Spin-Labeled Nucleotide Mobility in the Boundary of the EcoRI Endonuclease Binding Site

Abstract

A complex consisting of the EcoRI endonuclease site-specifically bound to spin-labeled DNA 26mers was prepared to provide a model system for studying possible conformational changes resulting from protein binding. EPR was used to monitor the mobility of the spin labels that were strategically placed in position 6, 9, or 11 with respect to the dyad axis of the 26mer. These positions are located within the flanking region on either side of the EcoRI hexamer binding site. This allows the monitoring of potential distal structural changes in the DNA helix caused by protein binding. The spectral line shapes indicate that the spin label closest to the EcoRI endonuclease binding site, i.e., in position 6, is most influenced by the binding event. The EPR data are analyzed according to a model that distinguishes between spectral effects due to a change in the hydrodynamic shape of the complex and those resulting from local variations in the spin-label mobility as characterized by a local order parameter S. S reflecting the motional restriction of the spin-labeled base is 0.20 ± 0.01 for all three oligomers as well as for the two complexes with the label in position 9 or 11, while the position 6 labeled complex yields S=0.25. To further evaluate the origin of the slightly larger EPR effect observed with position 6 labeled material, molecular dynamics (MD) simulations were used to explore the space accessible to the probes in positions 6, 9, and 11. MD results gave similar nitroxide trajectories for all three labeled 26mers in the absence or presence of EcoRI. Thus, the small position 6 effect is attributed to a structural distortion in the major groove of the DNA at this location possibly corresponding to a bend induced by protein binding. The observation that the spectral changes are small indicates the absence of any significant structural disruption being propagated along the helix as a result of protein binding. Also, the fact that the line shape of the 26mers did not change as expected from hydrodynamic theory in view of the significant increase in molecular volume upon protein binding suggests that there are additional relaxation processes involving the protein and nucleic acid.     

Species identification and tree-ring dating of wood boxes excavated from the Shinan shipwreck,Korea

The Shinan shipwreck, which was excavated in the southwestern sea of Korea in the 1970s, was a Chinese trade ship from the Yuan Dynasty, traveling from China to Japan in the early 14th century (A.D. 1323). Anatomical examination indicated that the wood boxes carrying thousands of Chinese porcelain pieces on the Shinan shipwreck were made of either Cryptomeria japonica or Cunninghamia spp. The former grows in South China and Japan, and the latter in China and Taiwan. Therefore, we could not confine the origin of the wood to a single country by wood identification. However, we could date 21 wood boxes using tree-ring chronologies of C. japonica from western Japan. The outermost ring with sapwood was dated to A.D. 1316. The results from the tree-ring dating indicated that the wood boxes on the Shinan shipwreck were of Japanese rather than Chinese origin.     

Functional adaptation rather than ecogeographical rules determine body-size metrics along a thermal cline with elevation in the Chinese pygmy dormouse (Typhlomys cinereus)

Phenotypic plasticity is crucial for how organisms respond to variation in their environment, affecting their diversity and distribution, especially in the light of rapid environmental change. Ecogeographical rules predict an association between specific adaptive morphological and physiological traits with cooler conditions due to higher latitude, elevation, or climate change. Such ecogeographical effects are often most evident in ancient species due to continuous selective adaptation occurring over long periods of time. Here, we use the suitably ancient Chinese pygmy dormouse (Typhlomys cinereus) to test whether body-size, appendage length and heart size vary in accordance with Bergmann's, Allen's and Hesse's rule, respectively. Based on a sample of 67 adult individuals (female, n = 29; male n = 38) trapped at 37 sites transcending an elevational range from 414 to 1757 m, we tested for trait concordance with Bergmann's rule (body mass, length and SMI), Allen's rule (length of tail, foot, ear, snout), and Hesse's rule (wet and dry heart mass). Effects of elevation (and thus temperature lapse rate; calculated as 0.61 °C per 100 m) on body size, appendage length and heart size, were tested by fitting Standardized Major Axis (SMA) models. We observed substantial heterogeneity in morphometric traits allowing for the detection of ecogeographical clines. However, none conformed with Bergmann's, Allen's (except ear size), or Hesse's rule. However, our results indicate some support for Geist's rule of net primary productivity. We conclude that pervasive functional life-history adaptations in this blind, arboreal, echolocating ancient species exceeded selection for morphological energy efficiency constraints, with the notable exception of reduced ear pinnae size at colder, elevated sites. This is an important consideration for predicting how species, and populations in general, may adapt to human induced rapid environmental change, contrary to expectations of warming driving selection for smaller body-size.     

Ecosystem evolution of Lake Gusinoe (Transbaikal region, Russia)

Lake Gusinoe is situated on a basin originating from Paleozoic and Mesozoic deposits. The recorded history of the lake's ecosystem evolution is no more than 300 years. The present lake drainage basin was formed mainly in the Cenozoic era, but during the past century, major anthropogenic impacts on the lake have occurred. The human-influenced evolution of the ecosystem began in the 1940s with the development of opencut coal mining nearby the lake. Population increase and the building of the Gusinoozersk State Regional Power Plant, the Trans-Mongolian Railroad and an associated station, and military installations were the major sources of anthropogenic impacts. Since the early 1950s about five species of fish have been introduced into Lake Gusinoe or have invaded the lake, and at least six of the native species have disappeared or are in danger of extinction. From our recent investigations, the present environment of the Lake Gusinoe Basin (Gusinoozersk Basin) is divided into four zones hydrogeochemically: (1) ultrafreshwater, (2) freshwater, (3) mineralized water, and (4) hyposaline and saltwater. Some additional data on changes of the chemical components of the drainage basin waters, as well as on the transition of zooplankton and zoobenthic fauna, are presented in consideration of the risk of industrial development, and the perspectives are discussed.     

Migration of herbaceous woodland flora into post-agricultural black alder woods planted on wet and fertile habitats in south western Poland

Because post-agricultural black alder woods have not been the subject of studies on forest recovery, the aim of the research was to investigate the process of colonization of their herb layer by woodland flora. Migration rates of 51 forest plant species in the herb layer of alder woods planted on abandoned meadows, bordering meso- and eutrophic forests, were studied. Mean migration rates calculated for typical wet alderwoods reached 1.20–1.60 m yr⁻¹, for oak-hornbeam forests 1.17–1.63 m yr⁻¹, and for alder-ash carrs 0.79–1.26 m yr⁻¹, exceeding those reported in studies conducted in less fertile, drier sites. Although migration rates for many species exceeded 2 or 3 m, there was a group of slow colonizing species, mainly ancient woodland indicators. Species migration patterns fitted either the model based on the establishment of isolated individuals, or the model of a wave front. The age of the recent forests and the presence of Urtica dioica in their herb layer are the main factors explaining the species composition in post-agricultural black alder woods.     

Origin of European rabbit (Oryctolagus cuniculus) in a Mediterranean island: Zooarchaeology and ancient DNA examination

Mammalian species presently living on Mediterranean islands have been brought in by man. The question of their geographical origin and of the time of their introduction is often a matter of debate. We studied this problem using a population of rabbits (European rabbit: Oryctolagus cuniculus) living in Zembra, an island off Tunisia. Archaeological surveys show that rabbit has been introduced to the island by Bronze Age or Roman people, between the IIIrd Millenium B.C. and the IIIrd century A.D. Part of the 16S-rRNA gene of mitochondrial DNAs from fossil bones of different ages (dated back to 130–390 A.D.) was characterized and compared to that of present day rabbits of differing geographical origin. The data suggest that animals present on Zembra in late Roman times belonged to the same maternal lineage as present populations from Northern Spain and Southern France.     

Comparative Study on the Chloroplast RPL32-TRNL Nucleotide Variation within and Genetic Differentiation among Ancient Tea Plantations of Camellia sinensis var.assamica and C.taliensis (Theaceae) from Yunnan,China

In order to assess genetic diversity and population structure, nine Camellia sinensis var.assamica and three C.taliensis populations from Yunnan, China were evaluated. Based on nucleotide variation of 94 cpDNA RPL32-TRNL sequences, a total of seven distinct haplotypes were detected in the studied populations. It was apparent that C.sinensis var.assamica (h=0.728,π =0.00469) possessed higher levels of genetic diversity than C.taliensis (h =0.610, π =0.00225). However, genetic differentiation among populations of C.sinensis varassamica (Gst=0.580, FST=0.612) was lower than that among C.taliensis populations (Gst=0.696, FST=0.773). Our AMOVA analysis further revealed that the majority of variation was partitioned among populations of the two taxa, while C.sinensis var.assamica (6121%) showed lower level of genetic differentiation than C.taliensis (77.34%). In comparisons to C.taliensis, genetic diversity within C.sinensis var.assamica largely varied among populations, ranging from 0 to 0.809 and from 0 to 0.00487 for haplotype and nucleotide diversity, respectively. Conservation strategies were finally discussed and proposed to efficiently protect ancient tea plantations in China.     

荷花反季节栽培技术试验

在可调控温湿度的薄膜温室大棚内,采用‘冬花红’（冬荷）、‘蝶恋花’、‘香雪海’3个荷花品种进行反季节栽培试验,摸索出一套适合东莞地区的荷花反季节栽培技术,并于12月初成功培育出盛开的荷花,实现夏荷冬开、延长荷花观赏期的目的。     

The neglected side of speciation in ancient lakes: phylogeography of an inconspicuous mollusc taxon in lakes Ohrid and Prespa

The morphologically remarkable endemic fauna within ancient lakes has received much attention in the literature. More inconspicuous taxa, however, often lack detailed molecular and morphometrical examination, although their proportion of the endemic fauna of an ancient lake must not be underestimated. Consequently, a better understanding of evolutionary patterns and processes within these lakes requires more knowledge about the often-neglected inconspicuous taxa. In the present study, we focus on the notoriously cryptic pea clam genus Pisidium (Bivalvia: Sphaeriidae). Though the genus is widely distributed, most endemic species are reported only from ancient lakes, including the European ancient sister lake system of Ohrid and Prespa on the Balkan Peninsula. Here we test for the first time hypotheses on the evolution of the endemic pea clams in this European biodiversity hotspot by molecular means. Combining a broad 16S phylogeny (comprising most European pea clam species), network analyses and morphometrical analyses, we found interesting biogeographical patterns and provide evidence for cryptic species in both lakes. Furthermore, we confirmed the proposed sister-species relationship of the endemics P. edlaueri in Lake Ohrid and P. maasseni in Lake Prespa, and we suggest scenarios of the endemic pea clam evolution within both lakes. The patterns of speciation found in the genus Pisidium are compared to patterns in morphologically distinct molluscan groups in lakes Ohrid und Prespa.     

Concurrent evolution of ancient sister lakes and sister species: the freshwater gastropod genus <Emphasis Type="Italic">Radix</Emphasis> in lakes Ohrid and Prespa

Ancient sister lakes are considered to be ancient lakes lying in close geographic proximity, sharing a related origin and significant time of co-existence, usually having hydrological connection as well as a balanced degree of faunal overlap and distinctness. A paradigm for studying sister lake relationships are the ancient lakes Ohrid and Prespa in the Balkans, which are characterized by high degrees of endemicity. Three general patterns of endemic species can be distinguished for these lakes: (1) taxa that are endemic to either lake, with no close relatives in the respective sister lake, (2) closely related but distinct endemic taxa in both lakes (sister species) and (3) shared endemic taxa occurring in both lakes. In the present paper, two endemic freshwater pulmonate gastropod species, Radix relicta (Lake Ohrid) and R. pinteri (Lake Prespa), are used to study the evolution of presumed sister species based on biogeographical and comparative DNA data from world-wide Radix taxa. Phylogenetic, phylogeographical and parametric bootstrap analyses all suggest a sister group relationship of R. relicta and R. pinteri (pattern 2 of endemic diversity). Sister to these two taxa is the widespread R. ampla, which does not occur in the vicinity of lakes Ohrid and Prespa. The southern feeder spring complexes of Lake Ohrid are inhabited by another lineage (Radix sp. 1), which resembles Radix relicta in morphology/anatomy. For Lake Prespa, the widespread R. auricularia was reported in addition to the endemic R. pinteri. Comparative phylogenetic data favour a western Adriatic zoogeographical affinity of lakes Ohrid and Prespa over an Aegean-Anatolian faunal connection. The status of lakes Ohrid and Prespa as sister lakes is evaluated in the light of current knowledge on gastropod speciation and endemism in these hotspots of biodiversity.