bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genomic and structural aspects of protein evolution
Authors: Chothia Cyrus , Gough Julian 
Published: March 2009

It has been known for more than 35 years that, during evolution, new proteins are formed by gene duplications, sequence and structural divergence and, in many cases, gene combinations. The genome projects have produced complete, or almost complete, descriptions of the protein repertoires of over 600 distinct organisms. Analyses of these data have dramatically increased our understanding of the formation of new proteins. At the present time, we can accurately trace the evolutionary relationships of about half the proteins found in most genomes, and it is these proteins that we discuss in the present review. Usually, the units of evolution are protein domains that are duplicated, diverge and form combinations. Small proteins contain one domain, and large proteins contain combinations of two or more domains. Domains descended from a common ancestor are clustered into superfamilies. In most genomes, the net growth of superfamily members means that more than 90% of domains are duplicates. In a section on domain duplications, we discuss the number of currently known superfamilies, their size and distribution, and superfamily expansions related to biological complexity and to specific lineages. In a section on divergence, we describe how sequences and structures diverge, the changes in stability produced by acceptable mutations, and the nature of functional divergence and selection. In a section on domain combinations, we discuss their general nature, the sequential order of domains, how combinations modify function, and the extraordinary variety of the domain combinations found in different genomes. We conclude with a brief note on other forms of protein evolution and speculations of the origins of the duplication, divergence and combination processes.
Comparison of in situ time-series of temperature with gridded sea surface temperature datasets in the North Atlantic
Authors: Hughes Sarah L. , Holliday N. Penny , Colbourne Eugene , Ozhigin Vladimir , Valdimarsson Hedinn , Østerhus Svein , Wiltshire Karen 
Published: March 2009

Abstract
Hughes, S. L., Holliday, N. P., Colbourne, E., Ozhigin, V., Valdimarsson, H., Østerhus, S., and Wiltshire, K. 2009. Comparison of in situ time-series of temperature with gridded sea surface temperature datasets in the North Atlantic. – ICES Journal of Marine Science, 66: 1467–1479. Analysis of the effects of climate variability and climate change on the marine ecosystem is difficult in regions where long-term observations of ocean temperature are sparse or unavailable. Gridded sea surface temperature (SST) products, based on a combination of satellite and in situ observations, can be used to examine variability and long-term trends because they provide better spatial coverage than the limited sets of long in situ time-series. SST data from three gridded products (Reynolds/NCEP OISST.v2., Reynolds ERSST.v3, and the Hadley Centre HadISST1) are compared with long time-series of in situ measurements from ICES standard sections in the North Atlantic and Nordic Seas. The variability and trends derived from the two data sources are examined, and the usefulness of the products as a proxy for subsurface conditions is discussed.
Leuconostoc citreum HJ‐P4 (KACC 91035) regulates immunoglobulin E in an ovalbumin‐induced allergy model and induces interleukin‐12 through nuclear factor‐kappa B and p38/c‐Jun N‐terminal kinases signaling in macrophages
Authors: Kang Hee , Oh Yoo‐Joung , Ahn Kyoo‐Seok , Eom Hyun‐Ju , Han NamSoo , Kim Yoon‐Bum , Sohn Nak‐Won 
Published: March 2009

ABSTRACT Leuconostoc citreum (L. citreum) HJ‐P4 (KACC 91035) is one of the major predominant species in kimchi fermentation in Korea. The purpose of the present study was to test the immunomodulatory capacity of L. citreum to modulate the IgE‐mediated allergic response and to examine the involvement of NF‐κB and MAPK in IL‐12 production in macrophages. Balb/c mice were sensitized with OVA/alum and oral administration of L. citreum to the mice began before or after the OVA sensitization. Protein and mRNA expression of Th1 cytokines in splenocytes by L. citreum in vitro was measured. The role of NF‐κB and MAPK such as p38, ERK1/2 and JNK in L. citreum‐induced IL‐12 was investigated in peritoneal macrophages and RAW264.7 cell lines. L. citreum inhibited the serum levels of total IgE, IgG1 and IgG2a altogether and increased OVA‐specific IFN‐γ production in splenocytes from pre‐ and post‐sensitized animals. However, the downregulation of IL‐4 and IL‐5 production was observed only in the pre‐sensitization group. The ability of L. citreum to stimulate IFN‐γ was dependent on its induction of IL‐12. NF‐κB, p38 and JNK were mainly involved in L. citreum‐induced IL‐12 production. In conclusion, the current study demonstrated that L. citreum is able to regulate serum IgE generation at the induction and effector phases of allergic response through overall control over antibody production and that its involvement of IL‐12 production was mediated through NF‐κB and p38/JNK. Taken together, the use of L. citreum can be useful in preventing the development and progression of IgE production.
Association between antibody response against cytomegalovirus strain‐specific glycoprotein H epitopes and HLA‐DR
Authors: Ishibashi Kei , Tokumoto Tadahiko , Shirakawa Hiroki , Hashimoto Koichi , Kushida Nobuhiro , Yanagida Tomohiko , Shishido Keiichi , Aikawa Ken , Yamaguchi Osamu , Toma Hiroshi , Tanabe Kazunari , Suzutani Tatsuo 
Published: March 2009

ABSTRACTThe gH of CMV is a major target for strain‐specific neutralizing antibodies. To verify whether there is a correlation between HLA‐DR type and strain‐specific antibodies, antibodies against CMV gH in potential donors and recipients for renal transplantation were investigated. Among 471 subjects, 404 (86%) showed reactivity to CMV gH, but no antibodies against gH were detected in 67 (14%) subjects. The positive rates were over 80% in most HLA subpopulations. Fewer subjects with HLA‐DR10 and DR11 had antibodies to CMV gH than did those without HLA‐DR10 and DR11. HLA‐DR10 and DR11 may be associated with fewer/non‐responders for strain‐specific neutralizing antibodies.
Alcohol‐related cirrhosis—early abstinence is a key factor in prognosis, even in the most severe cases
Authors: Verrill Clare , Markham Hannah , Templeton Alexa , Carr Norman J. , Sheron Nick 
Published: March 2009

ABSTRACTAims  To determine the effect of pathological severity of cirrhosis on survival in patients with alcohol‐related cirrhosis.Design  Liver biopsies from 100 patients were scored for Laennec score of severity of cirrhosis, and medical notes were reviewed to determine various clinical factors, including drinking status. Up‐to‐date mortality data were obtained using the National Health Service Strategic Tracing Service.Setting  Southampton General Hospital between 1 January 1995 and 31 December 2000.Participants  A total of 100 consecutive patients with biopsy proven alcohol‐induced liver cirrhosis.Measurements  Laennec score of severity of cirrhosis and mortality.Findings  Most surprisingly, the severity of cirrhosis on biopsy had little impact on survival; indeed, early death was more likely in patients with the least severe cirrhosis. Abstinence from alcohol at 1 month after diagnosis of cirrhosis was the more important factor determining survival with a 7‐year survival of 72% for the abstinent patients versus 44% for the patients continuing to drink.Conclusions  It is never too late to stop drinking, even with the most severe degrees of cirrhosis on biopsy. Early drinking status is the most important factor determining long‐term survival in alcohol‐related cirrhosis.
Are adolescents who moderate their cannabis use at lower risk of later regular and dependent cannabis use?
Authors: Swift Wendy , Coffey Carolyn , Carlin John B. , Degenhardt Louisa , Calabria Bianca , Patton George C. 
Published: March 2009

ABSTRACTAims  To examine whether moderation of cannabis use among adolescent cannabis users is associated with reductions in cannabis use frequency and risk of dependence in young adulthood.Design  Ten‐year representative cohort study with six surveys in adolescence (mean age 14.9–17.4 years) and two in young adulthood (mean age 20.7 and 24.1 years).Participants  Inception cohort of 1943 Victorian secondary school students (96% response rate), with 1520 (78% of adolescent participants) interviewed in the final wave.Measurements  Participants were classified into six groups according to the maximum level of adolescent use and the extent of subsequent moderation in such use: non‐users, occasional to abstinence, occasional persisting, weekly to abstinence, weekly to occasional and weekly persisting. Outcome measures were weekly+ cannabis use and DSM‐IV cannabis dependence at 20 and 24 years.Findings  Thirty‐one per cent reported cannabis use during adolescence. Most adolescent users had moderated their use: from occasional to abstinence (71% of occasional users), weekly to abstinence or weekly to occasional (28% and 48% of weekly+ users, respectively). By age 24, both occasional use groups were at similar, elevated risk of regular and dependent cannabis use compared to non‐users. Weekly+ adolescent users were at greatest risk of these outcomes, although the weekly to abstinence group exhibited lower risk than those in the weekly persisting and weekly to occasional groups, who were at similar risk.Conclusions  While many young people have dynamic cannabis use patterns, a pattern of moderating adolescent cannabis use was associated with less risk of later problematic use than among those persisting, but risks were still elevated substantially compared with never‐users.
Post induction arrhythmia in a renal patient: an unexpected risk factor
Authors: Srivastava A. , Ahmed Khan M. , Watkiss J. 
Published: March 2009

SummaryA 44 year‐old woman was anaesthetised for a transplant nephrectomy. About 10 min after induction of anaesthesia she had several runs of ventricular tachycardia followed by ventricular fibrillation requiring 30 s of cardiopulmonary resuscitation, after which she reverted to sinus rhythm. Review of her chest X‐ray, suggested that the haemodialysis catheter (Permcath™) position may have precipitated this event. However, subsequent investigation found that she had toxic serum levels of sotalol, with a prolonged corrected QT interval on the electrocardiogram. She was started on sotalol while her renal graft was functioning well but it was not reviewed when the graft started to fail and she had to commence haemodialysis. This led to the accumulation of sotalol and explains her serum sotalol value of 7.1 mg.l−1 on the day of the event. Concentrations greater than 2.5 mg.l−1 are generally considered toxic.
Mortality related to anaesthesia in France: analysis of deaths related to airway complications*
Authors: Auroy Y. , Benhamou D. , Péquignot F. , Bovet M. , Jougla E. , Lienhart A. 
Published: March 2009

SummaryDeath certificates from the French national mortality database for the calendar year 1999 were reviewed to analyse cases in which airway complications had contributed to peri‐operative death. Respiratory deaths (and comas) found in a previous national 1978–82 French survey (1 : 7960; 95% CI 1 : 12 700 to 1 : 5400) were compared with the death rate found in the present one: 1 : 48 200 (95% CI 1 : 140 000 to 1 : 27 500). In 1999, deaths associated with failure of the breathing circuit and equipment were no longer encountered and no death was found to be related to undetected hypoxia in the recovery unit. Deaths related to difficult intubation also occurred at a lower rate than in the previous report (1 : 46 000; 95% CI 1 : 386 000 to 1 : 13 000) in 1978–82 vs 1 : 176 000 (95% CI 1 : 714 000 to 1 : 46 000) in 1999, a fourfold reduction. In most cases, there were both inadequate practice and systems failure (inappropriate communication between staff, inadequate supervision, poor organisation). This large French survey shows that deaths associated with respiratory complications during anaesthesia have been strikingly reduced during this 15‐year period.
Point of care measurement of plasma creatinine in critically ill patients with acute kidney injury
Authors: Udy A. , O’Donoghue S. , D’Intini V. , Healy H. , Lipman J. 
Published: March 2009

SummaryWe report the utility of an enzymatic point of care system for estimation of plasma creatinine concentration in critically ill patients with acute kidney injury. Multiple measurements were obtained from a heterogenous population admitted to a multi‐disciplinary intensive care unit. The acute kidney injury network guidelines were used to identify and stratify patients based on the creatinine concentration. Central laboratory values were used as comparators to assess the precision and bias of the system. Overall, point of care measurements correlated well with central pathology results (R2 = 0.991, p < 0.001), although there tended to be a small negative bias in patients with acute kidney injury (3 μmol.l−1). The accuracy of point of care measurement is within clinically acceptable limits and given the much shorter turn around time can be used to identify and monitor patients with acute kidney injury in the critical care environment.
Effects of the maternal and pre‐adult host plant on adult performance and preference in the pea aphid, Acyrthosiphon pisum
Authors: McLEAN AILSA H. C. , FERRARI JULIA , GODFRAY H. C. J. 
Published: March 2009

Abstract 1. The taxon known as the pea aphid, Acyrthosiphon pisum, is composed of a series of host plant associated populations and is widely used as a model system to explore ecological speciation and the evolution of specialisation. It is thus important to know how maternal and pre‐adult experience influences host plant utilisation in this species.2. The relative importance of the maternal and pre‐adult host plant for adult fecundity and host preference was investigated using three aphid clones collected from Lathyrus pratensis and maintained on Lathyrus or Vicia faba.3. No significant effects of the maternal host plant on offspring fecundity were detected.4. The host plant on which the aphid grew up influenced adult fecundity, although in a complex way that depended on both the adult host plant species and when after transfer to the test plant fecundity was assessed.5. All three clones preferred to colonise Lathyrus over Vicia, and this preference was stronger for aphids raised on Lathyrus.6. The significance of the results for studies of the evolution of specialisation and speciation that employ A. pisum is discussed.
Plant traits and wood fates across the globe: rotted, burned, or consumed?
Authors: CORNWELL WILLIAM K. , CORNELISSEN JOHANNES H. C. , ALLISON STEVEN D. , BAUHUS JÜRGEN , EGGLETON PAUL , PRESTON CAROLINE M. , SCARFF FIONA , WEEDON JAMES T. , WIRTH CHRISTIAN , ZANNE AMY E. 
Published: March 2009

AbstractWood represents the defining feature of forest systems, and often the carbon in woody debris has a long residence time. Globally, coarse dead wood contains 36–72 Pg C, and understanding what controls the fate of this C is important for predicting C cycle responses to global change. The fate of a piece of wood may include one or more of the following: microbial decomposition, combustion, consumption by insects, and physical degradation. The probability of each fate is a function of both the abiotic environment and the wood traits of the species. The wood produced by different species varies substantially in chemical, micro‐ and macro‐morphological traits; many of these characteristics of living species have ‘afterlife’ effects on the fate and turnover rate of dead wood. The colonization of dead wood by microbes and their activity depends on a large suite of wood chemical and anatomical traits, as well as whole‐plant traits such as stem‐diameter distributions. Fire consumption is driven by a slightly narrower range of traits with little dependence on wood anatomy. Wood turnover due to insects mainly depends on wood density and secondary chemistry. Physical degradation is a relatively minor loss pathway for most systems, which depends on wood chemistry and environmental conditions. We conclude that information about the traits of woody plants could be extremely useful for modeling and predicting rates of wood turnover across ecosystems. We demonstrate how this trait‐based approach is currently limited by oversimplified treatment of dead wood pools in several leading global C models and by a lack of quantitative empirical data linking woody plant traits with the probability and rate of each turnover pathway. Explicitly including plant traits and woody debris pools in global vegetation climate models would improve predictions of wood turnover and its feedback to climate.
Response of plants and the dominant microarthropod,Cryptopygus antarcticus, to warming and contrasting precipitation regimes in Antarctic tundra
Authors: DAY THOMAS A. , RUHLAND CHRISTOPHER T. , STRAUSS SARAH L. , PARK JI‐HYUNG , KRIEG MICHELLE L. , KRNA MATTHEW A. , BRYANT DAVID M. 
Published: March 2009

AbstractWe examined the influence of warming and supplemental precipitation on plant production and abundance of the dominant microarthropod, the springtailCryptopygus antarcticus(Collembola), in tundra dominated by the vascular plantsColobanthus quitensisandDeschampsia antarcticaalong the Antarctic Peninsula. Tundra cores were placed in plots near Palmer Station where they were warmed with infrared heaters in combination with receiving supplemental precipitation. Diel canopy air and soil temperatures and air vapor pressure deficits in warmed plots were elevated 0.8 °C, 2.2 °C and 0.13 kPa, respectively. After two growing seasons, total aboveground plant production was greater under warming as a result of enhanced production byC. quitensis, which more than offset declines in moss biomass. Total aboveground plant production was also greater under supplemental precipitation primarily as a result of enhanced moss production. Total aboveground plant production was greatest under the combination of warming and supplemental precipitation, primarily as a result of enhancedC. quitensisproduction.C. antarcticuswere more abundant in cores receiving supplemental precipitation and there was a strong treatment interaction; these springtails were most abundant in warmed cores receiving supplemental precipitation. Over 50% of the variability in the abundance ofC. antarcticuscould be explained by differences in aboveground plant biomass. However, plant production did not appear directly responsible for differences inC. antarcticusabundance; when we examinedC. antarcticusabundance per unit of aboveground plant biomass, differences in its abundance among treatments were still apparent implying these differences were not the direct result of plant biomass. The responses ofC. antarcticuswere consistent with its known moisture and thermal preferences, suggesting that abiotic factors played a dominant role in controlling its abundance. Precipitation regime had large impacts on warming responses and these were species specific, illustrating the importance of future precipitation regimes in predicting system responses to warming.
Cognate Hsp70 gene is induced during deep larval diapause in the moth Sesamia nonagrioides
Authors: Gkouvitsas T. , Kontogiannatos D. , Kourti A. 
Published: March 2009

AbstractThe complete cDNA sequences of Heat shock cognate protein 70 (SnoHsc70) and Heat shock protein 70 (SnoHsp70) were determined from the corn stalk borer Sesamia nonagrioides (Lef.). They encode 653 amino acids (Hsc70) and 633 amino acids (Hsp70), with calculated molecular masses of 71.5 kDa and 70.2 kDa respectively. SnoHsc70 is constitutively expressed, and SnoHsp70 is heat‐inducible in non‐diapausing insects. SnoHsp70 is down regulated during diapause, while SnoHsc70 is induced as the larvae enter deep diapause. High temperature stress during diapause has no further effect on transcript levels of SnoHsc70. Our results show that SnoHsc70 may play important roles in assisting protein conformation during specific stages of diapause.
Identification of a new member of the PBAN family of neuropeptides from the fire ant, Solenopsis invicta
Authors: Choi M.‐Y. , Vander Meer R. K. 
Published: March 2009

AbstractNeuropeptide hormones produced by neurosecretory cells in the central or peripheral nervous systems regulate various physiological and behavioral events during insect development and reproduction. PBAN/Pyrokinin is a major neuropeptide family, characterized by a 5‐amino‐acid C‐terminal sequence, FXPRLamide. This family of peptides has been implicated in regulating various physiological functions including, pheromone biosynthesis, muscle contraction, diapause induction or termination, melanization, and puparium formation in different insect species. In the present study, we report a new member of the PBAN family from the red imported fire ant, Solenopsis invicta, Soi‐PBAN, composed of 26‐AA (GSGEDLSYGDAYEVDEDDHPLFVPRL). Three additional peptides were deduced from Soi‐PBAN cDNA: 15‐AA (TSQDIASGMWFGPRL), 8‐AA (QPQFTPRL) and 9‐AA (LPWIPSPRL), that correspond to diapause hormone (DH), β‐neuropeptide (NP), and γ‐NP, which are found in many lepidopteran moths. Five peptides, DH, α, β, γ NPs, and PBAN are encoded from PBAN genes of lepidopteran moths, but in the fire ant the α‐NP is missing. Each of the four synthetic peptides from the fire ant Soi‐PBAN cDNA showed significant pheromonotropic activity in a moth model, indicating that these peptides are cross‐reactive. Soi‐β‐NP induced the highest amount of pheromone production of the four peptides evaluated. The Soi‐DH homologue had the lowest pheromonotropic activity, but was still significantly greater than control values. When the deduced amino acid sequences (entire ORF domains) from Soi‐PBAN cDNA were compared with other known sequences, the fire ant was most similar to the honey bee, but phylogenetically distant from moth and beetle species. Soi‐PBAN (26‐AA) unlike the other three peptides shows a low degree of sequence identity with honeybee PBAN (33‐AA). Based on the amino acid sequences encoded from insect PBAN genes identified to date, neuropeptide diversity is correlated with the taxonomic or phylogenetic classification of Insecta. From the present study we report the first neuropeptide identified and characterized from the central nervous system of Formicidae.
Stability of bifidobacteria in powdered formula
Authors: Abe Fumiaki , Miyauchi Hirofumi , Uchijima Ayako , Yaeshima Tomoko , Iwatsuki Keiji 
Published: March 2009

SummaryTwo stability tests of bifidobacteria in powdered formula were conducted. In a strain comparison test, three kinds of bifidobacterial powders; Bifidobacterium longum BB536, Bifidobacterium breve M‐16V and Bifidobacterium infantis M‐63 powders, admixed in follow‐up formula were used. In a commercial product evaluation, powdered formulas for toddlers containing bifidobacteria sold in the Indonesian market were analysed. When the inactivation rate constant of each sample, which was used as an index of the loss rate, was determined from the stability tests, B. longum was the most stable strain. The mean inactivation rate constant of commercial products was significantly lower than those obtained in strain comparison, although the same strains (B. longum BB536 and B. breve M‐16V) were used. A possible reason was the lower water activity of commercial products compared to the follow‐up formula. Also, higher storage temperature yielded lower stability in all strains or samples, which obeys the Arrhenius theory.