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1.
Aims Chalk grasslands are subject to vegetation dynamics that range from species-rich open grasslands to tall and encroached grasslands, and woods and forests. In grasslands, earthworms impact plant communities and ecosystem functioning through the modification of soil physical, chemical and microbiological properties, but also through their selective ingestion and vertical transportation of seeds from the soil seed bank. Laboratory experiments showed that seed–earthworm interactions are species specific, but little is known on the impact of seed–earthworm interactions in the field. The overall aim of this study was to better understand seed–earthworm interactions and their impact on the plant community. First we analyzed the composition of seedlings emerging from casts after earthworm ingestion. Then we compared seedling composition in casts to the plant composition of emerging seedlings from the soil and of the aboveground vegetation along four stages of the secondary succession of chalk grasslands.Methods Four stages of the secondary succession of a chalk grassland—from open sward to woods—were sampled in Upper Normandy, France, in February 2010. Within each successional stage (×3 replicates), we sampled the standing vegetation, soil seed bank at three soil depths (0–2, 2–5 and 5–10cm) and earthworm surface casts along transects. Soil and cast samples were water sieved before samples were spread onto trays and placed into a greenhouse. Emerging seedlings were counted and identified. Effect of successional stage and origin of samples on mean and variability of abundance and species richness of seedlings emerging from casts and soil seed banks were analyzed. Plant compositions were compared between all sample types. We used generalized mixed-effect models and a distance-based redundancy multivariate analysis.Important findings Seedling abundance was always higher in earthworm casts than in the soil seed bank and increased up to 5-fold, 4-fold and 3.5-fold, respectively, in the tall grassland, woods and encroached grassland compared to the soil surface layer. Species richness was also higher in earthworm casts than in the soil seed bank in all successional stages, with a 4-fold increase in the encroached grassland. The plant composition of the standing vegetation was more similar to that of seedlings from casts than to that of seedlings from the soil seed bank. Seedlings diversity emerging from casts in the tall and encroached grasslands tended toward the diversity found in woods. Our results indicate that earthworms may promote the emergence of seedlings. We also suggest that the loss of some plant species in the seed bank and the tall grass vegetation in intermediary successional stages modify the local conditions and prevent the further establishment of early-successional plant species. 相似文献
2.
利用高效液相色谱证实了环毛蚓（Pheretima sp.)蚓粪中至少存在两种植物激素（IAA和GA3）,蚓粪中IAA和GA3的含量分别可达13.9mg/kg和49.9mg/kg。为原土的13.6和8.2倍,采用包括蚓粪提取液,原土提取液,Haogland营养液,蒸馏水,IAA,GA3等在内的11种供试液进行绿豆插条不定根发生的生物试验,结果表明,在相同条件下,蚓粪提取液处理的绿豆插条比其它处理提早3天出现不定根,统计证明,与原土提取液,Haogland营养液,蒸馏水等处理相比,蚓粪提取液处理可显提高绿豆插条不定根的数量,长度和生物量,蚓粪提取液对不定根发生数量的诱导效应与85-170μmol/L的IAA溶液相当,但从不定根根长和根生长量来看,蚓粪提取液的效果优于IAA。 相似文献
3.
William Buckland not only was an eccentric scientist either liked or disliked by his peers but, in the early 1800s, was also the foremost authority on coprolites. The latter were a source of considerable amusement to some of his friends. 相似文献
4.
Andrey A. Lebedev Michail N. Isupov 《Acta Crystallographica. Section D, Structural Biology》2014,70(9):2430-2443
The presence of pseudo‐symmetry in a macromolecular crystal and its interplay with twinning may lead to an incorrect space‐group (SG) assignment. Moreover, if the pseudo‐symmetry is very close to an exact crystallographic symmetry, the structure can be solved and partially refined in the wrong SG. Typically, in such incorrectly determined structures all or some of the pseudo‐symmetry operations are, in effect, taken for crystallographic symmetry operations and vice versa. A mistake only becomes apparent when the Rfree ceases to decrease below 0.39 and further model rebuilding and refinement cannot improve the refinement statistics. If pseudo‐symmetry includes pseudo‐translation, the uncertainty in SG assignment may be associated with an incorrect choice of origin, as demonstrated by the series of examples provided here. The program Zanuda presented in this article was developed for the automation of SG validation. Zanuda runs a series of refinements in SGs compatible with the observed unit‐cell parameters and chooses the model with the highest symmetry SG from a subset of models that have the best refinement statistics. 相似文献
5.
The recent development of multi‐collector inductively coupled plasma mass spectrometry (MC‐ICP‐MS) notably in the disciplines of earth sciences, now allows the precise measurement of isotope ratios, even at low concentration. Non‐traditional isotope systems, such as alkaline earth (Ca, Mg) and transition (Cu, Fe, Zn) metals are now being measured in a variety of biological tissues, including bone and teeth. Although our understanding of the environmental and biological mechanisms behind the fractionation of such elements is still in its infancy, some of these isotopes are suspected to fractionate along the food chain, as has been reported in the literature for calcium, magnesium and zinc. Other geochemical methods, such as concentration analyses, permit a prior assessment of diagenesis in the fossils and such an approach indicates that in some circumstances, not only enamel but also dentine or bone can preserve its original biogenic composition. The aims here are to: review the current knowledge surrounding these various isotopic tools; address their potential preservation in biological apatite; and provide the palaeobiologist with a guide to the different toolkits available, including a discussion of their potential applications in vertebrate palaeobiology with a case study involving two mammal assemblages from the Pleistocene of Europe. 相似文献
6.
Anna Z. Urbisz Patrick Martin Moïssou Lagnika &#x;ukasz Chajec Piotr
wi&#x;tek 《Journal of morphology》2021,282(1):98-114
Ovaries of Haplotaxis sp. were studied in active and nonactive states, that is, in a sexually mature specimen and in specimens outside of the reproductive period. Two pairs of ovaries were found in segments XI and XII. Especially in the nonactive state, they were in close contact with copulatory glands. Each ovary was composed of germ cells interconnected with syncytial cysts, which were enveloped by a layer of somatic cells. Within cysts each germ cell had one ring canal connecting it to the common anuclear cytoplasmic mass called a cytophore. During oogenesis clustering germ cells differentiated into nurse cells and oocytes; thus, the oogenesis was recognized as meroistic. Vitellogenic oocytes were detached from the ovaries and continued yolk absorption within the body cavity. Because recent studies have shown the variety of ovaries and germ line cyst organization in clitellates and suggest their evolutionary conservatism at the family or subfamily level, the data presented here can be valid in understanding the phylogenetic relationships among Clitellata. In this context, ovaries found in Haplotaxis sp. resembled those of the “Tubifex” type. “Tubifex” ovaries are characteristic for numerous microdrile taxa (tubificines, limnodriloidines, propappids, lumbriculids, and leech‐like branchiobdellids) and can be regarded as the primary character for these Clitellata in which germ‐line cysts are formed during early oogenesis. As the family Haplotaxidae is currently considered to be paraphyletic and the species studied here belongs to Haplotaxidae sensu stricto, our results support the close relationship of Haplotaxidae sensu stricto to the clade consisting of Lumbriculidae, Branchiobdellida, and Hirudinida, in which lumbriculids are sister to the latter two. 相似文献
7.
Cory L. Brooks Ryan J. Blackler Sandra Gerstenbruch Paul Kosma Sven Müller‐Loennies Helmut Brade Stephen V. Evans 《Acta Crystallographica. Section D, Structural Biology》2008,64(12):1250-1258
A difference of seven conservative amino‐acid substitutions between two single‐chain antibodies (scFvs) specific for chlamydial lipopolysaccharide does not significantly affect their molecular structures or packing contacts, but dramatically affects their crystallization. The structure of the variable domain (Fv) of SAG173‐04 was solved to 1.86 Å resolution and an Rcryst of 18.9% in space group P212121. Crystals of the homologous SAG506‐01 diffracted to 1.95 Å resolution and appeared at first to have Patterson symmetry I4/m or P4/mmm; however, no solution could be found in space groups belonging to the former and refinement in the only solution corresponding to the latter (in space group P43212) stalled at Rfree = 30.0%. Detailed examination of the diffraction data revealed that the crystal was likely to be twinned and that the correct space group was P212121. Both translational pseudo‐symmetry and pseudo‐merohedral twinning were observed in one crystal of SAG506‐01 and pseudo‐merohedral twinning was observed for a second crystal. The final R factor for SAG506‐01 after refinement in P212121 was 20.5%. 相似文献
8.
Ian J. MacRae Jennifer A. Doudna 《Acta Crystallographica. Section D, Structural Biology》2007,63(9):993-999
The crystal structure of the enzyme Dicer from Giardia intestinalis was solved to 3.3 Å resolution by MAD using crystals belonging to space group P21212 [Macrae et al. (2006), Science, 311 , 195–198]. These crystals were derived from crystals that diffracted X‐rays to 3.0 Å resolution but were refractory to structure determination because they were twinned. It is shown here that the original Dicer crystals represent an unusual case of perfect pseudo‐merohedral twinning of orthorhombic crystals. Before the twinning problem was overcome, it was possible to calculate a low‐resolution electron‐density map in space group P41 that was used to build a partial molecular model. Experimental phases were sufficient to identify heavy‐atom sites that indicated space‐group inconsistency, leading to identification of the true space group. This information guided the search for different crystallization conditions that yielded untwinned crystals and ultimately a fully interpretable electron‐density map. 相似文献
9.
Alan A. Simpson Narayanasamy Nandhagopal James L. Van Etten Michael G. Rossmann 《Acta Crystallographica. Section D, Structural Biology》2003,59(12):2053-2059
The Phycodnaviridae, Iridoviridae and related viruses, with diameters of 1500–2000 Å, are formed from large trigonal arrays of hexagonally close‐packed capsomers forming the faces of icosahedra [Yan et al. (2000), Nature Struct. Biol. 7 , 101–103; Nandhagopal et al. (2002), Proc. Natl Acad. Sci. USA, 99 , 14758–14763]. Caspar and Klug predicted that such structures could be assembled from hexameric capsomers [Caspar & Klug (1962), Cold Spring Harbor. Symp. Quant. Biol. 27 , 1–24], as was subsequently found in numerous icosahedral viruses. During the course of evolution, some viruses, including the virus families mentioned above, replaced hexameric capsomers with pseudo‐hexameric trimers by gene duplication. In large dsDNA icosahedral viruses, the capsomers are organized into `pentasymmetrons' and `trisymmetrons'. The interactions between the trimeric capsomers can be divided into three groups, one between similarly oriented trimers and two between oppositely oriented trimers (trimers related by an approximately sixfold rotation). The interactions within a trisymmetron belong to the first class, whereas those between trisymmetrons and within the pentasymmetron are of the other two types. Knowledge of these distances permits a more accurate fitting of the atomic structure of the capsomer into the cryo‐electron microscopy (cryoEM) reconstruction of the whole virus. The adoption of pseudo‐hexagonal capsomers places these viruses into a subset of the Caspar and Klug surface lattices. 相似文献
10.
Mia K. Grand Hein Putter Arthur Allignol Per K. Andersen 《Biometrical journal. Biometrische Zeitschrift》2019,61(2):290-298
Pseudo‐observations have been introduced as a way to perform regression analysis of a mean value parameter related to a right‐censored time‐to‐event outcome, such as the survival probability or the restricted mean survival time. Since the introduction of the approach there have been several extensions from the original setting. However, the proper definition and performance of pseudo‐observations under left‐truncation has not yet been addressed. Here, we look at two types of pseudo‐observations under right‐censoring and left‐truncation. We explored their performance in a simulation study and applied them to data on diabetes patients with left‐truncation. 相似文献
11.
Lisa L. Sandell Hiroshi Kurosaka Paul A. Trainor 《Genesis (New York, N.Y. : 2000)》2012,50(11):844-850
Here, we describe a relatively inexpensive and easy method to produce high quality images that reveal fine topological details of vertebrate embryonic structures. The method relies on nuclear staining of whole mount embryos in combination with confocal microscopy or conventional wide field fluorescent microscopy. In cases where confocal microscopy is used in combination with whole mount nuclear staining, the resulting embryo images can rival the clarity and resolution of images produced by scanning electron microscopy (SEM). The fluorescent nuclear staining may be performed with a variety of cell permeable nuclear dyes, enabling the technique to be performed with multiple standard microscope/illumination or confocal/laser systems. The method may be used to document morphology of embryos of a variety of organisms, as well as individual organs and tissues. Nuclear stain imaging imposes minimal impact on embryonic specimens, enabling imaged specimens to be utilized for additional assays. genesis 2012. © 2012 Wiley Periodicals, Inc. 相似文献
12.
The entire muscle system of Nerilla antennata, Nerillidium sp. and Trochonerilla mobilis was three-dimensionally reconstructed from whole mounts. In juvenile and adult specimens the F-actin musculature subset was stained with FITC-conjugated phalloidin and visualized with a confocal laser scanning microscope (cLSM). The muscle system shows the following major organization: 1) circular muscles are totally absent in the body wall; 2) the longitudinal muscles are confined in two ventral and two dorsal thick bundles; 3) additional longitudinal muscles are located in the ventro- and dorsomedian axis; 4) three segmental pairs of ventral oblique muscles elongate into the periphery: the main dorsoventral muscles that run along the body side posterior and dorsally and the anterior and posterior oblique parapodial muscles, which contribute to the ventral chaetal sacs; 5) one segmental pair of dorsal oblique parapodial muscles, contributing to the dorsal chaetal sacs; 6) five to seven small dorsoventral muscles per segment; and 7) complex head and pharyngeal musculature. These results support the belief that absence of circular muscles in the polychaete body wall is much more widely distributed than is currently presumed. 相似文献
13.
Enrique Carredano Bjrn Kauppi Devapriya Choudhury S. Ramaswamy 《Acta Crystallographica. Section D, Structural Biology》2000,56(3):313-321
Two trigonal crystal structures of naphthalene 1,2‐dioxygenase from Pseudomonas sp. NCIB 9816‐4 have been refined at 2.6 Å resolution. The space group is R3, with four heterodimers in the asymmetric unit. The crystallographic threefold axis coincides with the symmetry axis of the active molecule, a mushroom‐shaped α3β3 hexamer. The crystal is formed by symmetrical contacts between the hexamers on three different interaction surfaces, one on the β‐subunit and the other two on the α‐subunits. Nickel ions mediate one of the α‐subunit interactions. The two other types of packing contacts sustain two interlaced and almost independent crystal patterns with significantly different temperature factors. The space group of the individual crystal patterns is R32, with the corresponding twofold axes parallel to each other. The interactions between the crystal patterns separate the two parallel twofolds, eliminating the twofold symmetry for the whole crystal. The differences in temperature factors among the molecules in the asymmetric unit have been refined and are different for the two refined structures. An analysis of the structure factors of the pseudo‐equivalent reflections showed that their differences lie in their phases and not in their amplitudes, suggesting that Rmerge is not an appropriate indicator for revealing the correct point group. 相似文献
14.
The distribution and configuration of nephridia and gonoducts are described for seven species from seven genera of the interstitial polychaete family Nerillidae. The ciliated nephridia and gonoducts were identified by tubulin staining and examined with a confocal laser scanning microscope. The following species of the seven to nine-segmented nerillids were examined: Leptonerilla prospera, Nerilla antennata (nine segments); Nerillidium mediterraneum, Trochonerilla mobilis, Gen. sp. A (eight segments); and Aristonerilla brevis, Paranerilla limicola (seven segments). Two of the examined species are hermaphroditic (N. mediterraneum and Gen. sp. A). Segmented nephridia can be found from the first to the last segment, with a total of two to five pairs. One to three pairs of segmented spermioducts are present in all species. One pair of gonoducts is found in all species, except for P. limicola, where they are absent. Nephridia vary in length from half to almost twice the length of a segment and may be curled up in loops. In A. brevis and P. limicola the nephridia are discontinuously ciliated. The distribution and configuration of spermioducts and gonoducts are also variable, although to a lesser extent. The spermioduct distribution is generally consistent within genera and therefore of systematic significance. Nephridia and gonoducts are never found together in the same segments, and the results indicate that gonoducts and nephridia have developed from the same anlagen. The distribution patterns of nephridia and gonoducts are discussed with respect to segmentation, systematics, and development. 相似文献
15.
距今14～16亿年的华北地区高于庄组黑色层状、结核状和透镜状燧石与叠层石的黑色硅质部分中保存着极丰富的原核和真核生物微化石.宏观藻类在该组的页岩中亦已发现.本组为评估中元古代生命状况、古环境和前显生宙生物地层提供了重要的生物信息.迄今为止在高于庄组地层中已有百余个化石种被人们认识.根据古植物和古环境的特征这些生物种类可分为三个不同的组合,即:1.颤藻和色球藻组合,出现在高于庄组一段,代表浅水藻席建造者和居住者与一些可能的外来浮游生物的种类;2.念珠藻组合,仅发生在该组的二段,还含一些底栖藻席建造者或居住者的种类;3.第四段的色球藻组合,它代表了潮间带至亚潮带的藻席建造者和外来的种类.元古代燧石中的微化石,尤其是蓝藻化石,尽管在元古代它们就已不断趋向于多样化,但由于它们形态上的保守性,对环境的指示比对地质时代的指示更有价值.高于庄组微化石的特点和大多数链状念珠藻垂直层理保存的事实表明:1.高于庄组微化石的个体大小随时间趋向于增大;2.高于庄组的沉积可能是处于一个淡水环境,且沉积率可能等于或少于微生物的生长率;3. 高于庄组织沉积模式可能是从潮间带至亚潮带或深海,然后再至潮间带或潮上带;4.当高于庄组沉积时真核生物亦已出现. 相似文献
16.
Susan Heffron Stephan Watkins Rhonda Moeller Aise Huma Taban Rafal Butowt Dean DellaPenna Frances Jurnak 《Acta Crystallographica. Section D, Structural Biology》2003,59(12):2088-2093
The first polygalacturonase from a plant, tomato fruit PG2, has been crystallized and data have been collected to a resolution of 1.87 Å. The autoindexing program strongly favors one of the primitive orthorhombic cells. A plausible molecular‐replacement solution for two molecules in the asymmetric unit has been found for data assigned to space group P212121. Although the numerical criteria and the electron‐density maps are reasonable for this solution, manually adjusted models do not refine to an R factor below 0.48. Visual inspection of hkl Bragg planes does not reveal a breakdown in mm symmetry. Nevertheless, the correct space group has been determined to be P21, with similar unit‐cell parameters, a β angle of 90.04° and four molecules in the asymmetric unit. The Rsym of 0.053 for data processed in P212121 is very similar to the Rsym of 0.047 for the same data processed in P21. Comparisons of the intermediate results using the P212121 and P21 data sets are provided and the subtle indications of an initial erroneous space‐group assignment are discussed. 相似文献
17.
Myzostomids are minute, soft-bodied, marine worms associated with echinoderms since the Carboniferous. Due to their long history
as host-specific symbionts, they have acquired a highly derived body plan that obscures their phylogenetic affinities to other
metazoans. Because certain organs are serially arranged a closer relationship between polychaetes and myzostomids has repeatedly
been discussion. We presented here a review on the ultrastructure of myzostomids with the most recent analyses that concern
their phylogenetic position. The ultrastructure of the integument, digestive system, excretory system and nervous system are
summarized. Unpublished information on the gametogenesis and reproductive systems of myzostomids are also exposed with a view
on their reproductive process. 相似文献
18.
M Novo A Almodóvar R Fernández D Trigo DJ Díaz-Cosín G Giribet 《Molecular ecology》2012,21(15):3776-3793
Many recent studies on invertebrates have shown how morphology not always captures the true diversity of taxa, with cryptic speciation often being discussed in this context. Here, we show how diversification patterns can be very different in two clades of closely related earthworms in the genus Hormogaster stressing the risk of using nonspecific substitution rate values across taxa. On the one hand, the Hormogaster elisae species complex, endemic to the central Iberian Peninsula, shows morphological stasis. On the other hand, a clade of Hormogaster from the NE Iberian Peninsula shows an enormous morphological variability, with 15 described morphospecies. The H. elisae complex, however, evolves faster genetically, and this could be explained by the harsher environmental conditions to which it is confined—as detected in this study, that is, sandier and slightly poorer soils with lower pH values than those of the other species in the family. These extreme conditions could be at the same time limiting morphological evolution and thus be responsible for the observed morphological stasis in this clade. Contrarily, Hormogaster species from the NE Iberian Peninsula, although still inhabiting harsher milieu than other earthworm groups, have had the opportunity to evolve into a greater morphological disparity. An attempt to delimit species within this group following the recently proposed general mixed Yule‐coalescent method showed a higher number of entities than expected under the morphospecies concept, most probably due to the low vagility of these animals, which considerably limits gene flow between distant conspecific populations, but also because of the decoupling between morphological and genetic evolution in the H. elisae complex. 相似文献
19.
Markus G. Rudolph Christer Wingren Michael P. Crowley Yueh‐hsiu Chien Ian A. Wilson 《Acta Crystallographica. Section D, Structural Biology》2004,60(4):656-664
T10 is a non‐classical class Ib‐like major histocompatibility complex (MHC) cell‐surface antigen which binds directly to certain γδ T‐cell receptors in the absence of any exogenous and endogenous ligands, such as peculiar lipids or glycolipids. The crystal structure at 2.5 Å resolution of murine T10 was determined by molecular replacement using data from an almost perfectly twinned monoclinic crystal. The space group is P21, with unit‐cell parameters a = 78.2, b = 70.0, c = 139.2 Å, β = 106.8°. Self‐rotation function analysis and various intensity statistics revealed the presence of pseudo‐merohedral twinning, but these tests underestimated the true twin fraction of α ≃ 0.46. Native Patterson analyses pointed to the presence of pseudo‐translation among the four molecules present in the asymmetric unit. Data analysis, structure determination and model refinement are discussed. 相似文献
20.