Determinants of laminin polymerization revealed by the structure of the α5 chain amino-terminal region

The polymerization of laminin into a cell-associated network--a key step in basement membrane assembly--is mediated by the laminin amino-terminal (LN) domains at the tips of the three short arms of the laminin αβγ-heterotrimer. The crystal structure of a laminin α5LN-LE1-2 fragment shows that the LN domain is a β-jelly roll with several elaborate insertions that is attached like a flower head to the stalk-like laminin-type epidermal growth factor-like tandem. A surface loop that is strictly conserved in the LN domains of all α-short arms is required for stable ternary association with the β- and γ-short arms in the laminin network.     

Phylogenetic relationships between cultivated and wild species of the genusBeta revealed by DNA “fingerprinting”

Forty-one accessions of the genusBeta representing wild and cultivated species of all sections were analyzed by DNA fingerprinting. Four sugar beet minisatellite DNA probes revealed characteristic banding patterns with Southern-hybridizedBeta DNA restricted withHindIII. A total of 111 polymorphic RFLP bands were scored across all accessions. Cluster analysis based on genetic similarity estimates for all 820 combinations of accessions revealed the following results. (1) All accessions could unambiguously be identified by a characteristic RFLP banding pattern. (2) The sugar beet cultivars examined displayed a low level of genetic diversity; they showed high similarity toB. Vulgaris ssp.maritima but low genetic similarity to the other wild species of section I. (3) In most cases, the present taxonomic classification of the genusBeta was confirmed. Species of sections II, III, and IV were clearly distinguishable from those of section I except forB. Macrocarpa, which showed high similarity to wild species of section II. In a second experiment, 108 single-copy RFLP probes from sugar beet were Southern hybridized withB. procumbens DNA. A surprisingly low degree of homology (34%) was found. The results are discussed with regard to the taxonomic classification of the genusBeta.     

Reproductive biology of the lane snapper,Lutjanus synagris (Linnaeus 1758) (Perciformes,Lutjanidae), in the Maranhão continental shelf,Northeast of Brazil

Environmental Biology of Fishes - To clarify the reproductive activity of lane snapper, Lutjanus synagris, a total of 359 specimens of lane snapper were collected in partnership with an artisanal...     

Elver Invasion, Population Structure and Growth of Marbled eels Anguilla marmorata in a Tropical River on Réunion Island in the Indian Ocean

Winter skates, Leucoraja ocellata, exposed to 80% and 50% seawater (SW) exhibited rapid and significant weight gains followed by a slight recovery to new steady state levels within 8 days. Skates were acclimated at each salinity (100% SW [N = 16], 80% SW [N = 8], 50% SW [N = 8]), anesthetized (MS222) and bled from the caudal vein. In 100% SW, skate plasma (930mOsm/kg) was slightly hyperosmotic to the external medium (922mOsm/kg). Plasma osmolality decreased with seawater dilution, but became increasingly hyperosmotic to the bathing media. The environmental dilutions resulted in significant, but disproportionate changes in plasma Cl^–, P^–, Na⁺, Ca⁺, Mg⁺, trimethylamine oxide (TMAO) and urea concentrations. Mean corpuscular [Hb] and milliliter RBC water measurements suggest that skate red cells swelled less at each dilution than predicted for a passive erythrocyte osmometer. Concentrations of the major RBC solutes K⁺, urea, TMAO and Cl^– decreased by 8, 25, 5 and 21%, respectively in 80% SW. In 50% SW, K⁺, urea, TMAO and Cl^– concentrations decreased by 9, 47, 36 and 15%, respectively. Quantitatively, the other measured intracellular electrolytes (Mg⁺, Na⁺, P^– and Ca⁺) also exhibited disproportionate changes in concentration. Our results indicate that L. ocellata is a euryhaline elasmobranch that can tolerate significant reduction in the external salinity through the release of both ions and urea from the extracellular compartments while retaining electrolytes at the expense of urea in the intracellular compartment.     

Genetic differentiation and intraspecific structure of Eastern Tropical Pacific spotted dolphins,Stenella attenuata,revealed by DNA analyses

Mitochondrial DNA (mtDNA) control region sequences and microsatellite loci length polymorphisms were used to investigate genetic differentiation in spotted dolphins (Stenella attenuata) in the Eastern Tropical Pacific and to examine the intraspecific structure of the coastal subspecies (Stenella attenuata graffmani). One-hundred and thirty-five animals from several coastal areas and 90 offshore animals were sequenced for 455 bp of the mitochondrial control region, resulting in 112 mtDNA haplotypes. Phylogenetic analyses and the existence of shared haplotypes between the two subspecies suggest recent and/or current gene flow. Analyses using χ², F _ST (based on haplotype frequencies) and Φ_ST values (based on frequencies and genetic distances between haplotypes) yielded statistically significant separation (randomized permutation values P<0.05) among four different coastal populations and between all but one of these and the offshore subspecies (overall F _ST=0.0691). Ninety-one coastal animals from these four geographic populations and 50 offshore animals were genotyped for seven nuclear microsatellite loci. Analysis using F _ST values (based on allelic frequencies) yielded statistically significant separation between most coastal populations and offshore animals, although no coastal populations were distinguished. These results argue for the existence of some genetic isolation between offshore and inshore populations and among some inshore populations, suggesting that these should be treated as separate units for management purposes.     

Molecular basis of α1-antitrypsin deficiency revealed by the structure of a domain-swapped trimer

α(1)-Antitrypsin (α1AT) deficiency is a disease with multiple manifestations, including cirrhosis and emphysema, caused by the accumulation of stable polymers of mutant protein in the endoplasmic reticulum of hepatocytes. However, the molecular basis of misfolding and polymerization remain unknown. We produced and crystallized a trimeric form of α1AT that is recognized by an antibody specific for the pathological polymer. Unexpectedly, this structure reveals a polymeric linkage mediated by domain swapping the carboxy-terminal 34 residues. Disulphide-trapping and antibody-binding studies further demonstrate that runaway C-terminal domain swapping, rather than the s4A/s5A domain swap previously proposed, underlies polymerization of the common Z-mutant of α1AT in vivo.     

Topographical analysis of trypsin active site structure by means of the “inverse substrate” method

Trypsin-specific substrate analogs, “inverse substrates,” carrying the fluorescent dimethylaminonaphthalene group were synthesized. Preparation of acyl trypsins in which the fluorescent group is attached to the catalytic residue through a spacer group of various chain lengths was successfully carried out by use of these inverse substrates. The topographical structure of the trypsin active site vicinity was estimated on the basis of the fluorescence spectra of these acyl trypsins.     

The composition,structure, and dynamics of the nekton of the upper epipelagic layer in the Aleutian and Commander basins,western Bering Sea,in the fall seasons of 2002–2013

The data on the composition and abundance of nekton species and their interannual variations within the upper epipelagic layer (0–50 m) in the Aleutian and Commander basins in the western Bering Sea that are considered in the article were collected during complex surveys that were conducted by the Pacific Research Fisheries Center in September and October of 2002–2013. The core species structures of the nekton communities in these two areas were similar: the chum salmon Oncorhynchus keta and the boreopacific gonate squid Boreoteuthis borealis were the most abundant species. Simpson’s dominance index varied synchronously in both areas, with higher values in the Aleutian Basin, until 2009. In the subsequent years, the values of the index for the studied areas became equal and varied asynchronously. An analysis of abundance showed that two types of species structure most often prevailed (with the dominance of either chum salmon or squid); in some years the species structure differed from that in other years. Species of the low-boreal and low-boreal-subtropical complexes were more abundant in the Commander Basin, reaching particularly high proportions in 2006, 2008, and 2012. Certain species showed similarity in the year-to-year dynamics of their abundance; however, these coincidences were frequently accidental. After the climate regime shift in 2006–2007, the total biomass of nekton in the Aleutian Basin decreased from 3241 to 1736 kg/km² (46%); in the Komandorskiye Basin it decreased from 2459 to 1976 kg/km² (20%).     

Lateral root formation in the strawberry Fragaria × ananassa Duch. revealed by histone H4 in situ hybridisation

Abstract

Our study was carried out in bench rhizotrons using the Camarosa variety of strawberry (Fragaria × ananassa Duch.), by exciding the apex of fast-growing primary roots at two distances (1 or 8 cm) from the apex. It was demonstrated that new lateral meristems were rapidly induced by excision of the root apex at either distance; after 24 h, histone H4 in situ hybridisation detected groups of cell-organising root primordia just a few millimetres below the cut. After a further 24 h, new lateral roots were about to protrude from the original root. Results show that lateral roots can be formed anywhere along the primary roots of strawberry plants from a few stem cells distributed along the pericycle close to the protoxylem arches.     

Population structure in the endangered Blanca Cacereña bovine breed demonstrated by RAPD analyses

RAPD analyses have been used to determine the genetic diversity and the population structure of the endangered Blanca Cacere?a bovine breed. Genetic variability was evaluated on the basis of 1048 loci produced by 71 primers. RAPD produced a number of polymorphic loci (30.44%), and it has been proved to be a useful method for evaluating polymorphisms in this breed. The dendrograms based on simililarity indexes and on Nei's genetic distances between 60 animals and the value of genetic differentiation among subpopulations (F(ST)) showed a clear population substructure defined by herds and a scarce genetic flow among herds. Analysis of molecular variance (AMOVA) showed that 32.4% of the total variance was due to differences among herds and confirmed the clustering found. The results of the present study allow us to plan more adequate mating in order to maintain the genetic diversity and to improve the efficiency of conservation for the Blanca Cacere?a bovine breed.     

Prey Selection,Vertical Migrations and the Impacts of Harvesting Upon the Population Dynamics of a Predator-Prey System

A model is developed to describe the interaction between a predator and two prey types located in different regions. Conditions for stability and persistence are analysed. The effects of harvesting the predators are investigated by making the predator mortality rate habitat dependent. Results demonstrate that for any given set of parameter values there is a value of the intrinsic preference of the predator for each prey type at which the system undergoes a Hopf bifurcation. Above this critical value the system evolves towards a stable equilibrium, whereas below it, stable limit cycles arise by Hopf bifurcations. Simulations demonstrate that the presence of demographic stochasticity may destabilise oscillatory populations, thereby causing population extinctions. An application of the model to the foraging behaviour of North Sea cod is described. It is shown that if the preferred prey is more productive, it is likely that the equilibrium will be stable, whereas if the less preferred prey is more productive, populations are likely to display cycles and in the stochastic case become extinct. As cod fishing mortality is increased, the point of bifurcation and region of parameter space for which the system is unstable decreases. An increased understanding of how cod behave may enable fish stocks to be managed more successfully, for example by indicating where marine reserves should be placed.     

Predicted distributions and abundances of the sea turtle ‘lost years’ in the western North Atlantic Ocean

Oceanic dispersal characterizes the early juvenile life-stages of numerous marine species of conservation concern. This early stage may be a ‘critical period’ for many species, playing an overriding role in population dynamics. Often, relatively little information is available on their distribution during this period, limiting the effectiveness of efforts to understand environmental and anthropogenic impacts on these species. Here we present a simple model to predict annual variation in the distribution and abundance of oceanic-stage juvenile sea turtles based on species’ reproductive output, movement and mortality. We simulated dispersal of 25 cohorts (1993–2017) of oceanic-stage juveniles by tracking the movements of virtual hatchling sea turtles released in a hindcast ocean circulation model. We then used estimates of annual hatchling production from Kemp's ridley Lepidochelys kempii (n = 3), green Chelonia mydas (n = 8) and loggerhead Caretta caretta (n = 5) nesting areas in the northwestern Atlantic (inclusive of the Gulf of Mexico, Caribbean Sea and eastern seaboard of the U.S.) and their stage-specific mortality rates to weight dispersal predictions. The model's predictions indicate spatial heterogeneity in turtle distribution across their marine range, identify locations of increasing turtle abundance (notably along the U.S. coast), and provide valuable context for temporal variation in the stranding of young sea turtles across the Gulf of Mexico. Further effort to collect demographic, distribution and behavioral data that refine, complement and extend the utility of this modeling approach for sea turtles and other dispersive marine taxa is warranted. Finally, generating these spatially-explicit predictions of turtle abundance required extensive international collaboration among scientists; our findings indicate that continued conservation of these sea turtle populations and the management of the numerous anthropogenic activities that operate in the northwestern Atlantic Ocean will require similar international coordination.     

Expression patterns of several floral genes during flower initiation in the apical buds of apple (Malus × domestica Borkh.) revealed by in situ hybridization

The apple (Malus?×?domestica Borkh.) is one of the commercially important fruit crops in the worldwide. The apple has a relatively long juvenile period (up to 4?years) and a long reproductive period between the flower initiation and the mature fruit (14?C16?months), which prevent the fruit breeding. Therefore, the understanding of the flowering system is important to improve breeding efficiency in the apple. In this study, to examine the temporal and spatial expression patterns of the floral genes, MdTFL1, MdAP1 (MdMASD5), AFL2, and MdFT, we conducted in situ hybridization analysis in the apple shoot apex. In vegetative phase, MdTFL1 was expressed on the rib meristem zone. When vegetative meristem began converting into inflorescence meristem, the expression level of MdTFL1 was drastically decreased. At the early stage of inflorescence meristem, the expression levels of AFL2, MdFT, and MdAP1 were up-regulated in the leaf primordia and the upper region of cell layers on the shoot apex. In late stage, the expression levels of AFL2 and MdAP1 were up-regulated in the young floral primordia. At a more advanced stage, high expression of MdAP1 was observed in the inflorescence primordium through the inner layer of sepal primordia and the outer layer of receptacle primordia and floral axis. Our results suggest that AFL2, MdFT, and MdAP1 affect to convert from the vegetative meristem into the inflorescence meristem after the decline of MdTFL1 expression. After that, AFL2 and MdAP1 promote the formation of the floral primordia and floral organs.     

Population and group structure of western lowland gorillas (Gorilla gorilla gorilla) at Lokoué, Republic of Congo

During a 17-month study at the Lokoué clearing in Odzala National Park, Republic of Congo, we identified 377 western lowland gorillas. This population included 31 solitary males, 37 breeding groups, and eight nonbreeding groups. Its age- and sex-class structure was similar to those observed at two other clearings in the same forest block. However, the size of breeding groups varied with site (either clearing or forest sites). At Lokoué, breeding groups (mean size: 8.2 gorillas; range: 3-15) included a single silverback male and, on average, 3.2 adult females. Nonbreeding groups (mean size: 5.5; range: 2-15) were devoid of adult females. Five of the nonbreeding groups were composed predominantly of blackbacks, subadult males, and juveniles, and thus fit the definition of all-male groups previously observed in mountain gorillas. Our study confirms that 1) one-male breeding groups are the norm in western gorillas, and 2) all-male groups occur in this species. Despite frequent changes in members due to migrations of the males, the persistence of these all-male groups indicates that they may play an important role in the life of migrating males. Variations in population structure, and group composition and type among gorilla populations are discussed. However, a further understanding of the evolution of group-living in gorillas requires detailed ecological studies conducted in parallel with studies of the population structure and dynamics of these groups.     

Analysis of bacterial core communities in the central Baltic by comparative RNA–DNA-based fingerprinting provides links to structure–function relationships

Understanding structure–function links of microbial communities is a central theme of microbial ecology since its beginning. To this end, we studied the spatial variability of the bacterioplankton community structure and composition across the central Baltic Sea at four stations, which were up to 450 km apart and at a depth profile representative for the central part (Gotland Deep, 235 m). Bacterial community structure was followed by 16S ribosomal RNA (rRNA)- and 16S rRNA gene-based fingerprints using single-strand conformation polymorphism (SSCP) electrophoresis. Species composition was determined by sequence analysis of SSCP bands. High similarities of the bacterioplankton communities across several hundred kilometers were observed in the surface water using RNA- and DNA-based fingerprints. In these surface communities, the RNA- and DNA-based fingerprints resulted in very different pattern, presumably indicating large difference between the active members of the community as represented by RNA-based fingerprints and the present members represented by the DNA-based fingerprints. This large discrepancy changed gradually over depth, resulting in highly similar RNA- and DNA-based fingerprints in the anoxic part of the water column below 130 m depth. A conceivable mechanism explaining this high similarity could be the reduced oxidative stress in the anoxic zone. The stable communities on the surface and in the anoxic zone indicate the strong influence of the hydrography on the bacterioplankton community structure. Comparative analysis of RNA- and DNA-based community structure provided criteria for the identification of the core community, its key members and their links to biogeochemical functions.     

Pressure-dependent changes in the structure of the melittin α-helix determined by NMR

A novel method is described, which uses changes in NMR chemical shifts to characterise the structural change in a protein with pressure. Melittin in methanol is a small -helical protein, and its chemical shifts change linearly and reversibly with pressure between 1 and 2000 bar. An improved relationship between structure and HN shift has been calculated, and used to drive a molecular dynamics-based calculation of the change in structure. With pressure, the helix is compressed, with the H—O distance of the NH—O=C hydrogen bonds decreased by 0.021 ± 0.039 Å, leading to an overall compression along the entire helix of about 0.4 Å, corresponding to a static compressibility of 6 ×10^–6 bar^–1. The backbone dihedral angles and are altered by no more than ± 3° for most residues with a negative correlation coefficient of –0.85 between _i and _i–1, indicating that the local conformation alters to maintain hydrogen bonds in good geometries. The method is shown to be capable of calculating structural change with high precision, and the results agree with structural changes determined using other methodologies.     

Population structure of the malaria vector Anopheles darlingi in Rondônia, Brazilian Amazon, based on mitochondrial DNA

Anopheles darlingi is the most important Brazilian malaria vector, with a widespread distribution in the Amazon forest. Effective strategies for vector control could be better developed through knowledge of its genetic structure and gene flow among populations, to assess the vector diversity and competence in transmitting Plasmodium. The aim of this study was to assess the genetic diversity of An. darlingi collected at four locations in Porto Velho, by sequencing a fragment of the ND4 mitochondrial gene. From 218 individual mosquitoes, we obtained 20 different haplotypes with a diversity index of 0.756, equivalent to that found in other neotropical anophelines. The analysis did not demonstrate significant population structure. However, haplotype diversity within some populations seems to be over-represented, suggesting the presence of sub-populations, but the presence of highly represented haplotypes complicates this analysis. There was no clear correlation among genetic and geographical distance and there were differences in relation to seasonality, which is important for malarial epidemiology.