X-Ray Characterization of Melanins—I

The intrinsic local structure characterization of natural sepia melanin and L-dopa and tyrosine synthetic melanin powder has been carried out by X-ray diffraction using synchrotron radiation. The derived structure factor, S(q), shows six significant diffuse peaks within the q-range from 0.3 Å^-1 to 16 Å^-1 in the reciprocal space (q= (4π sin θ)/λ, 2θ is the scattering angle). The Fourier transform of S(q), which yields the radial distribution function (RDF), gives us information in real space of a 1.42 Å distance averaged over the C-C, C-O and C-N bond lengths as well as peaks at 2.40-2.41 Å, 3.67-3.71 Å and 4.67-4.70 Å discrete neighbor distances. There is a great similarity in the scattering intensity profiles of the natural and synthetic melanins indicating that the synthetically prepared material may be essentially similar to “real” melanin in its local atomic arrangements. An evidence of a prepeak at q = 0.45 Å^-1 has been confirmed which indicates a preferred length scale of ～ 13-20 Å that corresponds to the initial particle size in colloidal melanin solutions.     

QuantiSpec — Quantitative mass spectrometry data analysis of N-metabolically labeled proteins

For relative protein quantitation by mass spectrometry we metabolically labeled E. coli bacteria with ¹⁵N-enriched diets. Proteins extracted from ¹⁵N-labeled and unlabeled E. coli bacteria were mixed, separated by two-dimensional gel electrophoresis and enzymatically digested. The resulting tryptic peptides were analyzed by MALDI mass spectrometry. For the relative protein quantitation we developed fully automated software, QuantiSpec (Quantitative Mass Spectrometry Analysis Software), which uses data from MALDI TOF mass spectrometry and the Mascot database search engine. QuantiSpec detects natural as well as partially or fully labeled peptide isotope distributions. For each identified peptide the ¹⁵N incorporation rate is determined by comparing the experimental to a set of theoretical isotope patterns based on the peptide sequence. Relative quantitation is accomplished by calculating the signal intensity ratios for each ¹⁴N/¹⁵N peptide pair.     

Calorimetric Glucose Determination by Glucose Oxidase —Methylene Blue

The reaction between glucose and methylene blue, catalyzed by glucose oxidase (GOD)was analysed calorimetrically. The amount of heat produced under saturating methylene blue concentrations ( > 10^?2 mol/1)was measured with glucose concentration and time as parameters (kinetic procedure) Kinetic constants (pseudo one substrate kinetics) were derived from the experimental data: K_M(glucose)= 1.18 × 10^?3 mol/l and V_max = 0.085 J/mg GOD min (3.89 · 10^?6 mol/mg GOD min) Comparison of caloric with optical measurements gave an enthalpy of reaction of 22.52 kJ/mol. Considering the observed substrate inhibition, glucose determinations are possible up to glucose concentrations of 0.1 mol/l.     

Picomole assay for N-methylhistidine by gas chromatography—Mass spectrometry

A simple, sensitive method for measuring N^τ-methylhistidine in biological samples using a deuterated internal standard and methane chemical ionization gas chromatography-mass spectrometry is described. After sample preparation, a single analysis can be completed in 3 min; analysis in duplicate, including sample preparation for 40 samples, can be completed at a rate of 15 min per sample. Nanomole amounts of N^τ-mmethylhistidine in urine or plasma samples are determined with a precision of 0.5%. Picomole amounts, released during in vitro rat epitrochlaris muscle incubations, are measured with a precision of 10%.     

Coral—the world's most diverse symbiotic ecosystem

Zooxanthellate corals (i.e. those harbouring Symbiodinium) are the main builders of the world's shallow‐water marine coral reefs. They represent intimate diverse symbioses between coral animals, single‐celled photosynthetic dinoflagellates (Symbiodinium spp.), other microscopic eukaryotes, prokaryotes and viruses. Crabs and other crustaceans, worms, sponges, bivalves and hydrozoans, fishes, sea urchins, octopuses and sea stars are itinerant members of these ‘rainforests of the sea’. This review focuses on the biodiversity of scleractinian coral animals and their best studied microscopic epi‐ and endosymbionts. In relation to coral‐associated species diversity, Symbiodinium internal transcribed spacer region sequence types tally 10²–10³ or up to ~15 different operational taxonomic units (OTUs, or putative species at the 97% sequence identity level; this cut‐off was chosen based on intragenomic sequence diversity observed in monoclonal cultures) and prokaryotes (mostly bacterial) total 10²–10⁴ OTUs. We analysed all publically accessible 16S rRNA gene sequence data and found Gammaproteobacteria were extremely abundant, followed by Alphaproteobacteria. Notably, Archaea were poorly represented and ‘unassigned OTUs’ were abundant in data generated by high‐throughput DNA sequencing studies of corals. We outline and compare model systems that could be used in future studies of the coral holobiont. In our future directions, we recommend a global coral sampling effort including substantial attention being paid to method of coral tissue acquisition, which compartments (mucus, tissue, skeleton) to explore, broadening the holobiont members considered and linking biodiversity with functional investigations.     

STRUCTURE—FUNCTION RELATIONSHIPS OF NA+/K+-PUMPS EXPRESSED INXENOPUSOOCYTES

During the last years we have examined structure—function relationships in the Na⁺/K⁺-ATPase with respect to interactions of the external cations with the pump molecule. We have analysed in voltage-clamp experiments the influence of extracellular Na⁺and K⁺on the current generated by Na⁺/K⁺-pumps expressed inXenopusoocytes. Our results demonstrated that external Na⁺and K⁺have to pass an access channel in the electrical field of the membrane to reach their binding sites. This external access, therefore, is voltage-dependent and is affected by lysine residues within the cytoplasmic N-terminus, by glutamic acid residues in intramembraneous domains, the ouabain sensitivity and phosphorylation by protein kinases.     

Mechanism for Macrophage Activation against Corynebacterium parvum—Participation of T Cells and Its Lymphokines

It is well known that Corynebacterium parvum activates macrophages to produce tumor necrosis factor (TNF). It is suspected that the activation of macrophages by C. parvum requires T-cell participation. The purpose of this study was to confirm that T cells participate in the activation of macrophages by C. parvum. TNF production in vitro from the spleen cells of BALB/c- + / + mice was abrogated completely by the pre-treatment of spleen cells with anti-Ia antiserum and complement, indicating that Ia+ cells are the source of TNF. TNF production was not elicited at all in BALB/c-nu/nu mice. However, there was an increase in the number of Ia+ cells as well as an increase in the weight of spleen and liver. Supernatant from a culture of spleen cells stimulated with phytohemagglutinin-P (a PHA-induced lymphokine) made it possible for BALB/c-nu/nu mice to produce TNF, associated with an induction of Lyt-1⁺ cells and Lyt-2⁺ cells. However, treatment with the lymphokine did not augment the increases of Ia⁺ cells or liver and spleen weights. These results suggest that increasing the number of Ia⁺ cells is not sufficient to bring about TNF production; Ia⁺ cells must also be stimulated by T cells or T-cell lymphokines in order to produce TNF. These results suggest that T cells play an essential role in the activation of Ia⁺ cells against C. parvum.     

Collagen functionalized with unsaturated cyclic anhydrides—interactions in solution and solid state

Maleic anhydride (CMA) and itaconic anhydride modified collagen (CITA) were prepared as precursors for production of interpenetrated polymer networks (IPN). Calculated values for Huggins coefficient in aqueous diluted and semi‐diluted solutions of modified collagen indicated a slightly tendency of aggregation for itaconic anhydride‐modified collagen. In semi‐diluted solution collagen (Coll) and CMA present slightly differences in the thixotropic behavior, while CITA has a pronounced thixotropic behavior. Flow and oscillatory measurements revealed an elastic behavior of the collagen solutions, pure and modified with MA or ITA, as the storage modulus (G′) has always a superior value compared with the loss modulus (G″). The denaturation temperature (T_d) of unmodified collagen increased from 34^oC to 40^oC for CMA and to 39^oC for CITA respectively, by formation of covalent bonds that stabilize the triple helix. © 2013 Wiley Periodicals, Inc. Biopolymers 101: 228–236, 2014.     

Trichocysts—Paramecium's Projectile‐like Secretory Organelles

This review summarizes biogenesis, composition, intracellular transport, and possible functions of trichocysts. Trichocyst release by Paramecium is the fastest dense core‐secretory vesicle exocytosis known. This is enabled by the crystalline nature of the trichocyst “body” whose matrix proteins (tmp), upon contact with extracellular Ca²⁺, undergo explosive recrystallization that propagates cooperatively throughout the organelle. Membrane fusion during stimulated trichocyst exocytosis involves Ca²⁺ mobilization from alveolar sacs and tightly coupled store‐operated Ca²⁺‐influx, initiated by activation of ryanodine receptor‐like Ca²⁺‐release channels. Particularly, aminoethyldextran perfectly mimics a physiological function of trichocysts, i.e. defense against predators, by vigorous, local trichocyst discharge. The tmp's contained in the main “body” of a trichocyst are arranged in a defined pattern, resulting in crossstriation, whose period expands upon expulsion. The second part of a trichocyst, the “tip”, contains secretory lectins which diffuse upon discharge. Repulsion from predators may not be the only function of trichocysts. We consider ciliary reversal accompanying stimulated trichocyst exocytosis (also in mutants devoid of depolarization‐activated Ca²⁺ channels) a second, automatically superimposed defense mechanism. A third defensive mechanism may be effectuated by the secretory lectins of the trichocyst tip; they may inhibit toxicyst exocytosis in Dileptus by crosslinking surface proteins (an effect mimicked in Paramecium by antibodies against cell surface components). Some of the proteins, body and tip, are glycosylated as visualized by binding of exogenous lectins. This reflects the biogenetic pathway, from the endoplasmic reticulum via the Golgi apparatus, which is also supported by details from molecular biology. There are fragile links connecting the matrix of a trichocyst with its membrane; these may signal the filling state, full or empty, before and after tmp release upon exocytosis, respectively. This is supported by experimentally produced “frustrated exocytosis”, i.e. membrane fusion without contents release, followed by membrane resealing and entry in a new cycle of reattachment for stimulated exocytosis. There are some more puzzles to be solved: Considering the absence of any detectable Ca²⁺ and of acidity in the organelle, what causes the striking effects of silencing the genes of some specific Ca²⁺‐release channels and of subunits of the H⁺‐ATPase? What determines the inherent polarity of a trichocyst? What precisely causes the inability of trichocyst mutants to dock at the cell membrane? Many details now call for further experimental work to unravel more secrets about these fascinating organelles.     

Prion protein—Semisynthetic prion protein (PrP) variants with posttranslational modifications

Deciphering the pathophysiologic events in prion diseases is challenging, and the role of posttranslational modifications (PTMs) such as glypidation and glycosylation remains elusive due to the lack of homogeneous protein preparations. So far, experimental studies have been limited in directly analyzing the earliest events of the conformational change of cellular prion protein (PrP^C) into scrapie prion protein (PrP^Sc) that further propagates PrP^C misfolding and aggregation at the cellular membrane, the initial site of prion infection, and PrP misfolding, by a lack of suitably modified PrP variants. PTMs of PrP, especially attachment of the glycosylphosphatidylinositol (GPI) anchor, have been shown to be crucially involved in the PrP^Sc formation. To this end, semisynthesis offers a unique possibility to understand PrP behavior invitro and invivo as it provides access to defined site‐selectively modified PrP variants. This approach relies on the production and chemoselective linkage of peptide segments, amenable to chemical modifications, with recombinantly produced protein segments. In this article, advances in understanding PrP conversion using semisynthesis as a tool to obtain homogeneous posttranslationally modified PrP will be discussed.     

Determination of taurine metabolism by measurement of N-enriched taurine in cat urine by gas chromatography—mass spectrometry

To understand the biological function of taurine, a study of taurine kinetics in the cat was undertaken. This paper describes a method developed for the accurate determination of ¹⁵N-taurine enrichment in cat urine by gas chromatography—mass spectrometry. ¹⁵N-Taurine was given to six animals as an oral bolus dose of 20 mg/kg body weight, and the urine was pooled on a daily basis. The hydrolysed or non-hydrolysed urine samples (for total and free taurine, respectively) were directly derivatized without further purification. The N-pentafluorobenzoyl di-n-butyl amide derivative obtained was analysed, and the fragment [M — (di-n-butyl amide)]⁺, carrier of the labelled nitrogen atom, was selectively recorded at m/z 302 (¹⁴N-taurine) and m/z 303 (¹⁵N-taurine). Calibration curves prepared in hydrolysed and non-hydrolysed urine samples spiked with ¹⁵N-taurine gave similar slopes to the calibration curve prepared in water. The average coefficient of variation observed for the mole percent excess in the non-hydrolysed samples was 1.22% (n = 92) and for the hydrolysed urine 1.00% (n = 98). There was no significant difference between free and total taurine enrichment. The half-life of taurine in cat body was found to be 29.3 ± 2.9 h and 35.0 ± 1.4 h for free and total taurine, respectively (non-significant). The taurine body pool, calculated by extrapolation of the curve to zero time, had a value of 137 ± 22 ng/kg and 157 ± 11 mg/kg for free and total taurine, respectively.     

Inhibition of escherichia coli glucosamine synthetase by novel electrophilic analogues of glutamine—comparison with 6-diazo-5-oxo-norleucine

A series of electrophilic glutamine analogues based on 6-diazo-5-oxo-norleucine has been prepared, using novel synthetic routes, and evaluated as inhibitors of Escherichia coli. glucosamine synthetase. The γ-dimethylsulphonium salt analogue of glutamine was found to be one of the most potent inactivators of this enzyme yet reported, with an apparent second order rate constant (k₂/K_i) of 3.5×10⁵ M⁻¹ min⁻¹.     

Protein profile of basal prostate epithelial progenitor cells—stage‐specific embryonal antigen 4 expressing cells have enhanced regenerative potential in vivo

The long‐term propagation of basal prostate progenitor cells ex vivo has been very difficult in the past. The development of novel methods to expand prostate progenitor cells in vitro allows determining their cell surface phenotype in greater detail. Mouse (Lin^?Sca‐1⁺ CD49f⁺ Trop2^high‐phenotype) and human (Lin^? CD49f⁺ TROP2^high) basal prostate progenitor cells were expanded in vitro. Human and mouse cells were screened using 242 anti‐human or 176 antimouse monoclonal antibodies recognizing the cell surface protein profile. Quantitative expression was evaluated at the single‐cell level using flow cytometry. Differentially expressed cell surface proteins were evaluated in conjunction with the known CD49f⁺/TROP2^high phenotype of basal prostate progenitor cells and characterized by in vivo sandwich‐transplantation experiments using nude mice. The phenotype of basal prostate progenitor cells was determined as CD9⁺/CD24⁺/CD29⁺/CD44⁺/CD47⁺/CD49f⁺/CD104⁺/CD147⁺/CD326⁺/Trop2^high of mouse as well as human origin. Our analysis revealed several proteins, such as CD13, Syndecan‐1 and stage‐specific embryonal antigens (SSEAs), as being differentially expressed on murine and human CD49f⁺ TROP2⁺ basal prostate progenitor cells. Transplantation experiments suggest that CD49f⁺ TROP2^high SSEA‐4^high human prostate basal progenitor cells to be more potent to regenerate prostate tubules in vivo as compared with CD49f⁺ TROP2^high or CD49f⁺ TROP2^high SSEA‐4^low cells. Determination of the cell surface protein profile of functionally defined murine and human basal prostate progenitor cells reveals differentially expressed proteins that may change the potency and regenerative function of epithelial progenitor cells within the prostate. SSEA‐4 is a candidate cell surface marker that putatively enables a more accurate identification of the basal PESC lineage.     

Adapt or die—Response of large herbivores to environmental changes in Europe during the Holocene

Climate warming and human landscape transformation during the Holocene resulted in environmental changes for wild animals. The last remnants of the European Pleistocene megafauna that survived into the Holocene were particularly vulnerable to changes in habitat. To track the response of habitat use and foraging of large herbivores to natural and anthropogenic changes in environmental conditions during the Holocene, we investigated carbon (δ¹³C) and nitrogen (δ¹⁵N) stable isotope composition in bone collagen of moose (Alces alces), European bison (Bison bonasus) and aurochs (Bos primigenius) in Central and Eastern Europe. We found strong variations in isotope compositions in the studied species throughout the Holocene and diverse responses to changing environmental conditions. All three species showed significant changes in their δ¹³C values reflecting a shift of foraging habitats from more open in the Early and pre‐Neolithic Holocene to more forest during the Neolithic and Late Holocene. This shift was strongest in European bison, suggesting higher plasticity, more limited in moose, and the least in aurochs. Significant increases of δ¹⁵N values in European bison and moose are evidence of a diet change towards more grazing, but may also reflect increased nitrogen in soils following deglaciation and global temperature increases. Among the factors explaining the observed isotope variations were time (age of samples), longitude and elevation in European bison, and time, longitude and forest cover in aurochs. None of the analysed factors explained isotope variations in moose. Our results demonstrate the strong influence of natural (forest expansion) and anthropogenic (deforestation and human pressure) changes on the foraging ecology of large herbivores, with forests playing a major role as a refugial habitat since the Neolithic, particularly for European bison and aurochs. We propose that high flexibility in foraging strategy was the key for survival of large herbivores in the changing environmental conditions of the Holocene.     

Trend in Pacific walrus (Odobenus rosmarus divergens) tusk asymmetry, 1990–2014

We used the basal circumference of Pacific walrus (Odobenus rosmarus divergens) tusks (upper canine teeth, n = 21,068 pairs) to estimate fluctuating asymmetry (FA1 index) from 1990 to 2014. The mean difference in circumference between paired tusks was ?0.006 (SEM = 0.002) cm and approximately normally distributed. Measurement error was 0.6 (0.02)%, similar between biologists and lay persons (P = 0.83), and ≤15% of FA1. Tusk FA1 was greatest in 1990 then declined by 56% (P = 0.0001) through 2014. Male and female trends differed (P = 0.0001) and male FA1 was 40% greater (P = 0.0001) and the rate of decline 28% steeper (P = 0.3) than females. A quartic polynomial model (r² = 0.66, w_i = 0.685) fit the trend for female data better than simpler forms, whereas a linear model (r² = 0.55, w_i = 0.693) was a better fit for male data. Walrus tusk FA1 reflected periods when the population was stressed due to food limitations and then recovered, and perhaps when females began to experience the loss of preferred sea ice habitat in summer and FA1 is an easily monitored indicator. More work is needed to confirm the link between FA1, individual fitness, and adaptive potential.     

In situ measurement of fine root water absorption in three temperate tree species—Temporal variability and control by soil and atmospheric factors

Miniature heat balance-sap flow gauges were used to measure water flows in small-diameter roots (3–4 mm) in the undisturbed soil of a mature beech–oak–spruce mixed stand. By relating sap flow to the surface area of all branch fine roots distal to the gauge, we were able to calculate real time water uptake rates per root surface area (J_s) for individual fine root systems of 0.5–1.0 m in length. Study aims were (i) to quantify root water uptake of mature trees under field conditions with respect to average rates, and diurnal and seasonal changes of J_s, and (ii) to investigate the relationship between uptake and soil moisture θ, atmospheric saturation deficit D, and radiation I. On most days, water uptake followed the diurnal course of D with a mid-day peak and low night flow. Neighbouring roots of the same species differed up to 10-fold in their daily totals of J_s (<100–2000 g m⁻² d⁻¹) indicating a large spatial heterogeneity in uptake. Beech, oak and spruce roots revealed different seasonal patterns of water uptake although they were extracting water from the same soil volume. Multiple regression analyses on the influence of D, I and θ on root water uptake showed that D was the single most influential environmental factor in beech and oak (variable selection in 77% and 79% of the investigated roots), whereas D was less important in spruce roots (50% variable selection). A comparison of root water uptake with synchronous leaf transpiration (porometer data) indicated that average water fluxes per surface area in the beech and oak trees were about 2.5 and 5.5 times smaller on the uptake side (roots) than on the loss side (leaves) given that all branch roots <2 mm were equally participating in uptake. Beech fine roots showed maximal uptake rates on mid-summer days in the range of 48–205 g m⁻² h⁻¹ (i.e. 0.7–3.2 mmol m⁻² s⁻¹), oak of 12–160 g m⁻² h⁻¹ (0.2–2.5 mmol m⁻² s⁻¹). Maximal transpiration rates ranged from 3 to 5 and from 5 to 6 mmol m⁻² s⁻¹ for sun canopy leaves of beech and oak, respectively. We conclude that instantaneous rates of root water uptake in beech, oak and spruce trees are above all controlled by atmospheric factors. The effects of different root conductivities, soil moisture, and soil hydraulic properties become increasingly important if time spans longer than a week are considered.     

RATES OF GROWTH,RESPIRATION AND PHOTOSYNTHESIS OF UNICELLULAR ALGAE AS RELATED TO CELL SIZE—A REVIEW1,2

The decline of growth rate with increasing species size of unicellular algae grown under uniform conditions is quantified by applying to published data the equation, growth, (cell · time)^?1= a (cell carbon)^b where a and b are coefficients. The degree of size-dependence might be highest under optimal conditions of growth where b is 0.75. Respiration rate is shown to decline with size in the same manner. It is postulated that gross photosynthesis and processes underlying growth are similarly size-dependent. Growth, efficiency (net over gross photosynthesis) cannot be shown to be size-dependent. Cell size, expressed as carbon, is proposed as a scaling factor in comparative algal physiology.     

Determination of free salsolinol concentrations in human urine using gas chromatography—mass spectrometry

The urine concentrations of free salsolinol were determined in six healthy volunteers, using a gas chromatographic—mass spectrometric method with electron-capture negative-ion chemical ionization after derivatization with pentafluoropropionyl anhydride. The sensitivity of this method allows the quantification of salsolinol concentrations of 0.55 pmol/ml. The synthesis of [²H₄]salsolinol from dopamine and [²H₄]acetaldehyde via a Pictet—Spengler condensation is described; [²H₄]salsolinol was used as the internal standard for salsolinol quantification. The urine concentrations of free salsolinol ranged from ca. 1 to 6 pmol/ml.     

Stable isotope analyses—A method to distinguish intensively farmed from wild frogs

Consumption of frog legs is increasing worldwide, with potentially dramatic effects for ecosystems. More and more functioning frog farms are reported to exist. However, due to the lack of reliable methods to distinguish farmed from wild‐caught individuals, the origin of frogs in the international trade is often uncertain. Here, we present a new methodological approach to this problem. We investigated the isotopic composition of legally traded frog legs from suppliers in Vietnam and Indonesia. Muscle and bone tissue samples were examined for δ¹⁵N, δ¹³C, and δ¹⁸O stable isotope compositions, to elucidate the conditions under which the frogs grew up. We used DNA barcoding (16S rRNA) to verify species identities. We identified three traded species (Hoplobatrachus rugulosus, Fejervarya cancrivora and Limnonectes macrodon); species identities were partly deviating from package labeling. Isotopic values of δ¹⁵N and δ¹⁸O showed significant differences between species and country of origin. Based on low δ¹⁵N composition and generally little variation in stable isotope values, our results imply that frogs from Vietnam were indeed farmed. In contrast, the frogs from the Indonesian supplier likely grew up under natural conditions, indicated by higher δ¹⁵N values and stronger variability in the stable isotope composition. Our results indicate that stable isotope analyses seem to be a useful tool to distinguish between naturally growing and intensively farmed frogs. We believe that this method can be used to improve the control in the international trade of frog legs, as well as for other biological products, thus supporting farming activities and decreasing pressure on wild populations. However, we examined different species from different countries and had no access to samples of individuals with confirmed origin and living conditions. Therefore, we suggest improving this method further with individuals of known origin and history, preferably including samples of the respective nutritive bases.