Two new species of <Emphasis Type="Italic">Parspina</Emphasis> Pearse, 1920 (Digenea: Cryptogonimidae) from freshwater fishes (Gymnotiformes) of the Paraná River basin in Argentina

Two new species of the cryptogonimid genus Parspina Pearse, 1920 are described from gymnotiform fishes of the Paraná River basin, P. carapo n. sp. from the banded knifefish Gymnotus carapo Linnaeus and P. virescens n. sp. from the glass knifefish Eigenmannia virescens (Valenciennes). Parspina carapo differs from P. virescens in the number of oral spines (32–39 vs 30–33) and their length (28–47 vs 16–28 μm), the distribution of tegumental spines and their anchorage, the types of sensory papillae on the body surface (three vs two types), the extent of body length posterior to the caeca (5 vs 13% of the total body length), the dimensions of the pars prostatica (52 × 34 vs 24 × 10 μm), and in the absence of a gonotyl (vs presence). Both P. carapo and P. virescens differ from P. bagre Pearse, 1920 and P. argentinensis (Szidat, 1954) in the number of oral spines (20–21 and 21–28 in the latter pair) and their length (28–32 and 35–60 μm), and in total body length. Additionally, the two new species differ from P. argentinensis in the arrangement of the vitelline follicles (one continuous band vs two groups on each side of the body) and in having a smaller pars prostatica (149 × 49 μm in the latter). Parspina carapo is the fifth intestinal helminth found in G. carapo, and P. virescens is the first found in E. virescens.     

沙质草地3种优势植物叶片光合生理对增温和降水减少的响应北大核心CSCD

以沙质草地优势物种猪毛蒿、胡枝子和糙隐子草为研究对象,利用开顶式生长室(OTC)模拟增温,研究降水减少20%、40%和60%与增温的交互作用对3种典型植物叶片光合气体交换特征及叶绿素荧光特征的影响,以揭示沙质草地3种优势植物对气候变化的响应规律。结果显示:(1)与自然温度相比,OTC模拟增温增加了猪毛蒿C_(i),显著降低了胡枝子G_(s)、P_(n)和T_(r)、糙隐子草G_(s)和P_(n)、猪毛蒿WUE和L_(s),也显著降低了猪毛蒿和胡枝子F_(v)/F_(m)和F_(v)/F_(o)。(2)无论增温与否,随着降水减少幅度的增加,猪毛蒿G_(s)和P_(n)呈下降趋势,且中度以上的干旱胁迫下(降水减少>40%)胡枝子和糙隐子草P_(n)显著低于对照。(3)在自然温度条件下,轻度干旱胁迫时(降水减少20%)猪毛蒿T_(r)显著低于对照,重度干旱胁迫时(降水减少60%)其WUE、F_(v)/F_(m)和F_(v)/F_(o)显著低于对照;重度干旱胁迫时,胡枝子C_(i)显著高于对照,差异幅度达10.7%,L_(s)显著低于对照,轻度干旱胁迫时(降水减少20%)其F_(v)/F_(m)和F_(v)/F_(o)显著高于中度以上的干旱胁迫;中度以上的干旱胁迫下糙隐子草T_(r)和G_(s)显著低于对照,重度干旱胁迫时,其C_(i)、F_(v)/F_(m)和F_(v)/F_(o)显著低于对照,WUE和L_(s)显著高于对照。(4)增温与降水减少交互作用下,所有处理猪毛蒿C_(i)均高于对照,差异幅度分别达4.5%,6.0%和8.4%;胡枝子T_(r)均显著低于对照,差异幅度达57.8%;重度干旱胁迫时猪毛蒿L_(s)和WUE显著低于对照,糙隐子草F_(v)/F_(m)和F_(v)/F_(o)随降水减少而降低,中度以上的干旱胁迫时其值显著低于对照。(5)相关性分析表明,3个优势物种的P_(n)与F_(v)/F_(m)和F_(v)/F_(o)均呈显著正相关关系,其中猪毛蒿和糙隐子草的P_(n)—F_(v)/F_(m)和P_(n)—F_(v)/F_(o)斜率明显高于胡枝子。研究表明,气候变暖会在一定程度上加剧降水减少对沙质草地3种群落优势物种光合作用的抑制。     

蛹虫草磷酸甲羟戊酸激酶和焦磷酸甲羟戊酸脱羧酶基因的功能分析

【目的】确定蛹虫草甲羟戊酸途径中的2个关键酶——磷酸甲羟戊酸激酶(CmErg8)和焦磷酸甲羟戊酸脱羧酶(CmErg19)的功能及其对麦角甾醇和虫草素含量的影响。【方法】通过生物信息学分析鉴定蛹虫草中CmErg8和CmErg19,并采用酵母互补确定其功能是否保守;以蛹虫草尿嘧啶营养缺陷型CmΔpyrG为背景菌株,利用农杆菌介导的转化方法对CmErg8和CmErg19进行过表达,观察其对麦角甾醇和虫草素含量的影响。【结果】CmErg8和CmErg19不能互补酵母erg8和erg19突变体的温度敏感表型;CmErg8和CmErg19过表达菌株中麦角甾醇和虫草素含量均有所增加,特别是CmErg19基因过表达可以使虫草素含量提升5倍左右。【结论】本研究揭示了蛹虫草CmErg8和CmErg19的功能,并且发现蛹虫草麦角甾醇合成通路基因可能会影响虫草素含量。     

Mutually exclusive distribution of the sap and eag S-layer genes and the lytB/lytA cell wall hydrolase genes in Bacillus thuringiensis

Recently, two Bacillus thuringiensis strains were reported to synthesize parasporal inclusion bodies made not of the expected crystal (Cry) proteins but rather of the surface layer proteins (SLP) Sap (encoded by sap) and EA1 (encoded by eag), respectively. Whether the presence of the sap and eag genes is restricted to these two B. thuringiensis strains or ubiquitous in B. thuringiensis is unknown. We report here the distribution of the sap and eag genes in B. thuringiensis. Strains in the Bacillus cereus group were added for comparison purposes. We show that sap and eag are either present in tandem in 35% of the B. thuringiensis strains analysed and absent in 65% of the strains. When absent, a different tandem, the lytB/lytA cell wall hydrolase genes, is present. The distribution of the sap and eag S-layer and the lytB/lytA cell wall hydrolase genes is not species-specific in B. thuringiensis, B. cereus and Bacillus weihenstephanensis. Bacillus anthracis and Bacillus mycoides harbor sap and eag but not lytB/lytA. The sap, eag and lytB/lytA genes were absent in Bacillus pseudomycoides. Clearly, the distribution of the sap and eag S-layer and the lytB/lytA cell wall hydrolase genes in B. thuringiensis and in the Bacillus cereus group is mutually exclusive. We also showed that two genes involved in cell wall metabolism, csaA and csaB, are present not only upstream of the sap and eag S-layer genes, but also upstream of the lytB/lytA tandem in strains where sap and eag are absent. Bootstrapped neighbor-joining trees were inferred from the translated amino acid sequences of sap, eag and the tandem lytB/lytA, respectively.     

3种卫矛属植物叶片秋冬季转色期生理生化特征研究

以疏花卫矛(Euonymus laxiflorus)、丝棉木(E.maackii)和卫矛(E.alatus)3种卫矛属植物为试验材料,测定叶片转色期叶色参数和相关生理生化指标,探讨各项指标的变化规律和内在联系,为优良色叶植物的筛选提供依据。结果表明:(1)转色期,疏花卫矛的明亮度参数L~*和色素参数b~*(黄/蓝)呈上升趋势,色素参数a~*(红/绿)变化不大;丝棉木的L~*和b~*呈先上升后下降的单峰曲线,a~*呈上升趋势;卫矛的L~*和b~*变化不大,a~*呈上升趋势。(2)3种植物的叶绿素含量在转色期呈明显下降趋势;疏花卫矛的花色素苷相对含量、花色素苷/叶绿素的值较为平稳,类胡萝卜素/叶绿素的值呈上升趋势;丝棉木和卫矛的花色素苷相对含量、花色素苷/叶绿素的值均呈上升趋势,类胡萝卜素/叶绿素的值保持平稳。(3)3种植物苯丙氨酸解氨酶(PAL)活性呈下降趋势,查尔酮异构酶(CHI)活性呈先上升后下降的单峰曲线;卫矛的过氧化物酶(POD)和多酚氧化酶(PPO)活性保持平稳,疏花卫矛和丝棉木的POD活性呈上升趋势,疏花卫矛的PPO活性保持平稳,丝棉木的PPO活性呈下降趋势。(4)疏花卫矛和卫矛的可溶性糖和淀粉的质量分数呈先上升后下降的单峰曲线,丝棉木的可溶性糖和淀粉的质量分数呈上升趋势。(5)相关性分析显示,疏花卫矛呈现黄色主要是因为叶绿素的分解,丝棉木和卫矛呈现红色是因为花色素苷的合成,可溶性糖、淀粉、CHI对花色素苷的合成有一定作用,POD对叶片呈现红色有促进作用,PAL和PPO活性对花色素苷的合成无显著影响。     

What can we learn about the lipid vesicle structure from the small-angle neutron scattering experiment?

Small-angle neutron scattering (SANS) on the unilamellar vesicle (ULV) populations (diameter 500 and 1,000 Å) in D₂O was used to characterize lipid vesicles from dimyristoylphosphatidylcholine (DMPC) at three phases: gel L_β′, ripple P_β′ and liquid L_α. Parameters of vesicle populations and internal structure of the DMPC bilayer were characterized on the basis of the separated form factor (SFF) model. Vesicle shape changes from nearly spherical in the L_α phase to elliptical in the P_β′ and L_β′ phases. This is true for vesicles prepared via extrusion through pores with the diameter 500 Å. Parameters of the internal bilayer structure (thickness of the membrane and the hydrophobic core, hydration and the surface area of the lipid molecule) were determined on the basis of the hydrophobic–hydrophilic (HH) approximation of neutron scattering length density across the bilayer ρ(x) and of the step function (SF) approximation of ρ(x). DMPC membrane thickness in the L_α phase (T=30°C) demonstrates a dependence on the membrane curvature for extruded vesicles. Prepared via extrusion through 500 Å diameter pores, vesicle population in the L_α phase has the following characteristics: average value of minor semi-axis 266±2 Å, ellipse eccentricity 1.11±0.02, polydispersity 26%, thickness of the membrane 48.9±0.2 Å and of the hydrophobic core 19.9±0.4 Å, surface area 60.7±0.5 Ų and number of water molecules 12.8±0.3 per DMPC molecule. Vesicles prepared via extrusion through pores with the diameter 1,000 Å have polydispersity of 48% and membrane thickness of 45.5±0.6 Å in the L_α phase. SF approximation was used to describe the DMPC membrane structure in L_β′ (T=10°C) and P_β′ (T=20°C) phases. Extruded DMPC vesicles in D₂O have membrane thickness of 49.6±0.5 Å in the L_β′ phase and 48.3±0.6 Å in the P_β′ phase. The dependence of the DMPC membrane thickness on temperature was restored from the SANS experiment.     

Differences in susceptibility of introduced and native white grub species to entomopathogenic nematodes from various geographic localities

Invasive, non-native, white grubs (Coleoptera: Scarabaeidae) cause significant damage in urban landscapes. Although the lack of natural enemies in their new home is often suggested as an important factor in the establishment and spread of invasive species, the potential of incumbent generalist parasites and pathogens to delay their establishment and spread has not been explored. We compared the susceptibility of the introduced Popillia japonica and the native Cyclocephala borealis to 16 species and strains of entomopathogenic nematodes isolated from within or outside the geographic ranges of the two scarabs. We found large variation in the virulence of the species/strains of nematodes with over 50% mortality of P. japonica produced by Heterorhabditis zealandica strain X1 and H. bacteriophora strain GPS11 and of C. borealis by H. zealandica and H. bacteriophora strains KMD10 and NC1. Heterorhabditis indica and H. marelatus caused less than 20% mortality of both scarab species. When considered as a group the nematode species and strains from within and outside the geographic ranges of either P. japonica or C. borealis did not differ in virulence towards either scarab species. Dose response studies with selected nematode species and strains against P. japonica and two additional non-native species Anomala (Exomala) orientalis and Rhizotrogus majalis and the native C. borealis indicated that R. majalis was the least susceptible and P. japonica and A. orientalis were as susceptible as the native C. borealis. Heterorhabditis zealandica was significantly more virulent than any other species or strain against P. japonica with a LC₅₀ of 272 IJs/grub. The LC₃₀ and LC₅₀ values for H. zealandica were also the lowest among the four nematode species/strains tested against A. orientalis and C. borealis. The LC₅₀ values for H. zealandica and H. megidis (UK strain) were significantly lower for the native C. borealis than the introduced A. orientalis. H. zealandica also showed the highest penetration efficiency and the lowest encapsulation in P. japonica and C. borealis grubs. Results suggest that the introduction of the exotic H. zealandica into the front-line states with respect to the movement of P. japonica and A. orientalis should be explored as a tactic to delay their establishment and spread. The results also suggest that the manipulation of the indigenous H. bacteriophora populations may help in delaying spread and mitigating losses caused by the invasive grub species.     

捕食者对空心莲子草叶甲种群的生物胁迫

广食性捕食者广泛捕食植食性昆虫,常被用于有害生物的生物防治,也因此影响植食性昆虫对杂草的生物效果。空心莲子草叶甲(Agasicles hygrophila)(鞘翅目:叶甲科Chrysomelidae)作为入侵恶性杂草空心莲子草(Alternanthera philoxeroides)(苋科:莲子草属Alternanthera)的专性天敌,从美国的弗罗里达州引入中国,在释放地防治空心莲子草取得了较好的防治效果。虽然空心莲子草叶甲在引入地均已建立田间种群并有一定程度的自然扩散,但丰富的食物资源,并未使空心莲子草叶甲的自然种群数量变得繁荣,因此其未能有效抑制空心莲子草的扩散蔓延。在野外调查时发现空心莲子草生境中存在大量广食性捕食者。这些广食性捕食者是抑制空心莲子草叶甲种群数量扩张的生物胁迫因子吗?为此,选择捕食性昆虫龟纹瓢虫(Propylaea japonica)(鞘翅目:瓢虫科Coccinellidae)、蜘蛛类捕食者拟水狼蛛(Pirata subpiraticus)(蜘蛛目:狼蛛科Lycosidae)与斜纹猫蛛(Oxyopes sertatus)(蜘蛛目:猫蛛科Oxyopidae)为捕食者,分别以空心莲子草叶甲各虫态为猎物,构建简单的捕食者-猎物系统,在室内检测了上述3种捕食者对空心莲子草叶甲各虫态在不同密度下的日捕食量,以期了解捕食者对空心莲子草叶甲的捕食作用,客观评估空心莲子草叶甲的生物防治效能。研究结果表明:捕食者龟纹瓢虫、斜纹猫蛛与拟水狼蛛均捕食空心莲子草叶甲的卵粒及1龄、2龄幼虫,斜纹猫蛛与拟水狼蛛捕食3龄幼虫,捕食者的捕食量均随着猎物密度的升高而增加,寻找效应降低。三者均不捕食成虫。除拟水狼蛛对3龄幼虫的捕食用Holling II模型拟合不呈显著相关关系外,其余捕食反应均拟合Holling II模型并显著相关。通过拟合方程得出捕食者对空心莲子草叶甲卵粒的理论日最大捕食量为:斜纹猫蛛10.9粒,拟水狼蛛为6.2粒,龟纹瓢虫为5.6粒;对1龄幼虫的理论日最大捕食量为:斜纹猫蛛为17.1头;拟水狼蛛为35.8头,龟纹瓢虫为10.4头;对2龄幼虫的理论日最大捕食量为:斜纹猫蛛为6.6头,拟水狼蛛为11.2头,龟纹瓢虫为2.9头;对3龄幼虫的理论日最大捕食量为:斜纹猫蛛捕食12.3头,拟水狼蛛为1.1头。研究结果证实了捕食者可通过捕食作用降低空心莲子草叶甲种群密度,削弱空心莲子草叶甲对空心莲子草的控害效能,是空心莲子草叶甲种群存活的生物胁迫因子。建议在提高空心莲子草叶甲田间种群数量,达到对空心莲子有效的持续控制效果方面开展进一步研究。     

Effects of ATP-sensitive Potassium Channel Regulators on Chloride Channels in the Sarcoplasmic Reticulum Vesicles from Rabbit Skeletal Muscle

The lipid bilayer technique was used to examine the effects of the ATP-sensitive K⁺ channel inhibitor (glibenclamide) and openers (diazoxide, minoxidil and cromakalim) and Cl⁻ channel activators (GABA and diazepam) on two types of chloride channels in the sarcoplasmic reticulum (SR) from rabbit skeletal muscle. Neither diazepam at 100 μm nor GABA at 150 μm had any significant effect on the conductance and kinetics of the 75 pS small chloride (SCl) channel. Unlike the 150 pS channel, the SCl channel is sensitive to cytoplasmic glibenclamide with K _i ∼ 30 μm. Glibenclamide induced reversible decline in the values of current (maximal current amplitude, I _max and average mean current, I′) and kinetic parameters (frequency of opening F _o , probability of the channel being open P _o and mean open time, T _o , of the SCl channel. Glibenclamide increased mean closed time, T _c , and was a more potent blocker from the cytoplasmic side (cis) than from the luminal side (trans) of the channel. Diazoxide increased I′, P _o , and T _o in the absence of ATP and Mg²⁺ but it had no effect on I _max and also failed to activate or remove the glibenclamide- and ATP-induced inhibition of the SCl channel. Minoxidil induced a transient increase in I′ followed by an inhibition of I _max, whereas cromakalim reduced P _o and I′ by increasing channel transitions to the closed state and reducing T _o without affecting I _max. The presence of diazoxide, minoxidil or cromakalim on the cytoplasmic side of the channel did not prevent [ATP] _cis or [glibenclamide] _cis from blocking the channel. The data suggest that the action(s) of these drugs are not due to their effects on the phosphorylation of the channel protein. The glibenclamide- and cromakalim-induced effects on the SCl channel are mediated via a ``flicker' type block mechanism. Modulation of the SCl channel by [diazoxide] _cis and [glibenclamide] _cis highlights the therapeutic potential of these drugs in regulating the Ca²⁺-counter current through this channel. Received: 2 September 1997/Revised: 20 March 1998     

The taxonomy of the family Paramphistomidae Fischoeder, 1901 with special reference to the morphology of species occurring in ruminants. II. Revision of the genus Paramphistomum Fischoeder, 1901

Summary The genus Paramphistomum Fischoeder, 1901 is redefined and restricted and only the following species are retained and considered valid: P. cervi (Zeder, 1790) (type species); P. liorchis Fischoeder, 1901; P. gracile Fischoeder, 1901 P. epiclitum Fischoeder, 1904; P. gotoi Fukui, 1922, P. ichikawai Fukui, 1922; P. leydeni Näsmark, 1937 and P. hiberniae Willmott, 1950. These are redescribed and illustrated. A new species, Paramphistomum cephalophi is described and illustrated from the black-fronted duiker (Cephalophus nigrifrons) in Rwanda. It differs from the rest of the species in the genus by the presence of an anterior sphincter in the pharynx and the characteristic posterior notch of the acetabular rim. Scanning electron photomicrographs of the tegumental surfaces of the species in the genus are provided. Cotylophoron indicum Stiles & Goldberger, 1910 (=Paramphistomum thapari Price & McIntosh, 1953), C. madrasense Gupta, 1958, C. chauhani Gupta & Gupta, 1972, Paramphistomum indicum Stiles & Goldberger, 1910 (in part), P. malayi Lee & Lowe, 1971 and Srivastavaia indica Singh, 1970 are considered synonyms of Paramphistomum epiclitum Fischoeder, 1904. Paramphistomum indicum Stiles & Goldberger, 1910 (in part) and P. bombayiensis Gupta & Verma in Gupta & Nakhasi, 1977 are regarded as synonyms of Paramphistomum gracile Fischoeder, 1901. P. scotiae Willmott, 1950, P. julimarinorum Velázquez-Maldonado, 1976, P. nicabrasilorum Velázquez- Maldonado, 1976, P. procapri Wang, 1979 and Cotylophoron skrjabini Mitskevich, 1958 are considered synonyms of Paramphistomum leydeni Näsmark, 1937. Cotylophoron vigisi Davydova, 1963 is considered synonymous with Paramphistomum ichikawai Fukui, 1922. Paramphistomum birmense Railliet, 1924, P. microon Railliet, 1924, P. chinensis Hsu, 1935 and P. pseudocuonum Wang, 1979 are regarded as species inquirendae.The genera Liorchis Velichko, 1966 and Srivastavaia Singh, 1970 are synonymized with Paramphistomum Fischoeder, 1901.A key to the species of the genus is provided.Part of a thesis approved by the University of London for the award of the Ph.D. degree.Part of a thesis approved by the University of London for the award of the Ph.D. degree.     

Relationships and divergence of some taxa of the subfamily Lycodinae (Zoarcidae,Pisces) based on molecular-genetic and morphological data

An integrated molecular-genetic and morphological study of 14 species of 6 genera of Zoarcidae of the subfamily Lycodinae was performed. A high coincidence of study results obtained using both methods was found. The generic independence of the genus Petroschmidtia that includes species P. albonotata and P. toyamensis was justified. It was shown that species L. schmidti and L. nigrocaudatus belong to the genus Lycogrammoides; and the generic status of the genus Bothrocarichthys with species B. microcephalus and of the genus Allolepis with species A. hollandi was restored. The studied taxa fall into three large monophyletic groups that include species of the genus Petroschmidtia, species of the genus Lycodes, and species of the genera Bothrocara, Allolepis, Bothrocarichthys, and Lycogrammoides. Taxa of the last group are characterized by a large complex of morphological differences from the first two groups, including the absence of ventral fins. A key to species and genera of Lycogrammoides and Bothrocarichthys was compiled. The problem of determination of the time of divergence of the studied zoarcid-like fish using the concept of “molecular clock” and its calibration according to paleontological and paleogeographic data is discussed.     

Effects of light quality,CO2 tensions and NO 3 +− concentrations on the inorganic nitrogen metabolism of Chlamydomonas reinhardii

The blue light dependent utilization of nitrate by green algae under common air and high irradiances, besides its assimilatory nature, is associated with the release of NO₂ ^– and NH₄ ⁺ to the culture medium. If the CO₂ content of the sparging air was increased up to 2%, previously excreted NO₂ ^– and NH₄ ⁺ were rapidly assimilated. When under air and high irradiances the cell density in the culture reached values corresponding to 25 g Ch 1.ml^-1, no further growth was observed and the highest values of NO₃ ^– consumption and NO₂ ^– and NH₄ ⁺ release were attained. Besides low CO₂ tensions, increasing NO₃ ^– concentrations in the medium stimulated the release of NO₃ ^– and NH₄ ⁺. Under CO₂-free air the consumption of NO₃ ^– and the release of NO₂ ^– and NH₄ ⁺ on a total N bases were almost stoichiometric and their rates saturated at much lower irradiances than under air. Under CO₂-free air high rates of NO₂ ^– release were only observed under the blue radiations that were effectively absorbed by photosynthetically active pigments, i.e. 460 nm, but not under 404 and 630 nm radiations. However, the simultaneous illumination of the cells with 404 and 630 nm monochromatic light showed a remarkable synergistic effect on NO₂ ^– release.The results are discussed in terms of the close relationship between C and N metabolism, the photosynthetic reducing power required to convert NO _inf3 ^sup± -N into R – NH₂-N and the blue light activation of nitrate reductase.     

Improvement of the transfucosylation activity of α-l-fucosidase from Thermotoga maritima for the synthesis of fucosylated oligosaccharides in the presence of calcium and sodium

The influence of CaCl₂ and NaCl in the hydrolytic activity and the influence of CaCl₂ in the synthesis of fucosylated oligosaccharides using α-l-fucosidase from Thermotoga maritima were evaluated. The hydrolytic activity of α-l-fucosidase from Thermotoga maritima displayed a maximum increase of 67% in the presence of 0.8 M NaCl with water activity (a_w) of 0.9672 and of 138% in the presence of 1.1 M CaCl₂ (a_w 0.9581). In addition, the hydrolytic activity was higher when using CaCl₂ compared to NaCl at a_w of 0.8956, 0.9581 and 0.9672. On the other hand, the effect of CaCl₂ in the synthesis of fucosylated oligosaccharides using 4-nitrophenyl-fucose as donor substrate and lactose as acceptor was studied. In these reactions, the presence of 1.1 M CaCl₂ favored the rate of transfucosylation, and improved the yield of synthesis duplicating and triplicating it with lactose concentrations of 58 and 146 mM, respectively. CaCl₂ did not significatively affect hydrolysis rate in these reactions. The combination of the activating effect of CaCl₂, the decrement in a_w and lactose concentration had a synergistic effect favoring the synthesis of fucosylated oligosaccharides.

     

DNA barcoding of Oryza: conventional,specific, and super barcodes

Key message

We applied the phylogenomics to clarify the concept of rice species, aid in the identification and use of rice germplasms, and support rice biodiversity.

Abstract

Rice (genus Oryza) is one of the most important crops in the world, supporting half of the world’s population. Breeding of high-yielding and quality cultivars relies on genetic resources from both cultivated and wild species, which are collected and maintained in seed banks. Unfortunately, numerous seeds are mislabeled due to taxonomic issues or misidentifications. Here, we applied the phylogenomics of 58 complete chloroplast genomes and two hypervariable nuclear genes to determine species identity in rice seeds. Twenty-one Oryza species were identified. Conspecific relationships were determined between O. glaberrima and O. barthii, O. glumipatula and O. longistaminata, O. grandiglumis and O. alta, O. meyeriana and O. granulata, O. minuta and O. malampuzhaensis, O. nivara and O. sativa subsp. indica, and O. sativa subsp. japonica and O. rufipogon. D and L genome types were not found and the H genome type was extinct. Importantly, we evaluated the performance of four conventional plant DNA barcodes (matK, rbcL, psbA-trnH, and ITS), six rice-specific chloroplast DNA barcodes (psaJ-rpl33, trnC-rpoB, rps16-trnQ, rpl22-rps19, trnK-matK, and ndhC-trnV), two rice-specific nuclear DNA barcodes (NP78 and R22), and a chloroplast genome super DNA barcode. The latter was the most reliable marker. The six rice-specific chloroplast barcodes revealed that 17% of the 53 seed accessions from rice seed banks or field collections were mislabeled. These results are expected to clarify the concept of rice species, aid in the identification and use of rice germplasms, and support rice biodiversity.

     

Mitochondrial capture and incomplete lineage sorting in the diversification of balitorine loaches (Cypriniformes,Balitoridae) revealed by mitochondrial and nuclear genes

Tang, Q.‐Y., Liu, S.‐Q., Yu, D., Liu, H.‐Z. & Danley, P.D. (2012) Mitochondrial capture and incomplete lineage sorting in the diversification of balitorine loaches (Cypriniformes, Balitoridae) revealed by mitochondrial and nuclear genes. —Zoologica Scripta, 41, 233–247. Understanding the diversification of species is a central goal of evolutionary biological studies. One powerful tool to investigate the speciation process is molecular systematics. Here, we use molecular methods to investigate the evolution of balitorine loaches belonging to two genera, Lepturichthys and Jinshaia. Both genera contain only two species (Lepturichthys fimbriata, Lepturichthys dolichopterus and Jinshaia sinensis and Jinshaia abbreviata), all of which are endemic to China. These species share many morphological and ecological characters and exhibit overlapping distributions in the Upper Yangtze River. In this study, we used two mitochondrial genes (Cytb and COI) and one nuclear gene (RAG1) to investigate the phylogenetic relationships within and between these two genera. Phylogenetic analyses and network construction based on mitochondrial and nuclear genes consistently supported the monophyly of Jinshaia. In contrast, the mitochondrial and nuclear genes yielded conflicting results in Lepturichthys. The phylogenetic analyses of mitochondrial sequences identify two distinct Lepturichthys lineages, Lepturichthys A and Lepturichthys B. Lepturichthys A includes most of L. fimbriata individuals from the Upper Yangtze River and is the sister group to all Jinshaia species. Lepturichthys B consists of the remaining L. fimbriata individuals from the Upper and Middle Yangtze River, and all L. dolichopterus individuals from the Minjiang River in Southeastern China. However, the analysis of the nuclear sequence indicates that the genus Lepturichthys is monophyletic and is only distantly related to Jinshaia. This incongruence suggests that introgressive hybridization might have occurred between L. fimbriata (Lepturichthys A) and Jinshaia species. As a result of this hybridization event, L. fimbriata captured the mitochondrial genome of the sympatric Jinshaia species. This capture event appears to have occurred at least 1.74 million years ago. Additionally, L. fimbriata appears to be paraphyletic; the nuclear data indicated that L. dolichopterus forms a monophyletic clade nested within L. fimbriata. Because L. dolichopterus and L. fimbriata are allopatric and hybridization may not be possible, we suggest that the observed paraphyly of L. fimbriata is a product of incomplete lineage sorting. In addition, the reciprocal monophyly of J. sinensis and J. abbreviata could not be resolved. This may be the result of interspecific hybridization as these species occur sympatrically. However, incomplete lineage sorting may have caused the observed topology of the Jinshaia species. The data presented here illustrate the complex evolutionary history of the balitorine loach species: intergeneric hybridization and interspecific hybridization have likely occurred in this lineage. In addition, possible incomplete lineage sorting may further obscure the evolutionary history of this group. The complex relationships of the balitorine loaches provide a rich evolutionary system to study the creation of sympatric and sister species.     

Utility of the trnH–psbA Intergenic Spacer Region and Its Combinations as Plant DNA Barcodes: A Meta-Analysis

Background

The trnH–psbA intergenic spacer region has been used in many DNA barcoding studies. However, a comprehensive evaluation with rigorous sequence preprocessing and statistical testing on the utility of trnH–psbA and its combinations as DNA barcodes is lacking.

Methodology/Principal Findings

Sequences were searched from GenBank for a meta-analysis on the usefulness of trnH–psbA and its combinations as DNA barcodes. After preprocessing, we constructed full and matching data sets that contained 17 983 trnH–psbA sequences and 2190 sets of trnH–psbA, matK, rbcL, and ITS2 sequences from the same sample, repectively. These datasets were used to analyze the ability of trnH–psbA and its combinations to discriminate species by the BLAST and BLAST+P methods. The Fisher''s exact test was used to evaluate the significance of performance differences. For the full data set, the identification success rates of trnH–psbA exceeded 70% in 18 families and 12 genera, respectively. For the matching data set, the identification rates of trnH–psbA were significantly higher than those of the other loci in two families and four genera. Similarly, the identification rates of trnH–psbA+ITS2 were significantly higher than those of matK+rbcL in 18 families and 21 genera.

Conclusion/Significane

This study provides valuable information on the higher utility of trnH–psbA and its combinations. We found that trnH–psbA+ITS2 combination performs better or equally well compared with other combinations in most taxonomic groups investigated. This information will guide the optimal usage of trnH–psbA and its combinations for species identification.     

Influence of mixed antibiotics on Microcystis aeruginosa during the application of glyphosate and hydrogen peroxide algaecides

Antibiotics regulate various physiological functions in cyanobacteria and may interfere with the control of cyanobacterial blooms during the application of algaecides. In this study, Microcystis aeruginosa was exposed to H₂O₂ and glyphosate for 7 d in the presence of coexisting mixed antibiotics (amoxicillin, spiramycin, tetracycline, ciprofloxacin, and sulfamethoxazole) at an environmentally relevant concentration of 100 ng · L^?1. The mixed antibiotics significantly (P < 0.05) alleviated the growth inhibition effect of 15–45 μM H₂O₂ and 40–60 mg · L^?1 glyphosate. According to the increased contents of chlorophyll a and protein, decreased content of malondialdehyde, and decreased activities of superoxide dismutase and glutathione S‐transferase, antibiotics may reduce the toxicity of the two algaecides through the stimulation of photosynthesis and the reduction in oxidative stress. The presence of coexisting antibiotics stimulated the production and release of microcystins in the M. aeruginosa exposed to low concentrations of algaecides and posed an increased threat to aquatic environments. To eliminate the secondary pollution caused by microcystins, high algaecide doses that are ≥45 μM for H₂O₂ and ≥60 mg · L^?1 for glyphosate are recommended. This study provides insights into the ecological hazards of antibiotic contaminants and the best management practices for cyanobacterial removal under combined antibiotic pollution conditions.     

Ionic Currents across the Plasmalemma of Chara inflata Cells: II. EFFECTS OF EXTERNAL Na+, Ca2+ AND Cl- ON K+ AND Cl CURRENTS

The electrical conductance of the plasmalemma of cells of Charainflata, due to the diffusion of ions, consists predominantlyof K⁺, Cl^– and leak components. When the membrane electricalpotential difference is stepped in a negative direction witha voltage-clamp, the resulting inward current has componentsI_K, I_Cl and I_L (leak). During such voltage-clamp steps I_K isinactivated, and Ic activated with voltage-dependent half-times.Increases in the external NaCl concentration reduce the magnitudeof I_K and increase the magnitude of I_c, but reduce the half-timeof inactivation or activation. The NaCl-induced changes in I_kand I_Cl and their kinetics were more pronounced at pH₀ =6.5than at pH₀ =9.5. When the concentration of external CaCl₂ wasincreased, I_k, I_Cl and the half-time of inactivation, (T_1/2),of I_k were all reduced. The half-time of activation of I_Cl wasincreased. The NaCI-induced changes could result from increases in bothexternal ion concentration and osmotic pressure. Previous experimentshave shown that an increase in external osmotic pressure alonealters the properties of the conductances. In this paper weattempt to separate the purely ionic effects from the osmoticones. Key words: Chara inflata, ionic effects, K⁺ and Cl^– currents     

Effect of apple intake on fecal microbiota and metabolites in humans

The effects of apple intake on the fecal flora, water content, pH, and metabolic activities in eight healthy volunteers and the utilization of apple pectin in vitro were investigated. Although several isolates of Bifidobacterium, Lactobacillus, Enterococcus, and the Bacteroides fragilis group utilized apple pectin, most isolates of Escherichia coli, Collinsela aerofaciense, Eubacterium limosum, and Clostridium perfringens could not. When fecal samples from healthy adults were incubated in liquid broth with apple pectin present or absent, the numbers of Bifidobacterium and Lactobacillus in the former were higher than those in the later. After the intake of apples (2 apples a day for 2 weeks) by eight healthy adult humans, the number of bifidobacteria in feces increased (p < 0.05 on day 7 and p < 0.01 on day 14 of the intake period), and the numbers of Lactobacillus and Streptococcus including Enterococcus tended to increase. However, lecithinase-positive clostridia, including C. perfringens, decreased (p < 0.05), and Enterobacteriaceae and Pseudomonas tended to decrease. Moreover, the concentrations of fecal acetic acid tended to increase on apple intake. The fecal ammonia concentration showed a tendency to reduce and fecal sulfide decreased (p < 0.05) on apple intake. These findings indicate that apple consumption is related to an improved intestinal environment, and apple pectin is one of the effective apple components improving the fecal environment.