bluuebunny/crossref_metadata_2025 huggingface dataset:
RNA stem–loops: To be or not to be cleaved by RNAse III
Authors: Ritchie William , Legendre Matthieu , Gautheret Daniel
Published: February 2007

Most of the vertebrate genome is transcribed into RNA. Transcribed regions contain hundreds of thousands of potential duplex structures that could serve as substrates for RNAse III enzymes of microRNA (miRNA) maturation pathways. Yet, only a minority of these potential precursors make their way to the cytoplasm to form mature miRNAs. We question here what specific structural features make an RNA stem–loop structure an adequate primary or precursor miRNA. We address this question by comparing known pre-miRNAs to other predicted noncoding transcripts obtained from comparative genomics scans, using the structure comparison program RNAforester. By analyzing a classification tree of 1200 such RNA structures, we observe that pre-miRNAs cluster distinctly from other duplex structures of apparently similar size and free energy. The most distinctive features of nonprecursor duplexes are increased lengths and numbers of bulges and internal loops when compared to real miRNA precursors. Thanks to these characteristics, secondary structure comparison can predict the miRNA precursor status of a candidate stem–loop with a surprising accuracy. Furthermore, predicted noncoding transcripts tend to depart from miRNA precursor characteristics more strongly than randomly occurring duplex structures in genomic DNA. This result suggests that many noncoding RNAs may be under selection to dodge the RNAi pathway.
Dexmedetomidine: An Updated Review
Authors: Gerlach Anthony T , Dasta Joseph F
Published: February 2007

Objective:

To review recent literature on the safety and efficacy of dexmedetomidine.

Data Sources:

Articles were identified through searches of MEDLINE (1966–January 2007). Key words included dexmedetomidine, medetomidine, α2-agonist, and sedation. References from selected articles were reviewed for additional references.

Study Selection and Data Extraction:

Experimental and observational studies that focused on the safety and efficacy of dexmedetomidine in humans were selected.

Data Synthesis:

Dexmedetomidine is an α2-agonist for short-term sedation in critically ill patients. In postoperative patients, dexmedetomidine produced similar levels of sedation and times to extubation, with less opioid requirements compared with propofol. Dexmedetomidine has also been studied for sedation in critically ill medical and pediatric patients, as adjunct to anesthesia, and for procedural sedation. Hypotension, hypertension, and bradycardia are common adverse effects. Although dexmedetomidine is labeled only for sedation less than 24 hours, it has been administered for longer than 24 hours without apparent development of rebound hypertension and tachycardia.

Conclusions:

Dexmedetomidine is a safe and effective agent for sedation in critically ill patients. Further, well designed studies are needed to define its role as a sedative for critically ill medical, neurosurgical, and pediatric patients, as an adjunct to anesthesia, and as a sedative during procedures.
Phosholipase C-Related Inactive Protein Is Involved in Trafficking of γ2 Subunit-Containing GABAAReceptors to the Cell Surface
Authors: Mizokami Akiko , Kanematsu Takashi , Ishibashi Hitoshi , Yamaguchi Taku , Tanida Isei , Takenaka Kei , Nakayama Keiichi I. , Fukami Kiyoko , Takenawa Tadaomi , Kominami Eiki , Moss Stephen J. , Yamamoto Tsuneyuki , Nabekura Junichi , Hirata Masato
Published: February 2007

The subunit composition of GABAAreceptors is known to be associated with distinct physiological and pharmacological properties. Previous studies that used phospholipase C-related inactive protein type 1 knock-out (PRIP-1 KO) mice revealed that PRIP-1 is involved in the assembly and/or the trafficking of γ2 subunit-containing GABAAreceptors. There are two PRIP genes in mammals; thus the roles of PRIP-1 might be compensated partly by those of PRIP-2 in PRIP-1 KO mice. Here we used PRIP-1 and PRIP-2 double knock-out (PRIP-DKO) mice and examined the roles for PRIP in regulating the trafficking of GABAAreceptors. Consistent with previous results, sensitivity to diazepam was reduced in electrophysiological and behavioral analyses of PRIP-DKO mice, suggesting an alteration of γ2 subunit-containing GABAAreceptors. The surface numbers of diazepam binding sites (α/γ2 subunits) assessed by [3H]flumazenil binding were reduced in the PRIP-DKO mice as compared with those of wild-type mice, whereas the cell surface GABA binding sites (α/β subunits, assessed by [3H]muscimol binding) were increased in PRIP-DKO mice. The association between GABAAreceptors and GABAAreceptor-associated protein (GABARAP) was reduced significantly in PRIP-DKO neurons. Disruption of the direct interaction between PRIP and GABAAreceptor β subunits via the use of a peptide corresponding to the PRIP-1 binding site reduced the cell surface expression of γ2 subunit-containing GABAAreceptors in cultured cell lines and neurons. These results suggest that PRIP is implicated in the trafficking of γ2 subunit-containing GABAAreceptors to the cell surface, probably by acting as a bridging molecule between GABARAP and the receptors.
Activation of the Extracellular Signal-Regulated Kinase in the Amygdala Modulates Pain Perception
Authors: Carrasquillo Yarimar , Gereau Robert W.
Published: February 2007

The amygdala has been proposed to serve as a neural center for the modulation of pain perception. Numerous anatomical and behavioral studies demonstrate that exogenous manipulations of the amygdala (i.e., lesions, drug infusions) modulate behavioral responses to acute noxious stimuli; however, little is known about the endogenous molecular changes in the amygdala that contribute to alterations in nociceptive processing during persistent noxious stimuli that resemble pathological pain conditions. In the present study, we demonstrate that endogenous molecular changes in the amygdala play a crucial role in modulating long-lasting peripheral hypersensitivity associated with persistent inflammation and we further identify the extracellular signal-regulated kinase (ERK) as a molecular substrate underlying this behavioral sensitization. Using the formalin test as a mouse model of persistent inflammatory pain, we show that activation of ERK in the amygdala is both necessary for and sufficient to induce long-lasting peripheral hypersensitivity to tactile stimulation. Thus, blockade of inflammation-induced ERK activation in the amygdala significantly reduced long-lasting peripheral hypersensitivity associated with persistent inflammation, and pharmacological activation of ERK in the amygdala induced peripheral hypersensitivity in the absence of inflammation. Importantly, blockade of ERK activation in the amygdala did not affect responses to acute noxious stimuli in the absence of inflammation, indicating that modulation of nociceptive responses by amygdala ERK activation is specific to the persistent inflammatory state. Altogether, our results demonstrate a functional role of the ERK signaling cascade in the amygdala in inflammation-induced peripheral hypersensitivity.
Development of Inhibitory Mechanisms Underlying Selectivity for the Rate and Direction of Frequency-Modulated Sweeps in the Auditory Cortex
Authors: Razak Khaleel A. , Fuzessery Zoltan M.
Published: February 2007

Although it is known that neural selectivity for species-specific vocalizations changes during development, the mechanisms underlying such changes are not known. This study followed the development of mechanisms underlying selectivity for the direction and rate of frequency-modulated (FM) sweeps in the auditory cortex of the pallid bat, a species that uses downward FM sweeps to echolocate. In the adult cortex, direction and rate selectivity arise as a result of different spectral and temporal properties of low-frequency inhibition (LFI) and high-frequency inhibition (HFI). A narrow band of delayed HFI shapes rate selectivity for downward FM sweeps. A broader band of early LFI shapes direction selectivity. Here we asked whether these differences in LFI and HFI are present at the onset of hearing in the echolocation range or whether the differences develop slowly. We also studied how the development of properties of inhibitory frequencies influences FM rate and direction selectivity. We found that adult-like FM rate selectivity is present at 2 weeks after birth, whereas direction selectivity matures 12 weeks after birth. The different developmental time course for direction and rate selectivity is attributable to the differences in the development of LFI and HFI. Arrival time and bandwidth of HFI are adult-like at 2 weeks. Average arrival time of LFI gradually becomes faster and bandwidth becomes broader between 2 and 12 weeks. Thus, two properties of FM sweeps that are important for vocalization selectivity follow different developmental time courses attributable to the differences in the development of underlying inhibitory mechanisms.
Spatial and Temporal Distribution of Odorant-Evoked Activity in the Piriform Cortex
Authors: Rennaker Robert L. , Chen Chien-Fu F. , Ruyle Andrea M. , Sloan Andrew M. , Wilson Donald A.
Published: February 2007

Despite a remarkably precise spatial representation of odorant stimuli in the early stages of olfactory processing, the projections to the olfactory (piriform) cortex are more diffuse and show characteristics of a combinatorial array, with extensive overlap of afferent inputs and widespread intracortical association connections. Furthermore, although there is increasing evidence for the importance of temporal structure in olfactory bulb odorant-evoked output, little is known about how this temporal patterning is translated within cortical neural ensembles. The present study used multichannel electrode arrays and paired single-unit recordings in rat anterior piriform cortex to test several predictions regarding ensemble coding in this system. The results indicate that odorants evoke activity in a spatially scattered ensemble of anterior piriform cortex neurons, and the ensemble activity includes a rich temporal structure. The most pronounced discrimination between different odorants by cortical ensembles occurs during the first inhalation of a 2 s stimulus. The distributed spatial and temporal structure of cortical activity is present at both global and local scales, with neighboring single units contributing to coding of different odorants and active at different phases of the respiratory cycle. Finally, cross-correlogram analyses suggest that cortical unit activity reflects not only afferent input from the olfactory bulb but also intrinsic activity within the intracortical association fiber system. These results provide direct evidence for predictions stemming from anatomical- and theoretical-based models of piriform cortex.
The Role of Physiological Afferent Nerve Activity duringIn VivoMaturation of the Calyx of Held Synapse
Authors: Erazo-Fischer Emilio , Striessnig Jörg , Taschenberger Holger
Published: February 2007

We studied how afferent nerve activity affects thein vivomaturation of a fast glutamatergic CNS synapse, the calyx of Held. To address this question, we exploited the distinct presynaptic Ca2+channel subtypes governing transmitter release at the cochlear inner hair cell (IHC)–spiral neuron synaptic junction compared with those at higher synapses along the auditory pathways. We characterized the functional properties of calyx synapses in wild type (wt) compared with those developing inCaV1.3 subunit-deficient(CaV1.3−/−) mice.CaV1.3−/−mice are deaf because of an absence of glutamate release from IHC, which results in a complete lack of cochlea-driven nerve activity. Presynaptic Ca2+channel properties, Ca2+dependence of exocytosis, number of readily releasable quanta, and AMPA mEPSCs were unchanged in postnatal day 14 (P14) to P17 calyx synapses ofCaV1.3−/−mice. However, synaptic strength was augmented because presynaptic action potentials were broader, leading to increased quantal release, consistent with lower paired-pulse ratios and stronger depression during repetitive synaptic stimulation. Furthermore, asynchronous release after trains was elevated presumably because of higher residual Ca2+accumulating in the presynaptic terminals. Finally, we measured larger NMDA EPSCs with higher sensitivity to the NR2B subunit-specific antagonist ifenprodil in P14–P17 synapses ofCaV1.3−/−compared withwtmice. These results suggest that auditory activity is required for the adjustment of synaptic strength as well as for the downregulation of synaptic NMDA receptors during postnatal development of the calyx of Held. In contrast, properties of the presynaptic release machinery and postsynaptic AMPA receptors are unaffected by chronic changes in the level of afferent activity at this synapse.
Opioid Limbic Circuit for Reward: Interaction between Hedonic Hotspots of Nucleus Accumbens and Ventral Pallidum
Authors: Smith Kyle S. , Berridge Kent C.
Published: February 2007

μ-Opioid stimulation of cubic millimeter hedonic hotspots in either the nucleus accumbens shell (NAc) or the ventral pallidum (VP) amplifies hedonic “liking” reactions to sweetness and appetitive “wanting” for food reward. How do these two NAc–VP hotspots interact? To probe their interaction and limbic circuit properties, we assessed whether opioid activation of one hotspot recruited the other hotspot (neurobiologically) and whether opioid hedonic and incentive motivational amplification by either opioid hotspot required permissive opioid coactivation in the other (behaviorally). We found that NAc and VP hotspots reciprocally modulated Fos expression in each other and that the two hotspots were needed together to enhance sucrose “liking” reactions, essentially cooperating within a single hedonic NAc–VP circuit. In contrast, the NAc hotspot dominated for opioid stimulation of eating and food intake (“wanting”), independent of VP activation. This pattern reveals differences between limbic opioid circuits that control reward “liking” and “wanting” functions.
Developmental Homeostasis of Mouse Retinocollicular Synapses
Authors: Chandrasekaran Anand R. , Shah Ruchir D. , Crair Michael C.
Published: February 2007

Spontaneous retinal waves during development are thought to provide an instructive signal for precise retinotopic mapping by correlating the activity of neighboring retinal ganglion cells. In mutant mice (β2−/−) that lack correlated waves, retinocollicular map refinement is impaired.In vivorecordings reveal that neurons in the superior colliculus of β2−/−mice have large receptive fields and low peak visual responses, resulting in a conservation of total integrated response. We find that this “response homeostasis” is maintained on a cell-by-cell basis, and argue that it does not depend on regulation from the visual cortex during adulthood. Instead,in vitrorecordings show that homeostasis arises from the conservation of total synaptic input from the retina, and that it is maintained via different mechanisms over development. In the absence of correlated retinal waves, β2−/−neurons sample a larger number of weaker retinal inputs relative to controls after the first postnatal week. Once retinal waves are restored, developmental learning rules and homeostasis drive refinement so that fewer, stronger synapses are retained, as in wild-type mice, but from a larger retinal area. Homeostasis in neurons has been shown previously to regulate the gain of synaptic transmission in response to perturbations of activity. Our results suggest that during the development of sensory maps, a unique consequence of homeostatic mechanisms is the precise shaping of neuronal receptive fields in conjunction with activity-dependent competition.
Allelic Variation inRGS4Impacts Functional and Structural Connectivity in the Human Brain
Authors: Buckholtz Joshua W. , Meyer-Lindenberg Andreas , Honea Robyn A. , Straub Richard E. , Pezawas Lukas , Egan Michael F. , Vakkalanka Radhakrishna , Kolachana Bhaskar , Verchinski Beth A. , Sust Steven , Mattay Venkata S. , Weinberger Daniel R. , Callicott Joseph H.
Published: February 2007

Regulator of G-protein signaling 4 (RGS4) modulates postsynaptic signal transduction by affecting the kinetics of Gα-GTP binding. Linkage, association, and postmortem studies have implicated the gene encoding RGS4 (RGS4) as a schizophrenia susceptibility factor. Using a multimodal neuroimaging approach, we demonstrate that genetic variation inRGS4is associated with functional activation and connectivity during working memory in the absence of overt behavioral differences, with regional gray and white matter volume and with gray matter structural connectivity in healthy human subjects. Specifically, variation at oneRGS4single nucleotide polymorphism that has been associated previously with psychosis (rs951436) impacts frontoparietal and frontotemporal blood oxygenation level-dependent response and network coupling during working memory and results in regionally specific reductions in gray and white matter structural volume in individuals carrying the A allele. These findings suggest mechanisms in brain for the association ofRGS4with risk for psychiatric illness.
Neurotoxic and Gliotrophic Activity of a Synthetic Peptide Homologous to Gerstmann–Sträussler–Scheinker Disease Amyloid Protein
Authors: Fioriti Luana , Angeretti Nadia , Colombo Laura , De Luigi Ada , Colombo Alessio , Manzoni Claudia , Morbin Michela , Tagliavini Fabrizio , Salmona Mario , Chiesa Roberto , Forloni Gianluigi
Published: February 2007

Amyloid fibrils in Gerstmann–Sträussler–Scheinker (GSS) disease are composed of a fragment of the prion protein (PrP), the N and C termini of which correspond to ragged residues 81–90 and 144–153. A synthetic peptide spanning the sequence 82–146 (PrP 82–146) polymerizes into protease-resistant fibrils with the tinctorial properties of amyloid. We investigated the biological activity of PrP 82–146 and of two nonamyloidogenic variants of PrP 82–146 with scrambled amino acid sequence 106–126 or 127–146. Cortical neurons prepared from rat and mouse embryos were chronically exposed to the PrP 82–146 peptides (10–50 μm). PrP 82–146 and the partially scrambled peptides induced neuronal death with a similar dose–response pattern, indicating that neurotoxicity was independent of amyloid fibril formation. Neurotoxicity was significantly reduced by coadministration of an anti-oligomer antibody, suggesting that PrP 82–146 oligomers are primarily responsible for triggering cell death. Neurons from PrP knock-out (Prnp0/0) mice were significantly less sensitive to PrP 82–146 toxicity than neurons expressing PrP. The gliotrophic effect of PrP 82–146 was determined by [methyl-3H]-thymidine incorporation in cultured astrocytes. Treatment with PrP 82–146 stimulated [methyl-3H]-thymidine uptake 3.5-fold. This activity was significantly less when the 106–126 or 127–146 regions were disrupted, indicating that PrP 82–146 amyloid activates the gliotrophic response. Prnp0/0 astrocytes were insensitive to the proliferative stimulus of PrP 82–146. These results underline the role of cerebral accumulation of abnormally folded PrP fragments and indicate that cellular PrP governs the pathogenic process.
Regeneration of Inner Retinal Neurons after Intravitreal Injection of Ouabain in Zebrafish
Authors: Fimbel Shane M. , Montgomery Jacob E. , Burket Christopher T. , Hyde David R.
Published: February 2007

We examined the regenerative capacity of the adult zebrafish retina by intravitreal injection of a low ouabain concentration to rapidly damage the ganglion cell layer (GCL) and inner nuclear layer (INL) with minimal photoreceptor cell damage. By 24 h after ouabain injection, maximal numbers of terminal deoxynucleotidyl transferase-mediated biotinylated UTP nick end labeling (TUNEL)-positive cells were detected in the INL and GCL, with low numbers of TUNEL-positive cells in the outer nuclear layer. Immunolabeling revealed that ∼85% of the HuC/D-positive amacrine and ganglion cells were lost by 7 d post-ouabain injection (dpi). This ganglion cell loss was consistent with the small, but statistically significant, decrease in the optic nerve diameter. The regeneration response began within 1 dpi with increased proliferating cell nuclear antigen (PCNA) expression in both the INL and GCL. By 3 dpi, PCNA expression is primarily restricted to the Müller glia. By 5 dpi, most of the PCNA expression was localized to neuronal progenitors expressing theolig2:egfptransgene rather than the Müller glia. By 7 dpi, the neuronal progenitors began committing to the ganglion cell fate based on the coexpression of theatoh7:EGFPtransgene and the zn5 antigen. The regeneration of ganglion and amacrine cells continued until 60 dpi, when they reached 75% of their uninjected control number. This demonstrates that inner retinal damage, without extensive photoreceptor damage, is sufficient to induce a regeneration response that is marked by the Müller glial cells reentering the cell cycle to produce neuronal progenitor cells that regenerate INL and ganglion cells in the zebrafish retina.
Automatisches Reglertuning basierend auf Methoden des Control Performance Monitoring (Automatic Controller Tuning based on Control Performance Monitoring)
Authors: Jelali Mohieddine
Published: February 2007

Die Regelkreisüberwachung, auch Control Performance Monitoring (CPM) genannt, gewinnt in letzter Zeit immer mehr an Bedeutung als Komponente einer umfassenden und effektiven Anlagenüberwachung in der Prozessindustrie. Der Beitrag stellt neue Verfahren zum automatischen Reglertuning auf der Basis von Methoden und Indices des CPM vor. Sie zielen auf die Optimierung der Performance von Regelkreisen, die nach dem Bewertungsschritt als schwach/falsch eingestellt identifiziert werden. Die beschriebenen Reglertuningprozeduren liefern Einstellparameter, die eine mit PID-Reglern bestmögliche (stochastische) Performance im Sinne einer Maximierung des Performanceindex gewährleisten. Es erfolgt eine Klassifikation der Methoden in direkte und indirekte (d. h. iterative) Verfahren. Die Voraussetzungen und Eigenschaften von jeweils zwei Vertretern jeder Methodenklasse werden ausführlich dargestellt und verglichen.
Resistance, Rivalries, and Restaurants: Vietnamese Workers in Interwar France
Authors: Peters Erica J.
Published: February 2007

To complicate the well-researched story of the activities of colonial emigréés in France, this article focuses on the role of less visible groups. Despite rhetoric about intellectuals fusing with the people, there was no enduring Vietnamese student-worker alliance in interwar France. Workers formed their own organizations, notably the Association des Cuisiniers Indochinois and the Association Amicale des Indochinois (Travailleurs Manuels). Careful study of the expressed desires, daily practices, and networks of these working-class expatriates demonstrates that language and routines played as large a role as regional origin in dividing the Vietnamese community in interwar France.
From Patronage to "Outcomes": Vietnam's Communist Party Congresses Reconsidered
Authors: Gainsborough Martin
Published: February 2007

The article offers a revisionist approach to assessing the significance of Communist Party congresses in Vietnam. Analysis to date has focused on the presumed policy significance of a particular congress. The article argues that much more important than policy are outcomes, or what actually happens on the ground. Consequently, it is suggested that a more fruitful way to assess the significance of Vietnam's congresses is to view them first and foremost as occasions when access to patronage and political protection are circulated and then consider how outcomes emerge as a result of this.
Lýý Toéét in the City: Coming to Terms with the Modern in 1930s Vietnam
Authors: Dutton George
Published: February 2007

The emergence of popular journalism in 1930s Vietnam allowed for new forms of commentary on a transformed urban life, among them caricatures featuring LB Toéét, a villager bewildered by his encounters with the modern city. This article uses the LB To�t cartoons that appeared in the weekly journal Phong Hóóa [Mores] as a window on urban attitudes toward the modern. It suggests that the illustrations reveal a considerable ambivalence toward modernity on the part of Phong Hóóa's editors, despite their rhetorical commitment to the new and the modern.
The preservational fidelity of evenness in molluscan death assemblages
Authors: Olszewski Thomas D. , Kidwell Susan M.
Published: February 2007

The richness (number of species) and evenness (uniformity of species abundances) of death assemblages can differ from corresponding living communities due to processes such as between-habitat transport, environmental condensation, and differential taphonomic destruction. Analysis of 132 single-census live-dead comparisons of benthic molluscs from a variety of soft-bottom marine settings indicates thaton averageevenness does not differ greatly between live and dead assemblages, regardless of the particular depositional setting or grain size of associated sediment. However,individualdeath assemblages can deviate quite substantially from their corresponding living assemblages, especially if processed using a fine mesh. In addition, death assemblages collected using sieves with 2 mm mesh or coarser showed consistently and significantly greater evenness than corresponding living assemblages. These results are encouraging for broad-scale assessments of evenness in the fossil record based on the comparison ofaveragevalues (rather than for individual assemblages) and wheretrendsin evenness are the aim of the study.

Our live-dead comparisons of richness sample-size corrected by rarefaction revealed that death assemblages were on average ~1.45 times richer than the corresponding living assemblages regardless of rarefied size. In 63.6% of death assemblages both dead richness and dead evenness were greater than live, suggesting sufficient time-averaging to catch significant random or directional changes in the living community and/or introduction of individuals from outside the sampled habitat. In 12.9% of collections both dead richness and dead evenness were less than live, suggesting either rapid loss of dead shells so that dead diversity is depressed below the local living community or selective loss of taphonomically vulnerable taxa. In 18.2% of data sets dead richness was elevated but dead evenness was depressed relative to live: these are interpreted to reflect the addition of low-evenness allochthonous material. The remaining 4.5% of data sets had elevated dead evenness but depressed dead richness, suggesting that live and dead in this case may not be closely related.

In seven available time series, temporal volatility in living communities over 6–24 months was considerable but could not account for observed (mostly higher) evenness values in corresponding death assemblages, whose evenness and composition were quite stable in the few examined studies. A densely sampled spatial transect shows that changes in living-assemblage evenness along an environmental gradient were preserved in the corresponding death assemblages, although dead evenness at any location on the gradient was substantially higher than living evenness.
Changes in theoretical ecospace utilization in marine fossil assemblages between the mid-Paleozoic and late Cenozoic
Authors: Bush Andrew M. , Bambach Richard K. , Daley Gwen M.
Published: February 2007

We present a new three-dimensional theoretical ecospace for the ecological classification of marine animals based on vertical tiering, motility level, and feeding mechanism. In this context, analyses of a database of level-bottom fossil assemblages with abundance counts demonstrate fundamental changes in marine animal ecosystems between the mid-Paleozoic (461–359 Ma) and late Cenozoic (23–0.01 Ma). The average local relative abundance of infaunal burrowers, facultatively motile animals, and predators increased, whereas surface dwellers and completely non-motile animals decreased in abundance. Considering tiering, motility, and feeding together, more modes of life had high to moderate average relative abundance in the Cenozoic than in the Paleozoic. These results are robust to the biasing effects of aragonite dissolution in Paleozoic sediments and to heterogeneities in the latitudinal and environmental distributions of collections. Theoretical ecospace provides a unified system for future analyses of the utilization of ecologic opportunities by marine metazoa.
Coral reef development drives molluscan diversity increase at local and regional scales in the late Neogene and Quaternary of the southwestern Caribbean
Authors: Johnson Kenneth G. , Todd Jonathan A. , Jackson Jeremy B. C.
Published: February 2007

The late Neogene was a time of major environmental change in Tropical America. Global cooling and associated oceanographic reorganization and the onset and intensification of glaciation in the Northern Hemisphere during the past ten million years coincided with the uplift of the Central American isthmus and resulting changes in regional oceanographic conditions. Previous analyses of patterns of taxonomic turnover and the shifting abundances of major ecological guilds indicated that the regional shallow-water marine biota responded to these environmental changes through extinction and via a restructuring of local benthic food webs, but it is not clear whether this ecological response had an effect on the diversity of molluscan assemblages in the region. Changes in regional and local diversity are often used as proxies for similar ecological response to environmental change in large-scale paleontological studies, but a clear relationship between diversity and ecological function has rarely been demonstrated in marine systems dominated by mollusks. To explore this relationship, we have compiled a data set of the stratigraphic and environmental distribution of genera of mollusks in large new collections of fossil specimens from the late Neogene and Recent of the southwestern Caribbean. Analysis of a selection of ecological diversity measures indicates that within shelf depths, assemblages from deeper water (51–200 m) were more diverse than shallow-water (<50 m) assemblages in the Pliocene. Lower diversity for shallow-water assemblages is caused by increased dominance of a few superabundant taxa in each assemblage. This implies that studies of diversity of shelf benthos need to control for relatively fine scaled environmental conditions if they are to avoid interpreting artifacts of uneven sampling as true change of diversity. For shallow-water assemblages only, there was significant increase in local and regional diversity of bivalve assemblages after the late Pliocene. No parallel increase in gastropods could be detected, but this likely is because sample size was inadequate for documenting the diversity of gastropod assemblages following a steep post-Pliocene decline of average gastropod abundance. Both the increasing bivalve diversity and the decrease in average abundance of gastropod taxa correspond to an interval of increasing carbonate deposition and reef building in the region, and are likely a result of increased fine-scale habitat heterogeneity controlled by the local distribution of carbonate buildups. Each of these results demonstrates that documenting the ecological response of tropical marine ecosystems to regional environmental change requires a large volume of fine-scaled samples with detailed paleoenvironmental control. Such data sets are rarely available from the fossil record.
A quantitative null model of additive diversity partitioning: examining the response of beta diversity to extinction
Authors: Layou Karen M.
Published: February 2007

Paleobiological diversity is often expressed as α (within-sample), β (among-sample), and γ (total) diversities. However, when studying the effects of extinction on diversity patterns, only variations in α and γ diversities are typically addressed. A null model that examines changes in β diversity as a function of percent extinction is presented here.

The model examines diversity in the context of a hierarchical sampling strategy that allows for the additive partitioning of γ diversity into mean α and β diversities at varying scales. Here, the sampling hierarchy has four levels: samples, beds, facies, and region; thus, there are four levels of α diversity (α1, α2, α3, α4) and three levels of β diversity (β1, β2, and β3). Taxa are randomly assigned to samples within the hierarchy according to probability of occurrence, and initial mean α and β values are calculated. A regional extinction is imposed, and the hierarchy is resampled from the remaining extant taxa. Post-extinction mean α and β values are then calculated.

Both non-selective and selective extinctions with respect to taxon abundance yield decreases in α, β, and γ diversities. Non-selective extinction with respect to taxon abundance shows little effect on diversity partitioning except at the highest extinction magnitudes (above 75% extinction), where the contribution of α1 to total γ increases at the expense of β3, with β1 and β2 varying little with increasing extinction magnitude. The pre-extinction contribution of α1 to total diversity increases with increased probabilities of taxon occurrence and the number of shared taxa between facies. Both β1 and β2 contribute equally to total diversity at low occurrence probabilities, but β2 is negligible at high probabilities, because individual samples preserve all the taxonomic variation present within a facies. Selective extinction with respect to rare taxa indicates a constant increase in α1 and constant decrease in β3 with increasing extinction magnitudes, whereas selective extinction with respect to abundant taxa yields the opposite pattern of an initial decrease in α1 and increase in β3. Both β1 and β2 remain constant with increasing extinction for both cases of selectivity. By comparing diversity partitioning before and after an extinction event, it may be possible to determine whether the extinction was selective with respect to taxon abundances, and if so, whether that selectivity was against rare or abundant taxa.

Field data were collected across a Late Ordovician regional extinction in the Nashville Dome of Tennessee, with sampling hierarchy similar to that of the model. These data agree with the abundant-selective model, showing declines in α, β, and γ diversities, and a decrease in α1 and increase in β3, which suggests this extinction may have targeted abundant taxa.
A model of wear in curved mammal teeth: controls on occlusal morphology and the evolution of hypsodonty in lagomorphs
Authors: Bair Andrea R.
Published: February 2007

Cheek teeth of some mammalian herbivores exhibit pronounced changes in occlusal size and shape through wear, purportedly caused by strong curvature. Such changes are extreme in the upper cheek teeth of extinct, dentally archaic lagomorphs. Morphologic and taxonomic turnover in lagomorphs suggests that these dentally archaic forms may have been unable to develop hypselodont (ever-growing) cheek teeth. This study investigates how the interaction of tooth shape and wear can cause occlusal size and shape changes, and potentially impose structural constraints on crown height. These constraints may help explain extinction of mammals with teeth like archaic lagomorphs, evolution and diversification of other mammalian herbivores during the late Miocene, and the relative paucity of hypsodont cheek tooth shapes in extant mammals.

I first quantify two-dimensional curvature accounting for shape differences observed in hypsodont teeth, P4s of the archaic lagomorphsRussellagusandHesperolagomys, which exhibit pronounced change with wear, andOndatralower incisors, which show minimal change with wear. Using this quantification, I generate theoretical curvature morphologies and describe a geometric model of tooth wear that generates values for qualitative and quantitative aspects of the occlusal surface at different wear stages. Modeled results of wear surface topography and dimensions closely correspond to observed patterns inRussellagus, Hesperolagomys, andOndatra. Model results on wear in theoretical tooth morphologies identify two major shape factors influencing wear: orientation of the wear surface (incisor-like or cheek-tooth-like), and tooth curvature (“concentric” or “nonconcentric”). Modeled wear also suggests two geometric constraints on crown height. Teeth with nonconcentric curvatures can have crown height limited by potential tooth area. “Incomplete wear” in any tooth can present severe constraints on increasing crown height, causing structurally untenable morphologies in very tall-crowned to hypselodont teeth.
Ontogeny in the fossil record: diversification of body plans and the evolution of “aberrant” symmetry in Paleozoic echinoderms
Authors: Sumrall Colin D. , Wray Gregory A.
Published: February 2007

Echinoderms have long been characterized by the presence of ambulacra that exhibit pentaradiate symmetry and define five primary body axes. In reality, truly pentaradial ambulacral symmetry is a condition derived only once in the evolutionary history of echinoderms and is restricted to eleutherozoans, the clade that contains most living echinoderm species. In contrast, early echinoderms have a bilaterally symmetrical 2-1-2 arrangement, with three ambulacra radiating from the mouth. Branching of the two side ambulacra during ontogeny produces the five adult rays. During the Cambrian Explosion and Ordovician Radiation, some 30 clades of echinoderms evolved, many of which have aberrant ambulacral systems with one to four rays. Unfortunately, no underlying model has emerged that explains ambulacral homologies among disparate forms. Here we show that most Paleozoic echinoderms are characterized by uniquely identifiable ambulacra that develop in three distinct postlarval stages. Nearly all “aberrant” echinoderm morphologies can be explained by the paedomorphic ambulacra reduction (PAR) model through the loss of some combination of these growth stages during ontogeny. Superficially similar patterns of ambulacral reduction in distantly related clades have resulted from the parallel loss of homologous ambulacra during ontogeny. Pseudo-fivefold symmetry seen in Blastoidea and the true fivefold symmetry seen in Eleutherozoa result from great reduction and total loss, respectively, of the 2–1–2 symmetry early in ontogeny. These ambulacral variations suggest that both developmental and ecological constraints affect the evolution of novel echinoderm body plans.
Polychlorinated biphenyl contamination of the spider crab (Maja brachydactyla): Influence of physiological and ecological processes
Authors: Bodin Nathalie , Caisey Xavier , Abarnou Alain , Loizeau Véronique , Latrouite Daniel , Guellec Anne-Marie Le , Guillou Monique
Published: February 2007

Maja brachydactyla is a decapod crustacean widely distributed along the Northeast Atlantic coasts. The main objective of this work was to establish the influence of ontogenic factors, such as growth, aging, seasonal migrations, and reproduction, on the contamination of this species by polychlorinated biphenyls (PCBs). Two populations were studied: One in the Seine Bay (Eastern English Channel), which is exposed to greatly contaminated discharges from the Seine River, and one in the Iroise Sea (Western Brittany), which is little contaminated by such man-made compounds. At both sampling areas, PCB analysis revealed concentrations in hepatopancreas that were 10- and 50-fold higher than concentrations in gonads and muscle, respectively. Levels of 2,2′,4,4′,5,5′-hexachlorobiphenyl (CB153) increased with the age of the spider crabs, whereas their seasonal migrations had no direct effect. No significant sex effect was observed with regards to CB153 levels, but adult females exhibited PCB fingerprints different from those of males, probably because of the influence of the reproductive cycle on enzymatic system activity. Finally, spawning gave rise to a higher CB153 decontamination of female body burdens for specimens from the Iroise Sea than for those from the Seine Bay.
Desorption kinetics of hydrophobic organic chemicals from sediment to water: A review of data and models
Authors: Birdwell Justin , Cook Robert L. , Thibodeaux Louis J.
Published: February 2007

Resuspension of contaminated sediment can lead to the release of toxic compounds to surface waters where they are more bioavailable and mobile. Because the timeframe of particle resettling during such events is shorter than that needed to reach equilibrium, a kinetic approach is required for modeling the release process. Due to the current inability of common theoretical approaches to predict site-specific release rates, empirical algorithms incorporating the phenomenological assumption of biphasic, or fast and slow, release dominate the descriptions of nonpolar organic chemical release in the literature. Two first-order rate constants and one fraction are sufficient to characterize practically all of the data sets studied. These rate constants were compared to theoretical model parameters and functionalities, including chemical properties of the contaminants and physical properties of the sorbents, to determine if the trends incorporated into the hindered diffusion model are consistent with the parameters used in curve fitting. The results did not correspond to the parameter dependence of the hindered diffusion model. No trend in desorption rate constants, for either fast or slow release, was observed to be dependent on KOC or aqueous solubility for six and seven orders of magnitude, respectively. The same was observed for aqueous diffusivity and sediment fraction organic carbon. The distribution of kinetic rate constant values was approximately log-normal, ranging from 0.1 to 50 d−1 for the fast release (average ∼5 d−1) and 0.0001 to 0.1 d−1 for the slow release (average ∼0.03 d−1). The implications of these findings with regard to laboratory studies, theoretical desorption process mechanisms, and water quality modeling needs are presented and discussed.
Competition among zinc, manganese, and cadmium uptake in the freshwater alga Scenedesmus vacuolatus
Authors: Töpperwien Stefanie , Behra Renata , Sigg Laura
Published: February 2007

In the present study, Zn and Mn competition with Cd uptake was investigated in the freshwater alga Scenedesmus vacuolatus. Scenedesmus vacuolatus was exposed to experimental media with Cd and either Zn or Mn in short-term experiments; long-term experiments were undertaken to investigate the effect of growth on Cd accumulation. Cadmium accumulation in S. vacuolatus could be detected at very low exposure concentrations (free Cd2+, 2 × 10−14 to 1 × 10−11 M), and uptake was proportional to the free-Cd2+ concentration. Zinc was an effective competitive inhibitor of Cd uptake when the Zn2+ to Cd2+ ratio was greater than 14 in the exposure medium, whereas Mn competed with Cd for uptake above a Mn2+ to Cd2+ ratio of greater than 10,000. Binding constants for Cd and Zn affinity to the transport sites were determined (KZn and KCd). Values for KZn were slightly higher (log K = 9.4–9.8) than values for KCd (log K = 8.9–9.8). In contrast, Cd seemed not to compete with the Mn-binding sites for uptake over the Mn concentration range from 1 × 10−10 to 1 × 10−8 M. Determined values for the binding constants of Zn and Cd show that a simple model can be applied to predict Cd uptake at known Zn and Cd concentrations. The environmental implications of these results are discussed with respect to potential Cd toxicity for aquatic organisms.
Availability of polycyclic aromatic hydrocarbons from lampblack-impacted soils at former oil-gas plant sites in California, USA
Authors: Hong Lei , Luthy Richard G.
Published: February 2007

Lampblack-impacted soils at former oil-gas plant sites in California, USA, were characterized to assess the sorption of polycyclic aromatic hydrocarbons (PAHs) and the concentration-dependent effects of a residual oil tar phase on sorption mechanism and availability of PAHs. Nuclear magnetic resonance spectroscopy demonstrated similar aromaticity for both lampblack carbon and the oil tar phase, with pronounced resonance signals in the range of 100 to 150 ppm. Scanning-electron microscopic images revealed a physically distinct oil tar phase, especially at high concentrations in lampblack, which resulted in an organic-like film structure when lampblack particles became saturated with the oil tar. Sorption experiments were conducted on a series of laboratory-prepared lampblack samples to systematically evaluate influences of an oil tar phase on PAH sorption to lampblack. Results indicate that the sorption of PAHs to lampblack exhibits a competition among sorption phases at low oil tar contents when micro- and mesopores are accessible. When the oil tar content increases to more than 5 to 10% by weight, this tar phase fills small pores, reduces surface area, and dominates PAH sorption on lampblack surface. A new PAH partitioning model, Kd = KLB-C(1-ftar)° + ftarKtar (α = empirical exponent), incorporates these effects in which the control of PAH partitioning transits from being dominated by sorption in lampblack (KLB-C) to absorption in oil tar (Ktar), depending on the fraction of tar (ftar). This study illustrates the importance of understanding interactions among PAHs, oil tar, and lampblack for explaining the differences in availability of PAHs among site soils and, consequently, for refining site-specific risk assessment and establishing soil cleanup levels.
Cadmium uptake byCeriodaphnia dubiafrom different exposures: Relevance to body burden and toxicity
Authors: Sofyan Agus , Rosita Gina , Price David J. , Birge Wesley J.
Published: February 2007

Uptake of cadmium from water by freshwater animals has been well documented. However, little attention has been given to the importance of dietary and combined exposure as the source for uptake. In the present study, we compared cadmium uptake from waterborne (water-only), dietary (food-only), and combined (water plus food) exposures on the freshwater cladoceran Ceriodaphnia dubia. Major test end points included cadmium whole-body burdens, feeding rate, and reproduction. The C. dubia three-brood reproduction tests were conducted according to U.S. Environmental Protection Agency methods. The results indicated that cadmium was accumulated from both water and diet. Whereas the results showed that uptake from water was more rapid than uptake from diet, both uptakes occurred independently, and cadmium concentrations in C. dubia were additive from both sources. Furthermore, the present study found cadmium trophic transfer between primary producers (i.e., Pseudokirchneriella subcapitata) and primary consumers (i.e., C. dubia). Feeding rate was reduced from all avenues of exposure. Feeding reduction in combined exposure was affected additively by waterborne and dietary cadmium. Also, reductions in neonate production were observed after exposure to all three exposure types. Both body burden and reduced feeding affected C. dubia reproduction. These results indicate the importance of both waterborne and dietary cadmium exposures as the sources for metal uptake and toxicity.