Novel propargylamine-linked nucleosides for high throughput SNP genotyping by MALDI-TOF MS

The synthesis of positively charged and mass tagged nucleosides containing a quaternary ammonium functionality within the penultimate position of a primer is described. Neutralization of the sugar/thiophosphate backbone by alkylation increases the detection sensitivity in the mass spectrometric analysis by a factor of at least 100. The variable introduction of these novel compounds within the extension primers enables flexible design of multiplex genotyping reactions.     

Patterns of seed mass variation and their effects on seedling traits inAlliaria petiolata (Brassicaceae)

Seed mass is considered to be the least plastic component of reproductive yield. Yet, in invasive populations of garlic mustard, Alliaria petiolata, seed mass was highly variable (eightfold among populations, 2.5-7.5 fold within populations, two-threefold within individuals, and 1.4-1.8 fold within fruits). Variation in seed mass among populations explained nearly half of the total variance. Variation among seeds within fruits accounted for a further 25% of variance. Individual seed mass within a plant decreased with increased distance from the main stem, suggesting that access to parental resources limits seed size in a predictable manner. MANOVAs and Roy-Bargmann stepdown analyses revealed significant effects of seed mass, but not seed position (within a fruit or within an infructescence), on an array of subsequent seedling traits. Smaller seeds germinated significantly earlier, and seedlings from small seeds produced their first primary leaves significantly later and grew significantly taller. After accounting for seed mass as a covariate, only one seedling trait, date of first leaf emergence, was affected by seed position in a fruit. Differences in seed mass may therefore affect seedling recruitment via effects on early seedling growth in this weedy species.     

Does multiple paternity affect seed mass in angiosperms? An experimental test in Dalechampia scandens

Flowers fertilized by multiple fathers may be expected to produce heavier seeds than those fertilized by a single father. However, the adaptive mechanisms leading to such differences remain unclear, and the evidence inconsistent. Here, we first review the different hypotheses predicting an increase in seed mass when multiple paternity occurs. We show that distinguishing between these hypotheses requires information about average seed mass, but also about within‐fruit variance in seed mass, bias in siring success among pollen donors, and whether siring success and seed mass are correlated. We then report the results of an experiment on Dalechampia scandens (Euphorbiaceae), assessing these critical variables in conjunction with a comparison of seed mass resulting from crosses with single vs. multiple pollen donors. Siring success differed among males when competing for fertilization, but average seed mass was not affected by the number of fathers. Furthermore, paternal identity explained only 3.8% of the variance in seed mass, and siring success was not correlated with the mass of the seeds produced. Finally, within‐infructescence variance in seed mass was not affected by the number of fathers. These results suggest that neither differential allocation nor sibling rivalry has any effect on the average mass of seeds in multiply sired fruits in D. scandens. Overall, the limited paternal effects observed in most studies and the possibility of diversification bet hedging among flowers (but not within flowers), suggest that multiple paternity within fruits or infructescence is unlikely to affect seed mass in a large number of angiosperm species.     

Within and Between Plant Variation in Seed Number, Seed Mass and Germinability of Primula elatior: Effect of Population Size

Abstract: In this study, natural variation of seed mass and seed number between and within individual plants of P. elatior, a common forest herb on rich soils in Flanders, was investigated for both small (< 50 flowering individuals) and large (> 1000 flowering individuals) populations. The relationship between seed number and seed mass at both the between and within population level was also quantified. We also investigated how population size affected germinability of seeds through the effects of seed mass. Seed number varied by a factor of twenty, whereas seed mass spanned, on average, a 3.5 range. In both cases variation was highest among populations, indicating that population size has important effects on seed number and seed mass. Next, seed number-seed mass tradeoffs were significantly influenced by population size, with small populations showing strong negative relationships whereas in large populations seed mass was only marginally influenced by seed number. As to germination, larger seeds showed larger germination percentages only for the smallest population. In all other populations, seed mass had little effect on germination.     

Proteomics for routine identification of microorganisms

The invention of MALDI-TOF-MS enormously contributed to the understanding of protein chemistry and cell biology. Without this technique proteomics would most likely not be the important discipline it is today. Besides 'true' proteomics, MALDI-TOF-MS was applied for the analysis of microorganisms for their taxonomic characterization from its beginning. This approach has since been developed as a diagnostic tool readily available for routine, high-throughput analysis of microbial isolates from clinical specimens by intact-cell mass spectrometry (ICMS), the direct analysis of whole bacterial cell without a preceding fractionation or separation by chromatography or electrophoresis. ICMS exploits the reproducibility of mass fingerprints for individual bacterial and fungal strains as well as the high similarity of mass fingerprints within a species. Comparison of mass spectral data to genomic sequences emphasized the validity of peak patterns as taxonomic markers. Supported by comprehensive databases, MALDI-TOF-MS-based identification has been widely accepted in clinical laboratories within only a few years.     

Egg Size Versus Number of Offspring Trade-Off: Female Age Rather Than Size Matters in a Domesticated Arctic Charr Population

Understanding how organisms adjust reproductive allocation trade-offs between offspring size versus number (OSN trade-off) is a central question in evolutionary biology. In organisms with indeterminate growth, changes in OSN according to maternal size or age have been reported in numerous taxa. The relative contribution of age and size remains largely unclear, as they are often highly correlated. In this study, we investigated how females adjust the offspring size versus number trade-off and analyzed the relative contribution of female age and size in a domesticated population of Arctic charr Salvelinus alpinus (Linnaeus, 1758) that exhibit large variation in size within five age classes. Our results show that the reproductive output (i.e. as measured by the clutch mass), was strongly correlated to female mass and age suggesting that the proportion of resources allocated to reproduction do not vary along lifetime. Egg mass and fecundity (egg number) increased with female mass overall. However, within an age class, larger females had higher fecundity but egg mass was poorly related to female mass. At the population level, a positive relationship was observed between fecundity and egg mass but within each class age the relation was negative revealing a OSN trade-off. Overall, our results show that, in our model Arctic charr population, allocation trade-off to reproduction and the way females allocate to egg mass and fecundity is largely determined by their age rather than mass.     

A replicating module as the unit of mitochondrial structure and functioning

The mitochondrion within human cells in tissue culture is pleomorphic and highly dynamic. The organelle mass can exist as thousands of small ovoids or as one continuous reticulum. In either state, the mitochondrial mass is in constant thermal motion, as well as moving in approximately 0.8-microm jumps that are determined by, and related to, attachments with cytoskeletal elements. Many protein complexes, such as the pyruvate dehydrogenase (PDH) complex and DNA containing nucleoids, are dispersed through the mass and as though fixed by attachments to membranes, such that they can become distributed to all of the individual small ovoid mitochondria when the reticulum becomes fragmented. This leads us to propose that a replicating module is the repeating unit of mitochondrial structure. Studies to examine heterogeneity of functioning within the organelle mass are briefly reviewed.     

Diffusion and reaction within porous packing media: a phenomenological model

A phenomenological model has been developed to describe biomass distribution and substrate depletion in porous diatomaceous earth (DE) pellets colonized by Pseudomonas aeruginosa. The essential features of the model are diffusion, attachment and detachment to/from pore walls of the biomass, diffusion of substrate within the pellet, and external mass transfer of both substrate and biomass in the bulk fluid of a packed bed containing the pellets. A bench-scale reactor filled with DE pellets was inoculated with P. aeruginosa and operated in plug flow without recycle using a feed containing glucose as the limiting nutrient. Steady-state effluent glucose concentrations were measured at various residence times, and biomass distribution within the pellet was measured at the lowest residence time. In the model, microorganism/substrate kinetics and mass transfer characteristics were predicted from the literature. Only the attachment and detachment parameters were treated as unknowns, and were determined by fitting biomass distribution data within the pellets to the mathematical model. The rate-limiting step in substrate conversion was determined to be internal mass transfer resistance; external mass transfer resistance and microbial kinetic limitations were found to be nearly negligible. Only the outer 5% of the pellets contributed to substrate conversion. (c) 1993 Wiley & Sons, Inc.     

Taphonomy and palaeoecology of Late Triassic (Carnian) ammonoid concentrations from the Taurus Mountains,Turkey

The deposits of the Carnian Kas?mlar Formation within the Taurus Platform Units of south‐western Turkey represent an important archive of a Late Triassic ecosystem. New palaeontological information was obtained by analysing the Kasimlarceltites mass occurrence, located within the Kas?mlar Formation and named after the Lower Carnian (Julian) ammonoid genus Kasimlarceltites. This is the dominant taxon (> 94%) within the mass occurrence: nearly 775 million ammonoids and 50 million gastropods were extrapolated for the whole extension (at least 5 km²) of the Kasimlarceltites beds. This calculation is one of the main findings within this study, as it is the first time that such a fossil mass occurrence was quantified. Additionally, orientation measurements of the planispiral ammonoids and the helical gastropods enabled reconstructing the history of the mass occurrence and interpreting the underlying transport mechanisms. Further taphonomic aspects (e.g. biofabric, preservation, bioerosion or genetic classification) as well as comparisons with samples of the same acme zone from different localities near A?a?iyaylabel (AS IV, KA I‐II) point to a two‐phased genetic history. Accordingly, local mass mortality within the Kasimlarceltites fauna due to oxygen fluctuations or methane degassing may have initially led to a primary accumulation. These deposits were then reworked and redeposited basinward by gravity flows to create the present‐day secondary allochthonous concentrations.     

Effect of stem length to stem slender ratio of current-year twigs on the leaf display efficiency in evergreen and deciduous broadleaved trees

Aims Branches and leaves are the two main structural units of tree crown composition. Among the adaptive strategies of plants, the functional traits of branches and the relationships between branch traits and leaf traits determine the capacity of trees to access light and space. In this study, our objective is to test the hypothesis that leaf display efficiency is affected by the stem length to stem slender ratio within current-year twigs.Methods The stem length to stem slender ratios of current-year twigs were used as the proxy of stem structure traits. Leaf area ratio (total leaf area per stem mass), leaf density (leaf number per stem length) and leaf/stem mass ratio (total leaf mass per stem mass) were used as the proxies of leaf display efficiency. The relationship between stem structure traits and leaf display efficiency within current-year twigs were studied for 25 evergreen and 60 deciduous broadleaved woody species in Qingliang Mountain, Zhejiang, China. The standardized major axis estimation method was used to examine the scaling relationship between stem structural traits and leaf display efficiency within current-year twigs.Important findings The proxies of leaf display efficiency, measured by leaf area ratio, leaf density or leaf/stem mass ratio, were all significantly and negative correlated with stem length to stem slender ratio within current-year twigs in both evergreen and deciduous broadleaved woody species. This suggested that leaf display efficiency decreased with stem length to stem slender ratios within current-year twigs, which may reflect the role of mechanical safety and light within twigs. The slope of the relationship between leaf display efficiency and stem long-dimension structure traits in evergreen species was not significantly different from the one in deciduous species. In contrast, the y-intercept of the relationship between leaf density and stem long-dimension structure traits was significantly larger in evergreen species than in deciduous species, i.e. the leafing intensity of evergreen species was higher than that of deciduous species. Individual leaf area and specific leaf area were smaller in evergreen species than in deciduous species, which resulted in deciduous species have a larger leaf area per stem mass and leaf mass per stem mass at a given stem length to stem slender ratio compared to evergreen species. It may reflect the conservative adaptive strategy of high consumption and slow benefit in evergreen species. Our results demonstrated that leaf display efficiency could be affected by stem length, and would change with leaf life-span (deciduous versus evergreen).     

Distribution of mass within native thick filaments of vertebrate skeletal muscle

The distribution of mass within the vertebrate skeletal thick filament has been determined by scanning transmission electron microscopy. Thick and thin filaments from fresh rabbit muscle were mixed with tobacco mosaic virus (TMV), fixed with formaldehyde, dried onto thin carbon films and viewed in a computer-linked microscope. Electron scattering data from both TMV and thick filaments were analysed with reference to the long axis of the particles so that the distribution of mass within the particles could be determined. While TMV appeared to be a uniform rod at the resolution employed (4.3 nm), the thick filament was clearly differentiated along its length. M-line remnants at the centre of the filament were flanked by regions of low mass per unit length, corresponding to the bare zone of the filament, and then by the more massive cross-bridge regions. The mass per unit length was approximately constant through most of the cross-bridge zone and declined at the filament tips, in a manner consistent with a constant number of myosin molecules per 14.3 nm interval (crown) throughout the cross-bridge zone. Fourier analysis of the data failed to detect the expected 43 nm periodicity of C-protein. The total mass of the thick filament was 184 Mdalton (s.e.m., 1.6 X 10(6); n = 70). The mass of adhering M-line proteins was highly variable but, on average, was about 4 Mdalton. The total mass of the filament and the mass distribution in the cross-bridge zone are consistent with three myosin molecules per crown.     

The effect of light and seed mass on seed germination of common herbaceous species from the eastern Qinghai‐Tibet Plateau

Smaller seeds might encounter more severe selective pressure than larger ones because they have fewer food reserves and are more easily buried; thus, seed mass can be considered to be directly related to the effect of light on germination. To investigate the effect of light on seed germination and associated seed mass variation within a whole plant community, we compiled germination data for common herbaceous species from an alpine meadow on the eastern Qinghai‐Tibet plateau. The results showed the following. (i) Light had a general positive effect on seed germination. Under light, the proportion of species with lower germinability was decreased, mean germination percentage was increased by 20% and the speed of germination was doubled. (ii) Irrespective of light environment, species with medium‐sized seeds (seed mass ranging from 0.11 to 0.5 mg) had higher germination percentage and speed when compared with species within the largest seed mass group. (iii) The germination of smaller‐seeded species was more dependent on light stimulation than larger‐seeded ones. In darkness, the species within the smallest seed mass group had the lowest percentage and speed of germination; however, under light, the species within the largest seed mass group had the lowest percentage and speed of germination. Our results suggested that the germination characteristics and especially seeds’ response to light among species in the alpine meadow might be an adaptation to natural selective pressure.     

Identification of tyrosine 204 as the photo-cross-linking site in the DNA-EcoRI DNA methyltransferase complex by electrospray ionization mass spectrometry

We describe a highly sensitive strategy combining laser-induced photo-cross-linking and HPLC-based electrospray ionization mass spectrometry to identify amino acid residues involved in protein-DNA recognition. The photoactivatible cross-linking thymine isostere, 5-iodoracil, was incorporated at a single site within the sequence recognized by EcoRI DNA methyltransferase (GAATTC). UV irradiation of the DNA-protein complex at 313 nm results in a >60% cross-linking yield. SDS-polyacrylamide gel electrophoresis and mass spectrometry were used to analyze the covalent cross-linked complex. The total mass is consistent with covalent bond formation between one strand of DNA and the protein with 1:1 stoichiometry. Protease digestion of the cross-linked complex yields several peptide-DNA adducts that were purified by anion-exchange column chromatography. A combination of mass spectrometric analysis and amino acid sequencing revealed that tyrosine 204 was cross-linked to the DNA. Electrospray mass spectrometric analysis of the peptide-nucleoside adduct confirmed this assignment. Tyrosine 204 resides in a peptide motif previously thought to be involved in AdoMet binding and methyl transfer. Thus, amino acids within loop segments but outside of "DNA binding" motifs can be critical to DNA recognition. Our method provides an accurate characterization of picomole quantities of DNA-protein complexes.     

Multiple statistical analysis techniques corroborate intratumor heterogeneity in imaging mass spectrometry datasets of myxofibrosarcoma

MALDI mass spectrometry can generate profiles that contain hundreds of biomolecular ions directly from tissue. Spatially-correlated analysis, MALDI imaging MS, can simultaneously reveal how each of these biomolecular ions varies in clinical tissue samples. The use of statistical data analysis tools to identify regions containing correlated mass spectrometry profiles is referred to as imaging MS-based molecular histology because of its ability to annotate tissues solely on the basis of the imaging MS data. Several reports have indicated that imaging MS-based molecular histology may be able to complement established histological and histochemical techniques by distinguishing between pathologies with overlapping/identical morphologies and revealing biomolecular intratumor heterogeneity. A data analysis pipeline that identifies regions of imaging MS datasets with correlated mass spectrometry profiles could lead to the development of novel methods for improved diagnosis (differentiating subgroups within distinct histological groups) and annotating the spatio-chemical makeup of tumors. Here it is demonstrated that highlighting the regions within imaging MS datasets whose mass spectrometry profiles were found to be correlated by five independent multivariate methods provides a consistently accurate summary of the spatio-chemical heterogeneity. The corroboration provided by using multiple multivariate methods, efficiently applied in an automated routine, provides assurance that the identified regions are indeed characterized by distinct mass spectrometry profiles, a crucial requirement for its development as a complementary histological tool. When simultaneously applied to imaging MS datasets from multiple patient samples of intermediate-grade myxofibrosarcoma, a heterogeneous soft tissue sarcoma, nodules with mass spectrometry profiles found to be distinct by five different multivariate methods were detected within morphologically identical regions of all patient tissue samples. To aid the further development of imaging MS based molecular histology as a complementary histological tool the Matlab code of the agreement analysis, instructions and a reduced dataset are included as supporting information.     

Ultrastructural and histochemical observations on electroejaculated spermatophores of the palaemonid shrimp, Macrobrachium rosenbergii

Spermatophores obtained by electroejaculation from mature males of Macrobrachium rosenbergii were studied by light microscopy and by transmission and scanning electron microscopy. Upon electrical stimulation, single Spermatophores were usually extruded simultaneously from each gonopore and frequently became firmly adherent to one another forming a compound spermatophore. Individual Spermatophores were pod-shaped. 0.5-1 cm long, 2-3 mum in diameter and consisted of a lateral sperm mass, a medial mucus mass, and a noncellular capsule. The capsule was a single-layered PAS-reactive structure composed of fine, intertwining fibrils and almost completely surrounded the sperm and mucus masses. On its outer surface were large. AB-reactive globules of flocculent material partially surrounded by fingerlike extensions of a canaliculated reticulum composed of fine, intertwinning fibrils. The canaliculated reticulum may permit fluid imbibition by the spermatophore. Forming a central band within the capsule were many small membrane-less AB/PAS-reactive granules. The lateral sperm masses consisted of unistellatc spermatozoa embedded in an AB/PAS-reaetive matrix composed of globules of flocculent. AB-rcactive material and a highly plastic canaliculated and thread-filled reticulum. The reticulum itself consisted of fine, intertwining fibrils. The threads within the interstices of the reticulum were long, curving structures, 30-36 nm in diameter. The function(s) of the canaliculated and thread-filled reticulum within the sperm mass is not known at this time. The medial mucus mass was similar in fine structure and histochemical reactivity to the sperm mass, except that spermatozoa were lacking. It is apparent that the spermatophore of M. rosenbergii consists of relatively few complexly arranged structural and macromolecular components designed to transport and protect the spermatozoa.     

No evidence for a role of pollinator discrimination in causing selection on flower size through female reproduction

The preference for certain floral phenotypes by flower visiting animals may fuel the evolution of floral traits because variation in flower visitation rates may lead to fitness variation within a population. Here, I examine the importance of flower size for pollinator visitation rate, seed set, and seed mass in two alpine populations of the insect-pollinated herb Ranunculus acris L. during two seasons. There was no pollen limitation of seed set or mass. Pollinators discriminated strongly against flowers experimentally reduced in size. Despite this, there were no signs of any significant impact of flower size on female reproductive success. The results show that although pollinators discriminate strongly among floral phenotypes, this may not always result in female fitness differences within a population because seed set or mass is not limited by pollen availability alone. Probably abiotic environmental constraints prevent plants with high pollinator visitation from capitalizing on the high pollen deposition.     

Repeatability of hematocrits and body mass of Gray Catbirds

ABSTRACT.   Hematocrits may provide information about the physiological condition of birds, but, to be a useful measure, information is needed concerning how hematocrits vary among individuals and over time. We examined the repeatability of hematocrits in a population of Gray Catbirds ( Dumetella carolinensis ) in Pennsylvania at several time scales and also examined the repeatability of body mass, another measure commonly used as an indicator of condition. Both hematocrit ( r = 0.64) and mass ( r = 0.65) were repeatable ( P < 0.01) for first captures between years and between first and second captures within a year ( r = 0.41 and r = 0.50, respectively; P < 0.01), but not repeatable ( P > 0.05) between captures in different months within a year ( r = 0.11 for both). Repeatability of both measures differed by sex and age. Females exhibited repeatability of hematocrit and body mass only between years, while male hematocrits were repeatable between years and between first and second captures within a season. Male mass was repeatable for all time periods. Hematocrits of younger birds were repeatable between captures within a season and their body mass was repeatable between months and weeks while hematocrits of older birds were not repeatable and their body mass was repeatable only between captures in a season. Our results indicate that hematocrits and body mass had similar repeatability coefficients overall, but that hematocrits of Gray Catbirds were a consistent trait of individuals only across years. Because repeatability between captures and months depended on sex and age, we conclude that the hematocrit is a useful measure of individual performance only in limited circumstances.     

PROXIMATE AND ULTIMATE SOURCES OF WITHIN-INDIVIDUAL VARIATION IN SEED MASS IN PRUNELLA VULGARIS (LAMIACEAE)

Substantial variation in seed mass within individual seed parents is at odds with predictions of models for the evolution of optimum offspring size and with empirical observations of directional selection on seed mass. To elucidate the ultimate causes of this variation, I examined several proximal sources of within-individual variation in seed mass in the perennial herb Prunella vulgaris. Position of inflorescence, position of flower within an inflorescence, date of anthesis, and number of seeds produced per flower all explained some within-individual variation in seed mass. Hand pollination in the field failed to reveal any effect of pollen source (self pollen or outcross pollen) on seed mass. My results, in conjunction with those from studies of selection on seed mass in P. vulgaris, do not support hypotheses that within-individual variation in seed mass is favored by the pattern of natural selection on seed mass. Rather, the results suggest that seed parents are not capable of producing a uniform seed crop in the face of changes in resource availability in the course of a season. The inability to produce a uniform seed crop may persist because of selection for variability in traits correlated with seed mass or because of a true constraint on the evolution of uniform offspring size.     

Use of reconstituted metabolic networks to assist in metabolomic data visualization and mining

Metabolomics experiments seldom achieve their aim of comprehensively covering the entire metabolome. However, important information can be gleaned even from sparse datasets, which can be facilitated by placing the results within the context of known metabolic networks. Here we present a method that allows the automatic assignment of identified metabolites to positions within known metabolic networks, and, furthermore, allows automated extraction of sub-networks of biological significance. This latter feature is possible by use of a gap-filling algorithm. The utility of the algorithm in reconstructing and mining of metabolomics data is shown on two independent datasets generated with LC–MS LTQ-Orbitrap mass spectrometry. Biologically relevant metabolic sub-networks were extracted from both datasets. Moreover, a number of metabolites, whose presence eluded automatic selection within mass spectra, could be identified retrospectively by virtue of their inferred presence through gap filling.     

A new computational model to study mass inhomogeneity and hydrophobicity inhomogeneity in proteins

We propose a simple yet reliable computational framework that characterizes the differential mass and hydrophobicity distribution within structural classes of proteins. Radial partitioning of protein interior that could successfully distinguish the mass and hydrophobicity distribution patterns in extremophilic proteins from that in their structurally aligned mesophilic counterparts. Distance-dependent mass and hydrophobicity magnitudes could retrieve vital structural insights; needed to probe the hidden connections between packing, folding and stability within different structural classes of proteins, with causality. New computational markers; one, to represent the total mass content; other, related to hydrophobic centrality of proteins, are proposed as well. Results reveal that mass and hydrophobicity packing within extremophilic proteins is indeed more compact than that in their mesophilic counterparts. Analysis of structural constraints within them vindicate it. Total mass (and hydrophobicity) content is found to be maximum in α/β thermophilic proteins and minimum for the all-α mesophilic proteins. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.