Testate amoebae in late quaternary sediments of the Cape Mamontov Klyk (Yakutia)

The results of the analysis of Rhizopoda from permafrost sediments of the cryolithozone of northeastern Siberia are presented. Testate amoeba communities (Rhizopoda: Testaceafilosea, Testacealobosea) of the late Pleistocene and Holocene and modern habitats of the Cape Mamontov Klyk (the Laptev Sea coast in the vicinity of the Lena River estuary) have been researched. The paleocommunity structure was examined; assessment of rhizopod diversity in sediments of different (fluvial, alluvial, ice complex, alas, and alluvial-dealluvial) geneses was conducted.     

Fourier shape analysis of Globorotalia truncatulinoides from late Quaternary sediments in the southern Indian Ocean

Fourier shape analysis has been used to determine the morphological variation within the planktonic foraminifera,Globorotalia truncatulinoides from the southern Indian Ocean. Measured specimens are from 20 Recent core top samples distributed from 22°S (central gyre water mass) to 47°S (subantarctic water mass). Fourier analysis determined that the two most significant components of shape within this species are elongateness and conicalness which are characterized by harmonics 2 and 3, respectively. Mean harmonic 2 values are significantly correlated with the percentage of sinistral coiled individuals in each sample (r = +0.91). Mean values for harmonic 3 have a correlation coefficient with water temperature and salinity at 200 m of r = +0.85 and +0.88. Specimens become less elongate and more conical in a traverse from south to north.Fourier shape analysis of planktonic foraminifera was then shown to be useful in investigations of late Quaternary paleoceanographic problems. Four piston cores were examined from the southern Indian Ocean. Total faunal and oxygen isotope analyses provided the stratigraphic framework. The results indicated that the central gyre water mass remained relatively stable during glacial stages. The region of the Subtropical Convergence was strongly affected, however, by the northward migration of the Polar Front.     

The occurrence and fission-track ages of late neogene and quaternary volcanic sediments,Siwalik group,Northern Pakistan

Volcanic sediments, now mostly bentonites and bentonitic mudstones, occur throughout the Late Neogene and Quaternary Siwalik Group of northern Pakistan. A number of these deposits have been dated by the fission-track method, utilizing zircon phenocrysts from these deposits, and provide the chronometric constraints upon which a paleomagnetic stratigraphy is developed for the Siwalik Group. Notable in the occurrence of these altered tuff horizons is an apparent mode in their stratigraphic development from approximately 3.0 to 1.5 m.y. B.P. which coincides with the period of activity of the Dacht-e-Nawar volcanic complex of east-central Afghanistan. Fission-track ages of certain tuffs for critical areas of northern Pakistan are reported herein.     

Halophila ovalis in the Tropical Atlantic Ocean

A species of seagrass in the genus Halophila was found growing in a shallow lagoon on the west shore of Antigua in the Caribbean West Indies. Genetic analysis showed the plants were Halophila ovalis. In addition, the samples had no genetic deviation (using nrDNA sequences) from Halophila johnsonii, considered to be an endemic and endangered species in Florida, USA. Morphological analysis demonstrated the Antiguan Halophila to be well within the range of plant characteristics previously described in the literature for H. ovalis, except for leaf width and number of seeds per fruit, and again, not different from H. johnsonii and very closely related to H. ovalis from the Indo-Pacific. Ours is the first report of H. ovalis in the Tropical Atlantic bioregion.     

Cross-sectional analysis of late HAART initiation in Latin America and the Caribbean: late testers and late presenters

Background

Starting HAART in a very advanced stage of disease is assumed to be the most prevalent form of initiation in HIV-infected subjects in developing countries. Data from Latin America and the Caribbean is still lacking. Our main objective was to determine the frequency, risk factors and trends in time for being late HAART initiator (LHI) in this region.

Methodology

Cross-sectional analysis from 9817 HIV-infected treatment-naïve patients initiating HAART at 6 sites (Argentina, Chile, Haiti, Honduras, Peru and Mexico) from October 1999 to July 2010. LHI had CD4⁺ count ≤200cells/mm³ prior to HAART. Late testers (LT) were those LHI who initiated HAART within 6 months of HIV diagnosis. Late presenters (LP) initiated after 6 months of diagnosis. Prevalence, risk factors and trends over time were analyzed.

Principal Findings

Among subjects starting HAART (n = 9817) who had baseline CD4⁺ available (n = 8515), 76% were LHI: Argentina (56%[95%CI:52–59]), Chile (80%[95%CI:77–82]), Haiti (76%[95%CI:74–77]), Honduras (91%[95%CI:87–94]), Mexico (79%[95%CI:75–83]), Peru (86%[95%CI:84–88]). The proportion of LHI statistically changed over time (except in Honduras) (p≤0.02; Honduras p = 0.7), with a tendency towards lower rates in recent years. Males had increased risk of LHI in Chile, Haiti, Peru, and in the combined site analyses (CSA). Older patients were more likely LHI in Argentina and Peru (OR 1.21 per +10-year of age, 95%CI:1.02–1.45; OR 1.20, 95%CI:1.02–1.43; respectively), but not in CSA (OR 1.07, 95%CI:0.94–1.21). Higher education was associated with decreased risk for LHI in Chile (OR 0.92 per +1-year of education, 95%CI:0.87–0.98) (similar trends in Mexico, Peru, and CSA). LHI with date of HIV-diagnosis available, 55% were LT and 45% LP.

Conclusion

LHI was highly prevalent in CCASAnet sites, mostly due to LT; the main risk factors associated were being male and older age. Earlier HIV-diagnosis and earlier treatment initiation are needed to maximize benefits from HAART in the region.     

The burrowing crab Neohelice granulata affects the root strategies of the cordgrass Spartina densiflora in SW Atlantic salt marshes

Salt marshes are among the most productive systems of the world, with plant primary production limited by soil oxygen deficiency and nutrient availability. Nevertheless, root adaptations to anoxia and nutrient acquisition are different and often incompatible. The SW Atlantic salt marshes are characterized by high densities of the deep (up to 1 m) burrowing crab Neohelice granulata (Dana, 1851) that may change soil physical and chemical characteristics by burrow construction. In this work, we experimentally evaluated the hypothesis that crab burrowing can enhance soil oxygenation, causing changes in Spartina densiflora Brongniart below ground tissues from structures adapted to anoxia to systems adapted for nutrient acquisition. This response, in turn, would enhance plant productivity. Results from field observations show that oxygen availability is higher in zones with high burrow densities. As burrow densities increased, the plant root distribution changed from shallow (associated to low oxygen availability) to deeper and vertically homogeneous, with a positive correlation between burrow density and plant aboveground biomass. Experimental exclusion of crabs shows that they induce changes of root strategies from anoxia toleration to nutrient efficient acquisition, with increasing plant productivity. The invasive success that this plant shows in other parts of the world is likely to be due to their ability to tolerate harsh environmental conditions. Our results suggest that the morphological plasticity of S. densiflora is also important in their native zone given the characteristics of their specific habitat.     

The role of copper and quaternary structure on the conformational properties of Octopus vulgaris hemocyanin

Some structural properties of Octopus vulgaris hemocyanin have been investigated by fluorescence spectroscopy. The three-dimensional structure of Octopus hemocyanin is remarkably tight, resulting in a deep burial of almost all the tryptophyl residues of the protein. The hemocyanin conformation has been studied in the two main aggregation states (11 S, 50 S) of the protein, and with respect to the presence or absence of copper in the active site. Upon changing the pH of the solution, Octopus hemocyanin in the 50 S aggregation state can assume at least three different conformations. During the transition between each conformation the fluorescence quantum yield changes, but the environment of tryptophans does not change. Dissociation of the protein from 50 S to 11 S strongly enhances its susceptibility toward denaturating agents such as pH or temperature, and modifies the effects of fluorescence quenchers such as acrylamide. Moreover, these effects are more pronounced when copper is removed from the active site. A comparative analysis of the results shows that the subunit-subunit interactions exerted within the 50 S species are more important in the maintenance of the conformational stability than the copper ions present in the active sites. This behavior can be accounted for by the large amount of Ca(II) ions linked to 50 S hemocyanin.     

Experimental analysis of monogamy in the Caribbean cleaner goby, Gobiosoma evelynae

To investigate factors promoting monogamy, we studied the reproductive behaviour and ecology of the monogamous Caribbean cleaner goby at two sites near St Croix, U.S. Virgin Islands. We assessed mate fidelity and the amount of time required to acquire a new mate in experimentally widowed males and females. We also measured behavioural responses of pair members and single females to experimentally introduced conspecific intruders of both sexes. Finally, we evaluated the distribution of suitable habitat relative to existing goby territories. We found that pairs often separated due to males abandoning females and moving to a new territory, that most widowed fish soon acquired a new mate, and that there was strong aggression towards large same-sex intruders. We also found an abundance of suitable, unoccupied habitat. We conclude that pairs are maintained by intrasexual aggression that is related to both mate availability and other resources, such as high-quality, food-rich cleaning stations. Combined with observations of frequent pair separation, interterritory male movement, and relatively rapid remating by both sexes, these results suggest a complex mating system that is best classified as serial monogamy. Copyright 2003 Published by Elsevier Science Ltd on behalf of The Association for the Study of Animal Behaviour.      

The SW Atlantic burrowing crab Chasmagnathus granulatus Dana affects the distribution and survival of the fiddler crab Uca uruguayensis Nobili

In this paper, we address the question of whether the presence of the burrowing crab Chasmagnathus granulatus affects the habitat use of the fiddler crab Uca uruguayensis. Field samples showed that the species have a disjoint spatial distribution. Male fiddler crab density decreased in zones with C. granulatus, however, female density increased. Male fiddler crabs avoided feeding on sediment affected by C. granulatus and were more preyed. Predation was higher during the fiddler crab reproductive season and, probably due to predation risk, males showed lower reproductive display in shared zones. Field experiments shows that when C. granulatus were excluded, densities of U. uruguayensis increased mainly due to an increase in density of males. Habitat differentiation of these species may be because C. granulatus affects U. uruguayensis in several ways, including direct predation, disturbance and behavioural changes associated to predation risk. Males and females are affected differentially probably because of the extreme sexual dimorphism of this crab species. Coloration on enlarged claw and waving activities are all factors that increase predation risk for male and the presence of only one feeding claw may increase sediment-mediated effects.     

The quaternary structure of a unique phycobiliprotein: B-phycoerythrin from Porphyridium cruentum

B-phycoerythrin, from the unicellular red alga Porphyridium cruentum, was crystallized in the rhombohedral space group R3 with a=111.0Å and α=116.8° or A=B=189.1Å and C=60.1Å and γ=120°. Density measurements on the crystals indicate that the hexagonal unit cell can acconmodate three cylindrical molecules, 109Å in diameter and 60Å in height, each of approximately 275,000 daltons. The crystallographic symmetry of the unit cell requires at least 3-fold symmetry for the particle. However, the particle stoichiometry has been reported as (αβ)₆γ and this composition is also supported by SDS gel electrophoresis on the crystalline protein. These results are discussed in light of preliminary model calculations on the quaternary structure of B-phycoerythrin.     

Density of Monoporeia affinis and biogeochemistry in Baltic Sea sediments

This study focused on effects from Monoporeia affinis reworking and ventilation activities on benthic fluxes and mineralization processes during a simulated bloom event. The importance of M. affinis density for benthic solute (O₂, ΣNO₂⁻ + NO₃⁻, NH₄⁺ and HPO₄²⁻) fluxes and sediment reactivity (mobilization of NH₄⁺ and HPO₄²⁻) following additions of organic material to the sediment surface was experimentally investigated using sediment-water and closed sediment (jar) incubations. Three different densities of M. affinis were used to resemble a low, medium and high density situation (1300, 2500 and 6400 ind. m^− 2, respectively) of a natural amphipod community. The degradation of phytodetritus (Tetraselmis sp., 5 g C m^− 2) added to the sediment surface was followed over a period of 20 days. Benthic solute fluxes of O₂, ΣNO₂⁻ + NO₃⁻ and NH₄⁺ were generally progressively stimulated with increasing number of M. affinis, while no such correlation was found for HPO₄²⁻. Solute fluxes were initially enhanced 1 to 2 days after the addition of phytodetritius, caused by mineralization of the most labile organic material and a food-stimulated irrigation by the amphipods. There was no effect from the activity of M. affinis on total denitrification (Dtot = Dn + Dw) or denitrification utilizing nitrate from coupled nitrification/denitrification (Dn) for any of the densities examined. Denitrification utilizing overlying water nitrate (Dw) was only about 10% of Dtot. Dw was significantly enhanced for the highest M. affinis density investigated. The reactivity of the sediment decreased progressively with increasing density of M. affinis and with time of the experiment. However, enhanced ammonium production at least 6 days after the organic addition indicated excretion of N-containing organic compounds by M. affinis. In conclusion, large spatial and temporal variations in density of M. affinis may be of significant importance for benthic solute fluxes and overall mineralization of organic material in Baltic Sea sediments.     

Nypa megafossils from the Tertiary sediments of Northeast India

Nypa megafossils dominated by fruits are described from Oligocene and Lower Miocene sediments of Assam and Mizoram, respectively. The origin, past distribution and migration of Nypa are discussed in the light of recent findings. This study indicates that India might be the place of its origin. Its presence, along with some other coastal elements, reinforces the concept that the Bay of Bengal was extending considerably northward during these epochs than its present day boundary.     

Occurrence of Apicomplexa-like structures in the digestive gland of Strombus gigas throughout the Caribbean

The queen conch, Strombus gigas, is a marine resource of ecological and economical importance in the Caribbean region. Given its importance in this region, and the critical status of most populations, the reproductive biology of this species has been studied to support management decisions. It was from these studies that a generalized sporozoan infection was detected. This study describes the geographic distribution of a coccidian (Apicomplexa) parasite infecting the digestive gland of S. gigas throughout the Caribbean. The parasite was present in every location sampled. Based on histological analysis, the parasites from all locations are similar and appear to complete their life cycle within the digestive gland. The highest occurrence of the parasites was registered in samples from Puerto Rico (54 parasites per field) and Martinique (45 parasites per field). The lowest incidence was registered on the Mexican coast of Yucatan peninsula, at Alacranes and Chinchorro with 17 parasites per field. Data showed significant differences among sites (Kruskal Wallis H = 106.957; p ? 0.05). The abundance of parasites found in the digestive ducts and in the faeces suggests the liberation of parasites to the environment. A gradual decrease in abundance was found from East to West of the Caribbean sea.     

Hystrichokolpoma from pleistocene sediments in Okinawa-Jima,Japan

Three species of Hystrichokolpoma (Dinophyceae) are described from lower Pleistocene sediments of Okinawa-jima in the Ryukyu-Islands, Southwest Japan. Hystrichokolpoma pacifica and H. okinawaia are new. H. pacifica is characterized by subconical to short cylindrical, large processes with rectangular or pentagonal bases, and H wokinawaia by short cylindrical to tubiform, large processes with denticulate to foliate distal extremities. The paratabulation of Hystrichokolpoma is discussed.     

Sulphate reduction in oxic and sub-oxic North-East Atlantic sediments

Abstract Oxic and sub-oxic N.-E. Atlantic sediments were examined for sulphate-reducing activity. Oxygen and/or nitrate reduction are probably the dominant mineralisation processes in the abyssal plain sediment studied. A low rate of sulphate reduction (0.1 nmol SO²⁻₄/ml/day) was recorded in the surface 5 cm of the continental slope sediment, together with the presence of a range of sulphate-reducing bacteria (SRB). A higher activity of sulphate reduction (2.2 nmol SO²⁻₄/ml/day) occurred in the continental shelf sediment which led to a small decrease in pore water sulphate and an increase in titration alkalinity. This sediment contained approx. 10²–10³ acetate, lactate and propionate oxidising SRB/ml. No low- M _r organic acids were detected in these sediments. However, amendment with 75 μM acetate stimulated sulphate-reducing activity in the shelf sediment.     

Growth and quaternary alkaloid production in differentiating and non-differentiating strains of Ruta graveolens

Cultures of Ruta graveolens have been grown and maintained on Murashige and Skoog's medium supplemented with α-naphthalene acetic acid (1 mg/l.) and kinetin (0.1 mg/l.) or 2,4-dichlorophenoxyacetic acid (1 mg/l.), and glucose (30 g/l.). The production of dihydrofuroquinoline alkaloids has been investigated in these cultures. The present study showed that: (a) cultures of Ruta produced both differentiating and non-differentiating strains; (b) quaternary alkaloids (platydesminium, ribalinium and rutalinium) were present in all the strains and maximum contents were detected at 3-4 weeks growth; (c) high platydesminium and rutalinium content was associated with differentiation and callus formation, respectively; (d) changed concentrations of quaternary alkaloids were recorded in all the five strains grown on media supplemented with tryptophan and precursors (anthranilic acid, 5-methylanthranilic acid and 2,4-dihydroxyquinoline).     

Altitudinal variation in the late quaternary vegetational history of Northwest Greece

The palaeoecological sites of Gramousti lake and Rezina marsh, northwest Greece, although only 20 kin apart are at contrasting altitudes of 285 m a.s.1. and 1800 m a.s.1. Altitudinal difference between the two sites is shown to have a significant effect upon the postglacial vegetational history of the region. Rezina marsh is the highest and smallest site to be studied thus far in Greece and provides some of the first evidence for the location of cold‐stage temperate tree refugia. Migration of tree populations is shown to play an insignificant part in the vegetational development of the mountain region, demonstrating the importance of other factors (internal and external) in the diversity of the postglacial woodland.     

pH-induced quaternary assembly of Vitreoscilla hemoglobin: The monomer exhibits better peroxidase activity

pH-dependent (pH 6.0–8.0) quaternary structural changes of ferric Vitreoscilla hemoglobin (VHb) have been investigated using dynamic light scattering. The VHb exhibits a monomeric state under neutral conditions at pH 7.0, while the protein forms distinct homodimeric species at pH 6.0 and 8.0, respectively. The dissociation constant obtained using the Bio-Layer Interferometry technology indicates that, at pH 7.0, the monomer–monomer dissociation of VHb is about 6-fold or 5-fold higher (K_D = 6.34 μM) compared with that at slightly acidic pH (K_D = 1.05 μM) or slightly alkaline pH (K_D = 1.22 μM). The pH-dependent absorption spectra demonstrate that the heme microenvironment of VHb is sensitive to the changes of pH value. The maximum absorption band of heme group of VHb shifts from 402 nm to 407 nm when pH changes from 6.0 to 8.0. In addition, the fluorescence emission spectra of VHb, taken at excitation wavelength of 295 nm, suggest that the single Trp122 fluorescence quantum yields in VHb are decreased due to the formation of the homodimeric species. However, the circular dichroism spectra data display that the secondary structures of VHb are little affected by pH transitions. The pH-dependent peroxidase activity of VHb was also investigated in this study. The optimum pH for VHb using 2,2′-azino-bis-(3-ethylbenzothiazoline-6-sulfonic acid) as substrate is 7.0, which implies that the monomer state of VHb would exhibit better peroxidase activity than the homodimeric species of VHb at pH 6.0 and 8.0.     

Hyphomonas atlanticus sp. nov., isolated from the Atlantic Ocean and emended description of the genus Hyphomonas

A taxonomic study was carried out on strains 22II1-22F38^T and 22II-S13e, which were isolated from sea water and sediment from the Atlantic Ocean, respectively. The two strains were Gram-negative, oxidase and catalase positive, oval to pear shaped, and motile by a single polar flagellum. Phylogenetic analysis based on 16S rRNA gene sequences indicated that both strains belonged to the genus Hyphomonas, with highest sequence similarity (98.2%) to the type strains H. jannaschiana DSM 5153^T and H. johnsonii ATCC 43964^T. The genomic ANIm values and DNA-DNA hybridization estimate values between strain 22II1-22F38^T and seven type strains ranged from 82.84% to 84.10% and from 18.0% to 19.1%, respectively. Isolate 22II1-22F38^T had a G + C content of 58.3% and used Q-11 as the predominant respiratory quinone. The combined phenotypic and genotypic data showed that both strains represented a novel species of the genus Hyphomonas, for which the name Hyphomonas atlanticus sp. nov. is proposed, with the type strain being 22II1-22F38^T (=LMG 27916^T = MCCC 1A09418^T). In addition, we conclude that Hyphomonas hirschiana is a later synonym of Hyphomonas neptunium.