGs 2 and 3/4 is most consistent with the class of "divergence- first" models because a positive correlation was found between the relative age of the MRCA and the level of incompatibility for ICG 2 versus 3/4. On the other hand, the lack of such a correlation for ICGs 3 and 4 shows that (partial) incompatibility between these ICGs has arisen without strong divergence. The ecological (and to a lesser extent geographical) differences found between ICGs 3 and 4 suggest that selection for incompatibility, associated with host tree preference, has been important in the evolution of incompatibility between these two ICGs. The incongruence between the nuclear and mitochondrial trees for ICG 1 could be explained by a hybrid origin of this ICG, with different donors of the mitochondrial and nuclear sequences.

Hairpins involving both inverted and direct repeats are associated with homoplasious indels in non-coding chloroplast DNA of Taraxacum (Lactuceae: Asteraceae).

Sequence variation in 2.2 kb of non-coding regions of the chloroplast genome of eight dandelions (Taraxacum: Lactuceae) from Asia and Europe is interpreted in the light of the phylogenetic signal of base substitutions vs. indels (insertions-deletions). The four non-coding regions displayed a total of approximately 30 structural mutations of which 9 are potentially phylogenetically informative. Insertions, deletions, and an inversion were found that involved consecutive stretches of up to 172 bases. When compared to phylogenetic relationships of the chloroplast genomes based on nucleotide substitutions only, many homoplasious indels (33%) were detected that differed considerably in length and did not comprise simple sequence repeats typically associated with replication slippage. Though many indels in the intergenic spacers were associated with direct repeats, frequently, the variable stretches participated in inverted repeat stabilized hairpins. In each intergenic spacer or intron examined, nucleotide stretches ranging from 30 to 60 bp were able to fold into stabilized secondary structures. When these indels were homoplasious, they always ranked among the most stabilized hairpins in the non-coding regions. The association of higher order structures that involve both classes of repeats and parallel structural mutations in hot spot regions of the chloroplast genome can be used to differentiate among mutations that differ in phylogenetic reliability.

A search for diagnostic AFLP markers in Cichorium species with emphasis on endive and chicory cultivar groups.

The genus Cichorium consists of two widely cultivated species C. intybus (chicory) and C. endivia (endive) and four wild species, C. bottae, C. spinosum, C. calvum, and C. pumilum. A multivariate and an UPGMA (unweighted pair group method average) analysis based on AFLP (amplified fragment length polymorphism) markers were used to establish the genetic relationships among the species and cultivar groups of C. intybus and C. endivia. At the species level, the results correspond with previously obtained phylogenetic relationships in that C. bottae is the most divergent species, and C. intybus and C. spinosum, as well as C. endivia, C. pumilum, and C. calvum formed clusters. Based on the congruence between phylogenetic and genetic analyses, unique markers were expected for all species, however, hardly any specific marker was found except for C. bottae. The analysis of cultivar groups of C. intybus resembled the species analysis in two respects: (i) grouping of cultivars according to cultivar groups, and (ii) lack of markers unique to cultivar groups. In contrast to C. intybus, the cultivar series of C. endivia do not form distinct groups, which would reflect that crosses have been made among the various cultivar groups. The relationships among Cichorium species and cultivars will be useful for setting up a core collection of Cichorium, and stress the importance of inclusion of the wild species in the collection.

Amplified fragment length polymorphism (AFLP) markers reveal that population structure of triploid dandelions (Taraxacum officinale) exhibits both clonality and recombination.

Highly variable amplified fragment length polymorphism (AFLP) fingerprints of triploid apomictic dandelions obtained from three localities in an area where diploids are lacking were analysed to infer the predominant modes of reproduction. The distribution of markers was analysed using character compatibility to infer whether many genotypes agree with a tree-like structure in the data set. The presence of incompatible character state combinations (matrix incompatibility; MI) was used as a measure of genetic exchange. The detection of overrepresented genotypes, of which some were widespread, confirmed asexual reproduction. Not all genotypes were overrepresented; approximately half of the genotypes in the three localities were found only once. Because, in terms of genotype frequencies, only a part of the genetic variation is described, more important aspects of the molecular data such as relationships between markers or genotypes have been studied. The analysis of character compatibility indicated a disagreement of the data with a clonal structure. Nearly all genotypes contributed to MI and this contribution varied considerably among genotypes in each sampled locality. A gradual decrease of matrix incompatibility upon successive deletion of genotypes showing the highest contribution to MI indicated that marker distribution of virtually all genotypes disagreed with a tree-like structure in the data. This result suggested that many genotypes were separated by one or more sexual generations. Consistent with this conclusion was the fact that markers that show a low probability of contributing to MI are different in every sampled locality, which is most easily explained as the result of recombination. Apparently, asexual reproduction has resulted in overrepresented, widespread genotypes but sexual recombination has also substantially contributed to genetic variation in the sites studied.

Chloroplast DNA evidence for the evolution of Microseris (Asteraceae) in Australia and New Zealand after long-distance dispersal from western North America.

Restriction site mutations and trnL(UAA)-trnF(GAA) intergenic spacer length variants in the chloroplast genome were used to investigate the phylogenetic relationships among 53 Australian and New Zealand Microseris populations and to assess their position within their primarily North American genus. The study was performed to enhance understanding of evolutionary processes within this unique example of intercontinental dispersal and subsequent adaptive radiation. A southern blot method using four-base restriction enzymes and fragment separation on polyacryamide gels resulted in 55 mutations of which 30 were potentially phylogenetically informative. Most mutations were small indels of <162 bp, 80% of which were <20 bp. The small indels were useful for phylogenetic reconstruction of Australasian Microseris as judged by the high consistency indexes. The results confirmed the monophyly of the Australian and New Zealand Microseris. The occurrence of "hard" basal polytomies in the most parsimonious trees indicated that rapid radiation has occurred early in the history of the taxon. The monophyly of M. lanceolata, which includes the self-incompatible ecotypes of the Australian mainland, was confirmed. Within this species three clades were found that reflect more geographic distribution than morphological entities, suggesting that migration and possibly introgression between different ecotypes, or parallel evolution of similar adaptations, has occurred. One of the three clades was supported by a 162-bp deletion in the trnL-trnF spacer, while a subgroup of this exhibited also a tandemly repeated trnF exon. The data were inconclusive about the monophyly of the second Australasian species, M. scapigera, which comprises the New Zealand, Tasmanian, and autofertile ecotypes of Australia.

Evolution of the chloroplast genome and polymorphic ITS regions in Allium subg. Melanocrommyum.

Relationships based on PCR-RFLPs of non-coding regions of cpDNA indicate that some of the largest subgenera of the genus Allium and five of the largest sections of the Central Asian subg. Melanocrommyum are artificial. Internested synapomorphic mutations without homoplasy were found only in the chloroplast genomes of plants of subg. Melanocrommyum that occur in the border region of Tajikistan, Uzbekistan, Afghanistan, and Kyrgyzstan. Eighteen of 49 plants surveyed were polymorphic for their ITS regions. Even plants that had identical chloroplast genomes were polymorphic for nuclear ribosomal regions. These individuals had markedly different frequencies of ITS variants that were detected with various restriction enzymes. The geographic partitioning of chloroplast haplotypes and the fact that the ITS variants could not be ordered hierarchically can readily be envisioned to result from gene flow. Processes such as concerted evolution and parallel morphological evolution may also be partly responsible for the disconcordance of mutations in the chloroplast and nuclear genome. However, the chimeric nature of the nuclear ribosomal regions indicates that concerted evolution is not the dominating process in Allium subg. Melanocrommyum.

Molecular evolution of noncoding regions of the chloroplast genome in the Crassulaceae and related species.

Universal primers were used for PCR amplification of three noncoding regions of chloroplast DNA (cpDNA) in order to study sequence-length variation in the Crassulaceae and in related species. Several length mutations were observed that are of diagnostic value for evolutionary relationships in the Crassulaceae and the Saxifragaceae. Length variation and sequence divergence in the intergenic spacer between the trnL (UAA) 3' exon and the trnF (GAA) gene among 15 species were studied in detail by nucleotide-sequence analysis. A total of 50 insertion/deletion mutations were observed, accounting for a spacer-length variation in the range of 228-360 bp. Eighteen short direct repeat motifs (4-11 bp) and two inverted repeat motifs (7-11 bp) were found to be associated with length variation. Phylogenetic analysis of the sequence data indicated a pattern of relationships that was largely consistent with a previous analysis of cpDNA restriction-site variation. Evaluation of the level of homoplasy in insertion/deletion mutations within a phylogenetic framework revealed that only 1 out of 34 length mutations longer than 2 bp must have had multiple origins. The feasibility of the noncoding chloroplast DNA regions for molecular evolutionary studies is discussed.