Quantitative analysis of organelle abundance, morphology and dynamics

Recent data indicate that morphological characteristics of cell organelles are important for their function in the cell. These characteristics include not only their shape, number and size, but also their distribution in the cell. Moreover, the dynamics of processes that result in changes in these characteristics (e.g. organelle fission, fusion, autophagy, transport) influence the function of the cell. For a better understanding of these processes quantitative approaches are important. Here we give an overview of contemporary biochemical and microscopy methods that are used to quantify organelle abundance, morphology and the kinetics of the processes that cause changes in these properties.     

External morphology and abundance of mouthpart sensilla in Australian Gryllacrididae,Stenopelmatidae, and Tettigoniidae

Sensilla diversity and abundance were extremely high on the apex of the maxillary and labial palpi of two species of Gryllacrididae. The terminal segment of the maxillary palpi of these species had 9 and 15 sensilla types, respectively, and up to 2,834 sensilla. The labial palpi had 7 and 12 types, respectively, and up to 5,195 sensilla. Several types of multiporous smooth and ridged olfactory basiconic sensilla, and coeloconic, coelosphaeric, placoid, and multipapilliform sensilla occurred, as well as many trichoid sensilla and the more typical uniporous basiconic contact receptors. Two species of the closely related Stenopelmatidae were compared to the gryllacridids and found to have similar sensillar diversity and abundance, but three species of the more distantly related Tettigoniidae had only 4 or 5 sensilla types and a total number ranging from 320 to 960 on their maxillary palpi.     

Larval distribution, abundance, and stock structure of British Columbia herring

Pacific herring Clupea pallasi spawn in shallow and intertidal areas. Larval distributions and abundance of three major and several minor stocks were examined to determine if larvae mix among different spawning locations. The surveys were short, intensive, and occurred mainly within the first 30 days of larval life. Each major stock had a discrete larval distribution with continuous larval distributions within stock boundaries. Some overlap of distributions occurred among smaller stocks. Most larvae were found in inshore waters but there were no obvious oceanographic factors, such as fronts or eddies, to explain all the distributions. Estuarine circulation in inlets could promote larval retention in some areas. The results support the present geographic definitions for local herring stocks. The results are generally consistent with the concept of discrete larval distribution, including retention areas, as the basis for herring Stock Structure.     

Population structure, life histories and abundance of copepods in Tjeukemeer, the Netherlands

SUMMARY. The copepod zooplankton of Tjeukemeer was sampled at weekly intervals for 3 years (1969–1971), and ten species were recorded. Five species contributed more than 99% of all individuals collected. Acanthocyclops robustus is the most abundant species (66%), followed by Mesocyclops leuckarti (13%), Cyclops vicinus (11%), Eurytemora affinis (9%) and Diacyclops bicuspidatus (1%).
The ecology of the A. robustus population in Tjeukemeer differs from other A. robustus populations in that it dominates the open water zone. This is an additional argument for a taxonomic revision of the A. vernalis-robustus complex.
Seasonal periodicity in abundance of each species was very similar in 3 successive years.
All cyclopoid species went into diapause, A. robustus and M. leuckarti during winter, D. bicuspidatus and C. v. vicinus during summer. Most species diapause in a particular copepodite stage.
The seasonal variation in the population structure, the fecundity and the sex ratio are described. Both population structure and sex ratio were influenced by diapause and size-dependent mortality. The fecundity was more influenced by the water temperature and the age structure of the female population than by food situation or size of the females.     

Species diversity, abundance, and vertical size structure of rattans in Borneo and Java

We studied rattan communities in four forest types in Borneo and Java to clarify the pattern of species diversity and vegetation structure. Within six plots of 4.82 ha in total, we found 42 rattan species in six genera with 4,736 stems (≥20 cm long). There was a significant positive correlation between rattans and trees in species diversity, decreasing in the order mixed dipterocarp (for rattans: Shannon–Wiener diversity index, H′ = 2.87–3.34) > alluvial (1.96) > lower montane (1.43) > peat swamp forests (1.34). This pattern coincided with the diversity of the regional flora. The density of rattan stems (ha^–1) decreased in the order lower montane (5,997) > mixed dipterocarp (598–992) > alluvial (592) > peat swamp forests (162). The maximum height of rattans would be determined by the canopy height, rather than by the maximum tree height. The rattan stem volume ranged from 0.25 to 1.88 m³ ha⁻¹ and was not correlated with the stem density. The cool montane climate seemed to decrease the maximum height of rattans, and a few small rattans made denser colonies. Swampy environments apparently suppressed the survival of non-climbing rattans strongly, but that of tall climbing rattans less so.     

Spartina alterniflora loisel root structure and meiofaunal abundance

Meiofauna were collected from adjacent areas with and without Spartina alterniflora Loisel culms. Environmental complexity resulting from root structure cannot be determined by simply observing S. alterniflora culm distribution. There were no significant differences between the two areas with respect to root density or root sizes; however, the number of live roots was significantly higher in the area containing Spartina culms. Nematodes, the most abundant taxon were positively correlated with live root density. In contrast, the number of dead roots and harpacticoid copepods were higher in the area without culms. This study suggests that nematodes are positively associated with micro-oxygenated zones produced by live S. alterniflora roots. Other measures of biogenic structure, such as total root density or root size fractions are not important in affecting nematode abundance.     

Links between ammonia oxidizer community structure, abundance, and nitrification potential in acidic soils

Ammonia oxidation is the first and rate-limiting step of nitrification and is performed by both ammonia-oxidizing archaea (AOA) and bacteria (AOB). However, the environmental drivers controlling the abundance, composition, and activity of AOA and AOB communities are not well characterized, and the relative importance of these two groups in soil nitrification is still debated. Chinese tea orchard soils provide an excellent system for investigating the long-term effects of low pH and nitrogen fertilization strategies. AOA and AOB abundance and community composition were therefore investigated in tea soils and adjacent pine forest soils, using quantitative PCR (qPCR), terminal restriction fragment length polymorphism (T-RFLP) and sequence analysis of respective ammonia monooxygenase (amoA) genes. There was strong evidence that soil pH was an important factor controlling AOB but not AOA abundance, and the ratio of AOA to AOB amoA gene abundance increased with decreasing soil pH in the tea orchard soils. In contrast, T-RFLP analysis suggested that soil pH was a key explanatory variable for both AOA and AOB community structure, but a significant relationship between community abundance and nitrification potential was observed only for AOA. High potential nitrification rates indicated that nitrification was mainly driven by AOA in these acidic soils. Dominant AOA amoA sequences in the highly acidic tea soils were all placed within a specific clade, and one AOA genotype appears to be well adapted to growth in highly acidic soils. Specific AOA and AOB populations dominated in soils at particular pH values and N content, suggesting adaptation to specific niches.     

Bird abundance and species richness on Florida lakes: influence of trophic status,lake morphology,and aquatic macrophytes

Data from 46 Florida lakes were used to examine relationships between bird abundance (numbers and biomass) and species richness, and lake trophic status, lake morphology and aquatic macrophyte abundance. Average annual bird numbers ranged from 7 to 800 birds km^–2 and bird biomass ranged from 1 to 465 kg km^–2. Total species richness ranged from 1 to 30 species per lake. Annual average bird numbers and biomass were positively correlated to lake trophic status as assessed by total phosphorus (r = 0.61), total nitrogen (r = 0.60) and chlorophyll a (r = 0.56) concentrations. Species richness was positively correlated to lake area (r = 0.86) and trophic status (r = 0.64 for total phosphorus concentrations). The percentage of the total annual phosphorus load contributed to 14 Florida lakes by bird populations was low averaging 2.4%. Bird populations using Florida lakes, therefore, do not significantly impact the trophic status of the lakes under natural situations, but lake trophic status is a major factor influencing bird abundance and species richness on lakes. Bird abundance and species richness were not significantly correlated to other lake morphology or aquatic macrophyte parameters after the effects of lake area and trophic status were accounted for using stepwise multiple regression. The lack of significant relations between annual average bird abundance and species richness and macrophyte abundance seems to be related to changes in bird species composition. Bird abundance and species richness remain relatively stable as macrophyte abundance increases, but birds that use open-water habitats (e.g., double-crested cormorant, Phalacrocorax auritus) are replaced by species that use macrophyte communities (e.g., ring-necked duck, Aythya collaris).     

Amylose synthesized in vitro by amylosucrase: morphology, structure, and properties

The recombinant amylosucrase from Neisseria polysaccharea was used to synthesize in vitro amylose from sucrose as unique substrate. The morphology and structure of the insoluble residue were shown to depend only on the initial sucrose concentration (100, 300, or 600 mM), which controlled both the chain length and concentration at the precipitation stage. The average degree of polymerization (DP) in the precipitated product varied from 58 for the lowest initial sucrose concentration (100 mM) to 45 and 35 for higher sucrose concentrations (300 and 600 mM, respectively). The shorter chains (DP 35 and 45), produced in high yields (54 and 24 g/L respectively), precipitated as polycrystalline aggregates with exceptional crystallinity, without optimization of the reaction medium for crystallization. The longer chains (DP 58), produced in lower amount (2.9 g/L), formed networks similar to those observed for amylose gels. All synthesized products displayed a B-type crystal structure. Their melting behavior was also studied, the thermostability being higher for the precipitate containing the longer chains. Further thermal treatments were shown to still improve the crystallinity and yield substrates usable as new standards for the determination of the relative crystallinity of starchy products. The kinetics of chain elongation and aggregation were thoroughly investigated in order to explain how the action of amylosucrase resulted in such different amylose structures. These results emphasize the potentiality of amylosucrase in the design of amylodextrins with controlled morphology, structure, and physicochemical properties.     

Effects of substrate stiffness on cell morphology, cytoskeletal structure, and adhesion

The morphology and cytoskeletal structure of fibroblasts, endothelial cells, and neutrophils are documented for cells cultured on surfaces with stiffness ranging from 2 to 55,000 Pa that have been laminated with fibronectin or collagen as adhesive ligand. When grown in sparse culture with no cell-cell contacts, fibroblasts and endothelial cells show an abrupt change in spread area that occurs at a stiffness range around 3,000 Pa. No actin stress fibers are seen in fibroblasts on soft surfaces, and the appearance of stress fibers is abrupt and complete at a stiffness range coincident with that at which they spread. Upregulation of alpha5 integrin also occurs in the same stiffness range, but exogenous expression of alpha5 integrin is not sufficient to cause cell spreading on soft surfaces. Neutrophils, in contrast, show no dependence of either resting shape or ability to spread after activation when cultured on surfaces as soft as 2 Pa compared to glass. The shape and cytoskeletal differences evident in single cells on soft compared to hard substrates are eliminated when fibroblasts or endothelial cells make cell-cell contact. These results support the hypothesis that mechanical factors impact different cell types in fundamentally different ways, and can trigger specific changes similar to those stimulated by soluble ligands.     

Fish abundance and trophic structure from the commercial catch in Lake Patzcuaro, Mexico

The composition, abundance and trophic structure of the fish community in Lake Patzcuaro is analyzed, using data from eight samples taken from the commercial fishery acquired between August 1990 and April 1991. A total of 65 767 individuals, caught with gillnets selective to all fish and size, were analyzed. Eleven species (8 native and 3 exotic) were recorded during the study. Zooplanktivorous were the most representative species, amounting to 91% of the total number. Also, they were the most characteristic species (36.4%) when feeding habits were considered, followed by carnivore and omnivore (27.3% each), and herbivore (9.1%). Three species groups and three time-associated groups were detected by means of classification methods. Lake Patzcuaro's ichthyofauna is to be considered as a transitional community that has not reached equilibrium, particularly after the introduction of exotic species and local extinction of native species. However, Lake Patzcuaro has the greatest fishery production of all tropical lakes in the Central Plain of Mexico and it is mainly sustained by native species. The differential use of feeding resources by the fish species and the diversity in their habits must be taken into account to design strategies to maintain the fish structure (avoiding new introduction of exotic species) and the fish production in Lake Patzcuaro.     

Nonnative protein polymers: structure, morphology, and relation to nucleation and growth

Thermally induced aggregates of α-chymotrypsinogen A and bovine granulocyte-colony stimulating factor in acidic solutions were characterized by a combination of static and dynamic light scattering, spectroscopy, transmission electron microscopy, and monomer loss kinetics. The resulting soluble, high-molecular weight aggregates (∼10³-10⁵ kDa) are linear, semiflexible polymer chains that do not appreciably associate with one another under the conditions at which they were formed, with classic power-law scaling of the radius of gyration and hydrodynamic radius with weight-average molecular weight (M_w). Aggregates in both systems are composed of nonnative monomers with elevated levels of β-sheet secondary structure, and bind thioflavine T. In general, the aggregate size distributions showed low polydispersity by light scattering. Together with the inverse scaling of M_w with protein concentration, the results clearly indicate that aggregation proceeds via nucleated (chain) polymerization. For α-chymotrypsinogen A, the scaling behavior is combined with the kinetics of aggregation to deduce separate values for the characteristic timescales for nucleation (τ_n) and growth (τ_g), as well as the stoichiometry of the nucleus (x). The analysis illustrates a general procedure to noninvasively and quantitatively determine τ_n, τ_g, and x for soluble (chain polymer) aggregates, as well as the relationship between τ_n/τ_g and aggregate M_w.     

Skate assemblage on the eastern Patagonian Shelf and Slope: structure, diversity and abundance

The eastern Patagonian Shelf and continental slope of the south-west Atlantic Ocean support a high biodiversity and abundance of skates. In this study, meso-scale differences in the assemblages, spatial and seasonal distributions of skates are revealed among six habitat zones of the eastern Patagonian Shelf characterized by distinctive oceanographic conditions. Most skates belonged to temperate fauna, and their abundance was much greater in habitats occupied by temperate waters (north-western outer shelf) or mixed waters (northern slope) than in habitats occupied by sub-Antarctic waters (SASW) (south-eastern outer shelf and southern slope). Sub-Antarctic skates were not abundant on the shelf even in habitats occupied by SASW, occurring mainly in deep areas of the lower continental slope. The majority of temperate skates migrated seasonally, shifting northward in winter and spreading southward with warming waters in summer. Most temperate species had two peaks in female maturity (mainly spring and autumn) and spawned in the same habitats where they fed. It is hypothesized that the high biodiversity and abundance of skates on the Patagonian Shelf and Slope are due to the practical absence of their natural competitors, flatfishes, which occupy similar eco-niches elsewhere.     

Diversity of the diatom genus Fragilariopsis in the Argentine Sea and Antarctic waters: morphology, distribution and abundance

Fragilariopsis species composition and abundance from the Argentine Sea and Antarctic waters were analyzed using light and electron microscopy. Twelve species (F. curta, F. cylindrus, F. kerguelensis, F. nana, F. obliquecostata, F. peragallii, F. pseudonana, F. rhombica, F. ritscheri, F. separanda, F. sublinearis and F. vanheurckii) are described and compared with samples from the Frenguelli Collection, Museo de La Plata, Argentina. F. peragallii was examined for the first time using electron microscopy, and F. pseudonana was recorded for the first time in Argentinean shelf waters. New information on the girdle view is included, except for the species F. curta, F. cylindrus and F. nana, for which information already existed. In the Argentine Sea, F. pseudonana was the most abundant Fragilariopsis species, and in Antarctic waters, F. curta was most abundant. Of the twelve species of Fragilariopsis documented, four occurred in the Argentine Sea, nine in the Drake Passage and twelve in the Weddell Sea. F. curta, F. kerguelensis, F. pseudonana and F. rhombica were present everywhere.     

Community structure and habitat associations of parrotfishes on Oahu,Hawaii

Despite their ecological importance as bioeroders and their economic importance in commercial, artisanal, and recreational fisheries, there have been relatively few studies on parrotfish (Scaridae) ecology in Hawaii. Belt transects were conducted around the island of Oahu to survey current parrotfish distributions, size structure, species composition and associated habitats. Scarid communities in this heavily fished region are dominated by smaller species and smaller individuals within all species. Specific habitat characteristics such as rugosity, substrate diversity, and percent live coral cover were positively correlated with scarid numerical abundance. Scarids, however, were patchily distributed and were often absent from preferable habitats, suggesting that intense fishing pressure may be an important factor preventing these fish from fully exploiting available habitats. This study is the first thorough, broad-scale investigation of scarid community structure in Hawaii, and provides important information that has management and conservation implications for parrotfish in Hawaii and throughout tropical coral reef ecosystems.     

Correlations among morphology, beta-sheet stability, and molecular structure in prion peptide aggregates

The misfolding of proteins into beta-sheets and the subsequent aggregation of these sheets into fibrous networks underlies many diseases. In this paper, the role of peptide structure in determining the ordering of beta-sheet aggregates and the morphology of fibrils and protofibrils is dissected. Using a series of peptides based on residues 109-122 of the Syrian hamster prion protein (H1) with a range of substitutions at position 117, the link between side chain interactions and beta-sheet thermal stability has been investigated. The thermal stability of beta-sheets is associated with the peptides' ability to adopt the same alignment as wild-type H1, with residue 117 in register across all beta-strands [Silva, R. A. G. D., Barber-Armstrong, W., and Decatur, S. M. (2003) J. Am. Chem. Soc. 125, 13674-13675]. These aligned strands are capable of forming long, rigid, and twisted fibrils (as visualized by atomic force microscopy) which are thermostable. Peptides which do not adopt this strand alignment aggregate to form thin, flexible, and smooth protofibrils. The ability to form ordered aggregates, and thus to form twisted fibrils, is modulated by the structure of the side chain of residue 117.     

Taxonomy,morphology, and surface structure of Basidiobolus sp. isolate

The isolate under investigation was determined as Basidiobolus ranarum Eidam, 1886. Scanning electron micrographs elucidated the origin of a cap-like part of the conidiophore adhering to the conidium and showed new details of the surface of the fragment of conidiophore and proper papilla during their gradual separation. The attaching sac of nonattached anadhesive conidia was smooth and very turgid, but after attaching, there appeared depressions due to the loss of turgor.