A comparative map viewer integrating genetic maps for <Emphasis Type="Italic">Brassica</Emphasis> and <Emphasis Type="Italic">Arabidopsis</Emphasis>

Background  

Molecular genetic maps provide a means to link heritable traits with underlying genome sequence variation. Several genetic maps have been constructed for Brassica species, yet to date, there has been no simple means to compare this information or to associate mapped traits with the genome sequence of the related model plant, Arabidopsis.     

Deficiency of functional mannose-binding lectin is not associated with infections in patients with systemic lupus erythematosus

Infection imposes a serious burden on patients with systemic lupus erythematosus (SLE). The increased infection rate in SLE patients has been attributed in part to defects of immune defence. Recently, the lectin pathway of complement activation has also been suggested to play a role in the occurrence of infections in SLE. In previous studies, SLE patients homozygous for mannose-binding lectin (MBL) variant alleles were at an increased risk of acquiring serious infections in comparison with patients who were heterozygous or homozygous for the normal allele. This association suggests a correlation between functional MBL level and occurrence of infections in SLE patients. We therefore investigated the biological activity of MBL and its relationship with the occurrence of infections in patients with SLE. Demographic and clinical data were collected in 103 patients with SLE. Functional MBL serum levels and MBL-induced C4 deposition were measured by enzyme-linked immunosorbent assay using mannan as coat and an MBL- or C4b-specific monoclonal antibody. The complete MBL-dependent pathway activity was determined by using an assay that measures the complete MBL pathway activity in serum, starting with binding of MBL to mannan, and was detected with a specific monoclonal antibody against C5b-9. Charts were systematically reviewed to obtain information on documented infections since diagnosis of SLE. Major infections were defined as infections requiring hospital admission and intravenous administration of antibiotics. In total, 115 infections since diagnosis of lupus, including 42 major infections, were documented in the 103 SLE patients (mean age 41 ± 13 years, mean disease duration 7 ± 4 years). The percentage of SLE patients with severe MBL deficiency was similar to that in 100 healthy controls: 13% versus 14%, respectively. Although deposition of C4 to mannan and MBL pathway activity were reduced in 21% and 43% of 103 SLE patients, respectively, neither functional MBL serum levels nor MBL pathway activity was associated with infections or major infections in regression analyses. In conclusion, SLE patients frequently suffer from infections, but deficiency of functional MBL does not confer additional risk.     

Chirality matters: stereo-defined phosphorothioate linkages at the termini of small interfering RNAs improve pharmacology in vivo

A critical challenge for the successful development of RNA interference-based therapeutics therapeutics has been the enhancement of their in vivo metabolic stability. In therapeutically relevant, fully chemically modified small interfering RNAs (siRNAs), modification of the two terminal phosphodiester linkages in each strand of the siRNA duplex with phosphorothioate (PS) is generally sufficient to protect against exonuclease degradation in vivo. Since PS linkages are chiral, we systematically studied the properties of siRNAs containing single chiral PS linkages at each strand terminus. We report an efficient and simple method to introduce chiral PS linkages and demonstrate that Rp diastereomers at the 5′ end and Sp diastereomers at the 3′ end of the antisense siRNA strand improved pharmacokinetic and pharmacodynamic properties in a mouse model. In silico modeling studies provide mechanistic insights into how the Rp isomer at the 5′ end and Sp isomer at the 3′ end of the antisense siRNA enhance Argonaute 2 (Ago2) loading and metabolic stability of siRNAs in a concerted manner.     

On the Late Pleistocene and Holocene history of vegetation and human impact in the Ücker valley, north-eastern Germany

A high-resolution Late Pleistocene and Middle to Late Holocene pollen profile of regional significance is presented. The coring site is located in a mire between two lakes. Ober- and Unter-ückersee, in Brandenburg, north-eastern Germany. The study was carried out in an archaeological context. It provides information about the history of vegetation, climate and human impact in the ücker river valley and the surrounding hills, the Uckerm?rker Hügelland. Hence, it is an important contribution for the reconstruction of the past vegetation of this area of Brandenburg. Seven AMS ¹⁴C-dates based on pollen concentrates provide a chronology for the middle Holocene part of the profile. Phases of intensive human activity can be shown from the middle Neolithic times until the Roman Iron Age. Received February 1, 2000 / Accepted January 18, 2001     

Relationship between clinical signs and postmortem test status in cattle experimentally infected with the bovine spongiform encephalopathy agent

Background  

Various clinical protocols have been developed to aid in the clinical diagnosis of classical bovine spongiform encephalopathy (BSE), which is confirmed by postmortem examinations based on vacuolation and accumulation of disease-associated prion protein (PrP^d) in the brain. The present study investigated the occurrence and progression of sixty selected clinical signs and behaviour combinations in 513 experimentally exposed cattle subsequently categorised postmortem as confirmed or unconfirmed BSE cases. Appropriate undosed or saline inoculated controls were examined similarly and the data analysed to explore the possible occurrence of BSE-specific clinical expression in animals unconfirmed by postmortem examinations.     

Kinetic and Spectral Resolution of Multiple Nonphotochemical Quenching Components in Arabidopsis Leaves

Using novel specially designed instrumentation, fluorescence emission spectra were recorded from Arabidopsis (Arabidopsis thaliana) leaves during the induction period of dark to high-light adaptation in order to follow the spectral changes associated with the formation of nonphotochemical quenching. In addition to an overall decrease of photosystem II fluorescence (quenching) across the entire spectrum, high light induced two specific relative changes in the spectra: (1) a decrease of the main emission band at 682 nm relative to the far-red (750–760 nm) part of the spectrum (Δ F₆₈₂); and (2) an increase at 720 to 730 nm (Δ F₇₂₀) relative to 750 to 760 nm. The kinetics of the two relative spectral changes and their dependence on various mutants revealed that they do not originate from the same process but rather from at least two independent processes. The Δ F₇₂₀ change is specifically associated with the rapidly reversible energy-dependent quenching. Comparison of the wild-type Arabidopsis with mutants unable to produce or overexpressing the PsbS subunit of photosystem II showed that PsbS was a necessary component for Δ F₇₂₀. The spectral change Δ F₆₈₂ is induced both by energy-dependent quenching and by PsbS-independent mechanism(s). A third novel quenching process, independent from both PsbS and zeaxanthin, is activated by a high turnover rate of photosystem II. Its induction and relaxation occur on a time scale of a few minutes. Analysis of the spectral inhomogeneity of nonphotochemical quenching allows extraction of mechanistically valuable information from the fluorescence induction kinetics when registered in a spectrally resolved fashion.One of the most important photoprotective mechanisms against high-light (HL) stress in photosynthetic organisms is the nonphotochemical quenching (NPQ) of excitation energy, which is mostly due to thermal deactivation of pigment excited states in the antenna of PSII. There exist a number of literature reviews on the subject (Demmig-Adams and Adams, 1992; Horton et al., 1996; Horton and Ruban, 1999, 2005; Niyogi, 1999, 2000; Müller et al., 2001; Golan et al., 2004; Krause and Jahns, 2004). Chlorophyll (Chl) fluorescence, and in particular pulse amplitude-modulated (PAM) fluorometry as introduced by Schreiber et al. (1986), has become by far the dominant technique to measure NPQ in leaves, chloroplasts, and intact microorganisms (Krause and Weis, 1991; Govindjee, 1995; Maxwell and Johnson, 2000; Krause and Jahns, 2003; Schreiber, 2004), more recently often combined with specific NPQ mutant studies (Golan et al., 2004; Kalituho et al., 2006, 2007; Dall''Osto et al., 2007). In this technique, periodic saturating light pulses are applied, superimposed on the continuous actinic irradiation applied to induce NPQ, in order to transiently close the PSII reaction centers (RCs). Since the photochemistry contribution (photochemical quenching) is thus brought to zero, the method allows us to follow the dynamics of the NPQ development and relaxation by fluorescence in a relatively simple manner (Krause and Jahns, 2003, 2004).Mostly based on its relaxation kinetics, NPQ has been divided technically into the three kinetic components qE, qT, and qI, for the rapid, middle, and slow phases of relaxation (Horton and Hague, 1988), initially attributed to energy-dependent quenching, state transitions, and photoinhibitory quenching (Quick and Stitt, 1989). The rapidly forming and reversible part of NPQ, qE, is the most thoroughly studied. It is well established that this type of quenching is a finely regulated process in which the main governing factors are the proton gradient across the chloroplast thylakoid membrane, Δ pH (Wraight and Crofts, 1970; Briantais et al., 1979), the xanthophyll cycle (i.e. conversion of violaxanthin to antheraxanthin and zeaxanthin [Zx]; Demmig et al., 1987; Demmig-Adams, 1990; Demmig-Adams and Adams, 1992), and the action of the PsbS protein (Funk et al., 1995; Li et al., 2000, 2004; Niyogi et al., 2005). The actual molecular mechanism is still unknown, although there is no shortage of hypotheses and proposed quencher candidates: energy transfer from Chl to Zx in the major light-harvesting complex (LHCII; Frank et al., 2000); electron transfer from a carotenoid to Chl forming a Zx-Chl or lutein-Chl charge-transfer state (Holt et al., 2005; Avenson et al., 2009); direct or indirect quenching by the PsbS protein (Li et al., 2000; Niyogi et al., 2005); energy transfer from Chl to lutein in LHCII (Horton et al., 1991; Ruban et al., 2007) linked to the aggregation of or a conformational change in LHCII; and last but not least, a far-red (FR) light-emitting quenched Chl-Chl charge-transfer state formed by the aggregation of LHCII (Miloslavina et al., 2008). Quenching in the PSII RC has also been proposed (Weis and Berry, 1987; Finazzi et al., 2004; Huner et al., 2005; Ivanov et al., 2008) as an additional type of Zx-independent quenching. Alternatively, it has been suggested that quenching by lutein can complement the Zx-dependent quenching (Niyogi et al., 2001; Li et al. 2009). Johnson et al. (2009) have recently given support to the notion that both Zx-dependent and Zx-independent quenching originate from the same PsbS-dependent mechanism, which is modulated by Zx (Crouchman et al., 2006).While the rapidly relaxing phase qE is now well characterized in its dependence on the various factors, the much slower qT and qI phases are still controversial, and each of them may have contributions from more than one mechanism. The qI component has been traditionally attributed to photoinhibition of PSII (Somersalo and Krause, 1988), associated with coordinated degradation and repair of the photosystem (Powles and Björkman, 1982; Kyle, 1987; Krause, 1988; Aro et al., 1993; Long et al., 1994; Murata et al., 2007). Lately, though, it is more widely accepted that under most conditions the photoinhibition is low and qI, like qE, is a result of thermal deactivation of excited states. Different hypotheses have been put forward to account for its seeming irreversibility: persistent transmembrane Δ pH (Gilmore and Yamamoto, 1992), stable protonation of proteins (Horton et al., 1994), accumulation of inactive PSII reaction centers (Briantais et al., 1992; Schansker and van Rensen, 1999), or stable binding of Zx to CP29 (Färber et al., 1997). The connection of the qT phase with state transitions has been doubted as well, and in fact it is now thought that the fraction of energy redistributed from PSI to PSII under high-light conditions is negligible (Walters and Horton, 1991, 1993) and that the qT must have a different origin or that it has erroneously been ascribed as NPQ (Schansker et al., 2006).Along with the large amount of contradictory evidence on the nature and location of the NPQ quenching site(s), the question of whether the light-induced reversible NPQ represents one single mechanism of deexcitation located in a single site brought about by the combined action of PsbS and Zx (Johnson et al., 2009) or whether it comprises several parallel and largely independent mechanisms acting on different parts of the PSII antenna has not been finally answered. One way to answer this question might be to carefully examine the spectral properties of NPQ-related fluorescence changes. Quenching in different locations of the PSII antenna or with different mechanisms might give rise to a differential quenching in various parts of the PSII antenna that might affect the PSII fluorescence spectra in different ways. This appears possible, since the various pigment-protein complexes of the photosynthetic apparatus have slightly different absorption and emission spectra (Holzwarth, 1991; Holzwarth and Roelofs, 1992). However, in the vast majority of modulated Chl fluorescence instrumentation, including the most widely used PAM fluorometer (Schreiber et al., 1986), the signal is integrated over a broad wavelength range, usually covering the whole range of 710 nm or greater. This integration over the long-wave part of the spectrum has several undesirable consequences and is associated with the unnecessary loss of available information. For example, the fluorescence of PSII peaks in the region of 680 to 685 nm, whereas beyond 700 nm, the PSII fluorescence intensity drops to less than 20% of its peak intensity. In contrast, the fluorescence of intact PSI complexes is dominant in the region above 710 nm (Haehnel et al., 1982; Karukstis and Sauer, 1983; Holzwarth et al., 1985; Holzwarth, 1986; Slavov et al., 2008). Thus, the widely used instrumentation measures the NPQ parameters in a region with reduced PSII contribution and relatively high PSI contribution to total fluorescence, despite the fact that NPQ is generally considered to be primarily a PSII phenomenon. Only in a few studies has the fluorescence in the red and the FR region been separated in order to evaluate the contribution of PSI and its influence on the NPQ parameters (Genty et al., 1990; Peterson et al., 2001). NPQ might also shift the fluorescence properties of the PSII antenna complexes or give rise to entirely new fluorescing components (Miloslavina et al., 2008). This would remain undetected if the NPQ fluorescence changes are not resolved in the spectral domain. It follows from these considerations that a great deal of insight into the NPQ mechanisms and locations may be gained if the spectral dimension is added to the NPQ fluorescence characterization. Among the many advantages of such an approach, one would then be able to distinguish whether NPQ simply leads to a uniform decrease of PSII fluorescence across the emission range or whether this decrease is nonuniform, localized in specific pigment protein complexes, and/or whether new fluorescing species are actually being produced in the NPQ process.The HL-induced NPQ effects on the leaf fluorescence spectra have often been studied also at low temperature, where the differentiation between pigment sites is better (Krause et al., 1983; Demmig and Björkman, 1987; Ruban and Horton, 1994). However, the possibility to resolve the kinetics of NPQ development and relaxation is largely lost when performing the measurements at low temperatures. The 77 K spectra of leaves and thylakoid membranes are characterized by three main peaks, F₆₈₅, F₆₉₅, and F₇₃₀, believed to originate predominantly from Chl a in CP47 of PSII, a specific Chl in CP43 of PSII, and PSI, respectively (Satoh and Butler, 1978; van Dorssen et al., 1987; Andrizhiyevskaya et al., 2005; Komura et al., 2007). Fluorescence from the major LHCII peaks at 680 nm (Rijgersberg and Amesz, 1978) and from the PSII reaction center Chls at 683 nm (Roelofs et al., 1993; Andrizhiyevskaya et al., 2005). Low-temperature studies on the effects of HL irradiation are confined to the changes in the FR-to-red fluorescence ratio, which are the result of the quenching of PSII fluorescence or energy redistribution between the photosystems (state transitions). Ruban and Horton (1994) have shown that photochemical quenching in Guzmania is maximal at 688 nm, whereas nonphotochemical processes quench preferentially at 683 and 698 nm.In this study, we undertook a detailed investigation of the NPQ-associated spectral changes in the fluorescence spectra of Arabidopsis (Arabidopsis thaliana) measured at room temperature (RT) and at 77 K. It follows from the above discussion that deeper insight into the mechanisms of NPQ processes may be gained by combining the kinetic and the spectral information of the fluorescence changes occurring in NPQ. For this purpose, we developed a multiwavelength spectrometer with parallel detection, allowing us to follow the entire time-dependent fluorescence spectra of leaves during the induction and relaxation phases of NPQ with high sensitivity.Specific questions to be addressed in this study are the following. Are there more than one NPQ processes and NPQ sites? Are these processes occurring in a linked fashion or are they independent? How do they depend on the various cofactors known to affect NPQ, in particular regarding the roles of PsbS and Zx? Using this novel approach of adding the spectral information to the NPQ fluorescence changes, we discovered specific spectral changes associated with different NPQ components. By comparing the effects measured on various NPQ mutants of Arabidopsis, it is possible to assign these NPQ components to specific quenching processes. The results provide evidence that the total NPQ is a combination of several parallel and largely independent processes, likely occurring at different locations in the photosynthetic apparatus.     

Phylogeography of Plathymenia reticulata (Leguminosae) reveals patterns of recent range expansion towards northeastern Brazil and southern Cerrados in Eastern Tropical South America

Little is known about past vegetation dynamics in Eastern Tropical South America (ETSA). Here we describe patterns of chloroplast (cp) DNA variation in Plathymenia reticulata, a widespread tree in the ETSA Atlantic Forest and Cerrado biomes, but not found in the xeromorphic Caatinga. Forty one populations, comprising 220 individuals, were analysed by sequencing the trnS‐trnG and trnL‐trnL‐trnF cpDNA regions. Combined, they resulted in 18 geographically structured haplotypes. The central region of the sampling area, comprising Minas Gerais and Goiás Brazilian states, is a centre of genetic diversity and probably the most longstanding area of the distribution range of the species. In contrast, populations from northeastern Brazil and the southern Cerrados showed very low diversity levels, almost exclusively with common haplotypes which are also found in the central region. Coupled with a long‐branched star‐like network, these patterns suggest a recent range expansion of P. reticulata to those regions from central region sources. The recent origin of the species (in the early Pleistocene) or the extinction of some populations due to drier and cooler climate during the last glacial maximum could have been responsible for that phylogeographic pattern. The populations from northeastern Brazil originated from two colonization routes, one eastern (Atlantic) and one western (inland). Due to its high diversity and complex landscape, the central region, especially central‐north Minas Gerais (between 15°–18° S and 42°–46° W), should be given the highest priority for conservation.     

Chromosome spreading of associated transposable elements and ribosomal DNA in the fish Erythrinus erythrinus. Implications for genome change and karyoevolution in fish

Background  

The fish, Erythrinus erythrinus, shows an interpopulation diversity, with four karyomorphs differing by chromosomal number, chromosomal morphology and heteromorphic sex chromosomes. Karyomorph A has a diploid number of 2n = 54 and does not have differentiated sex chromosomes. Karyomorph D has 2n = 52 chromosomes in females and 2n = 51 in males, and it is most likely derived from karyomorph A by the differentiation of a multiple X₁X₂Y sex chromosome system. In this study, we analyzed karyomorphs A and D by means of cytogenetic approaches to evaluate their evolutionary relationship.