Integrating multiplicate data: A new trend for taxonomic study

Taxonomy today encompasses classifi cation, phylogeny, and evolution. A pressing challenge faced by taxonomists is harnessing the vast amount of genomic data to effectively conduct research on hyper‐diverse taxa.

Phylogenomic conflict analyses in the apple genus Malus s.l. reveal widespread hybridization and allopolyploidy driving diversification, with insights into the complex biogeographic history in the Northern Hemisphere

Phylogenomic evidence from an increasing number of studies has demonstrated that different data sets and analytical approaches often reconstruct strongly supported but conflicting relationships. In this study, 785 single-copy nuclear genes and 75 complete plastomes were used to infer the phylogenetic relationships and estimate the historical biogeography of the apple genus Malus sensu lato, an economically important lineage disjunctly distributed in the Northern Hemisphere and involved in known and suspected hybridization and allopolyploidy events. The nuclear phylogeny recovered the monophyly of Malus s.l. (including Docynia); however, the genus was supported to be biphyletic in the plastid phylogeny. An ancient chloroplast capture event in the Eocene in western North America best explains the cytonuclear discordance. Our conflict analysis demonstrated that ILS, hybridization, and allopolyploidy could explain the widespread nuclear gene tree discordance. One deep hybridization event (Malus doumeri) and one recent event (Malus coronaria) were detected in Malus s.l. Furthermore, our historical biogeographic analysis integrating living and fossil data supported a widespread East Asian-western North American origin of Malus s.l. in the Eocene, followed by several extinction and dispersal events in the Northern Hemisphere. We also propose a general workflow for assessing phylogenomic discordance and biogeographic analysis using deep genome skimming data sets.

The Distribution and Role of M1 and M2 Macrophages in Aneurysm Healing after Platinum Coil Embolization

BACKGROUND AND PURPOSE

Impairment of macrophage polarization from a proinflammatory macrophage type 1 (M1) population to an anti-inflammatory macrophage type 2 (M2) population is a hallmark of poor wound healing. In this study, we aimed to evaluate the distribution of M1 and M2 macrophages and to analyze their association with healing in aneurysms embolized by endovascular coiling.

MATERIALS AND METHODS

Elastase-induced aneurysms were created in female rabbits and subsequently embolized with platinum coils. Aneurysm occlusions were evaluated with angiographic imaging at 1 (n = 6), 3 (n = 5), or 6 (n = 6) months. Aneurysm tissues were harvested for histologic analysis, quantification of M1 and M2 macrophages by immunofluorescence, and collagen deposition determined by Masson trichrome staining. Histologic grading of aneurysm healing was also performed. Untreated aneurysms were used as controls (n = 6).

RESULTS

The M1 macrophage population was highest at 1 month posttreatment, progressively decreasing at 3 and 6 months. The M2 macrophage population progressively increased at 3 and 6 months posttreatment. The highest collagen deposition was at 6 months posttreatment. We found a moderate-to-weak direct correlation between the percentage of M2 macrophages and collagen deposition, as well as total histologic scores overall, and a strongly positive direct correlation between the percentage of M2 macrophages and total histologic scores at 6 months posttreatment.

CONCLUSIONS

Our data support the direct correlation between M2 macrophage polarization and healing in aneurysm tissues. Our results show a positive relationship between M2 macrophage populations and total histologic scores at later stages of healing after endovascular coiling. We conclude that interventions aimed at stimulating M2 macrophage expression locally may improve aneurysm healing after coil embolization.

A synopsis of the expanded Rhaphiolepis (Maleae, Rosaceae)

As part of the integrative systematic studies on the tribe Maleae, a synopsis of the expanded Rhaphiolepis is presented, recognizing 45 species. Three new forms were validated: R. bengalensis f. contracta B.B.Liu & J.Wen, R. bengalensis f. intermedia B.B.Liu & J.Wen, and R. bengalensis f. multinervata B.B.Liu & J.Wen, and four new combinations are made here: R. bengalensis f. angustifolia (Cardot) B.B.Liu & J.Wen, R. bengalensis f. gigantea (J.E.Vidal) B.B.Liu & J.Wen, R. laoshanica (W.B.Liao, Q.Fan & S.F.Chen) B.B.Liu & J.Wen, and R. latifolia (Hook.f.) B.B.Liu & J.Wen. Furthermore, one new name, Rhaphiolepis yui B.B.Liu & J.Wen is proposed here, and three taxa were reduced as new synonyms. We also provide lectotypification for 13 names: Crataegus bibas, Eriobotrya philippinensis, Mespilus spiralis, Opa integerrima, Photinia luzonensis, Rhaphiolepis brevipetiolata, R. ferruginea var. serrata, R. fragrans, R. gracilis, R. hainanensis, R. kerrii, R. indica subsp. umbellata var. liukiuensis, and R. parvibracteolata.

Typification of 23 names in Eriobotrya (Maleae, Rosaceae)

As part of a comprehensive systematic study on the genus Eriobotrya and its close relatives from the E & SE Asia, new typifications of 23 names are presented here, along with some nomenclatural notes of the names involved. We lectotypified 22 names including accepted names and synonyms. They are: E. acuminatissima, E. bengalensis var. angustifolia; E. bengalensis f. intermedia, E. brackloi, E. brackloi var. atrichophylla, E. elliptica var. petelotii, E. fragrans var. furfuracea, E. glabrescens, E. grandiflora, E. henryi, E. oblongifolia, E. petiolata, E. platyphylla, E. poilanei, E. prinoides, E. prinoides var. laotica, E. salwinensis, E. serrata, E. stipularis, Hiptage cavaleriei, Photinia longifolia, Symplocos seguinii. One neotype of Photinia dubia was also proposed in this study, and E. pseudoraphiolepis and Mespilus cuila were identified as superfluous names. In addition, we also summarized the typification of 18 names for taxonomic reference: E. angustissima, E. balgooyi, E. condaoensis, E. × daduheensis, E. elliptica, E. fulvicoma, E. fragrans, E. glabrescens var. victoriensis, E. hookeriana, E. latifolia, E. obovata, E. malipoensis, E. merguiensis, E. tengyuehensis, E. wardii, Mespilus bengalensis, Photinia deflexa, and M. japonica.

A special issue to mark the 90th Anniversary of College of Life Sciences, Zhejiang University

The College of Life Sciences (CLS) remains one of the most prestigious-and the oldest-colleges in Zhejiang University. This special issue, which includes 16 reviews contributed by our alumni and faculties, is dedicated to mark the 90th Anniversary of CLS. The reviews provide a glimpse of current progresses in the areas of life sciences such as biochemical processes and their association with diseases (Ding et al., 2019; Hu et al., 2019; Jin et al., 2019; Nie and Yi, 2019), cancer biology (Feng, 2019; Huang et al., 2019; Leonard and Zhang, 2019; Zhu F et al., 2019), plant and environmental microbiology (Li et al., 2019; Yang et al., 2019; Zhu XR et al., 2019), cell cycle (Gao and Liu, 2019; Zhang et al., 2019), RNA biology (Gudenas et al., 2019; Luo et al., 2019), and protein structural biology (Yang and Tang, 2019).

Eriobotrya Belongs to Rhaphiolepis (Maleae, Rosaceae): Evidence From Chloroplast Genome and Nuclear Ribosomal DNA Data

The Eriobotrya-Rhaphiolepis (ER) clade consists of about 46 species distributed in East and Southeast Asia. Although Eriobotrya and Rhaphiolepis have been supported to form a clade, the monophyly of Eriobotrya and Rhaphiolepis at the genus level has never been well tested and their phylogenetic positions in Maleae still remain uncertain. This study aims to reconstruct a robust phylogeny of the ER clade in the framework of Maleae with a broad taxon sampling and clarify the phylogenetic relationship between Eriobotrya and Rhaphiolepis. This study employed sequences of the whole plastome (WP) and entire nuclear ribosomal DNA (nrDNA) repeats assembled from the genome skimming approach and included 83 samples representing 76 species in 32 genera of Rosaceae, especially Maleae. The Maximum Likelihood (ML) and Bayesian Analysis (BI) based on three datasets, i.e., WP, coding sequences of plastome (CDS), and nrDNA, strongly supported the paraphyly of Eriobotrya, within which Rhaphiolepis was nested. Our plastid tree supported the sister relationship between the ER clade and Heteromeles, and the nrDNA tree, however, did not resolve the phylogenetic placement of the ER clade in Maleae. Strong incongruence between the plastid and the nuclear trees is most likely explained by hybridization events, which may have played an important role in the evolutionary history of the ER clade. Molecular, morphological, and geographic evidence all supports the merge of Eriobotrya with Rhaphiolepis, which has the nomenclatural priority. We herein transferred 36 taxa of Eriobotrya to Rhaphiolepis. We also proposed a new name, Rhaphiolepis loquata B.B.Liu & J.Wen, for the economically important loquat, as the specific epithet "japonica" was pre-occupied in Rhaphiolepis.

Resolving the systematic positions of enigmatic taxa: Manipulating the chloroplast genome data of Saxifragales

Accurately resolving the phylogeny of enigmatic taxa is always a challenge in phylogenetic inference. Such uncertainties could be due to systematic errors or model violations. Here, we provide an example demonstrating how these factors affect the positioning of Paeoniaceae within Saxifragales based on chloroplast genome data. We newly assembled 14 chloroplast genomes from Saxifragales, and by combining these genomes with those of 63 other angiosperms, three datasets were assembled to test different hypotheses proposed by recent studies. These datasets were subjected to maximum parsimony, maximum likelihood and Bayesian analyses with site-homogeneous/heterogeneous models, different data partitioning strategies, and the inclusion/exclusion of weak phylogenetic signals. Three datasets exhibited remarkable heterogeneity among sites and among taxa of Saxifragales. Phylogenetic analyses under homogeneous models or maximum parsimony showed a closer relationship of Paeoniaceae with herbaceous families in the order. Data partitioning strategies did not change the general tree topology. However, PhyloBayes analysis under the CAT+GTR model resulted in a relationship closer to woody families. We conclude that although genomic data significantly increase the phylogenetic resolution of enigmatic taxa with high support, the phylogenetic results inferred from such data might be analysis or signal dependent. The analytical pipeline outlined here combines phylogenomic inference methods with evaluation of lineage-specific rates of substitution, model selection, and assessment of systematic error. These methods would be applicable to resolve similar difficult questions in the tree of life.

Nonocclusive Mesenteric Ischaemia Induced by Diltiazem Overdose: A Case Report

Acute mesenteric ischaemia is a rare complication of calcium channel blocker (CCB) overdose. A previous study reported a case of mesenteric ischaemia induced by poisoning with CCBs other than diltiazem. We present a case of nonocclusive mesenteric ischaemia (NOMI) induced by diltiazem poisoning. Through this case report, we wish to emphasize that the clinicians should keep the possibility of intestinal ischaemia in mind from the early phase of calcium channel blocker poisoning. In addition, close monitoring and intense abdominal examination including the abdominal computed tomography scan should be done if CCBs poisoning patients complained of an abdominal pain.

Bacterial Contamination of Computer and Hand Hygiene Compliance in the Emergency Department

Introduction

The aim of this study was to determine the degree and nature of bacterial contamination of computer equipment in three Korean emergency departments (ED).

Methods

Hand hygiene practices of ED doctors and nurses were observed before contact with computer equipment. Microbiological swab samples were obtained from 112 multiple-user computer keyboards and electronic mice in the ED of three teaching hospitals. Isolated organisms were identified by a clinical microbiologist using Gram stain, colony morphology, and susceptibility test.

Results

Of the 112 samples, 103 (92.0%) showed growth of organisms on culture. Thirty-eight (33.9%) pieces of computer equipment yielded multiple bacterial species. Coagulase-negative Staphylococcus was the most common microorganism isolated (85.7%). Methicillin-resistant Staphylococcus aureus was obtained from two keyboards in two hospitals (1.8%). Hand hygiene compliance was observed on 29.9% occasions. Hand hygiene compliance after patient contact (38.0%) was higher than after other environmental contact (20.7%).

Conclusions

Multiple user computer equipment in the ED may serve as reservoirs for nosocomial infection. Hand hygiene should be performed before and after using all ED equipment, including computer equipment.

Bacterial Contamination of Computer and Hand Hygiene Compliance in the Emergency Department

Introduction

The aim of this study was to determine the degree and nature of bacterial contamination of computer equipment in three Korean emergency departments (ED).

Methods

Hand hygiene practices of ED doctors and nurses were observed before contact with computer equipment. Microbiological swab samples were obtained from 112 multiple-user computer keyboards and electronic mice in the ED of three teaching hospitals. Isolated organisms were identified by a clinical microbiologist using Gram stain, colony morphology, and susceptibility test.

Results

Of the 112 samples, 103 (92.0%) showed growth of organisms on culture. Thirty-eight (33.9%) pieces of computer equipment yielded multiple bacterial species. Coagulase-negative Staphylococcus was the most common microorganism isolated (85.7%). Methicillin-resistant Staphylococcus aureus was obtained from two keyboards in two hospitals (1.8%). Hand hygiene compliance was observed on 29.9% occasions. Hand hygiene compliance after patient contact (38.0%) was higher than after other environmental contact (20.7%).

Conclusions

Multiple user computer equipment in the ED may serve as reservoirs for nosocomial infection. Hand hygiene should be performed before and after using all ED equipment, including computer equipment. (Hong Kong j.emerg.med. 2012;19:387-393)

Multiple species of wild tree peonies gave rise to the 'king of flowers', Paeonia suffruticosa Andrews

The origin of cultivated tree peonies, known as the 'king of flowers' in China for more than 1000 years, has attracted considerable interest, but remained unsolved. Here, we conducted phylogenetic analyses of explicitly sampled traditional cultivars of tree peonies and all wild species from the shrubby section Moutan of the genus Paeonia based on sequences of 14 fast-evolved chloroplast regions and 25 presumably single-copy nuclear markers identified from RNA-seq data. The phylogeny of the wild species inferred from the nuclear markers was fully resolved and largely congruent with morphology and classification. The incongruence between the nuclear and chloroplast trees suggested that there had been gene flow between the wild species. The comparison of nuclear and chloroplast phylogenies including cultivars showed that the cultivated tree peonies originated from homoploid hybridization among five wild species. Since the origin, thousands of cultivated varieties have spread worldwide, whereas four parental species are currently endangered or on the verge of extinction. The documentation of extensive homoploid hybridization involved in tree peony domestication provides new insights into the mechanisms underlying the origins of garden ornamentals and the way of preserving natural genetic resources through domestication.

Evolution of the platycodonoid group with particular references to biogeography and character evolution

The Qinghai-Tibet Plateau (QTP) is an important center of origin and diversification for many northern temperate plants. The hypothesis "out-of-QTP" suggests that the majority of northern temperate plants have originated and dispersed from the QTP and adjacent regions. An interesting question is whether the biogeographic history of the platycodonoids (Campanulaceae), a group mainly distributed in the QTP and adjacent regions, coincides with the hypothesis "out-of-QTP"? Furthermore, how have the diagnostic characters of the platycodonoids evolved? In the present study, all 10 genera of the platycodonoids were sampled for molecular phylogeny and dating analyses, and ancestral states of distribution and characters were reconstructed. The results do not support the platycodonoids as an "out-of-QTP" group, but instead they might have descended from Tethyan ancestors. The dispersal and diversification of the platycodonoids in Asia might have been driven by the uplift of the QTP. The present study highlights the importance of the Tethyan Tertiary flora for the origin of the Sino-Himalayan flora and the influence of the uplift of QTP on diversification of northern temperate plants. In addition, character state reconstruction reveals that the inferior ovary, capsule, long-colpate pollen, and chromosome number 2n = 14 are probably ancestral states.

The development of a rapid prototyping prosthetic socket coated with a resin layer for transtibial amputees

This article proposes a type of transtibial socket composed of an inner layer fabricated by a rapid prototyping (RP) machine and an outer layer coated with unsaturated polyester resin. This work integrates contemporary technologies including a handheld scanner and CAD systems, to design a thin primary socket shape and then manufactures the socket using a fused deposition-modeling machine. To prevent breakage caused by the layer-based forming process and to reinforce flexural strength, the current research coats the preliminary RP socket with a layer of unsaturated polyester resin. After shaping the proximal brim of the resin-reinforced RP socket to match the specific stump, this study assembles and aligns a shank and a prosthetic foot to form a prosthesis set. After completing a trial safety walk wearing the prosthesis, which is satisfactory to the amputee and a registered prosthetist, this research measures interface pressures between the stump and the resin-reinforced RP socket. Experiment results demonstrate that the resin-reinforced RP socket is applicable for transtibial amputees. In addition to strengthening the FDM socket and producing consistent socket fit, this study also demonstrates a feasible procedure that employs current technologies to design and manufacture transtibial sockets without plaster moulds.

Accuracy of Web-based recording program for in-hospital resuscitation: laboratory study

OBJECTIVE

The purpose of this study was to assess the accuracy of a Web-based resuscitation recording program compared with the handwritten method.

METHODS

A Web site was developed to record in-hospital resuscitation events and a mock resuscitation was recorded using both the Web site and handwritten method by emergency nurses. Accurate recorded events and times were compared between the two methods through the use of a video clip. Paired t tests were used to compare differences in absolute timing error, the number of omitted events out of 11 reference events and total recorded events.

RESULTS

Twenty-one emergency nurses recorded simulated resuscitation events using both the handwritten and Web-based computerised recording system. The mean absolute timing errors were significantly lower using the computerised recording program (37.3 s (SD 17.1) versus 8.3 s (SD 5.3), p<0.001). The mean number of omissions for the computerised program was 1.8 (SD 0.8) compared with 1.4 (SD 1.1) for the handwritten method (p = 0.202). The mean number of total recorded events for the computerised program was 16.5 (SD 3.5) compared with 15.0 (SD 3.8) for the handwritten method (p = 0.063).

CONCLUSIONS

This study suggests that a Web-based recording program decreased timing error while causing no differences in the number of recorded or omitted events in a laboratory setting.

Behavior of meiotic chromosomes in Pinus wallichiana, P. strobus and their hybrid and nrDNA localization in pollen mother cells of the hybrid by using FISH

The complete process of meiosis was investigated in Pinus wallichiana, P. strobus and their artificial hybrid (F1) using microsporocytes. It is revealed that there were slightly lower chiasma frequency, lower ring bivalent frequency, lower meiotic index and distinctly higher frequency of aberrance (chromosomal bridges, fragments or micronuclei) in pollen mother cells (PMCs) of the hybrid (F1) than those of the parental species, which showed a certain degree of differentiation between homologous chromosomes of the two parents. However, relatively higher frequency of ring bivalents and higher meiotic index in all the three entities indicate the great stability of genomes of parental species, and the differentiation of genomes between the two parents must have been slight. Total nineteen signal loci of 18S rDNA were observed in nine bivalents of the hybrid (F1), among which one bivalent bears two loci, while the others have only one. It is suggested that distinct differentiation at genetic level existed in homologous chromosomes of the two parental species, whereas only slight differentiation at karyotypic and genomic levels take place between the parent species.

Cytoplasmic composition in Pinus densata and population establishment of the diploid hybrid pine

Sequence and restriction site analyses of the paternally inherited chloroplast rbcL gene and maternally inherited mitochondrial nad1 fragments from the same set of populations and individuals were used to investigate cytoplasmic composition and population establishment of Pinus densata, a diploid pine that originated through hybridization between P. tabuliformis and P. yunnanensis. Two variable sites and three chlorotypes (TT, TC and GC) were detected on the rbcL gene of the three pines. P. densata harboured the three chlorotypes, two of which (TT, GC) were characteristic of the parental species, respectively. The third chlorotype (TC) was distributed extensively in seven of the 10 P. densata populations analysed, and might represent a mutation type or have been derived from an extinct parent. The distribution of chlorotypes, together with that of mitotypes, indicated that significant founder effect and backcross happened during the population establishment of the hybrid pine. P. tabuliformis and P. yunnanensis had acted as both mother and father donors, i.e. bi-directional gene flow existed between the two parental species in the past. Population differentiation of P. densata is high, as detected from the cytoplasmic genomes: GST = 0.533 for cpDNA and GST = 0.905 for mtDNA. The differences in cytoplasmic composition among the hybrid populations suggest that the local populations have undergone different evolutionary histories.

Marked Intragenomic Heterogeneity and Geographical Differentiation of nrDNA ITS in Larix potaninii (Pinaceae)

Nuclear ribosomal DNA (nrDNA) of gymnosperms, especially Pinaceae, is characterized by slow concerted evolution and exhibits substantial ITS-region length variation (975-3663 bp), in sharp contrast to the narrow range (565-700 bp) in angiosperms. Here we examined intra- and intergenomic heterogeneity of the nrDNA internal transcribed spacer (ITS) region in four varieties of Larix potaninii, a species from the mountainous areas of western China. Two clones with more than a 100-bp deletion in ITS1 were detected in L. potaninii var. chinensis and L. potaninii var. australis, respectively. The deletion resulted in the loss of most part, including the motif sequence, of subrepeat 1 (SR1). Sequence divergence and phylogenetic analyses showed that some clones would be pseudogenes given their low GC content, high substitution rates, unique positions in the phylogenetic trees, or significant length variation. These clones might represent orphons or paralogues at minor loci resulting from large-scale gene or chromosome reorganization. Some recombinants characterized by chimeric structure and discordant phylogenetic positions in partitioned sequence analyses indicate that unequal crossing-over plays an important role in the process of nrDNA concerted evolution. In addition, some varieties of L. potaninii might have experienced an nrDNA founder effect parallel to their geographical isolation.

A phylogeny of the rice tribe Oryzeae (Poaceae) based on matK sequence data

Phylogenetic relationships were inferred using nucleotide sequences of the chloroplast gene matK for 26 species representing 11 genera of the tribe Oryzeae and three outgroup species. The sequenced fragments varied from 1522 base pairs (bp) to 1534 bp in length with 15.4% variable and 7.9% phylogenetically informative sites when the outgroups were excluded. The aligned sequences were analyzed by maximum parsimony and neighbor-joining methods. Analyses of the sequence data indicated that species of Oryzeae form a strongly supported monophyletic group, concordant with previous morphological and anatomical evidence. The tribe Oryzeae can be divided into two monophyletic lineages, corresponding to the traditionally recognized subtribes Oryzinae and Zizaniinae. The first subtribe consists of Oryza and Leersia, while the subtribe Zizaniinae includes the remaining genera. The matK sequence data did not support the close affinities of the monoecious genera in Oryzeae, implying the possibility of multiple origins of the floral structures in the tribe. It is noteworthy that Porteresia coarctata is closely related to Oryza species, suggesting that it should be treated as a member in the genus Oryza rather than a separate monotypic genus.

Maternal lineages of Pinus densata, a diploid hybrid

Previous morphological, allozyme and chloroplast DNA data have suggested that Pinus densata originated through hybridization between P. tabuliformis and P. yunnanensis. In the present study, sequence and restriction site analyses of maternally inherited mitochondrial nad1 intron were used to detect variation patterns in 19 populations of P. tabuliformis, P. yunnanensis and P. densata. A total of three mitotypes (A, B, C) were detected. All but one of the populations of P. yunnanensis possessed mitotype B while all populations of P. tabuliformis had mitotype A. Pinus densata populations, on the other hand, harboured both mitotypes A and B, which are characteristic of P. tabuliformis and P. yunnanensis, respectively. This result gives strong additional evidence supporting the hybrid origin of this diploid pine. The distribution of mitotypes indicated very different mating compositions and evolutionary history among P. densata populations. It seems that local founder populations and backcrosses may have played important roles in the early establishment of P. densata populations. The uplift of the Tibetan Plateau had a significant impact on the distribution of maternal lineages of P. densata populations.

Rapid and reliable identification of rice genomes by RFLP analysis of PCR-amplified Adh genes

The rice genus (Oryza L.) consists of 24 species with 10 recognized genome types. With the realization of many useful genes in species of wild rice, continuous efforts have been made to understand their genomic composition and relationships. However, the identification of rice genomes has often been difficult owing to complex morphological variation and formation of allotetraploids. Here we propose a rapid and reliable method for identifying rice genomes based on the restriction sites of PCR-amplified Adh genes. The experimental procedure was as follows: (i) amplify a portion of Adh1 and Adh2 genes with the locus-specific PCR primers; (ii) digest PCR products with restriction enzymes that distinguish different genomes; and (iii) run the digested products on 1.4% agarose gel, and photograph. Using various combinations of restriction digestion of the two Adh genes, all of the rice genomes can be identified.

High levels of genetic differentiation of Oryza officinalis Wall. ex Watt. from China

In order to determine the population genetic structure of wild rice (Oryza officinalis Wall. ex Watt.), an endangered tropical and subtropical species, allozyme diversity encoded by 24 loci was analyzed electrophoretically in 145 individuals of eight natural populations from Hainan, Guangxi, and Yunnan provinces, China. A fairly high genetic differentiation (F(ST) = 0.882 and mean I = 0.786) was found among the studied populations. Our results suggest that restricted gene flow may play a significant role in shaping such a population genetic structure. In addition, high genetic differentiation among populations within a geographically limited region may stem from a reduced population size and consequent genetic drift.

Clonality in wild rice (Oryza rufipogon, Poaceae) and its implications for conservation management

Correlations were examined between habitat characters and clonal structures determined by the RAPD (random amplified polymorphic DNA) assay in five populations of Oryza rufipogon in China. Nine of 175 decameric primers were used in the study because they reproducibly amplified polymorphisms. The extent of clonality together with the clonal and sexual reproductive strategies varied greatly among the five populations and correlated with the habitats where they occur. The populations under serious disturbance or seasonal drought tended to have small clones with relatively high clonal diversity caused by sexual reproduction, whereas the populations with little disturbance and sufficient supply of water were prone to have large clones with relatively low clonal variation and low sexual reproduction. Therefore, the dynamics of sexual vs. clonal reproduction of this species depended mainly on environmental factors, such as external disturbance and water supply, rather than latitudes indicated by previous study. These results have important implications for in situ conservation of O. rufipogon. Adequate external disturbance and water supply control are essential for maintaining high clone diversity of in situ conserved populations. According to the extent of clonality of the populations examined, we recommend that an interval of >12 m should be required for collecting samples for ex situ conservation and for population genetic studies to capture possible genetic diversity for O. rufipogon in China.

[A study on AFLP fingerprinting of land races of Panax ginseng L]

OBJECTIVE

To obtain more information on DNA fingerprintings of five land races of Chinese ginseng, namely, Damaya (DMY), Changbo (CB), Yuanbangyuanlu (YBYL) and Huangguo (HG).

METHODS

The five land races were detected by amplified restriction fragment polymorphism (AFLP) markers with 11 combined primers (M2, M3, M16, M20, M53, M56, M57, M68, M69, M72, M84 in Mse I).

RESULT AND CONCLUSION

Only 4.6% polymorphic sites was found. It was further verified that only a little diversity existed among the land races. The polymorphic sites of CB were much more than those of the others, which suggests that there are more heterozygotes in CB populations, and it is closer to wild ginseng than the others.

Allozyme diversity and population genetic structure of Pinus densata Master in northwestern Yunnan, China

We investigated the levels and patterns of genetic diversity of Pinus densata Master in Yunnan. Horizontal starch-gel electrophoresis was performed on macrogametophytes collected from nine populations in northwestern Yunnan, China. Compared with other gymnosperm species, P. densata has higher mean values for all measures of genetic diversity. Allozyme polymorphism (0.99 criterion) was 97.0% and 71.4% at the species and population levels, respectively. The average number of alleles per locus was 3.1 and 2.0 at the species and population levels. Mean expected heterozygosity was substantially higher in P. densata than average values investigated for other gymnosperms both at the population (Hep = 0.174 +/- 0.031) and at the species (Hes = 0.190) levels. Of the total genetic variation, less than 12% was partitioned among populations (GST = 0.112). Our allozyme survey supports the suggestion that the observed higher diversity in P. densata may be attributed partly to its hybrid origin between two genetically distinct species, P. yunnanensis and P. tabulaeformis. In addition, we suggest that introgression would give rise to the increase in genetic diversity occurring in P. densata.

[Comparison of ITS sequences between wild ginseng DNA and garden ginseng DNA]

OBJECTIVE

To compare the genetic differences between wild ginseng and garden ginseng (Panax ginseng).

METHOD

The sequences of ITS1 and ITS2 of wild ginsengs were determined on LKB DNA sequencing station through Si-liver Sequence DNA Sequencing System. The sequencies were aligned with DNA SIS software.

RESULTS AND CONCLUSION

The ITS1 and ITS2 of Panax were 220-221 and 222-224 bases in length respectively. In Panax ginsehg, the seqences of ITS1 were very stable, but ITS2 were changeable. The ITS2 sequences of No. 87 and No. 110 of the wild ginseng collected from Fusong Heilongjiang (China) were exactly the same as those of No. U41680(Jun Wen) and No. U41682(Jun Wen) of garden ginseng collected from Heilongjiang Province (China) and Korea respectively, but different from those of No. U41681(Jun Wen) from Hubei Province (China) in three bases (447, 449, 450) The result implies that the cultivated ginsengs may have been introduced from two different populations of the wild ginseng.

Phylogeny of rice genomes with emphasis on origins of allotetraploid species

The rice genus, Oryza, which comprises 23 species and 9 recognized genome types, represents an enormous gene pool for genetic improvement of rice cultivars. Clarification of phylogenetic relationships of rice genomes is critical for effective utilization of the wild rice germ plasm. By generating and comparing two nuclear gene (Adh1 and Adh2) trees and a chloroplast gene (matK) tree of all rice species, phylogenetic relationships among the rice genomes were inferred. Origins of the allotetraploid species, which constitute more than one-third of rice species diversity, were reconstructed based on the Adh gene phylogenies. Genome types of the maternal parents of allotetraploid species were determined based on the matK gene tree. The phylogenetic reconstruction largely supports the previous recognition of rice genomes. It further revealed that the EE genome species is most closely related to the DD genome progenitor that gave rise to the CCDD genome. Three species of the CCDD genome may have originated through a single hybridization event, and their maternal parent had the CC genome. The BBCC genome species had different origins, and their maternal parents had either a BB or CC genome. An additional genome type, HHKK, was recognized for Oryza schlechteri and Porteresia coarctata, suggesting that P. coarctata is an Oryza species. The AA genome lineage, which contains cultivated rice, is a recently diverged and rapidly radiated lineage within the rice genus.

RAPD variation within and between natural populations of the wild rice oryza rufipogon from china and brazil

Genetic variation within and between eight natural populations of Oryza rufipogon from China and Brazil was investigated at the DNA level by analysis of RAPD fragments. Out of 60 random primers, which were initially screened against DNA from four individuals, 20 generated highly reproducible RAPD fragments which were then used for further population analysis. With these primers, 95 discernible DNA fragments were produced and 78 (82.1%) were polymorphic, which indicated that high levels of genetic variation existed in these natural populations. In addition, the Chinese populations showed greater polymorphism than those from Brazil at both the population and regional levels. This is noteworthy considering that the Chinese populations are from a relatively restricted area of China. The factors responsible for these findings include the contrasting mating systems in the Brazilian and Chinese populations, and gene flow from annual cultivated rice to perennial natural populations in China. An Analysis of Molecular Variance (AMOVA) was used to apportion the variation between individuals within populations, between populations within regions, and between regions. Results showed that 61.8% of the total genetic diversity resided between the two continents, whereas only 14.9% and 23.3% was attributable to population differences within regions and to individual differences within a population, respectively. The great genetic differentiation between the Chinese and Brazilian populations is in agreement with recent treatment of the American form of O. rufipogon as a separate species, O. glumaepatula.

Chemoreception and perception of the bitterness of isohumulones

Psychophysical experiments were conducted to determine whether isohumulones share a common receptor mechanism with other bitter compounds, and whether parotid saliva flow affects perception of their bitterness. Findings from a study of inter-individual differences in sensitivity to 23 sweet and/or bitter compounds among 25 subjects using the time-intensity (TI) method suggest that isohumulone and tetrahydroisohumulone may share a common receptor mechanism with other bitter compounds except those with the thiourea moiety. Isohumulone and tetrahydroisohumulone displayed a unique dome-shaped TI profile. The bitterness of the two compounds took longer to develop, but it lasted as long as for other bitter stimuli. In a study of the relation between perception of bitterness in beer and parotid saliva flow in 20 young adults, no significant difference was found among the mean saliva flows triggered by 0, 15 and 30 mg/L of isohumulones added to beer, and no significant correlation was found between saliva flow and maximum intensity or total duration of bitterness.

Cheese acceptance and dairy product consumption in an older population

This study examined the acceptability of cheese products in a population of older adults in relation to their consumption of dairy products. The majority of the subjects liked hard cheeses (Cheddar, Provolone and Swiss) more than soft, ripened cheeses (Brie and blue cheese), and showed no significant difference in preference between regular and lowfat or fat-free processed cheese. A positive correlation was found between hedonic ratings and frequency of consumption across the five cheeses evaluated in the study. Almost one-half of the participants considered cheese to be a high calorie, high fat and high cholesterol food. This study suggests that lowfat or fat-free cheese products in the form of mild, hard or processed cheeses could successfully be incorporated in the diet of older adults to implement current dietary guidelines for fat and calcium consumption.