Genetic analysis of mortality in murine angiostrongyliasis costaricensis using SMXA recombinant inbred mouse strains

The SMXA recombinant inbred mouse strain set was produced by systematic inbreeding from the F2 generation of a cross between two progenitor inbred strains, A/J and SM/J, which differed markedly with respect to the patterns of infection with Angiostrongylus costaricensis. We have applied this set to genetic analysis of mouse susceptibility to this nematode infection. The mortality was variable among substrains of the SMXA RI strains, indicating the involvement of multiple genes. Linkage analysis showed several chromosomal regions closely linked to mortality; chromosome 6 (D6Rik86, 87; P0.001), 10 (D10Rik66–D10Mit12; P=0.0058), 13 (D13Rik79, 80; P=0.0096) and 17 (D17Mit28–D17Rik76; P=0.0088).     

Phenotypic and genomic characteristics of rhizobia isolated from Genista tinctoria root nodules

Forty three rhizobial strains isolated from root nodules of Genista tinctoria growing in England, Ukraine, and Poland were compared with 21 representatives of the recognized rhizobial species and two unclassified Bradyrhizobium sp. (Lupinus) strains by performing a numerical analysis of 102 phenotypic features and with the reference bradyrhizobia by simplified AFLP analysis with one restriction enzyme PstI and one selective primer PstI-A. All Genista tinctoria microsymbionts were slow-growing bradyrhizobia with generation time of 10–14 h, acid tolerant, salt sensitive, and antibiotic resistant. Cluster analysis based on the phenotypic properties of all bacteria included, grouped dyer's broom rhizobia together with Bradyrhizobium strains, and classified them into three major phena according to their geographic origin. Genista tinctoria nodule isolates were separated into three clusters with the strain composition as in a phenogrouping by AFLP patterns. The presented results, suggest the relationship of G. tincoria microsymbionts to Bradyrhizobium species and show the usefulness of AFLP analysis for differentiation and classification of the studied rhizobia.     

The phylogeny and systematics of the endemic Ethiopian Lophuromys flavopunctatus species complex based upon random amplified polymorphic DNA (RAPD) analysis

Random amplified polymorphic DNA (RAPD) analysis was performed to clarify systematics and phylogenetic relationships within the Ethiopian endemic representatives of Lophuromys flavopunctatus species complex. Data were analysed by both phenetic (UPGMA) and phylogenetic (neighbor-joining (NJ) and maximum parsimony) procedures. NJ and maximum parsimony analyses yielded identical phylogenetic trees that demonstrate the basal position of L. melanonyx with L. brevicaudus splitting next and sister-group relationship for L. brunneus–L. chrysopus. This phylogenetic pattern is congruent with inferences from allozymes for the considered species suggesting early divergence of Afroalpine species and recent origin of forest taxa. Thus, the results demonstrate that RAPD-PCR might be a useful technique for phylogenetic analysis at the species levels in vertebrates. Controversial taxonomy of L. brevicaudus, L. brunneus and L. chrysopus is clarified, with their specific ranks confirmed on the basis of tree topology and genetic distances.     

鹅掌楸贵州烂木山居群的微卫星遗传多样性及空间遗传结构

濒危植物鹅掌楸(Liriodendron chinense)目前仅零散分布于我国亚热带及越南北部地区, 残存居群生境片断化较为严重。研究濒危植物片断化居群的遗传多样性及小尺度空间遗传结构(spatial genetic structure)有助于了解物种的生态进化过程以及制定相关的保育策略。本研究采用13对微卫星引物, 对鹅掌楸的1个片断化居群进行了遗传多样性及空间遗传结构的研究, 旨在揭示生境片断化条件下鹅掌楸的遗传多样性及基因流状况。研究结果表明: 鹅掌楸烂木山居群内不同生境斑块及不同年龄阶段植株的遗传多样性水平差异不显著(P>0.05), 居群内存在寨内和山林2个遗传分化明显的亚居群。烂木山居群个体在200 m以内呈现显著的空间遗传结构, 而2个亚居群内的个体仅在20 m的距离范围内存在微弱或不显著的空间遗传结构。鹅掌楸的空间遗传结构强度较低(Sp = 0.0090), 且寨内亚居群的空间遗传结构强度(Sp = 0.0067)要高于山林亚居群(Sp = 0.0053)。鹅掌楸以异交为主, 种子较轻且具翅, 借助风力传播, 在一定程度上降低了空间遗传结构的强度。此外, 居群内个体密度及生境特征也对鹅掌楸的空间遗传结构产生了一定影响。该居群出现显著的杂合子缺失, 近交系数(F_IS)为0.099 (P < 0.01), 表明生境片断化的遗传效应正逐渐显现。因此, 对鹅掌楸的就地保护应注意维护与强化生境的连续性, 促进基因交流。迁地保护时, 取样距离应不小于20 m, 以涵盖足够多的遗传变异。     

绍兴黄酒酒药中酵母菌的物种资源

酒药是绍兴黄酒酿造中使用的重要糖化发酵剂。2013年绍兴黄酒冬酿期间,从绍兴地区5个主要黄酒生产企业,采集古越龙山、会稽山、塔牌、沈永和、女儿红及鉴湖等6个品牌酒药样本,在数量、种类和分布规律等方面对黄酒酒药内酵母菌物种资源进行了系统研究。研究发现,会稽山酒药和沈永和酒药蕴含酵母菌数量较多而且与其他样本相比差异显著（P<0.01）,而塔牌酒药中酵母菌数量显著少于其他5个品牌（P<0.05）。遵循酵母菌分类原则,从绍兴黄酒酒药中分离鉴定出3种酵母菌,扣囊复膜孢酵母Saccharomycopsis fibuligera、酿酒酵母Saccharomyces cerevisiae和隐球酵母Cryptococcus sp.。其中,扣囊复膜孢酵母Saccharomycopsis fibuligera在6个品牌黄酒酒药内的分布占有绝对优势,该种酵母菌可能对绍兴黄酒酒药的生产性能来说至关重要。比较分析酒药中酵母菌物种资源,可以为阐明绍兴黄酒的发酵机制提供基础数据和理论基础。     

Systematics of Mukdenia and Oresitrophe (Saxifragaceae): Insights from genome skimming data

Oresitrophe and Mukdenia (Saxifragaceae) are epilithic sister genera used in traditional Chinese medicine. The taxonomy of Mukdenia, especially of M. acanthifolia, has been controversial. To address this, we produced plastid and mitochondrial data using genome skimming for Mukdenia acanthifolia and Mukdenia rossii, including three individuals of each species. We assembled complete plastomes, mitochondrial CDS and nuclear ribosomal ETS/ITS sequences using these data. Comparative analysis shows that the plastomes of Mukdenia and Oresitrophe are relatively conservative in terms of genome size, structure, gene content, RNA editing sites and codon usage. Five plastid regions that represent hotspots of change (trnH-psbA, psbC-trnS, trnM-atpE, petA-psbJ and ccsA-ndhD) are identified within Mukdenia, and six regions (trnH-psbA, petN-psbM, trnM-atpE, rps16-trnQ, ycf1 and ndhF) contain a higher number of species-specific parsimony-informative sites that may serve as potential DNA barcodes for species identification. To infer phylogenetic relationships between Mukdenia and Oresitrophe, we combined our data with published data based on three different datasets. The monophyly of each species (Oresitrophe rupifraga, M. acanthifolia and M. rossii) and the inferred topology ((M. rossii, M. acanthifolia), O. rupifraga) are well supported in trees reconstructed using the complete plastome sequences, but M. acanthifolia and M. rossii did not form a separate clade in the trees based on ETS + ITS data, while the mitochondrial CDS trees are not well-resolved. We found low recovery of genes in the Angiosperms353 target enrichment panel from our unenriched genome skimming data. Hybridization or incomplete lineage sorting may be the cause of discordance between trees reconstructed from organellar and nuclear data. Considering its morphological distinctiveness and our molecular phylogenetic results, we strongly recommend that M. acanthifolia be treated as a distinct species.     

Genetic differentiation of two distinct chemotypes of Ferula communis (Apiaceae) in Sardinia (Italy)

The giant fennel, Ferula communis L. (Apiaceae) is a circum-Mediterranean species responsible of severe haemorrhagic intoxication of livestock. Electrophoretic analysis of 14 putative enzyme loci was carried out to assess genetic differentiation among poisonous and non-poisonous chemotypes of F. communis in Sardinia. Genetic structuring characterises all the five populations examined. However, differentiation was higher between poisonous and non-poisonous populations (P<0.00001), and was independent from geographic distances, suggesting a reduced gene flow between the two chemotypes.     

A major change in monsoon-driven productivity in the tropical Indian Ocean during ca 1.2–0.9 Myr: Foraminiferal faunal and stable isotope data

Tropical climate is variable on astronomical time scale, driving changes in surface and deep-sea fauna during the Pliocene–Pleistocene. To understand these changes in the tropical Indian Ocean over the past 2.36 Myr, we quantitatively analyzed deep-sea benthic foraminifera and selected planktic foraminifera from > 125 μm size fraction from Deep Sea Drilling Project Site 219. The data from Site 219 was combined with published foraminiferal and isotope data from Site 214, eastern Indian Ocean to determine the nature of changes. Factor and cluster analyses of the 28 highest-ranked species distinguished four biofacies, characterizing distinct deep-sea environmental settings. These biofacies have been named after their most dominant species such as Stilostomella lepidula–Pleurostomella alternans (Sl–Pa), Nuttallides umbonifer–Globocassidulina subglobosa (Nu–Gs), Oridorsalis umbonatus–Gavelinopsis lobatulus (Ou–Gl) and Epistominella exigua–Uvigerina hispido-costata (Ee–Uh) biofacies. Biofacies Sl–Pa ranges from ~ 2.36 to 0.55 Myr, biofacies Nu–Gs ranges from ~ 1.9 to 0.65 Myr, biofacies Ou–Gl ranges from ~ 1 to 0.35 Myr and biofacies Ee–Uh ranges from 1.1 to 0.25 Myr. The proxy record indicates fluctuating tropical environmental conditions such as oxygenation, surface productivity and organic food supply. These changes appear to have been driven by changes in monsoonal wind intensity related to glacial–interglacial cycles. A shift at ~ 1.2–0.9 Myr is observed in both the faunal and isotope records at Site 219, indicating a major increase in monsoon-induced productivity. This coincides with increased amplitude of glacial cycles, which appear to have influenced low latitude monsoonal climate as well as deep-sea conditions in the tropical Indian Ocean.     

Fcγ receptor IIA and IIIB polymorphisms are associated with susceptibility to cerebral malaria

Human FcγRIIA and FcγRIIIB exhibit genetic polymorphisms, FcγRIIA-131H/R and FcγRIIIB-NA1/NA2, coding for different capacities for IgG binding and phagocytosis. Recently, FcγRIIA-131R was reported to be associated with protection against high-density Plasmodium falciparum infection in Kenya. Furthermore, FcγRIIIB-NA1/NA2 polymorphism was shown to influence FcγRIIA function in an allele-specific manner. In this study, we examined a possible association of FcγRIIA-131H/R and FcγRIIIB-NA1/NA2 polymorphisms with malaria severity in 107 cerebral malaria patients, 157 non-cerebral severe malaria patients, and 202 mild malaria controls living in northwest Thailand. This study reveals that, with the FcγRIIIB-NA2 allele, the FcγRIIA-131H/H genotype is associated with susceptibility to cerebral malaria (OR 1.85, 95% CI 1.14–3.01; P=0.012), although these polymorphisms are not individually involved in the disease severity. Our results suggest that FcγRIIA-131H/R and FcγRIIIB-NA1/NA2 polymorphisms have an interactive effect on host defense against malaria infection.     

山葡萄种质资源DNA条形码通用序列的筛选

对山葡萄(Vitis amurensis)种质资源样品的ITS、ITS2、psb A-trn H、rbc L和mat K序列进行PCR扩增及测序,优化PCR反应的退火温度,比较各序列的扩增效率、测序成功率、品种间和品种内的差异及barcoding gap图,使用BLAST和NJ树法比较不同序列的鉴定能力,最终从5条DNA片段中筛选出可用于山葡萄种质资源鉴定的DNA条形码通用序列。结果表明,在采集的11份33个山葡萄样品中,psb A-trn H和ITS2序列的扩增与测序成功率较高,其品种间、品种内差异及barcoding gap较ITS、rbc L和mat K序列具有明显的优势,且ITS2序列能够鉴别psb A-trn H序列无法鉴别的品种。实验证明,ITS2和psb A-trn H序列是较适合鉴别山葡萄资源的DNA条形码序列组合。DNA条形码弥补了形态学鉴定的不足,可为山葡萄种质资源的准确鉴定提供科学依据。     

Effects of season on the yield and quality of agar from Gracilaria species (Gracilariaceae, Rhodophyta)

The effect of season on yield and physical properties of agars extracted from Gracia gracilis and G. bursa-pastoris were determined. The agar yield from G. gracilis was maximum during spring (30%) and minimum during autumn (19%). In G. bursa-pastoris, the agar yield was greatest in summer (36%) and lowest in winter (23%). Agar yield from G. bursa-pastoris was positively correlated with temperature (r=0.94; P<0.01) and salinity (r=0.97; P<0.01) and negatively with nitrogen content (r=−0.93; P<0.01). Agar gel strengths fluctuated from 229 to 828 g cm⁻² and 23 to 168 g cm⁻² for G. gracilis and G. bursa-pastoris, respectively. The gelling temperature showed significant seasonal variation for both species. Chemical analysis of agar from the two seaweeds indicated variation in 3,6-anhydrogalactose and sulfate content (P<0.01). Furthermore, there was an inverse correlation between the two chemical variables. In general, agar extracted from G. gracilis possessed better qualities than agar extracted from G. bursa-pastoris and can be considered a candidate for industrial use.     

DNA barcodes and microsatellites: How they complement for species identification in the complex genus Tamarix (Tamaricaceae)

DNA barcoding allows the identification of an organism by comparing the sequence of selected DNA regions (barcodes) with a previously compiled database, and it can be useful for taxonomic identification of species in complex genera, such as Tamarix. Many species of this genus show convergent morphology, which leads to frequent errors in their identification. Highly variable genetic markers, such as microsatellites or short sequence repeats (SSR), could be used to differentiate species where DNA barcodes fail. Here, we tested the ability of both, 5 different marker regions (rbcL, matK, ITS, trnH-psbA, and ycf1), and 14 microsatellites, to properly identify Tamarix species, especially those from the Mediterranean Basin, and compared the pros and cons of the different analytical methods for species identification. DNA barcoding allows the genetic identification of certain species in Tamarix. The two-locus barcodes matK + ITS and ITS + ycf1 were the best-performing combinations, allowing up to 69% and 70%, respectively, correct identification. However, DNA barcoding failed in phylogenetically close groups, such as many Mediterranean species. The use of SSR can aid the identification of species, and the combination of both types of data (DNA barcoding and SSR) improved the success. The combination of data was especially relevant in detecting the presence of hybridization processes, which are common in the genus. However, caution must be exercised when choosing the clustering methods for the SSR datasince different methods can lead to very different results.     

Population differentiation and phylogeography of Hygrophila pogonocalyx based on RAPDs fingerprints

Genetic variation of the endangered species, Hygrophila pogonocalyx Hayata (Acanthaceae), was estimated based on RAPD fingerprints. According to the criteria of the International Union for Conservation of Nature and Nature Resources, H. pogonocalyx is on the Red List Category due to its endangered status. Entomophilous plants of H. pogonocalyx are mostly pollinated by honeybees. Gene flow between populations is constrained by the migratory capacity of the pollinators. A survey based on RAPD fingerprinting using 50 random primers revealed the distribution of genetic variation following an “isolation by distance” model. A hierarchical AMOVA analyses indicated significant differentiation between geographical regions (Φ_ct=0.934; P=0.048), among populations (Φ_st=0.945; P<0.001), and among populations within region (Φ_sc=0.169; P<0.001). The differentiation between geographic populations may be ascribed to a long isolation since the formation of the Central Mountain Range 1 million years ago. In contrast to low levels of genetic variation in many endangered species, some genetic processes avoiding selfing may have evolved in H. pogonocalyx. Somatic mutation also possibly contributed to the variability maintenance within populations with limited size.     

A mathematical model on the effect of M. denticulata weed on different winter crops

Many weeds interfere with the productivity of wheat and other winter annual crops; however, one common weed Medicago denticulata, appears to have a beneficial effect. An experiment was conducted at Agricultural Experimental Farm of the Indian Statistical Institute, Giridih, Jharkhand to observe the effect of M. denticulata (a legume) on different crops yield of barley (Hordeum vulgare Sensu lato), linseed (Linum usitatissimum L.), Indian mustard [Brassica juncea (L.) Czernj. & Cosson] and wheat (Triticum aestivum L.). The commensalisms interaction was studied, in which one species benefits, while the other is unaffected, between the crops, M. denticulata and other weeds, to observe the role of medicago as biological control agent of other weeds for enhancement of crop productivity. Further, a statistical test was performed to establish the effect of M. denticulata and weed infestations based on one-step Markov structure of the covariance matrix of the biomass. This permitted development of a mathematical model of a crop–M. denticulata–other weeds system and their interactions through direct and indirect competition for resources. Crops yield decreased considerably due to the presence of other weeds, while it increased due to introduction of medicago and hence medicago acted as a controlling agent in a crop–M. denticulata–other weeds system. Our mathematical analysis supported the experimental findings. The model parameters are estimated through a nonlinear least square and stochastic differential equations. Moreover, some thresholds for the growth of medicago population came out from our analysis that may be used as a biological control threshold for the enhancement of crop productivity.     

Analysis of lycopene geometrical isomers in biological microsamples by liquid chromatography with coulometric array detection

Methods of analysis for determining low quantities of lycopene cis–trans isomers in biological tissues are needed. Development of two liquid chromatography (LC) methods based on the polymeric C₃₀ stationary phase equipped with coulometric electrochemical array detection (ED) is described. Separation of 13 lycopene isomers including prolycopene, (a novel tetra-cis-lycopene found in Tangerine tomatoes) was accomplished with both isocratic and gradient methods using different proportions of methanol, methyl tert.-butyl ether, water and 1 M ammonium acetate buffer. Carotenoids were detected at potential settings between 200 and 620 mV. Differences in generated current–voltage curves aided in tentative identification of trans carotenoid species and select cis isomers of lycopene. These methods were successfully applied in the analysis of small quantities of plasma, buccal mucosal cells, prostate and cervical tissues. Limits of detection for trans-lycopene by ED were found to be 50 fmol representing a 10- to 100-fold increase over conventional UV–Vis absorbance methods.     

后河保护区柳杉林中黏菌群落组成

柳杉是中国特有树种,对于广泛分布于森林生态系统的黏菌而言,单纯的柳杉林是一种特殊的生境。为探索柳杉林中黏菌的物种多样性,本研究在武陵山区东北部的湖北省后河国家级自然保护区柳杉林样地中采集柳杉树皮和凋落物,在120个培养湿室中,发生黏菌的湿室68个,占56.67%。从两种基物上获得黏菌6目7科12属24种,优势种为混淆筛菌Cribraria confusa,相对丰度达到19.01%。柳杉林凋落物上发生的黏菌种类和数量高于柳杉树皮,凋落物和柳杉树皮上发生的黏菌共有种为4种,种群间的Sørensen相似性系数为Cs=0.333。在不同季节间,黏菌物种的群落组成与多样性也表现出差异,春季Shannon-Wiener多样性指数Hʹ=0.2987±0.1564,夏季Hʹ=0.1105±0.0949,秋季Hʹ=0.1968±0.0589,冬季Hʹ=0.2726±0.0875。黏菌物种数量发生最多的是春季和冬季,均有15种,仅在春季发生的黏菌物种为粗壮发菌Comatricha suksdorfii、鲜黄绒泡菌Physarum luteolum、暗红团网菌Arcyria denudata和极小无丝菌Licea minima,仅在冬季发生的黏菌物种为钙丝绒泡菌Physarum decipiens、小筛菌Cribraria microcarpa和暗褐无丝菌Licea belmontiana。典型对应分析（canonical correspondence analyses,CCA）表明,影响柳杉林中黏菌物种群落组成与多样性的主要环境因素是基物类型。     

The relationship between leaf longevity and growth ring markedness in modern conifer woods and its implications for palaeoclimatic studies

Growth rings in modern conifer woods were quantitatively analysed to investigate the relationship between leaf longevity and the markedness of the growth ring boundary. Five conifer species exhibiting a wide range of Leaf Retention Times (LRTs) were examined in anatomical sections stored in the Jodrell Laboratory, Royal Botanic Gardens, Kew, Surrey, UK. The species studied were Larix decidua Mill. (deciduous), Pinus sylvestris L. (LRT=1–3 years), Picea abies (L.) H. Karst. (LRT=3–5 years), Cedrus libani A. Rich. (LRT=3–6 years), and Araucaria araucana (Molina) K. Koch (LRT=3–15 years). Two aspects of ring markedness were quantified: (1) the percentage of latewood in each growth ring increment and (2) the difference between the maximum and minimum radial cell diameters in the growth ring increment expressed as a percentage of the maximum cell diameter (percentage diminution). The product of these two parameters was calculated to give a Ring Markedness Index (RMI). Five growth ring increments were measured for each species from poorly provenanced specimens grown in southern England. Statistical analysis of these data shows that there is a significant inverse linear relationship between median LRT and percentage latewood (R²=0.86), percentage diminution (R²=0.77), and RMI (R²=0.91), at P<0.001. These data suggest that leaf longevity exerts an important control on growth ring markedness, in addition to the influence exerted by the growing environment (climatic and edaphic conditions). The significance of these results for the palaeoclimatic analysis of growth rings in fossil woods is discussed with reference to two case-studies: (1) the Early Carboniferous tropical climate of the British Isles and (2) the Early Cretaceous polar climate of the Antarctic Peninsula.     

High regional genetic differentiation of an endangered relict plant Craigia yunnanensis and implications for its conservation

Of the genus Craigia, widespread in the Tertiary, only two relict species survived to modern times. One species is now possibly extinct and the other one, Craigia yunnanensis, is severely endangered. Extensive surveys have located six C. yunnanensis populations in Yunnan province, southwest China. Using fluorescent amplified fragment length polymorphism (AFLP), the genetic diversity and population structure of these populations were examined. It was found that genetic diversity of C. yunnanensis was moderate at the species level, but low at regional and population levels. Analysis of population structure showed significant genetic differentiation between Wenshan and Dehong regions, apparently representing two geographically isolated for long time refuges. There are also clear indications of isolation between populations, which, together with anthropogenically caused decline of population size, will lead to general loss of the species genetic variation with subsequent loss of adaptive potential. To conserve the genetic integrity of C. yunnanensis, we recommend that ex-situ conservation should include representative samples from every population of the two differentiated regions (e.g. Wenshan and Dehong). The crosses between individuals originated from different regions should be avoided because of a high risk of outbreeding depression. As all the extant populations of C. yunnanensis are in unprotected areas with strong anthropogenic impact, there is no alternative to reintroduction of C. yunnanensis into suitable protected locations.     

Enzyme polymorphism in three species of Metanephrops (Decapoda: Nephropidae) from Taiwan

Electrophoretic analysis of 22 genetic Loci coding for 17 enzymes was used to investigate relationships among three species of Metanephrops (M. thomsoni M. formosanus and M. japonicus var) from Taiwan. Eleven Ioci are identically monomorphic in the three species. Only one Iocus Sdh was diagnostic for identification of the three species. Electrophoretically detectable variation was confined to three species of Metanephrops with Iow frequency — the unique alleles of ALk, Gdh, Gpi, Me-1 and 6-Pgdh. The proportion of polymorphic loci (0.95 level) ranged from 0.047 to 0.091 and expected average heterozygosity 0.0043–0.0232. Estimates of Nei's genetic distances between the three species suggest that M. formosanus and M. japonicus var. are closely related.