The Ste locus, a component of the parasitic cry-Ste system of Drosophila melanogaster, encodes a protein that forms crystals in primary spermatocytes and mimics properties of the beta subunit of casein kinase 2.

Males of Drosophila melanogaster lacking the Y chromosome-linked crystal locus show multiple meiotic alterations including chromosome disorganization and prominent crystal formation in primary spermatocytes. These alterations are due to the derepression of the X chromosome-linked Stellate sequences. To understand how the derepression of the Stellate elements gives rise to these abnormalities, we have expressed the protein encoded by the Stellate sequences in bacteria and produced an antibody against the fusion protein. Immunostaining of crystal- testes has clearly shown that the Stellate protein is a major component of the crystals. Moreover, in vitro experiments have shown that this protein can interact with the catalytic alpha subunit of casein kinase 2 enzyme, altering its activity.

Real-time monitoring of electrochemically active biofilm developing behavior on bioanode by using EQCM and ATR/FTIR

In the current study, the relationship between current and biomass and bio-adhesion mechanism of electrogenic biofilm on electrode were investigated using EQCM and ATR-SEIRAS linking electrochemistry. The results indicated that cellular biomass of biofilm on QCM-crystal surface showed maximum value of 6.0 μg/cm2 in initial batch and 11.5 μg/cm2 in the second batch on mature biofilm, producing a similar maximum current density of 110 μA/μg. Especially, the optimum cell biomass linking high electricity production ratio (110 μA/μg) occurred before maximum biomass coming, implying that over-growth mature biofilm is not an optimum state for enhancing power output of MFCs. On the other hand, the spectra using ATR-SEIRAS technique linking electrochemistry obviously exhibited water structure adsorption change at early biofilm formation and meanwhile the water adsorption accompanied the adsorbed bacteria and the bound cells population on the electrode increased with time. Meanwhile, the direct contact of bacteria and electrode via outer-membrane protein can be confirmed via a series spectra shift at amide I and amide II modes and water movement from negative bands displacing by adsorbed bacteria. Our study provided supplementary information about the interaction between the microbes and electrode beyond traditional electrochemistry.

The Early Miocene “Bisciaro volcaniclastic event” (northern Apennines, Italy): a key study for the geodynamic evolution of the central-western Mediterranean

The Early Miocene Bisciaro Fm., a marly limestone succession cropping out widely in the Umbria–Romagna–Marche Apennines, is characterized by a high amount of volcaniclastic content, characterizing this unit as a peculiar event of the Adria Plate margin. Because of this volcaniclastic event, also recognizable in different sectors of the central-western Mediterranean chains, this formation is proposed as a “marker” for the geodynamic evolution of the area. In the Bisciaro Fm., the volcaniclastic supply starts with the “Raffaello” bed (Earliest Aquitanian) that marks the base of the formation and ends in the lower portion of the Schlier Fm. (Late Burdigalian–Langhian p.p.). Forty-one studied successions allowed the recognition of three main petrofacies: (1) Pyroclastic Deposits (volcanic materials more than 90 %) including the sub-petrofacies 1A, Vitroclastic/crystallo-vitroclastic tuffs; 1B, Bentonitic deposits; and 1C, Ocraceous and blackish layers; (2) Resedimented Syn-Eruptive Volcanogenic Deposits (volcanic material 30–90 %) including the sub-petrofacies 2A, High-density volcanogenic turbidites; 2B, Low-density volcanogenic turbidites; 2C, Crystal-rich volcanogenic deposits; and 2D, Glauconitic-rich volcaniclastites; (3) Mixing of Volcaniclastic Sediments with Marine Deposits (volcanic material 5–30 %, mixed with marine sediments: marls, calcareous marls, and marly limestones). Coeval volcaniclastic deposits recognizable in different tectonic units of the Apennines, Maghrebian, and Betic Chains show petrofacies and chemical–geochemical features related to a similar calc-alkaline magmatism. The characterization of this event led to the hypothesis of a co-genetic relationship between volcanic activity centres (primary volcanic systems) and depositional basins (depositional processes) in the Early Miocene palaeogeographic and palaeotectonic evolution of the central-western Mediterranean region. The results support the proposal of a geodynamic model of this area that considers previously proposed interpretations.

Miocene palaeoclimate reconstructions from the North Alpine Foreland Basin in Germany

Early- and Middle-Miocene sediments of the North Alpine Foreland Basin (NAFB) in Southern Germany contain one of the world richest regional records of silicified wood. Here we analyze over 1,000 identifiable samples, belonging to 80 wood anatomical taxa from 61 stratigraphically well-dated localities using principally the Coexistence Approach. The samples investigated originate from fluvial sediments representing periods of intensified surface runoff in the NAFB and therefore represent and provide information pertaining to the wet end-member of the fluctuating climate system. The dry end of the climate system is represented in the profiles either by hiatuses or palaeosoils. The dataset is split into four xylofloras: (I) the Ortenburg xyloflora (Late Ottnangian; ~17.5 to 17.3 Ma) originating from a paratropical evergreen Carapoxylon (Xylocarpus) forest; (II) the Southern Franconian Alb xyloflora (Late Karpatian; 17.0 to ~16.3 Ma) originating from a subtropical semideciduous limestone forest; (III) the upper Older Series xyloflora (Early Badenian; ~16.3 to ~15.3 Ma) originating from a subtropical oak-laurel forest; and (IV) the upper Middle Series xyloflora (Middle Badenian; 14.3 to ~13.8 Ma) originating from a subtropical dry deciduous forest.

(Table S1) Boron isotope and trace element data and reconstructed carbonate system parameters, ODP Holes 122-761B and 154-926A

The middle Miocene Climatic Optimum (17-15 Ma; MCO) is a period of global warmth and relatively high CO2 and is thought to be associated with a significant retreat of the Antarctic Ice Sheet (AIS). We present here a new planktic foraminiferal d11B record from 16.6 to 11.8 Ma from two deep ocean sites currently in equilibrium with the atmosphere with respect to CO2. These new data demonstrate that the evolution of global climate during the middle Miocene (as reflected by changes in the cyrosphere) was well correlated to variations in the concentration of atmospheric CO2. What is more, within our sampling resolution (~1 sample per 300 kyr) there is no evidence of hysteresis in the response of ice volume to CO2 forcing during the middle Miocene, contrary to what is understood about the Antarctic Ice Sheet from ice sheet modelling studies. In agreement with previous data, we show that absolute levels of CO2 during the MCO were relatively modest (350-400 ppm) and levels either side of the MCO are similar or lower than the pre-industrial (200-260 ppm). These new data imply the presence of either a very dynamic AIS at relatively low CO2 during the middle Miocene or the advance and retreat of significant northern hemisphere ice. Recent drilling on the Antarctic margin and shore based studies indicate significant retreat and advance beyond the modern limits of the AIS did occur during the middle Miocene, but the complete loss of the AIS was unlikely. Consequently, it seems that ice volume and climate variations during the middle Miocene probably involved a more dynamic AIS than the modern but also some component of land-based ice in the northern hemisphere.

Distribution of foraminifera, pre-Pliocene foraminifera and macrofossil debris in sediment core CRP-2 (Table 1)

The stratigraphic distribution, assemblage content, paleoecology and age of foraminifera recovered in fourteen of sixteen samples from the 5.63 m thick CRP-2 (Lithostratigraphic Unit 2.2) are discussed. LSU 2.2 comprises four discrete lithologic beds. The upward sequence is informally referred to as the lower sand bed, diamicton bed, middle sand bed, and upper sand bed and it is surmised that these four units are closely related in time. The lower sand bed (~1.5m), which overlies lower Miocene sediments and from which it is separated by the Ross Sea Unconformity, contains traces of recycled Miocene diatoms but is otherwise barren of biogenic material. The diamicton bed (~2.42 m) contains 21 species of benthic foraminifera, with assemblages consistently dominated by Cassidulinoides porrectus, Ammoelphidiella antarctica, Rosalina cf. globularis, Cibicides refulgens, and Ehrenbergina glabra. The overlying middle sand bed (~1.9 m) contains 13 species. with C. porrectus and E. glabra dominant and A. antarctica less common than in the underlying diamicton bed. The upper sand bed (~0.46 m) contains four species and very few tests. The diamicton bed and middle sand bed assemblages are considered to be near in situ thanatocoenoses; and sediments interpreted as marine in origin but influenced by hyposaline waters and nearby ice. Planktic taxa are absent, perhaps indicating the presence of tidewater glaciers, sea ice and/or hyposaline surface waters. The small assemblage in the upper sand bed is more problematic and may be recycled. On the basis of foraminifera in the diamicton and middle sand beds. LSU 2.2 is assigned to the Pliocene. The overlying diamicton in LSU 2.1 contains abundant Quaternary foraminifera.

Magnetostratigraphy and biostratigraphy of ODP Leg 105 sites and DSDP Hole 12-112

During Ocean Drilling Program (ODP) Leg 105, three sites (Sites 645 through 647) were drilled in Baffin Bay and the Labrador Sea to examine the tectonic evolution and the climatic and oceanic histories of this region. Biostratigraphic and magnetostratigraphic results vary at each site, while stratigraphic resolution depends on the limited abundance of marker species and the completeness of the paleomagnetic record. Because of the paucity of planktonic microfossils and the poor paleomagnetic record signatures, stratigraphic determinations at Site 645 often rely on defining minimum temporal constraints on specific samples or stratigraphic intervals. The completed stratigraphy indicates that the sedimentary sequence recovered at Site 645 is early Miocene to Holocene in age. The magnetostratigraphy and biostratigraphies are better defined at Sites 646 and 647 in the Labrador Sea. Site 646 generally contains a well-developed magnetostratigraphy and calcareous microfossil biostratigraphy. This biostratigraphy is based on calcareous nannofossils and planktonic foraminifers typical of the North Atlantic Ocean. Siliceous microfossils are also present at Site 646, but they are restricted to upper Pliocene through Holocene sediments. The stratigraphic sequence recovered at Site 646 is late Miocene to Holocene in age. Based primarily on the calcareous nannofossil stratigraphy, the sequence recovered at Site 647 consists of lower Eocene to lower Oligocene, lower Miocene, upper Miocene, and upper Pliocene through Holocene sediments. Three hiatuses are present in this sequence: the older hiatus separates lower Oligocene sediments from lower Miocene sediments, another hiatus separates lower Miocene sediments from upper Miocene sediments, and the youngest one separates upper Miocene from upper Pliocene sediments. A magnetostratigraphy is defined for the interval from the Gauss/Matuyama boundary through the Brunhes (Clement et al., this volume). Both planktonic foraminifers and siliceous microfossils have restricted occurrences. Planktonic foraminifers occur in Pliocene and younger sediments, and siliceous microfossils are present in lower Miocene and lower Oligocene sediments. The near-continuous Eocene through lower Oligocene sequence recovered at Site 647 allows the calcareous nannofossils and diatom stratigraphies at this site to act as a Paleogene stratigraphic framework. This framework can be compared with the stratigraphy previously completed for DSDP Site 112.

Mineralogy, geochemistry, isotopic ratios and foraminifer occurrence in ODP Hole 183-1139A

Mixed terrigenous-pelagic sediments from the Oligocene-lower Miocene interval of Hole 1139A accumulated on the flank of an eroded alkalic volcano, Skiff Bank. In this study, I explore relationships among sediment fluxes, especially of organic carbon and the clay mineral by-products of silicate weathering, and lithologic, tectonic, climatic, and biologic forcing factors. Benthic foraminifers indicate that Skiff Bank had subsided to lower bathyal depths (1000-2000 m) by the Oligocene. Two prominent maxima in noncarbonate concentration at 28 and 22 Ma correspond to peaks in the terrigenous flux; also, high noncarbonate concentrations are associated with larger grain sizes (silt) and higher opal concentrations. These and higher-frequency variations of noncarbonate concentration were probably controlled by glacioeustatic/climatic changes, with higher noncarbonate concentrations caused by increased erosion during glacial lowstands. Around 27 Ma, benthic foraminiferal d18O values decreased 0.7 per mil as the noncarbonate concentration decreased after the 28-Ma maximum. A paucity of clay-sized sediment and clay minerals suggests that physical erosion, by waves and/or ice, predominated under weathering-limited conditions. Low organic carbon concentrations (~0.13 wt%) also suggest a harsh environment and/or poor preservation in coarse (>2 µm) sediments that were extensively bioturbated below the oxygen minimum zone.

Diversity of benthic foraminiferal faunas in Tertiary and Quaternary sediments of DSDP Hole 33-317_Site from the Manihiki Plateau, Pacific Ocean (Table 1)

A study is made of the benthic foraminifers (size fraction > 63 µm) recovered from 59 upper Eocene through Quaternary sediment samples at DSDP Site 317 (Leg 33), located at a depth of 2598 m in the central part of the Manihiki Plateau (South Pacific). The sediments cored are disturbed in only two samples. The stratigraphic assignements used are based on previous studies of planktic foraminifers and other microfossils. In total, 216 taxa are identified. A cluster analysis based on the 77 species which comprised 5% or more of the entire foraminiferal assemblage in at least one sample suggests the presence of 3 major biostratigraphic zones corresponding approximately to the following ages, zone A: middle Miocene-Quaternary; zones B-C: early Miocene-Oligocene; and zone D: Eocene. The most important faunal turnover occurred between the Eocene and the Oligocene; a less pronounced break took place between the early and the middle Miocene, and an additional minor turnover between the Oligocene and the early Miocene. Eighteen taxa are long-ranging, being recorded from the middle Eocene through the Pliocene-Quaternary. It is concluded that, in general, benthic foraminifers of the bathyal zone are poor worldwide stratigraphic guide fossils; the following taxa are conditionally considered as the most suitable in the Eocene-Quaternary sequence: Aragonia aragonensis, Quadrimorphina profunda, Nuttallides truempyi, Abyssamina poagi, Buliminella grata, Bulimina jarvisi, B. macilenta, Turrilina alsatica, Cibicides notocenicus, C. wuellerstorfi, Pyrgo murrhina. However, most of these species are relatively rare.

Description of lithofacies associations and their interpreted settings from sequences of sediment core CRP-1 (Table 2)

Cape Roberts Project drillcore 1 was obtained from Roberts Ridge, a sea-floor high located at 77°S, 16 km offshore from Cape Roberts in western McMurdo Sound, Antarctica. The recovered core is about 147 m long with the upper 43.15 metres below the sea floor (revised figure) being dated as Quarternary and the older part of the sequence being Miocene. The core includes nine facies: sandy diamict, muddy diamict, gravel/conglomerate, mud(stone), clay(stone) and carbonate. These facies occure in associations that are repeated in particulare sequences throughout the core, and are interpreted as representing different depositional environments through time. Seven lithofacies associations are interpreted as representing offshore shelf, ice protected/below wave-base; prodeltaic/offshore shelf; delta front/sandy shelf; ice system; subglacial till/rainout diamict/debris flow diamicts singly or in combination; and a carbonate-rich shelf bank. The facies associations are used to infer that the Quaternary section represents deposition on a polar shelf with perhaps two or three glacial fluctuations. The Quaternary carbonate unit indicates a period of ice sheet retreat, but local glacial activity may have increased with an increase in costal precipitation. The Miocene section represents polythermal glacial systems. The older Miocene section is glacially dominated whereas the younger section is much less so. The glacially dominated section may provide evidence for a major glacial advance thar resulted un a low stand of global eustatic sea level at that time. After the low stand, eustatic sea level was gradually rising during deposition of the younger section dominated more by non-glacial processes.

Electron transfer in acetohydroxy acid synthase as a side reaction of catalysis. implications for the reactivity and partitioning of the carbanion/enamine form of (alpha-hydroxyethyl)thiamin diphosphate in a "nonredox" flavoenzyme

Acetohydroxy acid synthases (AHAS) are thiamin diphosphate- (ThDP-) and FAD-dependent enzymes that catalyze the first common step of branched-chain amino acid biosynthesis in plants, bacteria, and fungi. Although the flavin cofactor is not chemically involved in the physiological reaction of AHAS, it has been shown to be essential for the structural integrity and activity of the enzyme. Here, we report that the enzyme-bound FAD in AHAS is reduced in the course of catalysis in a side reaction. The reduction of the enzyme-bound flavin during turnover of different substrates under aerobic and anaerobic conditions was characterized by stopped-flow kinetics using the intrinsic FAD absorbance. Reduction of enzyme-bound FAD proceeds with a net rate constant of k' = 0.2 s(-1) in the presence of oxygen and approximately 1 s(-1) under anaerobic conditions. No transient flavin radicals are detectable during the reduction process while time-resolved absorbance spectra are recorded. Reconstitution of the binary enzyme-FAD complex with the chemically synthesized intermediate 2-(hydroxyethyl)-ThDP also results in a reduction of the flavin. These data provide evidence for the first time that the key catalytic intermediate 2-(hydroxyethyl)ThDP in the carbanionic/enamine form is not only subject to covalent addition of 2-keto acids and an oxygenase side reaction but also transfers electrons to the adjacent FAD in an intramolecular redox reaction yielding 2-acetyl-ThDP and reduced FAD. The detection of the electron transfer supports the idea of a common ancestor of acetohydroxy acid synthase and pyruvate oxidase, a homologous ThDP- and FAD-dependent enzyme that, in contrast to AHASs, catalyzes a reaction that relies on intercofactor electron transfer.

The crystal structure of a bacterial Class II ketol-acid reductolsomerase: Domain conservation and evolution

Ketol-acid reductoisomerase (KARI; EC 1.1.1.86) catalyzes two steps in the biosynthesis of branched-chain amino acids. Amino acid sequence comparisons across species reveal that there are two types of this enzyme: a short form (Class 1) found in fungi and most bacteria, and a long form (Class 11) typical of plants. Crystal structures of each have been reported previously. However, some bacteria such as Escherichia coli possess a long form, where the amino acid sequence differs appreciably from that found in plants. Here, we report the crystal structure of the E. coli enzyme at 2.6 A resolution, the first three-dimensional structure of any bacterial Class 11 KARI. The enzyme consists of two domains, one with mixed alpha/beta structure, which is similar to that found in other pyridine nucleotide-dependent dehydrogenases. The second domain is mainly alpha-helical and shows strong evidence of internal duplication. Comparison of the active sites between KARI of E. coli, Pseudomonas aeruginosa, and spinach shows that most residues occupy conserved positions in the active site. E. coli KARI was crystallized as a tetramer, the likely biologically active unit. This contrasts with P. aeruginosa KARI, which forms a dodecamer, and spinach KARI, a dimer. In the E. coli KARI tetramer, a novel subunit-to-subunit interacting surface is formed by a symmetrical pair of bulbous protrusions.

Crisis management and risk communication: Why the food industry must get it right

There is public unease about food-related issues including food additives, food poisoning bacteria and GM ingredients. The public wants evidence of no risks, but all regulators can ever offer is no evidence of risk or evidence of a very small risk. The situation is complex because experts and non-experts can perceive the same risk in vastly different ways. The way in which the food industry manages crises and communicates risks will determine the public acceptance and success of new technologies such as GM foods and nanomaterials. There is a need for the food industry (including regulators and scientific experts) to sharpen up their risk communication skills to ensure that technical innovations are accepted by consumers, and crises such as food recalls do not undermine the public's confidence in the food industry. The AIFST has a key role to play in driving the risk communication process and allaying public unease about food-related issues.

Genes for the majority of group A streptococcal virulence factors and extracellular surface proteins do not confer an increased propensity to cause invasive disease

Background. The factors behind the reemergence of severe, invasive group A streptococcal (GAS) diseases are unclear, but it could be caused by altered genetic endowment in these organisms. However, data from previous studies assessing the association between single genetic factors and invasive disease are often conflicting, suggesting that other, as-yet unidentified factors are necessary for the development of this class of disease. Methods. In this study, we used a targeted GAS virulence microarray containing 226 GAS genes to determine the virulence gene repertoires of 68 GAS isolates (42 associated with invasive disease and 28 associated with noninvasive disease) collected in a defined geographic location during a contiguous time period. We then employed 3 advanced machine learning methods (genetic algorithm neural network, support vector machines, and classification trees) to identify genes with an increased association with invasive disease. Results. Virulence gene profiles of individual GAS isolates varied extensively among these geographically and temporally related strains. Using genetic algorithm neural network analysis, we identified 3 genes with a marginal overrepresentation in invasive disease isolates. Significantly, 2 of these genes, ssa and mf4, encoded superantigens but were only present in a restricted set of GAS M-types. The third gene, spa, was found in variable distributions in all M-types in the study. Conclusions. Our comprehensive analysis of GAS virulence profiles provides strong evidence for the incongruent relationships among any of the 226 genes represented on the array and the overall propensity of GAS to cause invasive disease, underscoring the pathogenic complexity of these diseases, as well as the importance of multiple bacteria and/ or host factors.

Palm kernel meal in broiler diets: effect on chicken performance and health

An increase in the production of palm kernel meal (PKM) coupled with the concern for continued availability of conventional feedstuffs in some parts of the world has led to research to establish the maximum inclusion level of palm kernel meal in broiler diets. The results suggested that palm kernel meal has no anti-nutritional properties and thus its inclusion is safe up to at least 40% in the diet, provided the diet is balanced in amino acids and metabolisable energy. Although feed digestibility is decreased due to high dietary fibre when PKM is included in the diet, the feed intake is increased. This makes total digestible nutrient intake relatively high. beta-mannan is the main component of palm kernel meal non-starch polysaccharide (NSP). Both mannose and manno-oligosaccharides have been reported to act as prebiotics. The inclusion of palm kernel meal in the diet improves the immune system of birds and reduces pathogenic bacteria and increases the population of nonpathogenic bacteria in the intestine. These two benefits should be considered as strong recommendations for using palm kernel meal in broiler diets, particularly in palm kernel meal producing countries, not only for increasing bird productivity but also to improve chicken health. Selective enzyme addition increases feed efficiency and digestibility as well as decreasing the moisture content of faeces.