Enzymatic Engineering of Polysialic Acid on Cells in Vitro and in Vivo Using a Purified Bacterial Polysialyltransferase

In vertebrates, polysialic acid (PSA) is typically added to the neural cell adhesion molecule (NCAM) in the Golgi by PST or STX polysialyltransferase. PSA promotes plasticity, and its enhanced expression by viral delivery of the PST or STX gene has been shown to promote cellular processes that are useful for repair of the injured adult nervous system. Here we demonstrate a new strategy for PSA induction on cells involving addition of a purified polysialyltransferase from Neisseria meningitidis (PST_Nm) to the extracellular environment. In the presence of its donor substrate (CMP-Neu5Ac), PST_Nm synthesized PSA directly on surfaces of various cell types in culture, including Chinese hamster ovary cells, chicken DF1 fibroblasts, primary rat Schwann cells, and mouse embryonic stem cells. Similarly, injection of PST_Nm and donor in vivo was able to produce PSA in different adult brain regions, including the cerebral cortex, striatum, and spinal cord. PSA synthesis by PST_Nm requires the presence of the donor CMP-Neu5Ac, and the product could be degraded by the PSA-specific endoneuraminidase-N. Although PST_Nm was able to add PSA to NCAM, most of its product was attached to other cell surface proteins. Nevertheless, the PST_Nm-induced PSA displayed the ability to attenuate cell adhesion, promote neurite outgrowth, and enhance cell migration as has been reported for endogenous PSA-NCAM. Polysialylation by PST_Nm occurred in vivo in less than 2.5 h, persisted in tissues, and then decreased within a few weeks. Together these characteristics suggest that a PST_Nm-based approach may provide a valuable alternative to PST gene therapy.     

Djinga cheekii sp. nov. (Podostemaceae) from Cameroon

A new species is added to the monotypic African genus Djinga. Djinga cheekii Ghogue, Huber & Rutish. (Podostemaceae) is described as a new species from Cameroon (Littoral Province) and its morphological affinities and conservation status are assessed. The main distinguishing characters are: stamens 2 (not 1 as in D. felicis), flower buds inside spathella strongly inclined (not only slightly inclined as in D. felicis), and stems lacking or only up to 6 mm long (not up to > 6 cm as in D. felicis). A molecular analysis revealed that D. cheekii is sister to D. felicis, and both together are sister to Ledermanniella linearifolia and L. pusilla which show completely inverted flower buds inside the spathella, as typical for the large and still artificial genus Ledermanniella.     

Tree Height Reduction After Selective Logging in a Tropical Forest

By harvesting scattered large trees, selective logging increases light availability and thereby stimulates growth and crown expansion at early‐life stage among remnant trees. We assessed the effects of logging on total and merchantable bole (i.e., lowest branch at crown base) heights on 952 tropical canopy trees in French Guiana. We observed reductions in both total (mean, ?2.3 m) and bole (mean, ?2.0 m) heights more than a decade after selective logging. Depending on local logging intensity, height reductions resulted in 2–13 percent decreases in aboveground tree biomass and 3–17 percent decreases in bole volume. These results highlight the adverse effects of logging at both tree and stand levels. This decrease in height is a further threat to future provision of key environmental services, such as timber production and carbon sequestration.     

The Mass Distance Fingerprint: a statistical framework for de novo detection of predominant modifications using high-accuracy mass spectrometry

We describe a statistical measure, Mass Distance Fingerprint, for automatic de novo detection of predominant peptide mass distances, i.e., putative protein modifications. The method's focus is to globally detect mass differences, not to assign peptide sequences or modifications to individual spectra. The Mass Distance Fingerprint is calculated from high accuracy measured peptide masses. For the data sets used in this study, known mass differences are detected at electron mass accuracy or better. The proposed method is novel because it works independently of protein sequence databases and without any prior knowledge about modifications. Both modified and unmodified peptides have to be present in the sample to be detected. The method can be used for automated detection of chemical/post-translational modifications, quality control of experiments and labeling approaches, and to control the modification settings of protein identification tools. The algorithm is implemented as a web application and is distributed as open source software.     

Qualitative and quantitative analyses of protein phosphorylation in naive and stimulated mouse synaptosomal preparations

Activity-dependent protein phosphorylation is a highly dynamic yet tightly regulated process essential for cellular signaling. Although recognized as critical for neuronal functions, the extent and stoichiometry of phosphorylation in brain cells remain undetermined. In this study, we resolved activity-dependent changes in phosphorylation stoichiometry at specific sites in distinct subcellular compartments of brain cells. Following highly sensitive phosphopeptide enrichment using immobilized metal affinity chromatography and mass spectrometry, we isolated and identified 974 unique phosphorylation sites on 499 proteins, many of which are novel. To further explore the significance of specific phosphorylation sites, we used isobaric peptide labels and determined the absolute quantity of both phosphorylated and non-phosphorylated peptides of candidate phosphoproteins and estimated phosphorylation stoichiometry. The analyses of phosphorylation dynamics using differentially stimulated synaptic terminal preparations revealed activity-dependent changes in phosphorylation stoichiometry of target proteins. Using this method, we were able to differentiate between distinct isoforms of Ca2+/calmodulin-dependent protein kinase (CaMKII) and identify a novel activity-regulated phosphorylation site on the glutamate receptor subunit GluR1. Together these data illustrate that mass spectrometry-based methods can be used to determine activity-dependent changes in phosphorylation stoichiometry on candidate phosphopeptides following large scale phosphoproteome analysis of brain tissue.     

Running energetics of the North American river otter: do short legs necessarily reduce efficiency on land?

Semi-aquatic mammals move between two very different media (air and water), and are subject to a greater range of physical forces (gravity, buoyancy, drag) than obligate swimmers or runners. This versatility is associated with morphological compromises that often lead to elevated locomotor energetic costs when compared to fully aquatic or terrestrial species. To understand the basis of these differences in energy expenditure, this study examined the interrelationships between limb morphology, cost of transport and biomechanics of running in a semi-aquatic mammal, the North American river otter. Oxygen consumption, preferred locomotor speeds, and stride characteristics were measured for river otters (body mass=11.1 kg, appendicular/axial length=29%) trained to run on a treadmill. To assess the effects of limb length on performance parameters, kinematic measurements were also made for a terrestrial specialist of comparable stature, the Welsh corgi dog (body mass=12.0 kg, appendicular/axial length=37%). The results were compared to predicted values for long legged terrestrial specialists. As found for other semi-aquatic mammals, the net cost of transport of running river otters (6.63 J kg(-1)min(-1) at 1.43 ms(-1)) was greater than predicted for primarily terrestrial mammals. The otters also showed a marked reduction in gait transition speed and in the range of preferred running speeds in comparison to short dogs and semi-aquatic mammals. As evident from the corgi dogs, short legs did not necessarily compromise running performance. Rather, the ability to incorporate a period of suspension during high speed running was an important compensatory mechanism for short limbs in the dogs. Such an aerial period was not observed in river otters with the result that energetic costs during running were higher and gait transition speeds slower for this versatile mammal compared to locomotor specialists.     

Phylogenetic utility of the nuclear gene arginine decarboxylase: an example from Brassicaceae

Arginine decarboxylase (ADC) is an important enzyme in the production of putrescine and polyamines in plants. It is encoded by a single or low-copy nuclear gene that lacks introns in sequences studied to date. The rate of Adc amino acid sequence evolution is similar to that of ndhF for the angiosperm family studied. Highly conserved regions provide several target sites for PCR priming and sequencing and aid in nucleotide and amino acid sequence alignment across a range of taxonomic levels, while a variable region provides an increased number of potentially informative characters relative to ndhF for the taxa surveyed. The utility of the Adc gene in plant molecular systematic studies is demonstrated by analysis of its partial nucleotide sequences obtained from 13 representatives of Brassicaceae and 3 outgroup taxa, 2 from the mustard oil clade (order Capparales) and 1 from the related order Malvales. Two copies of the Adc gene, Adc1 and Adc2, are found in all members of the Brassicaceae studied to data except the basal genus Aethionema. The resulting Adc gene tree provides robust phylogenetic data regarding relationships within the complex mustard family, as well as independent support for proposed tribal realignments based on other molecular data sets such as those from chloroplast DNA.      

Developmental Genetics and Morphological Evolution of Flowering Plants, Especially Bladderworts (Utricularia): Fuzzy Arberian Morphology Complements Classical Morphology

This review compares new developmental models on flowering andother vascular plants with evolutionary hypotheses formulatedby Agnes Arber (1879–1960) and like-minded botanists.Special emphasis is laid on philosophical basics such as perspectivism,pluralism about evolutionary modelling, continuum way of thinking,and fuzzy logic. Arber's perspective is best labelled as F uzzyA rberian M orphology (FAM Approach). Its proponents (‘FAMmers’)treat structural categories (e.g. ‘roots’, ‘shoots’,‘stems’, ‘leaves’, ‘stipules’)in vascular plants as concepts with fuzzy borderlines allowingintermediates (including transitional forms, developmental mosaics).The FAM Approach complements Cla ssical Plant M orphology (ClaMApproach), which is the traditional approach in botany. ClaMproponents (‘ClaMmers’) postulate that the structuralcategories of vascular plants are regarded as concepts withclear-cut borderlines and without intermediates. However, duringthe evolution of vascular plants, the root-shoot distinctionand the stem-leaf distinction have become blurred several timesdue to developmental changes, resulting in organs with uniquecombinations of features. This happened, for example, in thebladderworts (Utricularia, Lentibulariaceae). When focusingon the ‘leaf’, the FAM Approach is identical toArber's ‘partial-shoot theory of the leaf’ and Sinha's‘leaf shoot continuum model’. A compound leaf canrepeat the developmental pathway of the whole shoot, at leastto some degree. For example, compound leaves of Chisocheton(Meliaceae)with indeterminate apical growth and three-dimensional branchingmay be seen as developmental mosaics sharing some growth processeswith whole shoots! We focus here on the FAM Approach becausethis perspective is especially promising for developmental geneticistsstudying flowering and other vascular plants. Copyright 2001Annals of Botany Company Review, body plan, developmental mosaics, leaf development, history of botany, homeosis, homeotic genes, Lentibulariaceae, morphological evolution, process morphology, stipules, Utricularia, flowering plants     

Seasonal variability in otariid energetics: implications for the effects of predators on localized prey resources

Otariids, like other wild mammals, contend with a wide variety of energetic demands across seasons. However, due to the cryptic behaviors of this marine group, few studies have been able to examine longitudinal energetic costs or the potential impact of these costs on seasonal or annual prey requirements. Here we evaluated the changes in energy demand and intake of female California sea lions (Zalophus californianus) during reproductive (n=2 sea lions) and nonreproductive (n=3) periods. Monthly measurements included resting metabolic rate, blood hormone levels, body condition (blubber thickness and body mass), and caloric intake for adult sea lions throughout molting, late pregnancy, lactation, and postweaning. We found that maintenance energy demands decreased from 32.0 to 23.1 MJ d(-1) before pupping, remaining stable at 19.4+/-0.6 MJ d(-1) during lactation and postweaning. Energy intake rates to meet these demands showed marked changes with activity level and the reproductive cycle, reaching a peak intake of 3.6 times baseline levels during lactation. Translating this into prey demands, we find that 20,000 reproductively active females on San Nicolas Island rookeries would maximally require 4,950 metric tons of Pacific whiting during a month of the breeding season. This localized impact is reduced significantly with postbreeding dispersal and demonstrates the importance of considering spatial and temporal factors driving the energetic requirements of predators when designing marine protected areas.