bluuebunny/crossref_metadata_2025 huggingface dataset:
Molecular Characterization of Bacteriophages for Microbial Source Tracking in Korea
Authors: Lee Jung Eun , Lim Mi Young , Kim Sei Yoon , Lee Sunghee , Lee Heetae , Oh Hyun-Myung , Hur Hor-Gil , Ko GwangPyo
Published: September 2009

We investigated coliphages from various fecal sources, including humans and animals, for microbial source tracking in South Korea. Both somatic and F
+
-specific coliphages were isolated from 43 fecal samples from farms, wild animal habitats, and human wastewater plants. Somatic coliphages were more prevalent and abundant than F
+
coliphages in all of the tested fecal samples. We further characterized 311 F
+
coliphage isolates using RNase sensitivity assays, PCR and reverse transcription-PCR, and nucleic acid sequencing. Phylogenetic analyses were performed based on the partial nucleic acid sequences of 311 F
+
coliphages from various sources. F
+
RNA coliphages were most prevalent among geese (95%) and were least prevalent in cows (5%). Among the genogroups of F
+
RNA coliphages, most F
+
coliphages isolated from animal fecal sources belonged to either group I or group IV, and most from human wastewater sources were in group II or III. Some of the group I coliphages were present in both human and animal source samples. F
+
RNA coliphages isolated from various sources were divided into two main clusters. All F
+
RNA coliphages isolated from human wastewater were grouped with Qβ-like phages, while phages isolated from most animal sources were grouped with MS2-like phages. UniFrac significance statistical analyses revealed significant differences between human and animal bacteriophages. In the principal coordinate analysis (PCoA), F
+
RNA coliphages isolated from human waste were distinctively separate from those isolated from other animal sources. However, F
+
DNA coliphages were not significantly different or separate in the PCoA. These results demonstrate that proper analysis of F
+
RNA coliphages can effectively distinguish fecal sources.
The Olive Fly Endosymbiont, “CandidatusErwinia dacicola,” Switches from an Intracellular Existence to an Extracellular Existence during Host Insect Development
Authors: Estes Anne M. , Hearn David J. , Bronstein Judith L. , Pierson Elizabeth A.
Published: September 2009

As polyphagous, holometabolous insects, tephritid fruit flies (Diptera: Tephritidae) provide a unique habitat for endosymbiotic bacteria, especially those microbes associated with the digestive system. Here we examine the endosymbiont of the olive fly [Bactrocera oleae(Rossi) (Diptera: Tephritidae)], a tephritid of great economic importance. “CandidatusErwinia dacicola” was found in the digestive systems of all life stages of wild olive flies from the southwestern United States. PCR and microscopy demonstrated that “Ca.Erwinia dacicola” resided intracellularly in the gastric ceca of the larval midgut but extracellularly in the lumen of the foregut and ovipositor diverticulum of adult flies. “Ca.Erwinia dacicola” is one of the few nonpathogenic endosymbionts that transitions between intracellular and extracellular lifestyles during specific stages of the host's life cycle. Another unique feature of the olive fly endosymbiont is that unlike obligate endosymbionts of monophagous insects, “Ca.Erwinia dacicola” has a G+C nucleotide composition similar to those of closely related plant-pathogenic and free-living bacteria. These two characteristics of “Ca.Erwinia dacicola,” the ability to transition between intracellular and extracellular lifestyles and a G+C nucleotide composition similar to those of free-living relatives, may facilitate survival in a changing environment during the development of a polyphagous, holometabolous host. We propose that insect-bacterial symbioses should be classified based on the environment that the host provides to the endosymbiont (the endosymbiont environment).
Hydroxylation and Further Oxidation of Δ9-Tetrahydrocannabinol by Alkane-Degrading Bacteria
Authors: Rashidi Hassan , Akhtar Muhammad T. , van der Kooy Frank , Verpoorte Robert , Duetz Wouter A.
Published: September 2009

The microbial biotransformation of Δ9-tetrahydrocannabinol was investigated using a collection of 206 alkane-degrading strains. Fifteen percent of these strains, mainly gram-positive strains from the generaRhodococcus,Mycobacterium,Gordonia, andDietzia, yielded more-polar derivatives. Eight derivatives were produced on a mg scale, isolated, and purified, and their chemical structures were elucidated with the use of liquid chromatography-mass spectrometry,1H-nuclear magnetic resonance (1H-NMR), and two-dimensional NMR (1H-1H correlation spectroscopy and heteronuclear multiple bond coherence). All eight biotransformation products possessed modified alkyl chains, with hydroxy, carboxy, and ester functionalities. In a number of strains, β-oxidation of the initially formed C5carboxylic acid led to the formation of a carboxylic acid lacking two methylene groups.
Bacterial Community Composition of Stream Biofilms in Spatially Variable-Flow Environments
Authors: Besemer Katharina , Singer Gabriel , Hödl Iris , Battin Tom J.
Published: September 2009

Streams are highly heterogeneous ecosystems, in terms of both geomorphology and hydrodynamics. While flow is recognized to shape the physical architecture of benthic biofilms, we do not yet understand what drives community assembly and biodiversity of benthic biofilms in the heterogeneous flow landscapes of streams. Within a metacommunity ecology framework, we experimented with streambed landscapes constructed from bedforms in large-scale flumes to illuminate the role of spatial flow heterogeneity in biofilm community composition and biodiversity in streams. Our results show that the spatial variation of hydrodynamics explained a remarkable percentage (up to 47%) of the variation in community composition along bedforms. This suggests species sorting as a model of metacommunity dynamics in stream biofilms, though natural biofilm communities will clearly not conform to a single model offered by metacommunity ecology. The spatial variation induced by the hydrodynamics along the bedforms resulted in a gradient of bacterial beta diversity, measured by a range of diversity and similarity indices, that increased with bedform height and hence with spatial flow heterogeneity at the flume level. Our results underscore the necessity to maintain small-scale physical heterogeneity for community composition and biodiversity of biofilms in stream ecosystems.
Low Taxon Richness of Bacterioplankton in High-Altitude Lakes of the Eastern Tibetan Plateau, with a Predominance ofBacteroidetesandSynechococcusspp
Authors: Xing Peng , Hahn Martin W. , Wu Qinglong L.
Published: September 2009

Plankton samples were collected from six remote freshwater and saline lakes located at altitudes of 3,204 to 4,718 m and 1,000 km apart within an area of ca. 1 million km2on the eastern Tibetan Plateau to comparatively assess how environmental factors influence the diversity of bacterial communities in high-altitude lakes. The composition of the bacterioplankton was investigated by analysis of large clone libraries of 16S rRNA genes. Comparison of bacterioplankton diversities estimated for the six Tibetan lakes with reference data previously published for lakes located at lower altitudes indicated relatively low taxon richness in the Tibetan lakes. The estimated average taxon richness in the four Tibetan freshwater lakes was only one-fifth of the average taxon richness estimated for seven low-altitude reference lakes. This cannot be explained by low coverage of communities in the Tibetan lakes by the established libraries or by differences in habitat size. Furthermore, a comparison of the taxonomic compositions of bacterioplankton across the six Tibetan lakes revealed low overlap between their community compositions. About 70.9% of the operational taxonomic units (99% similarity) were specific to single lakes, and a relatively high percentage (11%) of sequences were <95% similar to publicly deposited sequences of cultured or uncultured bacteria. This beta diversity was explained by differences in salinity between lakes rather than by distance effects. Another characteristic of the investigated lakes was the predominance ofCyanobacteria(Synechococcus) andBacteroidetes. These features of bacterioplankton diversity may reflect specific adaptation of various lineages to the environmental conditions in these high-altitude lakes.
UropathogenicEscherichia coliSuppresses the Host Inflammatory Response via Pathogenicity Island GenessisAandsisB
Authors: Lloyd Amanda L. , Smith Sara N. , Eaton Kathryn A. , Mobley Harry L. T.
Published: September 2009

Extraintestinal pathogenicEscherichia colican successfully colonize the urinary tract of the immunocompetent host. In part, this is accomplished by dampening the host immune response. Indeed, thesisAandsisBgenes (shiA-likeinflammationsuppressor genesAandB) of uropathogenicE. colistrain CFT073, homologs of theShigella flexneriSHI-2 pathogenicity island geneshiA, suppress the host inflammatory response. A double deletion mutant (ΔsisAΔsisB) resulted in a hyperinflammatory phenotype in an experimental model of ascending urinary tract infection. The ΔsisAΔsisBmutant not only caused significantly more inflammatory foci in the kidneys of CBA/J mice (P= 0.0399), but these lesions were also histologically more severe (P= 0.0477) than lesions observed in mice infected with wild-type CFT073. This hyperinflammatory phenotype could be suppressed to wild-type levels by in vivo complementation of the ΔsisAΔsisBmutant with either thesisAorsisBgene intrans. The ΔsisAΔsisBmutant was outcompeted by wild-type CFT073 during cochallenge infection in the bladder (P= 0.0295) at 48 h postinoculation (hpi). However, during cochallenge infections, we reasoned that wild-type CFT073 could partially complement the ΔsisAΔsisBmutant. Consistent with this, the most significant colonization defect of the ΔsisAΔsisBmutant in vivo was observed during independent challenge relative to wild-type CFT073, with attenuation of the mutant observed in the bladder (P< 0.0001) and kidneys (P= 0.0003) at 6 hpi. By 24 and 48 hpi, the ΔsisAΔsisBmutant was no longer significantly attenuated in the bladder or kidneys, suggesting that thesisAandsisBgenes may be important for suppressing the host immune response during the initial stages of infection.
Complement Receptor 3 Deficiency Influences Lesion Progression duringLeishmania majorInfection in BALB/c Mice
Authors: Carter Cristina R. , Whitcomb James P. , Campbell Jessica A. , Mukbel Rami M. , McDowell Mary Ann
Published: September 2009

Leishmania majoris an obligately intracellular protozoan parasite that causes cutaneous leishmaniasis. Like numerous intracellular pathogens,Leishmaniaexploits cell surface receptors as a means of entry into host cells. Complement receptor 3 (CR3; also called CD11b/CD18), a β2integrin on phagocytic cells, is one such receptor. Ligation of CR3 has been shown to inhibit the production of interleukin-12, the cytokine that is pivotal in establishing the cell-mediated response necessary to combat intracellular infection. Here we investigate the role that CR3 plays in the establishment and progression of cutaneous leishmaniaisis in vivo. Dermal lesions of wild-type BALB/c mice are characteristically progressive and lead to extensive tissue necrosis coupled with elevated parasite burdens; CD11b-deficient BALB/c mice, however, demonstrate an intermediate phenotype characterized by chronic lesions and a reduced incidence of tissue damage. Infection followed by a reinfection challenge indicates that both susceptible (BALB/c) and resistant (C57BL/6) mice, regardless of CD11b status, develop resistance toL. major. In addition, CD11b does not bias the T helper cytokine response toL. majorinfection. Our results further indicate that CD11b is not necessary for disease resolution in resistant mice; rather, this protein appears to play a minor role in susceptibility.
σXIs Involved in ControllingBacillus subtilisBiofilm Architecture through the AbrB Homologue Abh
Authors: Murray Ewan J. , Strauch Mark A. , Stanley-Wall Nicola R.
Published: September 2009

A characteristic feature of biofilm formation is the production of a protective extracellular polymeric matrix. In the gram-positive bacteriumBacillus subtilis, the biofilm matrix is synthesized by the products of theepsABCDEFGHIJKLMNOoperon (hereafter called theepsoperon) andyqxM-sipW-tasAloci. Transcription from these operons is repressed by two key regulators, AbrB and SinR. Relief of inhibition is necessary to allow biofilm formation to proceed. Here we present data indicating that Abh, a sequence and structural homologue of AbrB, regulates biofilm architecture byB.subtiliswhen colony morphology and pellicle formation are assessed. Data indicating thatabhexpression is dependent on the environmental signals that stimulate the activity of the extracytoplasmic function σ-factor σXare shown. We demonstrate that expression ofslrR, the proposed activator ofyqxMtranscription, is positively controlled by Abh. Furthermore, Abh is shown to activate transcription from the promoter of theepsoperon through its control of SlrR. These findings add to the increasingly complex transcriptional network that controls biofilm formation byB.subtilis.
The β-Barrel Outer Membrane Protein Assembly Complex ofNeisseria meningitidis
Authors: Volokhina Elena B. , Beckers Frank , Tommassen Jan , Bos Martine P.
Published: September 2009

The evolutionarily conserved protein Omp85 is required for outer membrane protein (OMP) assembly in gram-negative bacteria and in mitochondria. ItsEscherichia colihomolog, designated BamA, functions with four accessory lipoproteins, BamB, BamC, BamD, and BamE, together forming the β-barrel assembly machinery (Bam). Here, we addressed the composition of this machinery and the function of its components inNeisseria meningitidis, a model organism for outer membrane biogenesis studies. Analysis of genome sequences revealed homologs of BamC, BamD (previously described as ComL), and BamE and a second BamE homolog, Mlp. No homolog of BamB was found. As inE. coli, ComL/BamD appeared essential for viability and for OMP assembly, and it could not be replaced by itsE. colihomolog. BamE was not essential but was found to contribute to the efficiency of OMP assembly and to the maintenance of OM integrity. AbamCmutant showed only marginal OMP assembly defects, but the impossibility of creating abamC bamEdouble mutant further indicated the function of BamC in OMP assembly. Anmlpmutant was unaffected in OMP assembly. The results of copurification assays demonstrated the association of BamC, ComL, and BamE with Omp85. Semi-native gel electrophoresis identified the RmpM protein as an additional component of the Omp85 complex, which was confirmed in copurification assays. RmpM was not required for OMP folding but stabilized OMP complexes. Thus, the Bam complex inN. meningitidisconsists of Omp85/BamA plus RmpM, BamC, ComL/BamD, and BamE, of which ComL/BamD and BamE appear to be the most important accessory components for OMP assembly.
The Response Regulator SprE (RssB) Modulates Polyadenylation and mRNA Stability inEscherichia coli
Authors: Carabetta Valerie J. , Mohanty Bijoy K. , Kushner Sidney R. , Silhavy Thomas J.
Published: September 2009

InEscherichia coli, the adaptor protein SprE (RssB) controls the stability of the alternate sigma factor RpoS (σ38and σS). When nutrients are abundant, SprE binds RpoS and delivers it to ClpXP for degradation, but when carbon sources are depleted, this process is inhibited. It also has been noted that overproduction of SprE is toxic. Here we show that null mutations inpcnB, encoding poly(A) polymerase I (PAP I), and inhfq, encoding the RNA chaperone Hfq, suppress this toxicity. Since PAP I, in conjunction with Hfq, is responsible for targeting RNAs, including mRNAs, for degradation by adding poly(A) tails onto their 3′ ends, these data indicate that SprE helps modulate the polyadenylation pathway inE. coli. Indeed, in exponentially growing cells,sprEdeletion mutants exhibit significantly reduced levels of polyadenylation and increased stability of specific mRNAs, similar to what is observed in a PAP I-deficient strain. In stationary phase, we show that SprE changes the intracellular localization of PAP I. Taken together, we propose that SprE plays a multifunctional role in controlling the transcriptome, regulating what is made via its effects on RpoS, and modulating what is degraded via its effects on polyadenylation and turnover of specific mRNAs.
Tryptophan Inhibits
Proteus vulgaris
TnaC Leader Peptide Elongation, Activating
tna
Operon Expression
Authors: Cruz-Vera Luis R. , Yang Rui , Yanofsky Charles
Published: September 2009

Expression of the
tna
operon of
Escherichia coli
and of
Proteus vulgaris
is induced by
l
-tryptophan. In
E. coli
, tryptophan action is dependent on the presence of several critical residues (underlined) in the newly synthesized TnaC leader peptide,
W
FNI
D
XX
L/I
XXXX
P
. These residues are conserved in TnaC of
P. vulgaris
and of other bacterial species. TnaC of
P. vulgaris
has one additional feature, distinguishing it from TnaC of
E. coli
; it contains two C-terminal lysine residues following the conserved proline residue. In the present study, we investigated
l
-tryptophan induction of the
P. vulgaris tna
operon, transferred on a plasmid into
E. coli
. Induction was shown to be
l
-tryptophan dependent; however, the range of induction was less than that observed for the
E. coli tna
operon. We compared the genetic organization of both operons and predicted similar folding patterns for their respective leader mRNA segments. However, additional analyses revealed that
l
-tryptophan action in the
P. vulgaris tna
operon involves inhibition of TnaC elongation, following addition of proline, rather than inhibition of leader peptide termination. Our findings also establish that the conserved residues in TnaC of
P. vulgaris
are essential for
l
-tryptophan induction, and for inhibition of peptide elongation. TnaC synthesis is thus an excellent model system for studies of regulation of both peptide termination and peptide elongation, and for studies of ribosome recognition of the features of a nascent peptide.
Complete Genome Sequence of
Lactobacillus johnsonii
FI9785, a Competitive Exclusion Agent against Pathogens in Poultry
Authors: Wegmann Udo , Overweg Karin , Horn Nikki , Goesmann Alexander , Narbad Arjan , Gasson Michael J. , Shearman Claire
Published: September 2009

Lactobacillus johnsonii
is a member of the acidophilus group of lactobacilli. Because of their probiotic properties, including attachment to epithelial cells, immunomodulation, and competitive exclusion of pathogens, representatives of this group are being intensively studied. Here we report the complete annotated genome sequence of
Lactobacillus johnsonii
FI9785, a strain which prevents the colonization of specific-pathogen-free chicks by
Clostridium perfringens
.
Complete Genome Sequence of
Robiginitalea biformata
HTCC2501
Authors: Oh Hyun-Myung , Giovannoni Stephen J. , Lee Kiyoung , Ferriera Steve , Johnson Justin , Cho Jang-Cheon
Published: September 2009

Robiginitalea biformata
HTCC2501, isolated from the Sargasso Sea by dilution-to-extinction culturing, has been known as an aerobic chemoheterotroph with carotenoid pigments and dimorphic growth phases. Here, we announce the complete sequence of the
R. biformata
HTCC2501 genome, which contains genes for carotenoid biosynthesis and several macromolecule-degrading enzymes.
Adaptive Variation in Rheotactic and Agonistic Behavior in Newly Emerged Fry of Chinook Salmon, Oncorhynchus tshawytscha, from Ocean- and Stream-Type Populations
Authors: Taylor Eric B.
Published: September 2009

Agonistic and rheotactic behavior and body morphology were compared in recently emerged, laboratory-reared chinook salmon (Oncorhynchus tshawytscha) from two "stream-type" and two "ocean-type" populations. Newly emerged chinook fry from the stream-type populations (Slim Creek and the Eagle River) were more aggressive than fry from the ocean-type populations (the Nanaimo and Harrison rivers). Slim Creek fry were consistently the most aggressive. There was no clear distinction in rheotactic behavior between stream- and ocean-type chinook; Harrison River, ocean-type chinook fry had the strongest downstream movement in "dark" current response tests, but fry from the other three populations had similar movement scores in both light and dark tests. Fry from the four populations were morphologically distinct; however, there was no clear separation in body morphology or coloration based on life history type. These differences exhibited in laboratory-reared fry indicate that they are, at least in part, inherited. I conclude that a fundamental genetic difference in agonistic behavior exists between stream- and ocean-type chinook juveniles. A genetic dichotomy between stream- and ocean-type chinook in rheotactic behavior and morphology, however, may be overidden by population-specific local adaptations, independent of life history type.
Response of Lake Michigan Benthic Algae to in situ Enrichment with Si, N, and P
Authors: Carrick Hunter J. , Lowe Rex L.
Published: September 2009

The possibility that benthic algae in the nearshore area of Lake Michigan might be growth limited by Si was tested using nutrient-releasing substrata. Nutrient treatments were Si, N + P, Si + N + P, and controls (CONT) and were sampled after 7, 14, and 31 d of exposure. Addition of Si alone had little stimulatory effect on algal biomass, while enrichment with Si + N + P led to the greatest increase in chlorophyll a, particulate Si, total biovolume, and diatom biovolume after 14 d of incubation (P < 0.0001). By day 31, communities on CONT and Si substrata exhibited little change in biomass and remained dominated by diatoms (98% of total biovolume), while algal biomass on both N + P and Si + N + P substrata increased more than eightfold (P < 0.0001) and consisted mainly of Stigeoclonium tenue (Chlorophyta) and Schizothrix calcicolas (Cyanophyta). These results indicate that benthic diatoms in Lake Michigan are not currently limited by Si, but may become Si limited following enrichment with N + P.
Allometric Models of Simuliid Growth Rates and Their Use for Estimation of Production
Authors: Morin Antoine , Constantin Michel , Peters Robert Henry
Published: September 2009

Growth rates of Prosimulium mixtum/fuscum, Stegopterna mutata, and Simulium vittatum are described in relation to individual mass, water temperature, and seston quality in the outlet of Lake Orford (southern Quebec) in the winter of 1985–86. Growth rates in mass (G, per day) of the three species were similar and inversely related to dry mass (DM, micrograms) following the power relationship G = 0.11 DM−0.28; neither water temperature nor seston abundance and quality varied sufficiently during the study period to have a significant influence on growth rates. The allometric model was used to estimate production of the three species, and the resulting estimates are compared with cohort methods and size–frequency estimates. Large larvae were responsible for most of the production, and most of the production occurred before the spring rise in water temperature. Measured growth rates in winter are significantly lower than those reported for simuliids in warmer waters. A reanalysis of published data shows that growth rates of simuliids increase as the square root of water temperature (T, degrees Celsius) (G = 0.08 DM−0.21 T0.48).
Dissolved Carbohydrate Distribution and Dynamics in Two Southeastern United States Reservoirs
Authors: Alberts James J. , Bowling John W. , Emmons Mark
Published: September 2009

Dissolved carbohydrate concentrations were measured in the waters of two southeastern United States reservoirs (Pond B and Par Pond) in 1982 and 1983 with attention to the influence of rooted aquatic macrophytes, spatial and temporal variability, and depth. Mean concentrations for all sampling locations were 2.86 ± 1.01 mg∙L−1 in Pond B and 1.72 ± 1.24 mg∙L−1 in Par Pond. There were no consistent spatial or temporal differences within a reservoir, nor were there consistent differences between macrophyte beds and open waters in either impoundment. Dissolved carbohydrate concentrations increased in both reservoirs during the day, reaching maxima in late afternoon, with an accompanying decrease in the dissolved organic carbon (DOC). The dissolved carbohydrates comprised 5.8–20.2% of the DOC in Par Pond and 25.7–42.3% of the DOC in Pond B. In both reservoirs, vertical profiles show the presence of carbohydrates at all depths during aerobic and anaerobic conditions. Midwater concentration maxima were present in Par Pond during periods of holomixis and stratification. The maxima were coincident with an intense pycnocline during periods of stratification; but during holomixis, the maximum was apparently unsupported by physical structure.
Bacterial Hydrolysis of Urea in the Tissues of Carcharhinid Sharks
Authors: Knight Ivor T. , Grimes D. Jay , Colwell Rita R.
Published: September 2009

Ureolytic activity was detected in liver homogenates of two carcharhinid shark species, Galeocerdo cuvieri and Negaprion brevirostris, employing 14C-labeled urea to monitor mineralization over 48 h. Significant (P < 0.05) urea hydrolysis was detected in liver homogenates within 48 h whereas no hydrolysis was detected in homogenates incubated with either ampicillin or the vibriostatic agent O/129, indicating bacterial mediation of the ureolytic activity. Urea hydrolysis could not be detected in blood samples. The autochthonous microflora of sharks has been found to contain ureolytic bacteria, and the present study supports the conclusion that they are present in organ tissues of healthy sharks but are not present in the blood.
Hydrographic Effects on the Vertical Distribution of Haddock (Melanogrammus aeglefinus) Eggs and Larvae on the Southwestern Scotian Shelf
Authors: Frank Kenneth T. , Page Fred H. , McRuer Jeff K.
Published: September 2009

Relationships between the density (sigma-t) structure of the water column and the depth distribution of haddock (Melanogrammus aeglefinus) eggs and larvae in May of 1985 and 1986 were investigated. During the early embryonic period the egg concentration decreased exponentially with depth; this contrasted sharply with stage IV eggs which showed a subsurface maximum, the location of which was determined by their specific gravity. Depth of the centre-of-mass (Zcrn) of stage IV eggs ranged from 13 to 47 m over the survey area whereas the sigma-t associated with the Zcm depth varied only slightly (CV = 0.4%) about a mean of 25.58. In stratified offshore waters, haddock eggs were aggregated at middepth but exhibited a progressively more uniform vertical distribution towards the weakly stratified nearshore. Where low-density water (sigma-t < 25.5) occurred near-shore eggs were concentrated at the deepest sampling stratum, suggesting that peak egg concentrations were below this level or possibly on the bottom. The depth distribution of haddock larvae was identical to that of late-stage eggs and was therefore established by buoyancy changes occurring during the embryonic period. Day and night Zcm was similar, averaging 28 and 31 m, respectively, and stability of the depth distribution of larvae appears to persist well into the juvenile period.
Spatial Comparison of Recent Growth in Postlarval Atlantic Cod (Gadus morhua) off Southwestern Nova Scotia: Inferior Growth in a Presumed Nursery Area
Authors: Suthers Iain M. , Frank Kenneth T. , Campana Steven E.
Published: September 2009

Spatial variation in distribution, age, and recent growth of postlarval cod (Gadus morhua) were examined off southwestern Nova Scotia during the early summer of 1985 and 1986. Ages ranged between 40–120 d posthatch throughout the sampling area, from the spawning grounds on Browns Bank, to nearshore (<55 m depth) and offshore regions 150 km north. The hatch-date distributions during 1986 between cruises 3 wk apart were significantly different in the nearshore, contrary to the age structure on the Bank which appeared more stable. These observations are consistent with retention of cod in the Browns Bank gyre, coupled with episodic leakage and northerly advection in the residual current. Recent growth determined from otolith increment widths was significantly less for those cod sampled at nearshore stations than for cod offshore and on the Bank. Recent growth was significantly correlated with Zooplankton biomass in a size range suitable for postlarval cod, while sea temperature was correlated in only one cruise. Nearshore areas had on average 25% of the Zooplankton biomass found on the Bank. Recent growth indices of the third and fourth week precapture were not significantly different between the nearshore and offshore, implying that the cod had shared a common environment, and common origin such as Browns Bank.
Demersal Fish Assemblages on the Scotian Shelf, Northwest Atlantic: Spatial Distribution and Persistence
Authors: Mahon Robin , Smith Robert W.
Published: September 2009

This study is based on 18 surveys, 12 in summer, and three each in spring and fall, with bottom trawls over the Scotian Shelf and Bay of Fundy. The data analysis sequence was: temporal and spatial aggregation of trawl sets; estimation of interspecies and intersite distance indices; clustering and ordination of sites and species, and discrimination of site groups using environmental variables. Nine species-groups, and 10 site-groups were defined, and displayed in a two-way table. Depth and temperature were the environmental variables most strongly associated with differences in assemblage structure among site-groups. Changes in assemblage structure from one area to another were distinct but apparently gradual, with no sharp assemblage boundaries. This pattern is expected if species are distributed independently on environmental gradients, rather than if assemblages consist of highly co-evolved, interdependent species. The observed spatial patterns were highly persistent through time. There are regions which are relatively homogeneous with regard to species composition and which can therefore be useful in dealing with bycatch problems. However, this study does not indicate the existence of discrete assemblages which might be appropriate as ecologically based fishery management units.
Performance of Domestic, Hybrid, and Wild Strains of Brook Trout, Salvelinus fontinalis, after Stocking: the Impact of Intra- and Interspecific Competition
Authors: Lachance Stephanie , Magnan Pierre
Published: September 2009

Wild and hybrid strains of brook trout, Salvelinus fontinalis, showed better rates of recovery (by angling) and yield (kilograms of fish recovered per kilogram planted) than a domestic strain, during the 2 yr following planting, in six small oligotrophic lakes of the Laurentian Shield. Native brook trout and white sucker, Catostomus commersoni, had a significant impact on planted brook trout. Recovery, percent of increment in weight and yield of each planted strain were inversely correlated with (1) the relative abundance of native brook trout, and (2) the occurrence of white sucker, supporting hypotheses of intra- and interspecific competition. Furthermore, the response variables were also inversely correlated with the number of potential competitors, indicating that the impact of native brook trout and white sucker was additive. The recovery in number of planted trout (both years and all strains) was approximately four times higher in lakes with effectively no competitors than in lakes containing both white sucker and native brook trout; the increase in weight was nearly three times higher, and the yield was more than nine times higher. The performances of planted fish were intermediate in the lake containing only native brook trout as competitor.
Measurement of Phosphorus Uptake Length in Streams: Comparison of Radiotracer and Stable PO4Releases
Authors: Mulholland Patrick J. , Steinman Alan D. , Elwood Jerry W.
Published: September 2009

Experimental releases of radiotracer and stable PO4were conducted on the same or consecutive days in a temperate first-order woodland stream to determine if both techniques resulted in similar measures of PO4uptake length (Sw). For each set of experiments, Swmeasured by radiotracer releases was substantially shorter than Swmeasured by stable PO4releases. For stable PO4releases, Swwas shorter for releases resulting in small increases in PO4concentration in water (7–12 μgP/L) than for releases resulting in larger increases in PO4concentration (84–163 μgP/L). Although the uptake rate of PO4increased with increasing [PO4] the increase in uptake rate was not sufficient to offset increases in downstream flux of PO4with stable PO4additions, thus resulting in longer Sw. A plot of PO4uptake rate against [PO4] suggested two uptake mechanisms: biologically controlled uptake at low [PO4] that appeared to become saturated at concentrations above approximately 5 μgP/L, and physical/chemical adsorption at high [PO4] that continued to increase with increasing concentration. Results indicate that stable PO4releases will overestimate ambient Swunless PO4increases are sufficiently small that they do not approach saturation of the biological community.
A Method for Forecasting the Timing of Ripeness in Pacific Herring (Clupea harengus pallasi) Females
Authors: Ware D. M. , Tanasichuk R. W.
Published: September 2009

A procedure was developed to forecast when Pacific herring females become ripe. The method uses a size-independent quantitative measure of maturity (D), which is the difference between the observed GSI (gonosomatic index) and the GSI expected at full maturity (Q) for a given body weight. We use D to segregate fish within samples, and then to split the samples into maturity groups. These groups often reflect discrete spawning waves. We regress mean D values for samples within a maturity group against date of collection to calculate when the observed GSI will equal Q, that is, when those females will be ripe. Analysis of data for 14 maturity groups indicates that the date of ripeness can be forecast with an average accuracy of 0.5 d, 5–6 d before it occurs. This procedure should be useful to fishery managers concerned with staging fisheries on mature fish and to investigators who need to know when a spawning stock reaches full maturity.
Influence of Four Species of Helminth Parasites on Orientation of Seaward Migrating Sockeye Salmon (Oncorhynchus nerka) Smolts
Authors: Garnick E. , Margolis L.
Published: September 2009

Each of four helminth parasite species, including the cestodes Eubothrium salvelini, Diphyllobothrium dendriticum, and Proteocephalus sp. and the nematode Philonema oncorhynchi, was found to influence the orientation of seaward-migrating sockeye salmon (Oncorhynchus nerka) smolts from the Great Central Lake area, Vancouver Island, British Columbia. Smolts placed in circular tanks were allowed to exit into evenly spaced bucket traps, and fish from five such runs were measured, sexed, and examined for the presence of parasites. Fish were categorized on the basis of infection status ("+" vs. "−") for each of the four parasite species found. The +/− groups did not differ for any of the parasite categories with respect to either bucket distributions or overall orientation directions. However, "−" groups did exhibit consistently greater departure from random distribution than their "+" counterparts. This finding suggests interference of parasites with smolt orientation, which could in turn have important implications for smolt survival. This finding also suggests that parasite infection may account to some extent for the considerable variability observed in the migratory behaviour of smolts.
Abundance of Oil Sardine (Sardinella longiceps) and Upwelling on the Southwest Coast of India
Authors: Longhurst Alan R. , Wooster Warren S.
Published: September 2009

The abundance of oil sardine (Sardinella longiceps) on the Malabar coast is highly variable on the decadal scale. During this century there have been several periods of relatively high abundance, and several major population crashes. O-group recruitment to the fishery begins towards the end of the summer monsoon, and its success is statistically related to sea level at Cochin just prior to onset of the monsoon. At this time, sea level indicates remote forcing of upwelling, rather than the wind-driven upwelling that occurs during the monsoon. Unusually early remote-forcing appears to inhibit subsequent recruitment, perhaps through exclusion of spawning fish from the neritic zone by oxygen-deficient upwelled water.
Effect of 6-, 12-, and 18-month Photoperiod Cycles on Smolting and Sexual Maturation in Juvenile Atlantic Salmon (Salmo salar)
Authors: Duston J. , Saunders R. L.
Published: September 2009

The results support the hypothesis that the commencement of smolting can occur during the decreasing phase of the annual photoperiod cycle, and sexual maturation during the increasing phase of the cycle, provided individuals have attained certain (unknown) growth thresholds. Thereafter the completion of smolting is entrained by the increasing phase of the photoperiod cycle, and sexual maturation by the decreasing phase. Three groups of Atlantic salmon (Salmo salar) were raised in freshwater for over 2 yr from the eyed egg stage under photoperiod cycles of either 6-, 12- (control), or 18-mo periodicity and an ambient 12-mo temperature cycle. Smolting was judged by changes in salinity tolerance and condition factor. All groups developed bimodal length–frequency distributions by December following hatch. Fish continued to be recruited into the upper modal group (UMG) beyond the shortest day of the photoperiod cycle, providing temperature was not limiting growth. The 6-, 12-, and 18-mo photoperiod cycles resulted in approximately 50, 60, and 100% of the populations being recruited into the UMG. Sexually mature male parr (1 + yr old) occurred only in the lower modal group of the 6- and 12-mo groups.
Genetic Control of Juvenile Life History Pattern in Chinook Salmon (Oncorhynchus tshawytscha)
Authors: Clarke W. Craig , Withler Ruth E. , Shelbourn John E.
Published: September 2009

To investigate the genetic basis for the difference in photoperiod responses between juvenile ocean-type and stream-type chinook salmon (Oncorhynchus tshawytscha), we conducted two crossing experiments and exposed the progeny to either a short- or long-day photoperiod for 10 wk from the time of first feeding. The first experiment examined the photoperiod response of pure and reciprocal crosses among red- and white-fleshed Quesnel River (stream-type) chinook salmon. The second experiment tested the photoperiod response of pure and reciprocal crosses between Quesnel River (stream-type) and Conuma River (ocean-type) chinook salmon. In both experiments, Quesnel chinook salmon fry (both red and white fleshed) sustained a high growth rate and developed a high degree of seawater adaptability only when exposed first to a short-day photoperiod for 10 wk and then to a long-day photoperiod. In contrast, the Conuma River chinook salmon grew rapidly and developed the increased seawater adaptability characteristic of smolts when reared on either photoperiod regime. Reciprocal Conuma–Quesnel hybrids displayed the ocean-type pattern of development, indicating that the photoperiod-independent phenotype is dominant and not under maternal control.
Deepwater Migrations of Chum Salmon (Oncorhynchus keta) along the Pacific Coast of Northern Japan
Authors: Ueno Yasuhiro
Published: September 2009

Mature chum salmon (Oncorhynchus keta) were caught in bottom trawls off lwate Prefecture, northern Japan, in autumn. To document the incidence and depth distribution of these catches, records were kept of salmon caught by five trawlers that fished along the Pacific coast of northern Honshu during September–December 1986. During this period, 4337 chum salmon were caught at bottom depths ranging from 150 to 460 m with most taken from 200 to 350 m. Gonads and stomach contents were examined for 100 of these salmon. All were mature and close to spawning. Thirty-nine of the 100 stomachs examined were empty and the remaining 61 contained only a small quantity of food, averaging 2.4 g. Chum salmon may move at these depths to avoid the high temperatures of surface waters (12–20 °C) found in this area and to follow temperatures close to their thermal preferendum (3–11 °C) which are found near bottom. This phenomenon appears to be an adaptation of chum salmon near the southern limit of their range.
Role of Predatory Fish in Community Dynamics of an Ephemeral Stream
Authors: Holomuzki Joseph R. , Stevenson R. Jan
Published: September 2009

In enclosed runs in a third-order ephemeral stream in west-central Kentucky, the effects of predatory sunfish (Lepomis) on benthic macroinvertebrates, benthic algae, and detritivory were compared (1) before stream intermittence, (2) after stream intermittence when transport was restricted, and (3) between substrata offering differential cover from fish predation. Ambient fish densities had little effect on total macrobenthic densities and processes on lower trophic levels before intermittence. Fish modestly affected macroinvertebrate densities after intermittence, when surface exchange of prey was interrupted by sections of dry stream. Among substrata, fish influenced macroinvertebrates on bedrock, but not on stony, coarse substrata. Densities of two taxa were significantly affected by fish, and this significantly altered the relative abundance of functional feeding groups in enclosures on bedrock by increasing the proportion of invertebrate predators in fish treatments. Macroinvertebrate densities in microhabitats on both substrata were not affected by fish presence. Dense growths of the stalked diatom Cymbella generally covered microhabitats and added structural complexity, particularly to bedrock surfaces. Unobstructed, natural migration of prey in the large (40 m2) fencelike enclosures (versus containers), ample refuge space, and low natural densities of fish were important in minimizing fish effects in enclosures.
Response of Amphipoda and Trichoptera to Lake Fertilization in the Canadian Arctic
Authors: Jorgenson John K. , Welch Harold E. , Curtis Martin F.
Published: September 2009

Small oligotrophic lakes at Saqvaqjuac, Northwest Territories, were fertilized with phosphorus and nitrogen after 2 yr of study and the response of macroinvertebrates to increased primary production was followed for 3 yr. The amphipod Gammarus lacustris lacustris (G. O. Sars) had a 2-yr life cycle, with three cohorts present in August. Biomass under natural conditions was approximately 0.1–0.2 g dry wt∙m−2. Gammarus responded immediately to a doubling of phytoplankton production with increased survival of young-of-year. Gammarus biomass increased steadily to 0.9 g dry wt∙m−2 and had not stabilized after 3 yr of fertilization. Trichoptera were represented by three species, with Grensia praeterita composing the bulk of the biomass, followed by Apatania zonella and an uncommon Hesperophylax species. Trichoptera biomass ranged from 0.04 to 0.3 g dry wt∙m−2 before fertilization. Response to increased primary production was slow, beginning in year 2 of fertilization. Trichoptera biomass had doubled by the third year of fertilization but was probably several years from equilibrium. Application of benthos models, in addition to the data, suggested that the production to biomass ratio was between 1 and 2, averaging 1.5.
Effect of Short-Duration Seawater Exposure on Plasma Ion Concentrations and Swimming Performance in Coho Salmon (Oncorhynchus kisutch) Parr
Authors: Brauner C. J. , Shrimpton J. M. , Randall D. J.
Published: September 2009

The effect of seawater (sw) on plasma ion concentrations and critical swimming velocity (Ucrit) was investigated in hatchery-reared coho salmon (Oncorhynchus kisutch) parr exposed to one of four treatments: 24 h of seawater exposure (SW1), 5–7 d of seawater (SW5), 24 h in seawater followed by 24 h in fresh water (SW-FW), and a freshwater control (FWC). Only the SW1 fish demonstrated a reduced Ucritand, at rest, elevated plasma [Na+], [Cl−], and [SO42−]. With exercise, SW1 fish were characterized by an increase in plasma ion concentrations and a decrease in both hematocrit (Hct) and muscle moisture content. There is a strong relationship between plasma [Na+] at rest and Ucrit, where an optimal swimming velocity is obtained in animals with resting levels of approximately 147 mEq∙L−1. Traditionally, the 24-h seawater challenge is used to test the hypoosmoregulatory ability in smolting salmonids, however, our data suggest that it may also predict the aerobic swimming potential of salmonids following seawater transfer. We suggest that the reduction in Hct and increase in plasma [Na+] result in reduced oxygen delivery to the muscle and that decrease in muscle moisture content impairs the contractile process.
Influence of Fat Content on Uptake and Depuration of the Off-flavor 2-Methylisoborneol by Channel Catfish (Ictalurus punctatus)
Authors: Johnsen Peter B. , Lloyd Steven W.
Published: September 2009

Channel catfish (Ictalurus punctatus) of different tissue fat contents (0.5–11.0%) were held in water containing approximately 0.5 μg/L of the off-flavor compound 2-methylisoborneol (MIB) for various times. A new analytical method was developed to quantify tissue burdens of MIB. Fish showed significant bioconcentration of MIB after 2 h and equilibrium by 24 h. The fatter fish (> 2.5% muscle fat) accumulated nearly three times more MIB than lean fish (< 2%). Purging fish in MIB-free water indicated that leaner fish depurate faster (8 h) than fatter fish (48 h). Fat content had more influence in determining the time for return to acceptable flavor than initial MIB concentration. Managing catfish production to harvest leaner fish could minimize the impact of off-flavor on fish producers.
MULTIDIMENSIONAL INDEPENDENT COMPONENT ANALYSIS FOR STATISTICAL ESTIMATIONS OF INDETERMINACIES IN ELECTROCARDIOGRAMS
Authors: CHAWLA M. P. S.
Published: September 2009

Independent component analysis (ICA) is a technique capable of separating independent components (ICs) from complex electrocardiogram (ECG) signals. The basic intention behind using multidimensional independent component analysis (MICA) is to find stable higher dimensional source signal subspaces. This study highlights the ability of ICA for parametrization of ECG signals to reduce the amount of redundant ECG data if any in a data set.

The aim of this paper is to justify the underlying theory of the use of ICA and how it can be extended to for MICA separation of the ECG signals for combinational leads to attain most useful diagnostic information, which was not discussed in other some similar previous publications in this field.

It is also investigated that the value of kurtosis coefficients for the ICs, which represents the noise component, can be further reduced using parametrized multidimensional independent component analysis (PMICA) technique. The indeterminacies available in the ECG data are also analyzed using modified version of Jade algorithm for PMICA and parametrized standard independent component analysis (PSICA). For the ECG data set, Jade algorithm is applied first to find smaller subspaces for MICA analysis and can therefore be regarded as a basis algorithm for PMICA analysis. The simulation results are obtained in Matlab environment to indicate that, ICA can definitely improve signal–noise ratio (SNR) in minimizing the reconstruction errors.

The future scope of MICA expected by author is that, by reconsidering the notion of ICA, a more general perspective can be envisioned: i.e. modified multidimensional independent component analysis (MMICA). It would be based on a morphological geometric parametrization (MGP) which would further reduce the indeterminacies involved in matrix-based modeling (MBM).