Distribution of live benthic Foraminifera at three oceanographically dissimilar sites in the northeast Atlantic: preliminary results

Live (i.e. rose Bengal stained) benthic foraminiferal assemblages in the 0–1 cm layer of multiple core samples were examined at three contrasting sites in the northeast Atlantic as part of the Natural Environment Research Council Deep Ocean Benthic Boundary Layer (BENBO) Thematic Programme. Sites A (3600 m water depth) and C (1900 m) were located in the Rockall Trough while Site B (1100 m) was in the Hatton–Rockall Basin. Wet-sorting sediment residues (>125 m fraction) revealed more abundant (98–190 individuals/10 cm²) and diverse (71–99 species /27 cm²) assemblages than found previously in studies employing dry-sorting techniques. At all three sites, the assemblages were numerically dominated by delicate soft-bodied and agglutinated species, most of which are undescribed. Calcareous taxa formed a relatively small proportion of the assemblages (23% of individuals at Site B, 13% at Site C and 7% at Site A). Conversely, the agglutinated hormosinaceans (mainly Reophax species) became more prominent with increasing depth and accounted for 8% of the assemblage at Site B, 33% at Site C and 51% at Site A. Foraminifera represented 67–81% of the fauna in the samples and greatly outnumbered the metazoans. The assemblage at Site A has similarities with abyssal assemblages, while those at Sites B and C contain characteristic bathyal species. At Site B, Uvigerina peregrina and Melonis barleeanum are abundant, suggesting that there are high organic carbon inputs at this site. Reduced species diversity was observed at Site A following the spring phytodetritus bloom due to the presence of large numbers of juvenile Hoeglundina elegans, although it is not clear whether this species is responding to phytodetritus inputs.     

OBSERVATIONS ON THE ECOLOGY OF BULINUS (PHYSOPSIS) GLOBOSUS (MORELET), B. (BULINUS) FORSKALII (EHRENBERG) AND LYMNAEA NATALENSIS (KRAUSS) IN RICE SWAMPS IN SIERRA LEONE.

Changes in population of Bulinus globosus, B. forskalii andLymnaea natalensis were studied in four different locationsnamed Sites A, B, C. and D in Bo town Sierra Leone. The snailpopulations and oxygen concentrations of water increased inthe rainy season. The biological oxygen demand did not havesignificant correlation with changes in snail populations inSites B and D. B. globosus was absent from Site A while B. forskaliiwas the predominant snail in Site C. Site D with the highestmean monthly conductivity of 176 µmhos contained 54% whileSite A with a similar reading of 90µmhos contained 1%of all snails found. (Received 22 May 1980;     

Cytochalasin B binding proteins in human erythrocyte membranes. Modulation of glucose sensitivity by site interaction and partial solubilization of binding activities

We have previously described three different cytochalasin B binding sites in human erythrocyte membranes, a D-glucose-sensitive site (Site I), a cytochalasin E-sensitive site (Site II), and a site (Site III) insensitive to both D-glucose and cytochalasin E. Ligand bindings to each of these sites were considered to be independent (Jung, C., and Rampal, A. (1977) J. Biol. Chem. 252, 5456-5463). However, we have obtained subsequently the following evidence which indicated that an interaction occurs between Sites II and III, and this modulates sensitivity of Site III to the sugar. The displacement of cytochalasin E greatly exceeds the sum of their independent displacements. This ghosts extracted with EDTA or 2,3-dimethylmaleic anhydride at low ionic strength lack Site II activity but retain Site I and III activities, and both of these activities are displaceable by D-glucose alone. This indicated that the removal of Site II from the membrane confers glucose sensitivity to Site III. These observations are consistent with a model that Sites II and III in the membrane exist in a close association through which unliganded Site II maintains the glucose insensitivity of Site III, and once site II is liganded or removed by extraction this association is disrupted and Site III becomes glucose-sensitive. The ghosts extracted with Triton X-100 retain a cytochalasin B binding activity similar to that of site II (Kd = 1.8 X 10(-7) M, cytochalasin E-sensitive, glucose-insensitive), whereas a binding activity similar to that of Site I (Kd = 4 X 10(-7) M, cytochalasin E-insensitive, glucose-sensitive) is recovered in the Triton extract. A cytochalasin B binding activity similar to that of Site II is solubilized by EDTA at low ionic strength.     

Book Notes

The Systems of Land Tenure in the Kikuyu Land Unit . H. E. L ambert
Hawaiian Antiquities (Moolelo Hawaii ). D avid M alo
Navaho Means People . L eonard M c C ombe , E von Z. V ogt , and C lyde K luckhohn
Paradox and Nirvana . R obert L awson S later
The North American Buffalo. A Critical Study of the Species in Its Wild State . F rank G ilbert R oe
The Wulfing Plates: Products of Prehistoric Americans . V irginia D rew W atson
The Medora Site. West Baton Rouge Parish, Louisiana . G eorge I. Q uimby
The Crable Site, Fulton County, Illinois. A Late Prehistoric Site in the Central Illinois Valley . H ale G illiam S mith
Archaeology of the Columbia-Fraser Region . M arian W. S mith
Cattle Point: A Stratified Site in the Southern Northwest Coast Region . A rden R. K ing
Hyperbrachycephaly as Influenced by Cultural Conditioning . J. F ranklin E wing
Surgery of the Shoulder . A. F. D e P alma
The Mark of Oppression, A Psychological Study of the American Negro . A bram K ardiner and L ionel O vesey
Race Relations: The Interaction of Ethnic Groups . B rewton B erry
The Sociology of Georg Simmel . Translated, edited, and with an introduction by K urt H. W olff
Social Behavior and Personality: Contributions of W. I. Thomas to Theory and Social Research . Edited by E dmund H. V olkart
Handbook of Latin American Studies : 1948, No. 14. F rancisco A guilera , ed
Area Studies in American Universities . W endell C. B ennett     

P-Bodies and Stress Granules: Possible Roles in the Control of Translation and mRNA Degradation

The control of translation and mRNA degradation is important in the regulation of eukaryotic gene expression. In general, translation and steps in the major pathway of mRNA decay are in competition with each other. mRNAs that are not engaged in translation can aggregate into cytoplasmic mRNP granules referred to as processing bodies (P-bodies) and stress granules, which are related to mRNP particles that control translation in early development and neurons. Analyses of P-bodies and stress granules suggest a dynamic process, referred to as the mRNA Cycle, wherein mRNPs can move between polysomes, P-bodies and stress granules although the functional roles of mRNP assembly into higher order structures remain poorly understood. In this article, we review what is known about the coupling of translation and mRNA degradation, the properties of P-bodies and stress granules, and how assembly of mRNPs into larger structures might influence cellular function.The translation and decay of mRNAs play key roles in the control of eukaryotic gene expression. The determination of eukaryotic mRNA decay pathways has allowed insight into how translation and mRNA degradation are coupled. Degradation of eukaryotic mRNAs is generally initiated by shortening of the 3′ poly (A) tail (Fig. 1A) (reviewed in Parker and Song 2004; Garneau et al. 2007) by the major mRNA deadenylase, the Ccr4/Pop2/Not complex (Daugeron et al. 2001; Tucker et al. 2001; Thore et al. 2003). Following deadenylation, mRNAs can be degraded 3′ to 5′ by the exosome (Anderson and Parker 1998; Wang and Kiledjian 2001). However, more commonly, mRNAs are decapped by the Dcp1/Dcp2 decapping enzyme and then degraded 5′ to 3′ by the exonuclease, Xrn1 (Decker and Parker 1993; Hsu and Stevens 1993; Muhlrad et al. 1994, 1995; Dunckley and Parker 1999; van Dijk et al. 2002; Steiger et al. 2003). In metazoans, a second decapping enzyme, Nudt16, also contributes to mRNA turnover (Song et al. 2010).Open in a separate windowFigure 1.Eukaryotic mRNA decay pathways. (A) General mRNA decay pathways. (B) Specialized decay pathways that degrade translationally aberrant mRNAs.The processes of mRNA decay and translation are interconnected in eukaryotic cells in many ways. For example, quality control mechanisms exist to detect aberrancies in translation, which then lead to mRNAs being degraded by specialized mRNA decay pathways (Fig. 1B). Nonsense-mediated decay (NMD) is one such mRNA quality control system that degrades mRNAs that terminate translation aberrantly. In yeast, aberrant translation termination leads to deadenylation-independent decapping (Muhlrad and Parker 1994), whereas in metazoan cells NMD substrates can be both decapped and endonucleolytically cleaved and degraded (reviewed in Isken and Maquat 2007). A second quality control system for mRNA translation is referred to as no-go decay (NGD) and leads to endonucleolytic cleavage of mRNAs with strong stalls in translation elongation (Doma and Parker 2006; reviewed in Harigaya and Parker 2010). Another mechanism of mRNA quality control is the rapid 3′ to 5′ degradation of mRNAs that do not contain translation termination codons, which is referred to as non-stop decay (NSD) (Frischmeyer et al. 2002; van Hoof et al. 2002). The available evidence suggests these specialized mechanisms function primarily on aberrant mRNAs that are produced by defects in splicing, 3′ end formation, or damage to RNAs.The main pathway of mRNA degradation is also in competition with translation initiation. Competition between the two processes was first suggested by the observation that removal of the poly (A) tail and the cap structure, both of which stimulate translation initiation, were the key steps in mRNA degradation. In addition, inhibition of translation initiation by strong secondary structures in the 5′UTR, translation initiation inhibitors, a poor AUG context, or mutations in initiation factors increases the rates of deadenylation and decapping (Muhlrad et al. 1995; Muckenthaler et al. 1997; Lagrandeur and Parker 1999; Schwartz and Parker 1999). Moreover, the cap binding protein eIF4E, known to stimulate translation initiation, inhibits the decapping enzyme, Dcp1/Dcp2, both in vivo and in vitro (Schwartz and Parker 1999; Schwartz and Parker 2000). Finally, many mRNA specific regulatory factors, (e.g., miRNAs or PUF proteins), both repress translation and accelerate deadenylation and decapping (reviewed in Wickens et al. 2002; Behm-Ansmant et al. 2006; Franks and Lykke-Anderson 2008; Shyu et al. 2008).In the simplest model, the competition between translation and mRNA degradation can be understood through changes in the proteins bound to the cap and poly (A) tail that then influence the accessibility of these structures to deadenylases and decapping enzymes. For example, given that the Ccr4/Pop2/Not deadenylase complex is inhibited by poly (A)-binding protein (Pab1) (Tucker et al. 2002), the effects of translation on deadenylation are most likely through dynamic changes in the association of Pab1 binding with the poly (A) tail. One possibility is that defects in translation initiation either directly or indirectly decrease Pab1 association with the poly (A) tail. Deadenylation is also affected by aspects of translation termination. For instance, premature translation termination in yeast accelerates poly (A) shortening as part of the process of NMD (Cao and Parker 2003; Mitchell and Tollervey 2003). The coupling of translation termination to deadenylation has been suggested to occur through direct interactions of the translation termination factor eRF3 with Pab1 (Cosson et al. 2002), which may lead to Pab1 transiently dissociating from the poly (A) tail. Interestingly, in yeast, once the poly (A) tail reaches an oligo (A) length of 10–12 residues, a length that reduces the affinity of Pab1, the mRNA can become a substrate for decapping and for binding of the Pat1/Lsm1-7 complex (Tharun and Parker 2001; Chowdhury et al. 2007), which enhances the rate of decapping. This exchange of the Pab1 protein for the Pat1/Lsm1-7 complex is part of the mechanism that allows decapping to be promoted following deadenylation.A similar mRNP dynamic is also likely to occur on the cap structure. Specifically, the competition between translation initiation and decapping suggests that prior to decapping, translation initiation factors are exchanged for decapping factors, thereby assembling a distinct “decapping” mRNP that is no longer capable of translation initiation (Tharun and Parker 2001). This idea is supported by the observation that some decapping activators also function as translational repressors (Coller and Parker 2005; Pilkington and Parker 2008; Nissan et al. 2010). Thus, mRNA decapping appears to occur in two steps, first inhibition of translation initiation and exchange of translation factors for the general repression/degradation machinery, and a second step whereby the mRNA is actually degraded. Thus, by understanding the changes in mRNP states between actively translating mRNAs and mRNAs that are translationally repressed and possibly stored or ultimately degraded we will better understand how the fate of mRNAs is controlled in the cytoplasm.     

Microbial community analysis of a coastal hot spring in Kagoshima, Japan, using molecular- and culture-based approaches

Ibusuki hot spring is located on the coastline of Kagoshima Bay, Japan. The hot spring water is characterized by high salinity, high temperature, and neutral pH. The hot spring is covered by the sea during high tide, which leads to severe fluctuations in several environmental variables. A combination of molecular- and culture-based techniques was used to determine the bacterial and archaeal diversity of the hot spring. A total of 48 thermophilic bacterial strains were isolated from two sites (Site 1: 55.6°C; Site 2: 83.1°C) and they were categorized into six groups based on their 16S rRNA gene sequence similarity. Two groups (including 32 isolates) demonstrated low sequence similarity with published species, suggesting that they might represent novel taxa. The 148 clones from the Site 1 bacterial library included 76 operational taxonomy units (OTUs; 97% threshold), while 132 clones from the Site 2 bacterial library included 31 OTUs. Proteobacteria, Bacteroidetes, and Firmicutes were frequently detected in both clone libraries. The clones were related to thermophilic, mesophilic and psychrophilic bacteria. Approximately half of the sequences in bacterial clone libraries shared <92% sequence similarity with their closest sequences in a public database, suggesting that the Ibusuki hot spring may harbor a unique and novel bacterial community. By contrast, 77 clones from the Site 2 archaeal library contained only three OTUs, most of which were affiliated with Thaumarchaeota.     

Effect of wastewater discharge on nutrient contamination of mangrove soils and plants

The ecological impact of sewage discharges to a mangrove wetland in Futian National Nature Reserve, the People's Republic of China was assessed by comparing the plant community, plant growth and nutrient status of soils and vegetation of a site treated with settled municipal wastewater (Site A) with those of a control adjacent site (Site B) which did not receive sewage. During the one year study, the total and available N and P, and organic carbon concentrations of mangrove soils in Site A did not significantly differ from those of Site B. In both sites, the soil organic C, total N, NH₄ ^}-N and total P content exhibited a descending trend from landward to seaward regions, with the lowest measurements obtained from the most foreshore location. Seasonal variation in N content of soil samples was more obvious than any difference between wastewater treated and the control sites. The soil N content was lower in spring and summer. This was attributed to the higher temperature in these seasons which facilitated degradation of organic matter and absorption of nitrogen by the plants for growth. No significant difference in plant community structure, plant growth (in terms of tree height and diameter) and biomass was found between Sites A and B. Leaf samples of the two dominant plant species, Kandelia candel and Aegiceras corniculatum collected from Site A had comparable content of organic carbon, N, P and K to those Site B. These preliminary results indicated that the discharge of a total volume of 2600 m³ municipal wastewater to an area of 1800 m² mangrove plants over the period of a year did not produce any apparent impact on growth of the plants. The soils and plant leaves of Site A were not contaminated, in terms of nutrient content, by the discharged sewage.     

The sites of thyroid hormone formation in rabbit thyroglobulin

Rabbit thyroglobulin (Tg) was labeled in vivo with 125I and purified by gel filtration. Separation by high performance liquid chromatography (HPLC) of tryptic digests of S-cyanoethylated Tg yielded four major iodothyronine-containing peaks, designated A, B, C, and D. These were further purified on HPLC and sequenced for identification of amino acid residues and for location of the iodothyronine by 125I counting. The published primary structure for bovine Tg, derived from cDNA sequencing of the Tg gene (Mercken, L., Simons, M.J., Swillens, S., Massaer, M., and Vassart, G. (1985) Nature 316, 647-651), permitted tentative location of the rabbit hormonogenic peptides within the Tg polypeptide chain. Site A, corresponding to bovine residue 5, contained 44% of Tgs [125I]T4 (thyroxine) and 25% of its [125I]T3 (triiodothyronine); its specific activity of iodine was higher than that for other sites, indicating priority of iodination. Site B, containing 24% of Tgs [125I]T4 and 18% of its [125I]T3, corresponded to bovine residue 2555. Site C, at the third residue from the C terminus (bovine residue 2748), was the major T3 site, accounting for over 50% of Tgs [125I]T3. The amino acid sequence around this site shows less homology among different animal species than do those flanking the other hormonogenic sites. Site D accounted for 17% of Tgs [125I]T4 and corresponded to bovine Tyr-1291, in the midportion of Tgs polypeptide chain. The three major T4-forming sites had the sequence Asp-Tyr (sites B and D) or Glu-Tyr (site A), while the sequence Ser-Tyr-Ser appeared to favor T3 synthesis (site C), suggesting an important influence of primary structure on hormonogenesis. We conclude that site A is the major T4-forming site and site C the major T3-forming one, but others are available and offer the opportunity for flexibility in meeting different demands for hormone formation.     

Two additional carbohydrate-binding sites of beta-amylase from Bacillus cereus var. mycoides are involved in hydrolysis and raw starch-binding

In the previous X-ray crystallographic study, it was found that beta-amylase from Bacillus cereus var. mycoides has three carbohydrate-binding sites aside from the active site: two (Site2 and Site3) in domain B and one (Site1) in domain C. To investigate the roles of these sites in the catalytic reaction and raw starch-binding, Site1 and Site2 were mutated. From analyses of the raw starch-binding of wild-type and mutant enzymes, it was found that Site1 contributes to the binding affinity to raw-starch more than Site2, and that the binding capacity is maintained when either Site1 or Site2 exists. The raw starch-digesting ability of this enzyme was poor. From inhibition studies by maltitol, GGX and alpha-CD for hydrolyses of maltopentaose (G5) and amylose ( (n) = 16) catalyzed by wild-type and mutant enzymes, it was found that alpha-CD is a competitive inhibitor, while, maltitol behaves as a mixed-type or competitive inhibitor depending on the chain length of the substrate and the mutant enzyme. From the analysis of the inhibition mechanism, we conclude that the bindings of maltitol and GGX to Site2 in domain B form an abortive ESI complex when amylose ( (n) = 16) is used as a substrate.     

Benthic Distribution of Sewage Sludge Indicated by Clostridium perfringens at a Deep-Ocean Dump Site

Clostridium perfringens in sediment samples collected at the Deep Water Municipal Sewage Sludge Disposal Site (also called the 106-Mile Site), off the coast of New Jersey, was enumerated. The counts of C. perfringens found in sediment samples collected within and to the southwest of the 106-Mile Site were significantly elevated (P < 0.01) compared with counts of samples from reference stations of similar depth (2,400 to 2,700 m), topography, and distance from the continental shelf, indicating that the benthic environment was contaminated by sewage dumping at this site. Low counts of C. perfringens in sediment samples collected at stations between the base of the continental shelf and the 106-Mile Site indicated that coastal runoff was not a significant source of contamination. Elevated counts were observed for samples up to 92 km to the southwest, whereas low counts were obtained for samples from stations to the east of the 106-Mile Site. This distribution is consistent with previous model predictions of sludge deposition. In areas heavily impacted by sludge dumping, C. perfringens counts were generally highest in the top 1 cm of sediment and exceeded 9,000 CFU g (dry weight) of sediment^-1. The patterns of C. perfringens dispersal observed in this study have proved useful for selection of heavily impacted areas and control stations for further ecological evaluation by a multidisciplinary research team.     

Early Occupations in Bighorn Canyon,Montana

Abstract

Excavation of the Mangus Site (24CB22l) in Bighorn Canyon, Montana revealed a stratum containing artifacts of the Agate Basin Complex. This occupation was dated by radiocarbon at 6740 B. C. and 6650 B. C. The Sorenson Site (24CB202) contained two early cultural levels, one of unknown cultural affiliation datedat 5850 B. C. and 5610 B. C. overlying a second unidentified occupation. Future investigations in Bighorn Canyon may produce artifacts allowing identification of these two occupations.     

Is Sexual Conflict an “Engine of Speciation”?

At the end of the last century, sexual conflict was identified as a powerful engine of speciation, potentially even more important than ecological selection. Earlier work that followed—experimental, comparative, and mathematical—provided strong initial support for this assertion. However, as the field matures, both the power of sexual conflict and constraints on the evolution of reproductive isolation as driven by sexual conflict are becoming better understood. From theoretical studies, we now know that speciation is only one of several possible evolutionary outcomes of sexual conflict. In line with these predictions, both experimental evolution studies and comparative analyses of fertilization proteins and of species richness show that sexual conflict leads to, or is associated with, reproductive isolation and speciation in some cases but not in others. Increased genetic variation (especially in females) without reproductive isolation is an underappreciated consequence of sexually antagonistic selection.By the end of 1990s, studies of sexual conflict and sexually antagonistic coevolution moved to the forefront of experimental and theoretical research in evolutionary biology (Rice and Holland 1997; Holland and Rice 1998; Rice 1998). Although the potential evolutionary importance of sexual conflict was anticipated and articulated from a theoretical point of view by Geoff Parker 20 years earlier (Parker 1979), the explosive interest in this topic was a result of groundbreaking experimental work with Drosophila melanogaster by Bill Rice (1993, 1996), which directly showed high potential for sexually antagonistic coevolution.Sexual conflict is a special case of intragenomic conflict (Rice and Holland 1997; Rice 1998; Crespi and Nosil 2013). Sexual conflict occurs if the interests of the sexes with regard to certain aspects of reproduction differ (Parker 1979; Arnqvist and Rowe 2005). Ultimately, sexual conflict arises because of the differences in the roles played by the sexes in the process of reproduction, which in turn lead to the differences between the sexes in the costs and benefits of mating and reproduction (Bateman 1948; Trivers 1972; Parker 1979). Sexual conflict can occur over mating rate (Rice and Holland 1997; Holland and Rice 1998; Rice 1998), offspring size (Haig 2000), parental care (Smith and Härdling 2000; Barta et al. 2002), the use of sperm (Ball and Parker 2003), epigenetic control of development (Rice et al. 2012), etc.Sexual conflict can occur through two genetic routes (Chapman and Partridge 1996; Parker and Partridge 1998). Within-locus conflict occurs when the locus controls a trait expressed in both sexes and the optimum trait values differ between the sexes. As a result, optimizing the trait value in one sex will lead to a fitness reduction in the other sex. Within-locus conflict can be resolved via a number of mechanisms, including the evolution of sex linkage, sex-specific expression of genes, gene duplication, and condition dependence (Bonduriansky and Chenoweth 2009; van Doorn 2009). Between-locus conflict occurs when there are two different (sets of) traits each expressed in one sex only but affecting the fitness of both sexes in opposite directions. In this case, adaptive changes in a trait of one sex cause deleterious fitness consequences for the other sex, which can be negated by the evolution in a trait of the other sex, which in turn will cause deleterious fitness consequences for the first sex. For example, males can evolve adaptations increasing their mating rate, which would be detrimental for females who would then evolve some counteradaptations to decrease the mating rate (Rice 1996).One particularly exciting idea that has emerged from studies of sexual conflict and sexually antagonistic coevolution is that sexual conflict can be an important “engine of speciation” (Rice 1996, 1998; Howard et al. 1998; Parker and Partridge 1998). In standard modern perspective, speciation is a result of genetic divergence between populations accompanied by the evolution of reproductive isolation (Howard and Berlocher 1998; Schluter 2000; Coyne and Orr 2004; Dieckmann et al. 2004; Gavrilets 2004). Genetic divergence can be driven by a variety of evolutionary factors, including mutation, random genetic drift, and natural, sexual, and social selection. Reproductive isolation can follow from a variety of mechanisms, resulting in incompatibilities (including genetic, developmental, morphological, ecological, and behavioral) of males and females from diverging populations or in a reduced fitness of their offspring. As was argued by Rice (1998), Parker and Partridge (1998), and others (e.g., Howard et al. 1998), sexual conflict can contribute to these processes in a number of ways.Below, I briefly summarize several, mostly verbal, theories of biological diversification caused by sexual conflict and then move to discussing some of the more concrete mathematical models and empirical data and patterns.     

Upper Albian ammonites from ODP Leg 171B off northern Florida

ODP Leg 171B investigated the sediments of the Blake Plateau off northern Florida and recovered 36 Upper Albian ammonites — one from Site 1050C, the others from Site 1052E. This unusually large number of specimens from an ODP site permits the dating of the interval between 668 to 621 m below sea-floor at Site 1052E as late Late Albian, Stoliczkaia ( S .) dispar ammonite zone. This zone is indicated by the genera Mortoniceras and Stoliczkaia ( S. ). Site 1050C (Interval 171B-1050C-31R-3, 0.80–0.86 m) cannot be dated more precisely than Late Aptian to Mid Cenomanian by ammonites. The fauna is cosmopolitan. Tetragonites jurinianus Puzosia mayoriana are widely distributed forms. Kossmatella muhlenbecki was thought to be restricted to a fairly small area around the Mediterranean, but the record off northern Florida presented here, indicates that it is not an endemic species; this is also true for Hemiptychoceras subgaultinum in the Albian. The event-like character of the ammonite-bearing interval at Site 1052E is unique. It is overlain by a laminated claystone succession; the top of this sequence is considered to represent maximum flooding (Oceanic Anoxic Event, OAE 1d). Ammonites perhaps profited from an increased nutrient supply derived from flooded coastal plains during a continuous transgression.     

PCR-based identification of thermotolerant free-living amoebae in Italian hot springs

Several thermal areas, also used for leisure purposes, may represent suitable habitats for free-living amoebae (FLAs), but few studies have been carried out in search for these organisms. The aim of this study was to assess the presence and distribution of FLAs by culture detection and molecular identification, over a one year-round sampling of two sites in Central Italy. Two geothermal springs (Site A and Site B) were investigated for a total of 36 water samples. Four sets of primers were used to amplify FLA DNA from all cultures positive for amoebic growth at both 37 °C and 45 °C. Overall, 33 (91.6%) water samples produced PCR amplification. Eleven taxa were identified. The array of identified species varied over the sampling period, and differed between the two hot springs, Site A harbouring 11 taxa compared to 5 of site B. However, both sites were characterized by the most common species Vermamoeba vermiformis and Naegleria australiensis. Acanthamoeba genotypes T4 and T15 were found at low frequency. Differences in the composition between the two sites could reflect environmental changes in biotic and chemical/physical parameters. From a public health perspective, the detection of potentially pathogenic amoebae could unveil a potential risk for humans.     

Dvl2-DIX结构域的SiteⅢ相关突变体结晶及其与Ccd1-DIX的共结晶

Dvl(Dishevelled)是Wnt信号通路传递的核心分子,无论内源的还是过表达的Dvl在细胞体内都能因自聚而形成puncta．研究已报道,Dvl主要通过其DIX结构域上的三个作用区域来介导自聚：SiteⅠ、SiteⅡ和SiteⅢ,其中SiteⅠ和SiteⅡ还参与了Dvl-DIX与Ccd1-DIX的异聚．为了进一步得到Dvl2-DIX上SiteⅠ和SiteⅡ的直接三维结构,本研究设计了一系列的SiteⅢ突变体．通过体内和体外实验进一步证实了这些突变氨基酸确实参与了Dvl2-DIX的自聚,然后对这些SiteⅢ突变体蛋白成功地进行了纯化和结晶,最终得到3.1Å的Dvl2-DIX(G65A)晶体数据．分析表明该晶体存在片层位移现象,需对数据进行一定修正后才能进行后续的结构分析．体外实验又证实了这些突变氨基酸不影响Dvl2-DIX与Ccd1-DIX的异聚,为了进一步研究Dvl2-DIX与Ccd1-DIX相互作用,我们对这些SiteⅢ突变体蛋白与Ccd1-DIX进行共结晶．最终获得Dvl2-DIX(G65A)与Ccd1-DIX复合物的初晶,利于进一步的晶体优化及数据收集．     

Thermosediminibacter oceani gen. nov., sp. nov. and Thermosediminibacter litoriperuensis sp. nov., new anaerobic thermophilic bacteria isolated from Peru Margin

A new group of anaerobic thermophilic bacteria was isolated from enrichment cultures obtained from deep sea sediments of Peru Margin collected during Leg 201 of the Ocean Drilling Program. A total of ten isolates were obtained from cores of 1–2 m below seafloor (mbsf) incubated at 60°C: three isolates came from the sediment 426 m below sea level with a surface temperature of 9°C (Site 1227), one from 252 m below sea level with a temperature of 12°C (Site 1228), and six isolates under sulfate-reducing condition from the lower slope of the Peru Trench (Site 1230). Strain JW/IW-1228P from the Site 1228 and strain JW/YJL-1230-7/2 from the Site 1230 were chosen as representatives of the two identified clades. Based on the 16S rDNA sequence analysis, these isolates represent a novel group with Thermovenabulum and Caldanaerobacter as their closest relatives. The temperature range for growth was 52–76°C with an optimum at around 68°C for JW/IW-1228P and 43–76°C with an optimum at around 64°C for JW/YJL-1230-7/2. The pH^25C range for growth was from 6.3 to 9.3 with an optimum at 7.5 for JW/IW-1228P and from 5 to 9.5 with an optimum at 7.9–8.4 for JW/YJL-1230-7/2. The salinity range for growth was from 0% to 6% (w/v) for JW/IW-1228P and from 0% to 4.5% (w/v) for JW/YJL-1230-7/2. The G+C content of the DNA was 50 mol% for both JW/IW-1228P and JW/YJL-1230-7/2. DNA–DNA hybridization yielded 52% similarity between the two strains. According to 16S rRNA gene sequence analysis, the isolates are located within the family, Thermoanaerobacteriaceae. Based on their morphological and physiological properties and phylogenetic analysis, it is proposed that strain JW/IW-1228P^T is placed into a novel taxa, Thermosediminibacter oceani, gen. nov., sp. nov. (DSM 16646^T=ATCC BAA-1034^T), and JW/YJL-1230-7/2^T into Thermosediminibacter litoriperuensis sp. nov. (DSM 16647^T =ATCC BAA-1035^T).An erratum to this article can be found at     

A late quaternary stratigraphy for DSDP Site 480, Gulf of California

The Coscinodiscus nodulifer A. Schmidt size-change stratigraphy is applied to the upper 17 cores (86 m) of DSDP Site 480 and the upper six cores (50 m) of Site 479, both from the Guaymas Basin slope, Gulf of California. This stratigraphy locates Oxygen Isotope Stage 2 (18,000 yrs BP) in Core 4, Section 1, Site 480, and Core 3, Section 2, Site 479, and the Stage boundary (24,000 yrs BP) in Core 5, Sections 1–2, Site 480.     

A complex array of positive and negative elements regulates the chicken alpha A-crystallin gene: involvement of Pax-6, USF, CREB and/or CREM, and AP-1 proteins.

The abundance of crystallins (> 80% of the soluble protein) in the ocular lens provides advantageous markers for selective gene expression during cellular differentiation. Here we show by functional and protein-DNA binding experiments that the chicken alpha A-crystallin gene is regulated by at least five control elements located at sites A (-148 to -139), B (-138 to -132), C (-128 to -101), D (-102 to -93), and E (-56 to -41). Factors interacting with these sites were characterized immunologically and by gel mobility shift experiments. The results are interpreted with the following model. Site A binds USF and is part of a composite element with site B. Site B binds CREB and/or CREM to enhance expression in the lens and binds an AP-1 complex including CREB, Fra2 and/or JunD which interacts with USF on site A to repress expression in fibroblasts. Sites C and E (which is conserved across species) bind Pax-6 in the lens to stimulate alpha A-crystallin promoter activity. These experiments provide the first direct data that Pax-6 contributes to the lens-specific expression of a crystallin gene. Site D (-104 to -93) binds USF and is a negative element. Thus, the data indicate that USF, CREB and/or CREM (or AP-1 factors), and Pax-6 bind a complex array of positive and negative cis-acting elements of the chicken alpha A-crystallin gene to control high expression in the lens and repression in fibroblasts.     

The catabolite activator protein stabilizes its binding site in the E. coli lactose promoter.

The effect of catabolite activator protein, CAP, on the thermal stability of DNA was examined. Site specific binding was studied with a 62 bp DNA restriction fragment containing the primary CAP site of the E. coli lactose (lac) promoter. A 144 bp DNA containing the lac promoter region and a 234 bp DNA from the pBR322 plasmid provided other DNA sites. Thermal denaturation of protein-DNA complexes was carried out in a low ionic strength solvent with 40% dimethyl sulfoxide, DMSO. In this solvent free DNA denatured below the denaturation temperature of CAP. The temperature stability of CAP for site specific binding was monitored using an acrylamide gel electrophoresis assay. Results show that both specific and non-specific CAP binding stabilize duplex DNA. Site specific binding to the 62 bp DNA produced a 13.3 degrees C increase in the transition under conditions where non-specific binding stabilized this DNA by 2-3 degrees C.