bluuebunny/crossref_metadata_2025_split huggingface dataset:
Co-evolution of proteins and solutions: protein adaptation versus cytoprotective micromolecules and their roles in marine organisms
Authors: Yancey Paul H. , Siebenaller Joseph F. 
Published: June 2015

ABSTRACTOrganisms experience a wide range of environmental factors such as temperature, salinity and hydrostatic pressure, which pose challenges to biochemical processes. Studies on adaptations to such factors have largely focused on macromolecules, especially intrinsic adaptations in protein structure and function. However, micromolecular cosolutes can act as cytoprotectants in the cellular milieu to affect biochemical function and they are now recognized as important extrinsic adaptations. These solutes, both inorganic and organic, have been best characterized as osmolytes, which accumulate to reduce osmotic water loss. Singly, and in combination, many cosolutes have properties beyond simple osmotic effects, e.g. altering the stability and function of proteins in the face of numerous stressors. A key example is the marine osmolyte trimethylamine oxide (TMAO), which appears to enhance water structure and is excluded from peptide backbones, favoring protein folding and stability and counteracting destabilizers like urea and temperature. Co-evolution of intrinsic and extrinsic adaptations is illustrated with high hydrostatic pressure in deep-living organisms. Cytosolic and membrane proteins and G-protein-coupled signal transduction in fishes under pressure show inhibited function and stability, while revealing a number of intrinsic adaptations in deep species. Yet, intrinsic adaptations are often incomplete, and those fishes accumulate TMAO linearly with depth, suggesting a role for TMAO as an extrinsic ‘piezolyte’ or pressure cosolute. Indeed, TMAO is able to counteract the inhibitory effects of pressure on the stability and function of many proteins. Other cosolutes are cytoprotective in other ways, such as via antioxidation. Such observations highlight the importance of considering the cellular milieu in biochemical and cellular adaptation.
Giving microbes their due – animal life in a microbially dominant world
Authors: McFall-Ngai Margaret J. 
Published: June 2015

ABSTRACTThe new technology of next-generation sequencing is changing our perceptions of the form and function of the biological world. The emerging data reveal an array of microbes that is more vast and more central to all biological processes than previously appreciated. Further, evidence is accumulating that the alliances of microbes with one another and with constituents of the macrobiological world are critical for the health of the biosphere. This contribution summarizes the basic arguments as to why, when considering the biochemical adaptations of animals, we should integrate the roles of their microbial partners.
Physiological strategies during animal diapause: lessons from brine shrimp and annual killifish
Authors: Podrabsky Jason E. , Hand Steven C. 
Published: June 2015

ABSTRACTDiapause is a programmed state of developmental arrest that typically occurs as part of the natural developmental progression of organisms that inhabit seasonal environments. The brine shrimp Artemia franciscana and annual killifish Austrofundulus limnaeus share strikingly similar life histories that include embryonic diapause as a means to synchronize the growth and reproduction phases of their life history to favorable environmental conditions. In both species, respiration rate is severely depressed during diapause and thus alterations in mitochondrial physiology are a key component of the suite of characters associated with cessation of development. Here, we use these two species to illustrate the basic principles of metabolic depression at the physiological and biochemical levels. It is clear that these two species use divergent molecular mechanisms to achieve the same physiological and ecological outcomes. This pattern of convergent physiological strategies supports the importance of biochemical and physiological adaptations to cope with extreme environmental stress and suggests that inferring mechanism from transcriptomics or proteomics or metabolomics alone, without rigorous follow-up at the biochemical and physiological levels, could lead to erroneous conclusions.
The environmentally tuned transcriptomes ofMytilusmussels
Authors: Lockwood Brent L. , Connor Kwasi M. , Gracey Andrew Y. 
Published: June 2015

ABSTRACTTranscriptomics is a powerful tool for elucidating the molecular mechanisms that underlie the ability of organisms to survive and thrive in dynamic and changing environments. Here, we review the major contributions in this field, and we focus on studies of mussels in the genus Mytilus, which are well-established models for the study of ecological physiology in fluctuating environments. Our review is organized into four main sections. First, we illustrate how the abiotic forces of the intertidal environment drive the rhythmic coupling of gene expression to diel and tidal cycles in Mytilus californianus. Second, we discuss the challenges and pitfalls of conducting transcriptomic studies in field-acclimatized animals. Third, we examine the link between transcriptomic responses to environmental stress and biogeographic distributions in blue mussels, Mytilus trossulus and Mytilus galloprovincialis. Fourth, we present a comparison of transcriptomic datasets and identify 175 genes that share common responses to heat stress across Mytilus species. Taken together, these studies demonstrate that transcriptomics can provide an informative snapshot of the physiological state of an organism within an environmental context. In a comparative framework, transcriptomics can reveal how natural selection has shaped patterns of transcriptional regulation that may ultimately influence biogeography.
Fluorescence and excited state dynamics of the deprotonated Schiff base retinal in proteorhodopsin
Authors: Bühl Elena , Braun Markus , Lakatos Andrea , Glaubitz Clemens , Wachtveitl Josef 
Published: June 2015

Abstract
The UV light absorbing species of proteorhodopsin with deprotonated Schiff base retinal was investigated using steady-state fluorescence and femtosecond pump-probe spectroscopy. Compared to the all-trans retinal with protonated Schiff base, the deprotonated chromophore absorbs at 365 nm and exhibits a blue-shifted fluorescence spectrum. The unusually long-lived excited state decays bi-exponentially with time constants of 8 ps and 130 ps to form a deprotonated 13-cis retinal as the primary photo-product.
Protein aggregate formation in oligodendrocytes: tau and the cytoskeleton at the intersection of neuroprotection and neurodegeneration
Authors: Richter-Landsberg Christiane 
Published: June 2015

Abstract
Oligodendrocytes are dependent on an intact, dynamic microtubule (MT) network, which participates in the elaboration and stabilization of myelin forming extensions, and is essential for cellular sorting processes. The microtubule-associated protein tau is constituent of oligodendrocytes. During culture maturation it is developmentally regulated and important for MT stability, MT formation and intracellular trafficking. Downregulation of tau impairs process outgrowth and the transport of myelin basic protein (MBP) mRNA to the cell periphery. Cells fail to differentiate into MBP-expressing, sheet-forming oligodendrocytes. Tau-positive inclusions originating in oligodendrocytes and white matter pathology are prominent in frontotemporal dementias, such as Pick’s disease, progressive supranuclear palsy and corticobasal degeneration. An impairment or overload of the proteolytic degradation systems, i.e. the ubiquitin proteasomal system and the lysosomal degradation pathway, has been connected to the formation of protein aggregates. Large protein aggregates are excluded from the proteasome and degraded by autophagy, which is a highly selective process and requires receptor proteins for ubiquitinated proteins, including histone deacetylase 6 (HDAC6). HDAC6 is present in oligodendrocytes, and α-tubulin and tau are substrates of HDAC6. In this review our current knowledge of the role of tau and protein aggregate formation in oligodendrocyte cell culture systems is summarized.
The encoding of addressee’s perspective in Kakataibo (Panoan, Peru)
Authors: Zariquiey Roberto 
Published: June 2015

AbstractThis paper studies forms attested in Kakataibo (Panoan, Peru) for situating the information presented by the speaker from the perspective of the addressee. The constructions discussed can satisfactorily be accounted for by means of the notions of epistemic status and epistemic stance, which have to do with the knowing status of speech act participants and how it is expressed in grammar. Salient characteristics of the mechanisms used in Kakataibo to encode addressee’s perspective are the diversity of the relevant forms, which come from two different paradigms, and the semantic and pragmatic features that play a role in their distribution.
Label-Free Rapid Detection of Pathogens with Antimicrobial Peptide Assisted Impedance Spectrometry
Authors: Jiang Keren , Etayash Hashem , Azmi Sarfuddin , Thakur Garima , Naicker Selvaraj , Kaur Kamaljit , Thundat Thomas 
Published: June 2015

ABSTRACTAn urgent need exist for developing handheld devices for rapid, sensitive, and specific detection method for pathogens. Here we demonstrate a rapid detection method for Gram-positive and Gram-negative bacteria using an impedance sensor array functionalized with antimicrobial peptides (AMPs). This impedance sensor screens pathogens in real-time and has comparable sensitivity with current detection methods like polymerase chain reaction (PCR) and immunoassay. Functionalized electrodes in array selectively bind to the corresponding bacteria strains, resulting in variations in the impedance modulus. Impedance variation is used to detect incubated bacterial cell concentration with a resolution of 1 cell µL-1. The dynamic range of detection for both Gram-positive and Gram-negative bacteria is found to be 103-106cfu mL-1. Micropatterned electrodes modified with AMPs in an impedimetric array offer an excellent platform for rapid and selective detection of pathogens in contaminated water and food products.
Micropaleontology in Multi-Disciplinary Research: Applications to OAE2 and KTB
Authors: Keller Gerta 
Published: June 2015

Abstract :
Today, it is virtually unthinkable to solve almost any geologic problem without microfossils, whether in terms of age control or environmental proxies. Perhaps the turning point came in 1980 with the impact hypothesis as cause for the end-Cretaceous mass extinction. Although this hypothesis initiated one of the longest running and most acrimonious scientific debates, its most lasting and positive effects include the introduction of really high-resolution biostratigraphy at the cm-scale and the beginning of truly interdisciplinary and multi-disciplinary studies. Rarely has there been a topic so popular, albeit contentious, that it attracted interest and attention by disciplines across the spectrum of earth sciences and beyond. This report highlights advances in high-resolution biostratigraphy and environmental studies based on major events in Earth’s history, such as the Oceanic Anoxic Event 2 (OAE2) and the Cretaceous-Tertiary boundary (KTB) mass extinction. It illustrates current age control, biostratigraphic resolution, stable isotope records with characteristic δ13C excursions and integration with other disciplines to derive environmental interpretations.
Effect of Temperature and Salinity on Stable Isotopic Composition of Shallow Water Benthic Foraminifera: A Laboratory Culture Study
Authors: Kurtarkar Sujata R. , Linshy V.N. , Saraswat Rajeev , Nigam Rajiv 
Published: June 2015

Abstract :
Quantitative estimation of past climatic parameters from stable isotopic composition of foraminifera relies on estimating the precise relationship between stable isotopic composition of the species analyzed and the physico-chemical factors of the seawater. This relationship can be established either on species collected from surface sediments or in plankton tows. Another method to establish such relationships is by subjecting the foraminiferal species to known physico-chemical parameters in the laboratory. In the present work, shallow water benthic foraminiferal species, Rosalina sp. and Pararotalia nipponica were subjected to different combinations of seawater temperature (25°C to 35°C) and salinity (25 psu to 37 psu) in the laboratory to assess their stable oxygen isotopic composition and its applicability in determining seawater temperature and salinity. The stable isotopic ratio of the species shows no consistent relationship with salinity. The relationship between δ18O foraminifera and seawater temperature is more consistent for P. nipponica than for Rosalina sp. Salinity appears to have less control on δ18O foraminifera as compared to the seawater temperature, within the studied salinity and temperature range. The study shows that the changes in δ18O of P. nipponica can be used effectively to infer past seawater temperature changes.
Sequence Stratigraphy of Late Cretaceous Successions in the Ramnad Sub-basin, Cauvery Basin, India
Authors: Nallapa Reddy A. , Jaiprakash B.C. , Rao M.V. , Chidambaram L. , Bhaktavatsala K.V. 
Published: June 2015

Abstract :
We interpret the subsurface distribution pattern of Late Cretaceous sandstone reservoirs in the Ramnad sub-basin within the framework of sequence stratigraphy via biostratigraphic and lithostratigraphic correlation with outcrop sections in the Ariyalur area of the Cauvery basin. The sequence stratigraphic surfaces recognized in outcrop sections can be correlated to subsurface sections by using biostratigraphic datum markers. By this method five 2nd and 3rd order sequences can be recognized in outcrops of the Ariyalur area based on sequence boundaries (SB): 1) the top of the Terani Formation (latest Aptian-earliest Albian SB1), 2) the Karai Formation (middle Turonian Marginotruncana sigali Zone SB2), 3) the Anaipadi member of Garudamangalam Formation (late Santonian Dicarinella asymetrica Zone SB3), 4) the Sillakudi Formation (late Campanian Globotruncanita calcarata Zone SB4), 5) the Ottakovil Formation (early late Maastrichtian Gansserina gansseri Zone SB5), and 6) the Kallamedu Formation (late Maastrichtian Abathomphalus mayaroensis Zone SB6). Examination of log profiles of the Koluvur, Ramnad, Perungulam, Chumaitangi, Kanjirangudi, Periapattinam, Ramanavalasai and Uchipuli structures show that sea level lowstands at the end of the middle Turonian, late Santonian and late Maastrichtian are associated with coarser clastic sediments in deeper parts of the basin. This suggests that low sea levels are associated with bypass of coarser clastics in shelf areas and deposition as fan deposits in the deeper parts of the basin. Major sea level falls thus significantly influence the distribution of coarser clastic sediments and the application of sequence stratigraphic concepts aids the understanding of sandstone reservoirs in the Ramnad sub-basin.
Sequence Stratigraphic Analysis of the Mixed Siliciclastic-Carbonate Sediments (Middle Jurassic) of the Patcham Island, Kachchh, Western India: An Ichnological Approach
Authors: Patel Satish J. , Joseph Jaquilin K. , Bhatt Nishith Y. 
Published: June 2015

Abstract:
The Middle Jurassic (Bajocian to Callovian) sequence of the Patcham Island, Kachchh, comprises mixed siliciclastic-carbonate sediments displaying transgressive-regressive cycles that record changes in the relative sea level condition. These mixed siliciclastic carbonate sediments are of varying composition representing six sedimentary facies namely, micritic sandstone, allochemic sandstone, sandy allochem limestone, sandy micrite, muddy micrite, and micritic mudrock along with the grey shale, allochemic limestone and ferruginous sandstone facies. These sedimentary facies are bioturbated with a total of 65 ichnospecies of 42 ichnogenera which are recurring throughout the sequence. The trace fossils are further grouped into nine trace fossil assemblages based on environmentally related traces based on diversity, frequency and preservational aspects (viz., Arenicolites, Asterosoma, Gyrochorte, Ophiomorpha, Planolites/Palaeophycus, Phycodes, Rhizocorallium, Skolithos and Thalassinoides assemblages). The sedimentary units (packages) coupled with ichnoassemblages reveal three transgressive system tracts (TST) and four regressive system tracts (RST) separated by flooding surfaces representing 3rd order transgressive-regressive (T-R) cycles bounded by regressive surfaces. In the T-R cycle, presence of the Rhizocorallium ichnoassemblage (TRC-II) and Arenicolites, Thalassinoides with Planolites-Palaeophycus assemblages (TRC-III) mark the flooding surfaces while the Skolithos assemblage with the Planolites-Palaeophycus assemblage (TRC-I), Arenicolites assemblage (TRC-II) and Planolites-Palaeophycus assemblage (TRC-III) mark the regressive surfaces. These soft ground ichnoassemblages mark the Skolithos and Cruziana ichnofacies conditions developed in progradational and retrogradational sequences and indicate cyclic changes in bathymetry within shoreface-offshore settings. An integrated sedimentological and ichnological approach has allowed the recognition of the internal organization of the sequence in absence of significant physical expressions of discontinuity surfaces at the T-R cycle scale.
Distribution of Benthic Ostracoda in surface and subsurface backwater sediments of Ernakulam, Kerala, Southwest coast of India: Microenvironmental Implications
Authors: Hussain S.M. , Kuleen E.C. , Jisha K. , Elumalai K. , Ravi G. 
Published: June 2015

Abstract:
Fourteen surface and two core sediment samples were collected from the backwaters of Cochin, Kerala, southwest coast of India, in order to study the systematics and distribution of Recent Ostracoda. The ostracod taxa were separated from the sediments applying standard micropaleontological techniques. A total of 20 Ostracod species belonging to 17 genera and 8 families were identified. Sediment parameters such as CaCO3, organic matter and sand-silt-clay ratio were estimated for the surface as well as core samples in order to determine the relationship between substrate and Ostracoda populations, and to evaluate the favoured substrate of dominant species populations. The down core distribution of sediment parameters and ostracod assemblages is presented. Based on this data we determine that ostracods favour silty-sandy substrate environments. The rate of sedimentation was determined based on the ratio between the carapace and open valves of Ostracoda. The benthic ostracod fauna recorded is characteristic of a tropical, brackish to epi-neritic environment and few warm, shallow marine species occur in the backwaters of Cochin, may be due to the tidal influence.
Paleoclimate and Paleoenvironment of the Naredi Formation (Early Eocene), Kutch, Gujarat, India
Authors: Khozyem Hassan , Adatte Thierry , Keller Gerta , Spangenberg Jorge E. , Saravanan N. , Bajpai Sunil 
Published: June 2015

Abstract :
The Naredi Formation of Kutch, Gujarat, India, is early Eocene in age and marks the first marine transgression above the last Deccan traps. Sediment deposition occurred in a shallow inner shelf environment that varied from a brackish lagoon to brackish, normal inner shelf and to marginal marine environments. The section can be divided into 2 main transgressive cycles interrupted by a regression phase that is marked by a well-defined sequence boundary marked by a root-bearing paleosoil. Three intervals yielded common to abundant benthic foraminiferal assemblages. Planktic foraminifera are few to rare and restricted to the top of the section, except for Chiloguembelina trinitatensis. An early Eocene age can be attributed to the Naredi section based primarily on larger benthic foraminifera (SBZ8 to SBZ11, equivalent to planktic foraminiferal biozones E4 to E6), rare planktic foraminifera, the stable isotope curve and its correlation with marine sections and sequence stratigraphy. Sediments of the transgression/regression cycles were derived from physical and chemical-weathering processes of basaltic rocks as indicated by the different geochemical proxies. Carbon isotope analyses of bivalve shells and organic matter reveal a negative excursion that is correlative with the global Early Eocene excursion. The presence of fish bones, fish teeth and organic matter can be related to the Early Eocene climatic optimum. Clay mineral data from the Naredi Formation indicate variably hot humid to arid climate conditions.
Strontium Isotope Stratigraphy of the Naredi Formation, Kutch Basin, India
Authors: Anwar Danish , Choudhary A.K. , Saraswati P.K. 
Published: June 2015

Abstract:
The Naredi Formation records the first marine transgression of the Cenozoic era in Kutch. Its age has remained equivocal and various workers have assigned different ages ranging from Late Palaeocene to Early and Middle Eocene. In this study we carried out strontium isotopic analysis of the foraminiferal shells of the Naredi Formation to determine its numerical age in order to resolve this controversy. The measured 87Sr/86Sr ratios, lying between 0.707727 and 0.707816, have been compared with the standard strontium isotope variation curve for the Cenozoic. Biostratigraphically, the formation ranges from shallow benthic zone SBZ 6 to SBZ 11 corresponding to planktonic foraminiferal zones P5 to P9 (Serra-Kiel et al., 1998). The biostratigraphically constrained Sr isotopic values indicate that the Naredi Formation is of Early Eocene age spanning from 50 to 55Ma.
Palaeoenvironmental Significance of Rectilinear Benthic Foraminifera in the Middle Eocene section of Matanomadh Sub-basin, Kutch
Authors: Khanolkar Sonal , Kumar Saraswati Pratul 
Published: June 2015

Abstract :
A lignite-bearing section at Matanomadh (N23°30′; E68°55′) in Kutch was examined for its foraminiferal assemblage. The section consists of lignite and carbonaceous shale in the lower part and mudstone in the upper part. The mudstone is characterized by a low diversity and moderate abundance of dwarf foraminifera. The presence of Halkyardia minima, Linderina kutchensis and Lockhartia alveolata suggests its correlation with Fulra Limestone exposed in the adjoining regions of Kutch. The smaller benthic foraminifera mainly include the species of Brizalina, Bulimina, Trifarina, Cibicides, Discorbis and Guttulina. The Rectilinear Benthic Foraminifera morphogroup (RBF) constituting up to 60% of the foraminiferal assemblage are characterized by large pores. These are typical characteristics of foraminiferal assemblages from low oxygen environment. The peak abundance of RBF occurs consistently at co-eval levels in several sections of Kutch. It is suggestive of dysoxic conditions in late Middle Eocene, corresponding to planktonic foraminiferal zone P13.