bluuebunny/crossref_metadata_2025 huggingface dataset:
Comorbid Schizophrenia and Substance Abuse: A Review of Epidemiology and Course
Authors: Westermeyer Joseph
Published: September 2006

Over the last dozen years, our knowledge regarding comorbid schizophrenia (SCZ) and substance use disorder (SUD) has evolved in several ways. First, the rate of lifetime comorbid SCZ‐SUD appears to have increased another 20–30%, so now about 70–80% of persons with SCZ have lifetime SUD. Second, early remission of SUD has become commonplace among patients with SCZ, perhaps outnumbering the number of SCZ‐only patients as well as those with active SCZ‐SUD. Third, sustained SUD remission is well demonstrated, though the rates may yet be low. Fourth, research on comorbid SCZ‐SUD is filling out our knowledge in many areas, including the characteristics of SCZ patients at risk for SUD, reasons SCZ patients seek out substances, effects of various substances on SCZ course and symptoms, and obstacles to SUD recovery in people with SCZ. The influence of SUD treatment and self‐help on epidemiology and course has not been adequately evaluated. Primary prevention and early treatment of SUD in SCZ patients are still relatively neglected, though they offer our greatest hope for enhancing the lives of people with SCZ and improving the cost efficacy of care.
Exploration of the Relationship between Drinking Intensity and Quality of Life
Authors: Stewart Scott H. , Hutson Alan , Connors Gerard J.
Published: September 2006

This work explored the association between quality of life and drinking intensity in the Project MATCH sample. Tobit regression models were evaluated to assess the relationship between quality of life indicators (eg, measures of depression, adverse consequences, and others) and drinks per drinking day (DDD), and to assess modification or confounding of DDD by subject characteristics and treatment type. Each quality of life indicator improved with decreased DDD. Gender and ethnicity modified the DDD effect for some outcomes, with DDD exerting a greater influence on quality of life in women and non‐Hispanic whites.
Using Addiction Severity Profiles to Differentiate Cocaine‐Dependent Patients with and without Comorbid Major Depression
Authors: Leventhal Adam M. , Mooney Marc E. , DeLaune Katherine A. , Schmitz Joy M.
Published: September 2006

This study compared pretreatment addiction severity profiles of 339 abusers in three diagnostic groups: cocaine dependence only (CO), cocaine dependence with substance‐induced major depression (SIMD), and cocaine dependence with independent major depression (IMD). Depressed subjects reported more severe problems than non‐depressed subjects across numerous domains, regardless of diagnostic etiology. These findings support the need for specialized treatment approaches targeting depressive symptoms or life stress for cocaine‐dependent patients with IMD or SIMD, though patients with IMD may require additional attention for chronic and comorbid psychiatric and medical problems.
A Gendered Analysis of Canadian Aboriginal Individuals Admitted to Inpatient Substance Abuse Detoxification: A Three‐Year Medical Chart Review
Authors: Callaghan Russell C. , Cull Randi , Vettese Lisa C. , Taylor Lawren
Published: September 2006

This study examined gender differences within a sample of Canadian Aboriginal individuals admitted to an inpatient, hospital‐based substance abuse detoxification program. Even though alcohol was the most frequent primary drug of detoxification for both genders, women received proportionately higher rates of cocaine or opiate detoxification diagnoses. In addition to a younger age, females reported higher rates of physical and sexual abuse. Women were also administered antidepressants, antibiotic medication protocols, and more medical evaluation tests. It appears that Canadian Aboriginal women have a diverse set of psychological and medical needs. This study demonstrates the need for detoxification programs to address the substantial rates of intravenous drug use and the associated risk of infectious disease (eg, Hepatitis C, HIV) among this treatment‐seeking population.
Self‐Harm and Suicidal Behavior in Women with Comorbid PTSD and Substance Dependence
Authors: Harned Melanie S. , Najavits Lisa M. , Weiss Roger D.
Published: September 2006

This study examined the frequency, methods, and correlates of self‐harm and suicidal behavior in 65 outpatient women with comorbid posttraumatic stress disorder (PTSD) and substance dependence (SD). Results showed high rates of suicide attempts, self‐harm, suicidal ideation, and self‐harm ideation for the prior three months. The most common methods were overdosing and cutting/scratching. Both PTSD and SD were perceived as contributing to self‐harm and suicidal behavior. Women who had and had not engaged in such behavior differed in SD diagnoses and reasons for staying safe, but not in the number or type of traumatic experiences, age at first trauma, or substance abuse diagnoses.
Lake Winnipeg, remnant of glacial Lake Agassiz, an efficient dispersal route of planktonic crustaceans through central and northern Canada
Authors: Patalas K.
Published: September 2006

Zooplankton in five lake regions once inundated by Lake Agassiz were compared with zooplankton of 10 other lake regions and in 5 Great Lakes in south—central Canada. The highest resemblance to a hypothetical composite of Lake Agassiz plankton, from 94 to 100 percent, was found in lakes of the Northern Manitoba, Northern Saskatchewan and Upper Mackenzie regions. Eighty nine to 94 percent of zooplankton from the Laurentian Great Lakes came from the Agassiz Lake fauna. The only other species found in the Great Lakes in 1969 were Eurytemora affinis, and Eubosmina coregoni, newcomers to the North American fauna from Europe.

The number of species shared with the hypothetical fauna of Lake Agassiz declines with the distance from this glacial lake. From 91 to 93 percent of Lake Agassiz species were found in Manitoba Western, Southern Manitoba and Alberta, 85 to 86 percent in New Brunswick and Newfoundland, 80 to 84 percent in Nova Scotia and Southern British Columbia and about 74 percent in the lakes of the Mackenzie Delta region.

Lake Agassiz appeared to be a very efficient south-north dispersion route. Of the 35 species originating from the Mississippi refugium, 24 species penetrated as far as the Upper Mackenzie region and 16 species reached the Mackenzie Delta. The north to south dispersion route was not as effective. Of the 15 species originating from the Beringia refugium, seven species reached the Upper Mackenzie area and 5 species penetrated only to Northern Manitoba and Northern Saskatchewan. The fact that they did reach so far south could be explained by two different hypotheses. In the first, Lake Agassiz did not extend as far north as suggested by Teller or Fisher and Smith but rather the northern boundary corresponded to that indicated by Elson, and Northern Manitoba and Northern Saskatchewan were part of Lake McConnell. The second hypothesis states that the most northern portion of Lake Agassiz according to the boundary suggested by Teller or by Fisher and Smith served in the very late stage as a wide connecting channel with Lake McConnell and allowed some Beringia species to penetrate south, but no further than to Reindeer Lake, or perhaps to Southern Indian Lake.
Significance of coupling of nitrification and nitrate reduction on water quality of a coastal lake that receives nitrate in diverted Mississippi River water
Authors: Miao Shenyu , DeLaune R. D. , Jugsujinda A.
Published: September 2006

Nitrification and denitrification rates were estimated simultaneously using a 15N dilution technique in sediment-water columns of Lake Cataouatche that receives diverted Mississippi River water. Labeled and unlabeled NO3 were added to surface water of replicated sediment-water columns and changes in the concentrations of labeled and non-labeled nitrate in water were determined over time. The average rate of total nitrite plus nitrate NO2 + NO3 decrease from the water columns was 16.2 mg N m−3 d−1, whereas 15N-labeled (NO2 + NO3)-N decreased at the rates of 5.8 mg 15N m−3 d−1 over the 57 d incubation period. The averaged rates of nitrate reduction and nitrification were 51.8 μmol N m−2 h−1 (43.5 mg N m−3 d−1) and 30.8 μ mol N m−2 h−1 (25.9 mg N m−3 d−1), respectively. Results indicate the lake sediment has capacity to process nitrate entering the system via denitrification. Nitrification occurring simultaneously at the sediment-water interface was also a significant process representing 59.4 percent of the denitrification rate. Water quality issues associated with nitrate levels in diverted Mississippi water entering Lake Cataouatche should consider both the coupling of nitrate reduction of river water nitrate and nitrification of nitrogen in nitrogen-enriched lake sediment. Nitrification in bottom sediment is a significant nitrate source and should be regarded as important factor in the determination of the maximum daily load of nitrate that the lake can effectively assimilate without adversely affecting water quality.
Integrated management of water resources in river basins in China
Authors: Zeng Wei-hua , Yang Zhi-feng , Jia Gen-suo
Published: September 2006

Along with population explosion and social economic development, human beings continuously intensify the exploitation and use of water resources. The trend of water shortage becomes more austere day by day, and the conflicts among sectors of water resources consumers are also becoming increasingly acute. There are major conflicts dealing with water resources conservation, farmland irrigation, and domestic water utilization, as well as those among upper and lower river reaches and sustainable consumption. These conflicts in different sectors, districts and time periods can not be reconciled through traditional scattered methods of management; the only solution is through integrated management of water resources in river basins.

This paper starts by analyzing the progressing course and problems of water resources management in river basins in China and abroad, stands on the practical problems of water resources management and systematically generates the model, organization structure and technical framework of integrated management of river basins that would meet the conditions in China. The study was based on the analysis of a complicated system of water resources in river basins, and on theories of conflict analysis.
A management focused investigation into phytoplankton blooms in a sub-tropical Australian estuary
Authors: Rissik David , Doherty Maria , van Senden David
Published: September 2006

Tidal flushing, primary production and phytoplankton and zooplankton communities were investigated to establish the processes leading to persistently high levels of phytoplankton (in excess of 15 to 60 μg l−1 chlorophyll a) in a particular reach of Berowra Estuary, a relatively large drowned river valley estuary in New South Wales, Australia. Residence times at the bloom site were sufficiently long to provide an opportunity for exponential growth of algae and to result in large accumulations of cells and high rates of primary production. Phytoplankton taxa over the study period were dominated by various diatoms, Chaetoceros, Pseudonitzschia, Thalassiosira and Skeletonema. Zooplankton biomass (wet weight of taxa between 90 and 900 μ m equivalent circular diameter), estimated using image analysis technology was significantly greater in the bloom area (200 mg m−3), than upstream (140 mg m−3) and downstream (120 mg m−3) sites. Numbers of individuals in the smallest zooplankton size classes were significantly related to chlorophyll a concentrations. The relationship decreased with increases in the particle size classes, showing an uncoupling between chlorophyll a concentrations and abundance of larger zooplankton. Residence times in the bloom reach were sufficient for secondary production (somatic and egg production) to occur in the zooplankton taxa present. Growth of phytoplankton under the conditions of nutrients, light and temperature exceeded losses due to zooplankton grazing and estuarine flushing, maintaining chlorophyll concentrations of more than 10 μ g·l−1.
Estimating the executive demands of a one-back choice reaction time task by means of the selective interference paradigm
Authors: Szmalec Arnaud , Vandierendonck André
Published: September 2006

The present study proposes a new executive task, the one-back choice reaction time (RT) task, and implements the selective interference paradigm to estimate the executive demands of the processing components involved in this task. Based on the similarities between a one-back choice RT task and the n-back updating task, it was hypothesized that one-back delaying of a choice reaction involves executive control. In three experiments, framed within Baddeley's (1986) working-memory model, a one-back choice RT task, a choice RT task, articulatory suppression, and matrix tapping were performed concurrently with primary tasks involving verbal, visuospatial, and executive processing. The results demonstrate that one-back delaying of a choice reaction interferes with tasks requiring executive control, while the potential interference at the level of the verbal or visuospatial working memory slave systems remains minimal.
Bend it like Beckham: Embodying the Motor Skills of Famous Athletes
Authors: Bach Patric , Tipper Steven P.
Published: September 2006

Observing an action activates the same representations as does the actual performance of the action. Here we show for the first time that the action system can also be activated in the complete absence of action perception. When the participants had to identify the faces of famous athletes, the responses were influenced by their similarity to the motor skills of the athletes. Thus, the motor skills of the viewed athletes were retrieved automatically during person identification and had a direct influence on the action system of the observer. However, our results also indicated that motor behaviours that are implicit characteristics of other people are represented differently from when actions are directly observed. That is, unlike the facilitatory effects reported when actions were seen, the embodiment of the motor behaviour that is not concurrently perceived gave rise to contrast effects where responses similar to the behaviour of the athletes were inhibited.
Continuous recruitment of naive T cells contributes to heterogeneity of antiviral CD8 T cells during persistent infection
Authors: Vezys Vaiva , Masopust David , Kemball Christopher C. , Barber Daniel L. , O'Mara Leigh A. , Larsen Christian P. , Pearson Thomas C. , Ahmed Rafi , Lukacher Aron E.
Published: September 2006

Numerous microbes establish persistent infections, accompanied by antigen-specific CD8 T cell activation. Pathogen-specific T cells in chronically infected hosts are often phenotypically and functionally variable, as well as distinct from T cells responding to nonpersistent infections; this phenotypic heterogeneity has been attributed to an ongoing reencounter with antigen. Paradoxically, maintenance of memory CD8 T cells to acutely resolved infections is antigen independent, whereas there is a dependence on antigen for T cell survival in chronically infected hosts. Using two chronic viral infections, we demonstrate that new naive antigen-specific CD8 T cells are primed after the acute phase of infection. These newly recruited T cells are phenotypically distinct from those primed earlier. Long-lived antiviral CD8 T cells are defective in self-renewal, and lack of thymic output results in the decline of virus-specific CD8 T cells, indicating that newly generated T cells preserve antiviral CD8 T cell populations during chronic infection. These findings reveal a novel role for antigen in maintaining virus-specific CD8 T cells during persistent infection and provide insight toward understanding T cell differentiation in chronic infection.
The requirement for Notch signaling at the β-selection checkpoint in vivo is absolute and independent of the pre–T cell receptor
Authors: Maillard Ivan , Tu LiLi , Sambandam Arivazhagan , Yashiro-Ohtani Yumi , Millholland John , Keeshan Karen , Shestova Olga , Xu Lanwei , Bhandoola Avinash , Pear Warren S.
Published: September 2006

Genetic inactivation of Notch signaling in CD4−CD8− double-negative (DN) thymocytes was previously shown to impair T cell receptor (TCR) gene rearrangement and to cause a partial block in CD4+CD8+ double-positive (DP) thymocyte development in mice. In contrast, in vitro cultures suggested that Notch was absolutely required for the generation of DP thymocytes independent of pre-TCR expression and activity. To resolve the respective role of Notch and the pre-TCR, we inhibited Notch-mediated transcriptional activation in vivo with a green fluorescent protein–tagged dominant-negative Mastermind-like 1 (DNMAML) that allowed us to track single cells incapable of Notch signaling. DNMAML expression in DN cells led to decreased production of DP thymocytes but only to a modest decrease in intracellular TCRβ expression. DNMAML attenuated the pre-TCR–associated increase in cell size and CD27 expression. TCRβ or TCRαβ transgenes failed to rescue DNMAML-related defects. Intrathymic injections of DNMAML− or DNMAML+ DN thymocytes revealed a complete DN/DP transition block, with production of DNMAML+ DP thymocytes only from cells undergoing late Notch inactivation. These findings indicate that the Notch requirement during the β-selection checkpoint in vivo is absolute and independent of the pre-TCR, and it depends on transcriptional activation by Notch via the CSL/RBP-J–MAML complex.
Persistent expression of autoantibodies in SLE patients in remission
Authors: Yurasov Sergey , Tiller Thomas , Tsuiji Makoto , Velinzon Klara , Pascual Virginia , Wardemann Hedda , Nussenzweig Michel C.
Published: September 2006

A majority of the antibodies expressed by nascent B cells in healthy humans are self-reactive, but most of these antibodies are removed from the repertoire during B cell development. In contrast, untreated systemic lupus erythematosus (SLE) patients fail to remove many of the self-reactive and polyreactive antibodies from the naive repertoire. Here, we report that SLE patients in clinical remission continue to produce elevated numbers of self-reactive and polyreactive antibodies in the mature naive B cell compartment, but the number of B cells expressing these antibodies is lower than in patients with active disease. Our finding that abnormal levels of self-reactive mature naive B cells persist in the majority of patients in clinical remission suggests that early checkpoint abnormalities are an integral feature of SLE.
Function of a STIM1 Homologue in C. elegans: Evidence that Store-operated Ca2+ Entry Is Not Essential for Oscillatory Ca2+ Signaling and ER Ca2+ Homeostasis
Authors: Yan Xiaohui , Xing Juan , Lorin-Nebel Catherine , Estevez Ana Y. , Nehrke Keith , Lamitina Todd , Strange Kevin
Published: September 2006

1,4,5-trisphosphate (IP3)-dependent Ca2+ signaling regulates gonad function, fertility, and rhythmic posterior body wall muscle contraction (pBoc) required for defecation in Caenorhabditis elegans. Store-operated Ca2+ entry (SOCE) is activated during endoplasmic reticulum (ER) Ca2+ store depletion and is believed to be an essential and ubiquitous component of Ca2+ signaling pathways. SOCE is thought to function to refill Ca2+ stores and modulate Ca2+ signals. Recently, stromal interaction molecule 1 (STIM1) was identified as a putative ER Ca2+ sensor that regulates SOCE. We cloned a full-length C. elegans stim-1 cDNA that encodes a 530–amino acid protein with ∼21% sequence identity to human STIM1. Green fluorescent protein (GFP)–tagged STIM-1 is expressed in the intestine, gonad sheath cells, and spermatheca. Knockdown of stim-1 expression by RNA interference (RNAi) causes sterility due to loss of sheath cell and spermatheca contractile activity required for ovulation. Transgenic worms expressing a STIM-1 EF-hand mutant that constitutively activates SOCE in Drosophila and mammalian cells are sterile and exhibit severe pBoc arrhythmia. stim-1 RNAi dramatically reduces STIM-1∷GFP expression, suppresses the EF-hand mutation–induced pBoc arrhythmia, and inhibits intestinal store-operated Ca2+ (SOC) channels. However, stim-1 RNAi surprisingly has no effect on pBoc rhythm, which is controlled by intestinal oscillatory Ca2+ signaling, in wild type and IP3 signaling mutant worms, and has no effect on intestinal Ca2+ oscillations and waves. Depletion of intestinal Ca2+ stores by RNAi knockdown of the ER Ca2+ pump triggers the ER unfolded protein response (UPR). In contrast, stim-1 RNAi fails to induce the UPR. Our studies provide the first detailed characterization of STIM-1 function in an intact animal and suggest that SOCE is not essential for certain oscillatory Ca2+ signaling processes and for maintenance of store Ca2+ levels in C. elegans. These findings raise interesting and important questions regarding the function of SOCE and SOC channels under normal and pathophysiological conditions.
Augur—a computational pipeline for whole genome microbial surface protein prediction and classification
Authors: Billion A. , Ghai R. , Chakraborty T. , Hain T.
Published: September 2006

Summary: The analysis of protein function is a challenge and a major bottleneck towards well-annotated and analysed microbial genomes. In particular, bacterial surface proteins present an opportunity for pharmacological intervention and vaccine development. We present Augur, an automatic prediction pipeline that integrates major surface prediction algorithms and enables comparative analysis, classification and visualization for gram-positive bacteria on a genomic scale.

Availability:  

Contact:  Andre.Billion@mikrobio.med.uni-giessen.de

Supplementary information: Supplementary data are available at Bioinformatics online.
SPEED: a molecular-evolution-based database of mammalian orthologous groups
Authors: Vallender Eric J. , Paschall Justin E. , Malcom Christine M. , Lahn Bruce T. , Wyckoff Gerald J.
Published: September 2006

Motivation: The abundance of nucleotide sequence information available has expanded horizons of inquiry for molecular evolution; however, the full potential of whole-genome analysis has not been realized because of inadequate tools. Here, we present one of the first toolkits to aid multidisciplinary high-throughput analysis.

Summary: SPEED was created to integrate molecular evolutionary data with existing genetic resources and provide a straightforward user interface to 17 352 orthologous gene groups, containing representatives from eight mammalian species and an avian outgroup.

Availability: See for access

Contact:  wyckoffg@umkc.edu

Supplementary information: A larger version of the data model and a site map are available online.
Probabilistic inference of transcription factor concentrations and gene-specific regulatory activities
Authors: Sanguinetti Guido , Lawrence Neil D. , Rattray Magnus
Published: September 2006

Motivation: Quantitative estimation of the regulatory relationship between transcription factors and genes is a fundamental stepping stone when trying to develop models of cellular processes. Recent experimental high-throughput techniques, such as Chromatin Immunoprecipitation (ChIP) provide important information about the architecture of the regulatory networks in the cell. However, it is very difficult to measure the concentration levels of transcription factor proteins and determine their regulatory effect on gene transcription. It is therefore an important computational challenge to infer these quantities using gene expression data and network architecture data.

Results: We develop a probabilistic state space model that allows genome-wide inference of both transcription factor protein concentrations and their effect on the transcription rates of each target gene from microarray data. We use variational inference techniques to learn the model parameters and perform posterior inference of protein concentrations and regulatory strengths. The probabilistic nature of the model also means that we can associate credibility intervals to our estimates, as well as providing a tool to detect which binding events lead to significant regulation. We demonstrate our model on artificial data and on two yeast datasets in which the network structure has previously been obtained using ChIP data. Predictions from our model are consistent with the underlying biology and offer novel quantitative insights into the regulatory structure of the yeast cell.

Availability: MATLAB code is available from

Contact:  guido@dcs.shef.ac.uk

Supplementary information: Supplementary Data are available at Bioinformatics online
Mineral minimization in nature's alternative teeth
Authors: Broomell Christopher C , Khan Rashda K , Moses Dana N , Miserez Ali , Pontin Michael G , Stucky Galen D , Zok Frank W , Waite J. Herbert
Published: September 2006

Contrary to conventional wisdom, mineralization is not the only strategy evolved for the formation of hard, stiff materials. Indeed, the sclerotized mouthparts of marine invertebrates exhibit Young's modulus and hardness approaching 10 and 1 GPa, respectively, with little to no help from mineralization. Based on biochemical analyses, three of these mouthparts, the jaws of glycerid and nereid polychaetes and a squid beak, reveal a largely organic composition dominated by glycine- and histidine-rich proteins. Despite the well-known metal ion binding by the imidazole side-chain of histidine and the suggestion that this interaction provides mechanical support in nereid jaws, there is at present no universal molecular explanation for the relationship of histidine to mechanical properties in these sclerotized structures.
Plant Material Exchanged between James Petiver (
ca
. 1663–1718) and Joan Salvador I Riera (1683–1725). I. The Balearic Plants Conserved in the Bc-Salvador and Bm-Sloane Herbaria
Authors: Ibáñez Neus , Montserrat Josep M , Soriano Ignasi , Camarasa Josep M
Published: September 2006

The BC-Salvador herbarium, conserved in the Botanic Institute of Barcelona, is the oldest plant collection known in Spain, with 4025 sheets collected between the late seventeenth century and the middle of the eighteenth. Joan Salvador, the main contributor, sent duplicates of some of these sheets to James Petiver and Hans Sloane; the sheets are now conserved as a part of the BM-Sloane herbarium. Both herbaria conserve the testimonies of the first well-known systematic explorations of the Balearic Islands carried out by Joan and Josep Salvador between 1711 and 1725. In this article we list the contents of
Petiveriana III
, published by Petiver in 1717, in which some Balearic plants are described as new taxa by Joan Salvador, and we point out the sheets of the BC-Salvador and BM-Sloane herbaria on which these diagnoses are based.
RETHINKING THE HISTORY OF SOLAR WIND STUDIES: EDDINGTON'S ANALYSIS OF COMET MOREHOUSE
Authors: Durham Ian T
Published: September 2006

Arthur Eddington's very early career is often overshadowed by his later accomplishments. For many years the work he performed at the Royal Observatory, Greenwich, was little studied. In some cases, citations to his work in major journals did not appear for more than three decades. One of his earliest works was a mathematical analysis of the shapes of the envelopes of Comet Morehouse, a non-periodic comet discovered in 1908. Eddington's description of the envelopes, in mathematical terms, as paraboloids projected in two dimensions as parabolas, was not studied in earnest until after his death. Although the primary conclusion of his work has recently been modified, there are several other statements he makes about the source of the creation of these envelopes that suggest he should be acknowledged as the first person to suggest that there is a continuous outflow of ions from the Sun.
Why I don't FRS my Tail: Augustus DE Morgan and the Royal Society
Authors: Higgitt Rebekah
Published: September 2006

The mathematician Augustus De Morgan chose not to become a Fellow of the Royal Society. This short article examines the reasons behind this choice and a sketch that he drew representing a satirical ‘Coat of Arms’ for the Society. Despite recent reform, De Morgan felt that the Society still represented aristocratic privilege rather than scientific attainment. In addition, his research into the history of the Society revealed past unfairness done in its name, for which it was yet to atone. De Morgan, who opposed and hoped to expose the presence of vested interests in the realm of science, was never to be convinced that the Royal Society represented and facilitated independent scientific endeavour.
Standardization of biological medicines: the first hundred years, 1900–2000
Authors: Bristow Adrian F , Barrowcliffe Trevor , Bangham Derek R
Published: September 2006

The use of materials of biological origin in medicine has a long history. These materials, including tissue, organ and microbial extracts, blood and its derivatives, antibodies and hormones, share the feature that for much of the last century the ability to characterize and quantify the active substance was limited. Quantification of these substances depends on biological standardization, a discipline that was refined to a science by the Medical Research Council from the 1920s onwards, and which, with contributions from several prominent Fellows of the Royal Society, including principally Sir Henry Dale, the UK has led the world to the present date.
Implications of a 3.472–3.333 Gyr-old subaerial microbial mat from the Barberton greenstone belt, South Africa for the UV environmental conditions on the early Earth
Authors: Westall Frances , de Ronde Cornel E.J , Southam Gordon , Grassineau Nathalie , Colas Maggy , Cockell Charles , Lammer Helmut
Published: September 2006

Modelling suggests that the UV radiation environment of the early Earth, with DNA weighted irradiances of about three orders of magnitude greater than those at present, was hostile to life forms at the surface, unless they lived in specific protected habitats. However, we present empirical evidence that challenges this commonly held view. We describe a well-developed microbial mat that formed on the surface of volcanic littoral sediments in an evaporitic environment in a 3.5–3.3 Ga-old formation from the Barberton greenstone belt. Using a multiscale, multidisciplinary approach designed to strongly test the biogenicity of potential microbial structures, we show that the mat was constructed under flowing water by 0.25 μm filaments that produced copious quantities of extracellular polymeric substances, representing probably anoxygenic photosynthesizers. Associated with the mat is a small colony of rods–vibroids that probably represent sulphur-reducing bacteria. An embedded suite of evaporite minerals and desiccation cracks in the surface of the mat demonstrates that it was periodically exposed to the air in an evaporitic environment. We conclude that DNA-damaging UV radiation fluxes at the surface of the Earth at this period must either have been low (absorbed by CO
2
, H
2
O, a thin organic haze from photo-dissociated CH
4
, or SO
2
from volcanic outgassing; scattered by volcanic, and periodically, meteorite dust, as well as by the upper layers of the microbial mat) and/or that the micro-organisms exhibited efficient gene repair/survival strategies.
The carbon cycle on early Earth—and on Mars?
Authors: Grady Monica M , Wright Ian
Published: September 2006

One of the goals of the present Martian exploration is to search for evidence of extinct (or even extant) life. This could be redefined as a search for carbon. The carbon cycle (or, more properly, cycles) on Earth is a complex interaction among three reservoirs: the atmosphere; the hydrosphere; and the lithosphere. Superimposed on this is the biosphere, and its presence influences the fixing and release of carbon in these reservoirs over different time-scales. The overall carbon balance is kept at equilibrium on the surface by a combination of tectonic processes (which bury carbon), volcanism (which releases it) and biology (which mediates it). In contrast to Earth, Mars presently has no active tectonic system; neither does it possess a significant biosphere. However, these observations might not necessarily have held in the past. By looking at how Earth's carbon cycles have changed with time, as both the Earth's tectonic structure and a more sophisticated biology have evolved, and also by constructing a carbon cycle for Mars based on the carbon chemistry of Martian meteorites, we investigate whether or not there is evidence for a Martian biosphere.
Searching for signatures of life on Mars: an Fe-isotope perspective
Authors: Anand M , Russell S.S , Blackhurst R.L , Grady M.M
Published: September 2006

Recent spacecraft and lander missions to Mars have reinforced previous interpretations that Mars was a wet and warm planet in the geological past. The role of liquid water in shaping many of the surface features on Mars has long been recognized. Since the presence of liquid water is essential for survival of life, conditions on early Mars might have been more favourable for the emergence and evolution of life. Until a sample return mission to Mars, one of the ways of studying the past environmental conditions on Mars is through chemical and isotopic studies of Martian meteorites. Over 35 individual meteorite samples, believed to have originated on Mars, are now available for lab-based studies. Fe is a key element that is present in both primary and secondary minerals in the Martian meteorites. Fe-isotope ratios can be fractionated by low-temperature processes which includes biological activity. Experimental investigations of Fe reduction and oxidation by bacteria have produced large fractionation in Fe-isotope ratios. Hence, it is considered likely that if there is/were any form of life present on Mars then it might be possible to detect its signature by Fe-isotope studies of Martian meteorites. In the present study, we have analysed a number of Martian meteorites for their bulk-Fe-isotope composition. In addition, a set of terrestrial analogue material has also been analysed to compare the results and draw inferences. So far, our studies have not found any measurable Fe-isotopic fractionation in bulk Martian meteorites that can be ascribed to any low-temperature process operative on Mars.
Physical conditions on the early Earth
Authors: Lunine Jonathan I
Published: September 2006

The formation of the Earth as a planet was a large stochastic process in which the rapid assembly of asteroidal-to-Mars-sized bodies was followed by a more extended period of growth through collisions of these objects, facilitated by the gravitational perturbations associated with Jupiter. The Earth's inventory of water and organic molecules may have come from diverse sources, not more than 10% roughly from comets, the rest from asteroidal precursors to chondritic bodies and possibly objects near Earth's orbit for which no representative class of meteorites exists today in laboratory collections. The final assembly of the Earth included a catastrophic impact with a Mars-sized body, ejecting mantle and crustal material to form the Moon, and also devolatilizing part of the Earth. A magma ocean and steam atmosphere (possibly with silica vapour) existed briefly in this period, but terrestrial surface waters were below the critical point within 100 million years after Earth's formation, and liquid water existed continuously on the surface within a few hundred million years. Organic material delivered by comets and asteroids would have survived, in part, this violent early period, but frequent impacts of remaining debris probably prevented the continuous habitability of the Earth for one to several hundred million years. Planetary analogues to or records of this early time when life began include Io (heat flow), Titan (organic chemistry) and Venus (remnant early granites).
Phosphorus in prebiotic chemistry
Authors: Schwartz Alan W
Published: September 2006

The prebiotic synthesis of phosphorus-containing compounds—such as nucleotides and polynucleotides—would require both a geologically plausible source of the element and pathways for its incorporation into chemical systems on the primitive Earth. The mineral apatite, which is the only significant source of phosphate on Earth, has long been thought to be problematical in this respect due to its low solubility and reactivity. However, in the last decade or so, at least two pathways have been demonstrated which would circumvent these perceived problems. In addition, recent results would seem to suggest an additional, extraterrestrial source of reactive phosphorus. It appears that the ‘phosphorus problem’ is no longer the stumbling block which it was once thought to be.
From volcanic origins of chemoautotrophic life to Bacteria, Archaea and Eukarya
Authors: Wächtershäuser Günter
Published: September 2006

The theory of a chemoautotrophic origin of life in a volcanic iron–sulphur world postulates a pioneer organism at sites of reducing volcanic exhalations. The pioneer organism is characterized by a composite structure with an inorganic substructure and an organic superstructure. Within the surfaces of the inorganic substructure iron, cobalt, nickel and other transition metal centres with sulphido, carbonyl and other ligands were catalytically active and promoted the growth of the organic superstructure through carbon fixation, driven by the reducing potential of the volcanic exhalations. This pioneer metabolism was reproductive by an autocatalytic feedback mechanism. Some organic products served as ligands for activating catalytic metal centres whence they arose. The unitary structure–function relationship of the pioneer organism later gave rise to two major strands of evolution: cellularization and emergence of the genetic machinery. This early phase of evolution ended with segregation of the domains Bacteria, Archaea and Eukarya from a rapidly evolving population of pre-cells. Thus, life started with an initial, direct, deterministic chemical mechanism of evolution giving rise to a later, indirect, stochastic, genetic mechanism of evolution and the upward evolution of life by increase of complexity is grounded ultimately in the synthetic redox chemistry of the pioneer organism.
Hyperthermophiles in the history of life
Authors: Stetter Karl O
Published: September 2006

Today, hyperthermophilic (‘superheat-loving’) bacteria and archaea are found within high-temperature environments, representing the upper temperature border of life. They grow optimally above 80°C and exhibit an upper temperature border of growth up to 113°C. Members of the genera,
Pyrodictium
and
Pyrolobus
, survive at least 1 h of autoclaving. In their basically anaerobic environments, hyperthermophiles (HT) gain energy by inorganic redox reactions employing compounds like molecular hydrogen, carbon dioxide, sulphur and ferric and ferrous iron. Based on their growth requirements, HT could have existed already on the early Earth about 3.9 Gyr ago. In agreement, within the phylogenetic tree of life, they occupy all the short deep branches closest to the root. The earliest archaeal phylogenetic lineage is represented by the extremely tiny members of the novel kingdom of Nanoarchaeota, which thrive in submarine hot vents. HT are very tough survivors, even in deep-freezing at −140°C. Therefore, during impact ejecta, they could have been successfully transferred to other planets and moons through the coldness of space.
Conditions for the emergence of life on the early Earth: summary and reflections
Authors: Jortner Joshua
Published: September 2006

This review attempts to situate the emergence of life on the early Earth within the scientific issues of the operational and mechanistic description of life, the conditions and constraints of prebiotic chemistry, together with bottom-up molecular fabrication and biomolecular nanofabrication and top-down miniaturization approaches to the origin of terrestrial life.
The origin of replicators and reproducers
Authors: Szathmáry Eörs
Published: September 2006

Replicators are fundamental to the origin of life and evolvability. Their survival depends on the accuracy of replication and the efficiency of growth relative to spontaneous decay. Infrabiological systems are built of two coupled autocatalytic systems, in contrast to minimal living systems that must comprise at least a metabolic subsystem, a hereditary subsystem and a boundary, serving respective functions. Some scenarios prefer to unite all these functions into one primordial system, as illustrated in the lipid world scenario, which is considered as a didactic example in detail. Experimentally produced chemical replicators grow parabolically owing to product inhibition. A selection consequence is survival of everybody. The chromatographized replicator model predicts that such replicators spreading on surfaces can be selected for higher replication rate because double strands are washed away slower than single strands from the surface. Analysis of real ribozymes suggests that the error threshold of replication is less severe by about one order of magnitude than thought previously. Surface-bound dynamics is predicted to play a crucial role also for exponential replicators: unlinked genes belonging to the same genome do not displace each other by competition, and efficient and accurate replicases can spread. The most efficient form of such useful population structure is encapsulation by reproducing vesicles. The stochastic corrector model shows how such a bag of genes can survive, and what the role of chromosome formation and intragenic recombination could be. Prebiotic and early evolution cannot be understood without the models of dynamics.
Endurance exercise training in common carp Cyprinus carpio L. induces proliferation of myonuclei in fast muscle fibres and slow muscle fibre hypertrophy
Authors: Martin C. I. , Johnston I. A.
Published: September 2006

Endurance exercise training (2·4–2·6 body lengths s−1, 16 h day−1 for 28 days) resulted in an increased density of myonuclei in fast muscle fibres relative to tank rested controls and induced slow muscle fibre hypertrophy. The results indicate that exercise is a powerful stimulus for the proliferation of myogenic cells and nuclear accretion.
Snailfishes of the central California coast: video, photographic and morphological observations
Authors: Stein D. L. , Drazen J. C. , Schlining K. L. , Barry J. P. , Kuhnz L.
Published: September 2006

Video and photographic images of snailfishes (Liparidae) collected by the Monterey Bay Aquarium Research Institute, augmented by specimens collected simultaneously, were analysed. Nine species in five genera were identified, including Careproctus melanurus, Careproctus ovigerus, Careproctus longifilis, Careproctus gilberti, Careproctus filamentosus, Osteodiscus cascadiae, Nectoliparis pelagicus, Paraliparis dactylosus and Rhinoliparis barbulifer. Voucher specimens were collected of all except C. melanurus, C. gilberti and C. filamentosus. In addition, individuals of the Paraliparis‘rosaceus’ species group were abundant but could not be identified to species. Many liparids were identified only to family, but an individual of a very distinctive unknown species, presumably undescribed, was videotaped. Relative abundance of C. melanurus was estimated, and several in situ snailfish behaviours are described for the first time.
Sex differentiation of the European eel in brackish and freshwater environments: a comparative analysis
Authors: Melià P. , Bevacqua D. , Crivelli A. J. , Panfili J. , De Leo G. A. , Gatto M.
Published: September 2006

Body growth parameters, age and total length at sex differentiation were compared in three European eel Anguilla anguilla populations from Mediterranean sites with different salinity. Whilst body growth was faster in brackish than in freshwater environments, the present analysis shows that body size at sex differentiation might be a physiological invariant.
First record of the white catfish Ameiurus catus in Great Britain
Authors: Britton J. R. , Davies G. D.
Published: September 2006

The North American catfish Ameiurus catus is recorded for the first time in Great Britain. An albino variety of 620 mm fork length and 4550 g was believed to have been an ornamental fish that was introduced subsequently into the wild.
Breeding behaviour and distribution of the tucunaréCichla aff. monoculus in a clear water river of the Bolivian Amazon
Authors: Muñoz H. , Van Damme P. A. , Duponchelle F.
Published: September 2006

The breeding behaviour and distribution of tucunaréCichla aff. monoculus were studied for 2 months during the breeding season in the Paraguá River, Bolivia. Tucunaré were more abundant in the old remnant channels and isolated lakes than in the main river channel. The breeding period was delayed for c. 1 month in the river compared to the old remnant channels and lakes. The batch fecundity ranged between 3712 and 10 355 for females weighing 460 and 1380 g, respectively. Gonad analysis of egg‐guarding or juvenile‐guarding females showed that a female was able to spawn more than once during the breeding season. Nests were significantly larger and deeper in the isolated lakes than in the old remnant channels and in the main river. The maximum depth of the nests also differed significantly, being deeper in the isolated lakes than in the river channel and in the old remnant channels.
Habitat use by triplefin species (Tripterygiidae) on rocky reefs in New Zealand
Authors: Feary D. A. , Clements K. D.
Published: September 2006

Habitat use and nesting sites of 12 triplefin species (Tripterygiidae) were investigated at 26 coastal and offshore rocky reef locations in north‐eastern New Zealand. Within these locations, 17 broad‐scale habitats and 14 fine‐scale habitats were surveyed using visual transects. In terms of broad‐scale habitat use, four species, Notoclinops segmentatus, Forsterygion lapillum, Forsterygion varium and Ruanoho whero showed a high similarity in distribution, irrespective of depth or habitat characteristics. The distributions of Bellapiscis lesleyae, Cryptichthys jojettae and Ruanoho decemdigitatus were relatively similar, being primarily confined to shallow habitats providing a high degree of shelter. Forsterygion flavonigrum, Forsterygion malcolmi and Notoclinops caerulepunctus were all predominantly found beyond 10 m, irrespective of habitat characteristics. Despite the majority of species using several distinct fine‐scale habitats, a high degree of variation was apparent between species, with the majority of species showing extremely low overlap of fine‐scale habitats used. Differences in fine‐scale habitat use were not apparent when comparing the nesting sites of species. All nests were found in fine‐scale habitats, presumably affording a high degree of shelter from predation and physical disturbance. Interspecific partitioning of spatial resources probably occurs by depth and microhabitat in this species assemblage in north‐eastern New Zealand.