Mass–length ratio of fibrin fibers from gel permeation and light scattering

Mass–length ratios of fibers in fibrin gels were obtained from measurements of the angular dependence of the intensity of light scattered by dilute gels and from the permeability of more concentrated gels. The permeability was determined by measuring the forced flow of buffer through a short column of gel held in a glass tube. The results obtained with the two methods are consistent. At high pH and high ionic strength the mass–length ratio is found to be that calculated for a protofibril, i.e., a double strand of fibrin molecules laid end to end at a separation of 450 Å. This same value is found under conditions where the polymerized fibrin is not gelled (pH 10.25) and where it is just gelled (pH 10.0). At pH 7.4, ionic strength 0.35, the fibers are found to have a higher mass–length ratio, the average fiber consisting of some three protofibrils associated laterally. At pH 7.4 and low ionic strength (0.10 M) the fibers are up to a hundred times more massive.     

Root length and diameter measurement using NIH Image: application of the line-intercept principle for diameter estimation

The objective of this study was to develop an image analysis algorithm for estimating the length versus diameter distribution of washed root samples. Image analysis was performed using a Macintosh computer and the public domain NIH Image program. After an appropriate binary image of roots was obtained, the image was processed to get the thinned image to calculate the length of the roots. The edge pixel of the binary image was then deleted and root length was calculated again. This `edge deletion–length calculation' cycle was repeated until no root pixel was left in the image. Repeated edge deletion removed one pixel layer from around the periphery of root objects in each iteration. The number of edge deletions, which is equivalent to the intercept length, can be used to estimate the root diameter. We used the vertical or horizontal intercept length, whichever was shorter. The accuracy of diameter estimation due to orientation of objects varied from 89.1 to 126.0%. Branching root systems consist of several orders of laterals, and as the root branches to a higher order, the diameter of the roots becomes smaller. Therefore, edge deletions eliminate sequentially from the highest order roots, which have the smallest diameter, to the lowest order roots, which have the widest diameter. Thus, the length and diameter of each root order can be calculated by the proposed method. For verification, images of copper wire of 0.23, 0.50, and 1.0 mm diameter were analyzed. The results showed reasonable agreement with the expected distribution of length versus diameter for randomly oriented objects, and consequently the wire length of each diameter could be estimated. The proposed method was tested for primary and secondary roots of water-cultured rice (Oryza sativa L.), and it was proven that the method can provide accurate length and diameter measurements for each root order.     

Accurate root length and diameter measurement using NIH Image: use of Pythagorean distance for diameter estimation

This report describes an image analysis algorithm to estimate the length versus diameter of washed root samples accurately. Image analysis was performed using a Macintosh computer and the public domain NIH Image program. The binary image of the roots was processed to get the thinned image to calculate the length of the roots. The pixels of the root in a binary image were then stripped off from around the periphery based on the pixel's Pythagorean distance from the nearest background pixel. The length of the remaining root in each stripping off process was calculated after the image was thinned. Images (300 dpi) of copper wire of 0.23, 0.5, 1.0 mm diameter were analyzed for verification of the usefulness of the procedure. The results showed that more than 93% of the wires in each diameter wire were calculated to be in diameter classes including the true diameter and its adjoining classes: 93.6% of the wires of 0.23 mm diameter appeared in the 0.098–0.38 mm diameter classes, 96.19% of the wires of 0.5 mm diameter appeared in the 0.38–0.61 mm diameter classes, and 96.17% of the wires of 1 mm diameter appeared in the 0.85–1.08 mm diameter classes. The proposed method was tested for primary and secondary roots of water-cultured rice (Oryza sativa L.) and it was proven that the method could provide accurate length and diameter measurements for each root order. In addition, it was found that the method could provide the lengths of the thick primary, thin primary, and secondary roots. The effectiveness of applying sharpening for the grayscale image before making the binary image is also discussed.     

Utilization of mass–energy balance regularities in the analysis of continuous-culture data

Material and energy balances for continuous-culture processes are described based on the facts that the heat of reaction per electron transferred to oxygen for a wide variety of organic molecules, the number of available electrons per carbon atom in biomass, and the weight fraction carbon in biomass are relatively constant. Energy requirements for growth and maintenance are investigated and related to the biomass energetic yield. The consistency of experimental data is examined using material and energy balances and the regularities identified above. When extracellular products are absent, the consistency of yield models containing separate terms for growth and maintenance may be investigated using organic substrate consumption, biomass production, oxygen consumption (or heat evolution), and carbon dioxide evolution rate data for a series of dilution rates. The consistency of continuous-culture data in the published literature is examined.     

Plant–pollinator networks in semi‐natural grasslands are resistant to the loss of pollinators during blooming of mass‐flowering crops

Mass‐flowering crops lead to spatial redistributions of pollinators and to transient shortages within nearby semi‐natural grasslands, but the impacts on plant–pollinator interactions remain largely unexplored. Here, we characterised which pollinator species are attracted by oilseed rape and how this affected the structure of plant–pollinator networks in nearby grasslands. We surveyed 177 networks from three countries (Germany, Sweden and United Kingdom) in 24 landscapes with high crop cover, and compared them to 24 landscapes with low or no oilseed rape during and after crop blooming. On average 55% of grassland pollinator species were found on the crop, which attracted 8–35% of individuals away from grasslands. However, networks in the grasslands were resistant to these reductions, since mainly abundant and highly mobile species were attracted. Nonetheless, simulations indicated that network structural changes could be triggered if > 50% of individuals were attracted to the crop (a value well‐above that found in our study system), which could affect community stability and resilience to further disturbance.     

The diameters of frozen-hydrated chromatin fibers increase with DNA linker length: evidence in support of variable diameter models for chromatin

The diameters of chromatin fibers from Thyone briareus (sea cucumber) sperm (DNA linker length, n = 87 bp) and Necturus maculosus (mudpuppy) erythrocytes (n = 48 bp) were investigated. Soluble fibers were frozen into vitrified aqueous solutions of physiological ionic strength (124 mM), imaged by cryo-EM, and measured interactively using quantitative computer image-processing techniques. Frozen-hydrated Thyone and Necturus fibers had significantly different mean diameters of 43.5 nm (SD = 4.2 nm; SEM = 0.61 nm) and 32.0 nm (SD = 3.0 nm; SEM = 0.36 nm), respectively. Evaluation of previously published EM data shows that the diameters of chromatin from a large number of sources are proportional to linker length. In addition, the inherent variability in fiber diameter suggests a relationship between fiber structure and the heterogeneity of linker length. The cryo-EM data were in quantitative agreement with space-filling double-helical crossed-linker models of Thyone and Necturus chromatin. The data, however, do not support solenoid or twisted-ribbon models for chromatin that specify a constant 30 nm diameter. To reconcile the concept of solenoidal packing with the data, we propose a variable-diameter solid-solenoid model with a fiber diameter that increases with linker length. In principle, each of the variable diameter models for chromatin can be reconciled with local variations in linker length.     

Global patterns in anuran–prey networks: structure mediated by latitude

Life on Earth is supported by an infinite number of interactions among organisms. Species interactions in these networks are influenced by latitude, evolutionary history and species traits. We performed a global‐scale literature analysis to build up a database of interactions between anuran communities and their preys, from a wide range of geographical areas, using a network approach. For this purpose, we compiled a total of 55 weighted anuran–prey interaction networks, 39 located in the tropics and 16 in temperate areas. We tested the influence of latitude, as well as anuran taxonomic, functional and phylogenetic richness on network metrics. We found that anuran–prey networks are not nested, exhibit low complementary specialization and modularity and high connectance when compared to other types of networks. The main effects on network metrics were related to latitude, followed by anuran taxonomic, functional and phylogenetic richness, a pattern similar to the emerging in mutualistic networks. Our study is the first integrated analysis of the structural patterns in anuran–prey antagonistic interaction networks in different parts of the world. We suggest that different processes, mediated mainly by latitude, are modeling the architecture of anuran–prey networks across the globe.     

Concentration of protein in fibrin fibers and fibrinogen polymers determined by refractive index matching

We have used refractive index matching to determine the concentration of protein in the fibers in fibrin clots and of needlelike crystals of native fibrinogen. Our results are in agreement with those of Carr and Hermans [(1978) Macromolecules 11 , 46–50], as determined by light scattering—namely, that protein makes up about 20% of the volume of the fiber. However, we have found that the protein concentration is strongly dependent on ionic strength. An increase in ionic strength caused a substantial drop in the protein concentration. In a buffer containing 100 mM NaCl, the protein concentration was 26.6–29.8 g of protein per 100 cm³ of polymer, and at 200 mM NaCl it was reduced to 22.1–23.1 g/100 cm³.     

The role of belowground competition and plastic biomass allocation in altering plant mass–density relationships

Metabolic scaling theory (MST) predicts a ‘universal scaling law’ for plant mass–density relationships, but empirical observations are more variable. Possible explanations of this variability include plasticity in biomass allocation between the above‐ and belowground compartment and different modes of competition, which can be asymmetric or symmetric. Although complex interactions of these factors are likely to occur, so far the majority of modelling and empirical studies has focussed on mono‐factorial explanations. We here present a generic individual‐based model, which allows exploring the plant mass–density relationship in realistic settings by representing plasticity of biomass allocation and different modes of competition in the above‐ and belowground compartment. Plants grew according to an ontogenetic growth model derived from MST. To evaluate the behavior of the simulated plants related to the allocation patterns and to validate model predictions, we conducted greenhouse experiments with tree seedlings. The model reproduced empirical patterns both at the individual and population level. Without belowground resource limitation, aboveground processes dominated and the slopes of mass–density relationships followed the predictions of MST. In contrast, resource limitation led to an increased allocation of biomass to belowground parts of the plants. The subsequent dominance of symmetric belowground competition caused significantly shallower slopes of the mass–density relationship, even though the growth of individual plants followed MST. We conclude that changes in biomass allocation induced by belowground resource limitation explain the deviations from the mass–density relationship predicted by MST. Taking into account the plasticity of biomass allocation and its linkage to the above‐ and belowground competition is critical for fully representing plant communities, in particular for correctly predicting their response of carbon storage and sequestration to changing environmental conditions.     

Electron microscopy of fine fibrin clots and fine and coarse fibrin films: Observations of fibers in cross-section and in deformed states

Fine fibrin clots and coarse and fine fibrin films (both ligated and unligated), formed by shrinkage of clots in one dimension, were examined by electron microscopy. Specimens of clots were prepared by critical point drying and by embedding and sectioning; specimens of films were prepared by embedding and sectioning only. In the fine clots, network junctions appeared to be formed by fiber segments in which two or more protofibrils were gently twisted around each other for distances of the order of 200 nm and then diverged to give trifunctional branch points. This topology appeared to be preserved in the fine films. It is proposed that the strength of the junctions is primarily provided by the twisting topology, though reinforced by non-covalent bonding involving the B sites uncovered by thrombin. In coarse films, bundles of protofibrils, lying primarily in the film plane, had diameters of 40 to 200 nm and were gently twisted around each other to form thicker cables. Uniaxial stretching, up to 100%, of either fine or coarse film before fixing caused suprisingly extensive orientation of the protofibrils or bundles. However, random orientation was recovered if a stretched ligated film was allowed to retract to its original dimensions before fixing. In a stretched coarse film sectioned perpendicular to the stretch direction, fiber bundles could be seen in cross-section; these were roughly circular with scalloped edges. The changes with stretching and recovery are discussed in relation to possible mechanisms of deformation and elastic energy storage.     

Effect of master mixes on the measurement of telomere length by qPCR

Molecular Biology Reports - Alterations in telomere length (TL) have been associated with several diseases and a method based on qPCR, the Monochrome Multiplex Real-Time Quantitative PCR (MMQPCR)...     

The effect of prefixation on the diameter of chromosome fibers isolated by the Langmuir trough-critical point method

The effect of prefixation on the diameter of chromosome fibers isolated by the Langmuir trough-critical point method has been investigated in several species of plants and animals. In barley, fibers isolated from endosperm without prefixation have an average diameter of between 240 and 250 A, and are similar in dimensions and structure to the chromosome fibers isolated from animals by this method. Chromosome fibers from other tissues of the same plant are smaller in diameter when isolated without prefixation, approximating 200 A. After prefixation in 2% buffered formalin, isolated fibers from the three barley tissues studied are reduced in diameter, to approximately 120-130 A for endosperm and leaflet and to 140 A for root tip. Chromosome fibers isolated from newt erythrocytes also show a significantly reduced diameter after formalin prefixation, to approximately 120 A.     

Determination of the optimal parasitoid‐to‐host ratio for efficient mass‐rearing of the parasitoid,Sclerodermus pupariae (Hymenoptera: Bethylidae)

Sclerodermus pupariae Yang et Yao (Hymenoptera: Bethylidae) is used as a potential biocontrol agent for several buprestid and cerambycid larvae. This study aimed to enhance the efficiency of mass‐rearing of this parasitoid by investigating the fitness gain of this bethylid wasp, including the proportion of successful parasitism and development, brood size, sex ratio, proportion of winged female offspring, body size and longevity of female offspring, under eight different maternal parasitoid density treatments using Thyestilla gebleri Faldermann as host in the laboratory. The results indicated that the foundress densities did not affect the parasitism or emergence rate of this parasitoid. Brood size of the parasitoids increased significantly when the number of maternal wasps ranged from one to four. However, further increases in foundress number did not affect the parasitoid brood size. The sex ratios of S. pupariae were always female‐biased. The proportions of male in the progeny colonies were <10% throughout all experimental treatments. The percentage of winged female progeny was not significantly influenced by the density of adult maternal parasitoids. Body sizes of parasitoids significantly declined with increasing maternal parasitoid densities. Although the parasitoid body size reduced when maternal wasp number was higher, it could be compromised by the relatively higher number of female offspring produced. Further, more than 70% of the parasitoids remained alive when they were stored at 12°C for four months throughout the experiments. These findings suggest that exposure of four female wasps to a single host larva would result in the highest fitness of S. pupariae. Our findings might provide a new approach to enhance the efficiency of mass‐rearing of this bethylid wasp.     

施肥对日本落叶松人工林细根直径、根长和比根长的影响

以辽宁东部山区16年生日本落叶松人工林为研究对象,探讨施肥对日本落叶松1～5级根序中细根直径、根长和比根长的影响.结果表明：随着根序等级的增加,日本落叶松细根平均直径和根长显著增加（P<0。05,P<0。01）、比根长则显著下降（P<0。01）.在日本落叶松的5级根序中,1级根的平均直径最细、根长最短、比根长最高,而5级根则相反;随着根序等级的增加,日本落叶松细根平均直径、根长和比根长的变异系数逐渐增大.除1级根外,土层对细根的平均直径、根长和比根长没有显著影响(P>0。05).与对照样地相比,施肥对各级细根平均直径、根长和比根长的影响主要表现在1～2级根上,对3级根序以上的细根影响不显著（P>0.05）.其中,施氮肥显著降低了1～2级根的平均直径（P<0.05）,施氮肥以及氮磷肥显著降低了表层土壤（0～10 cm）中1级根的平均根长（P<0.05）,表层土壤中细根的比根长在施氮肥的条件下显著增加（P<0.05）.     

Length–weight,length–length relationships and length at first maturity of fish species from the Paraná and Uruguay rivers,Argentina

Length–weight relationships (LWR) were estimated for 12 species, representing three orders and eight families of fishes from the Paraná and Uruguay rivers in Argentina: Acestrorhynchus pantaneiro, Cynopotamus argenteus, Pachyurus bonariensis, Pterodoras granulosus, Hypostomus commersoni, Pseudoplatystoma corruscans, Pimelodus maculatus, Parapimelodus valenciennis, Salminus brasiliensis, Prochilodus lineatus, Hoplias malabaricus and Leporinus obtusidens. For the last four species, the length at first spawning (L_m) was estimated using three different methods. The captures were made in shallow river areas during 2005–2013. Significant length–weight relationships were found for all species. None or few LWRs were previously available for these species.     

Weight–length relationships of six batoids in the Ecuadorian Pacific

Weight–length relationships (WLR) were estimated for six batoids, namely: Urotrygon chilensis, Narcine entemedor, Rhinobatos leucorhynchus, Rhinobatos planiceps, Rhinobatos prahli and Urobatis tumbesensis captured in the Ecuadorian Pacific. Data were collected between October 2013 and August 2014 in two artisanal fishing ports. In addition, this represents the first WLR estimations for five of the species.     

Mate choice by wild and mass‐reared females of the Mediterranean fruit fly

The sterile insect technique (SIT) is used to control Mediterranean fruit fly, Ceratitis capitata (Wiedemann), but its effectiveness is limited by low sexual competitiveness of mass‐reared males. This study investigated whether wild and mass‐reared [from a temperature sensitive lethal (tsl) genetic sexing strain] females display similar mate preferences and thus exert similar selective forces on the evolution of male courtship behaviour. Wild females preferred wild males over tsl males, whereas tsl females mated indiscriminately. The probability that mounting resulted in copulation was related to the duration of pre‐mount courtship for wild females, and wild males performed longer courtships than tsl males. Copulation occurred independently of courtship duration in tsl females. Counter to the aim of the SIT, female choice by tsl females appears to promote the evolution of male behaviour disfavoured by wild females.     

Filling the gap: Length–weight and length–length relationships of intertidal endemic fishes of the Brazilian Province Oceanic Islands

Length‐weight and length‐length relationships were determined for nine fish species of Rocas Atoll, Fernando de Noronha and Trindade Island. Samples were conducted in 2014 (Rocas) and 2015 (Noronha and Trindade) in tidepools using anaesthetic clove oil and hand nets to collect fish fauna. Four species (Stegastes rocasensis, Scartella itajobi, Starksia multilepis and Bathygobius brasiliensis) are endemic from the Noronha‐Rocas ridge, two are endemic from the Trindade‐Martin Vaz insular complex (Scartella poiti and Malacoctenus brunoi), and three species have a widespread distribution. All relationships are novel for science.     

Nutrient Fluxes from Land to Sea: Consequences of Future Scenarios on the Oder River Basin – Lagoon – Coastal Sea System

Eutrophication management is still one of the major challenges in the Baltic Sea region. Intense transformation processes in several Baltic Sea states have led to drastic changes in e.g., landuse and thereby nutrient emissions and water quality. Several future development directions are possible. The Oder catchment – lagoon – coastal water system serves as a pilot study area, since it has a major influence on the nutrient loads into the Baltic Sea and about 90% of the catchment is located in Poland, a state with transitional economy. Different scenarios for landuse changes in the Oder catchment are developed and their consequences on nutrient emissions simulated. Next to politically induced changes of agricultural landuse in general, specific aspects such as cultivation of energy maize and increased animal stocks are considered. Nitrogen emissions are likely to increase due to agricultural landuse changes whereas phosphorus emissions will not change or even decrease according to the application of the EC‐Urban Waste Water Treatment Directive. Resulting nitrogen loads to the Oder Lagoon could increase up to 23%, phosphorus loads could decrease by 11% compared to 2005. These trends may lead to higher nitrogen availability compared to phosphorus at least in the Oder lagoon. Interannual differences in discharge also have profound effects on nutrient emissions. A good status of the Oder river basin – lagoon – coastal sea system according to EC‐Directives is not very likely to be achieved under the investigated circumstances. (© 2011 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)