bluuebunny/crossref_metadata_2025 huggingface dataset:
Spatial and temporal pattern for the dentition in the Australian lungfish revealed with sonic hedgehog expression profile
Authors: Smith Moya M , Okabe Masataka , Joss Jean
Published: November 2008

We report a temporal order of tooth addition in the Australian lungfish where timing of tooth induction is sequential in the same pattern as osteichthyans along the lower jaw. The order of tooth initiation in
Neoceratodus
starts from the midline tooth, together with left and right ones at jaw position 2, followed by 3 and then 1. This is the pattern order for dentary teeth of several teleosts and what we propose represents a stereotypic initiation pattern shared with all osteichthyans, including the living sister group to all tetrapods, the Australian lungfish. This is contrary to previous opinions that the lungfish dentition is otherwise derived and uniquely different.
Sonic hedgehog
(
shh
) expression is intensely focused on tooth positions at different times corresponding with their initiation order. This deployment of shh is required for lungfish tooth induction, as cyclopamine treatment results in complete loss of these teeth when applied before they develop. The temporal sequence of tooth initiation is possibly regulated by
shh
and is know to be required for dentition pattern in other osteichthyans, including cichlid fish and snakes. This reflects a shared developmental process with jawed vertebrates at the level of the tooth module but differs with the lack of replacement teeth.
Uracil in DNA and its processing by different DNA glycosylases
Authors: Visnes Torkild , Doseth Berit , Pettersen Henrik Sahlin , Hagen Lars , Sousa Mirta M.L , Akbari Mansour , Otterlei Marit , Kavli Bodil , Slupphaug Geir , Krokan Hans E
Published: November 2008

Uracil in DNA may result from incorporation of dUMP during replication and from spontaneous or enzymatic deamination of cytosine, resulting in U:A pairs or U:G mismatches, respectively. Uracil generated by activation-induced cytosine deaminase (AID) in B cells is a normal intermediate in adaptive immunity. Five mammalian uracil-DNA glycosylases have been identified; these are mitochondrial UNG1 and nuclear UNG2, both encoded by the
UNG
gene, and the nuclear proteins SMUG1, TDG and MBD4. Nuclear UNG2 is apparently the sole contributor to the post-replicative repair of U:A lesions and to the removal of uracil from U:G contexts in immunoglobulin genes as part of somatic hypermutation and class-switch recombination processes in adaptive immunity. All uracil-DNA glycosylases apparently contribute to U:G repair in other cells, but they are likely to have different relative significance in proliferating and non-proliferating cells, and in different phases of the cell cycle. There are also some indications that there may be species differences in the function of the uracil-DNA glycosylases.
Hijacked DNA repair proteins and unchained DNA polymerases
Authors: Saribasak Huseyin , Rajagopal Deepa , Maul Robert W , Gearhart Patricia J
Published: November 2008

Somatic hypermutation of immunoglobulin (Ig) genes occurs at a frequency that is a million times greater than the mutation in other genes. Mutations occur in variable genes to increase antibody affinity, and in switch regions before constant genes to cause switching from IgM to IgG. Hypermutation is initiated in activated B cells when the activation-induced deaminase protein deaminates cytosine in DNA to uracil. Uracils can be processed by either a mutagenic pathway to produce mutations or a non-mutagenic pathway to remove mutations. In the mutagenic pathway, we first studied the role of mismatch repair proteins, MSH2, MSH3, MSH6, PMS2 and MLH1, since they would recognize mismatches. The MSH2–MSH6 heterodimer is involved in hypermutation by binding to U:G and other mismatches generated during repair synthesis, but the other proteins are not necessary. Second, we analysed the role of low-fidelity DNA polymerases η, ι and θ in synthesizing mutations, and conclude that polymerase η is the dominant participant by generating mutations at A:T base pairs. In the non-mutagenic pathway, we examined the role of the Cockayne syndrome B protein that interacts with other repair proteins. Mice deficient in this protein had normal hypermutation and class switch recombination, showing that it is not involved.
Non-homologous end joining in class switch recombination: the beginning of the end
Authors: Kotnis Ashwin , Du Likun , Liu Chonghai , Popov Sergey W , Pan-Hammarström Qiang
Published: November 2008

Immunoglobulin class switch recombination (CSR) is initiated by a B-cell-specific factor, activation-induced deaminase, probably through deamination of deoxycytidine residues within the switch (S) regions. The initial lesions in the S regions are subsequently processed, resulting in the production of DNA double-strand breaks (DSBs). These breaks will then be recognized, edited and repaired, finally leading to the recombination of the two S regions. Two major repair pathways have been implicated in CSR, the predominant non-homologous end joining (NHEJ) and the alternative end-joining (A-EJ) pathways. The former requires not only components of the ‘classical’ NHEJ machinery, i.e. Ku70/Ku80, DNA-dependent protein kinase catalytic subunit, DNA ligase IV and XRCC4, but also a number of DNA-damage sensors or adaptors, such as ataxia–telangiectasia mutated, γH2AX, 53BP1, MDC1, the Mre11–Rad50–NBS1 complex and the ataxia telangiectasia and Rad3-related protein (ATR). The latter pathway is not well characterized yet and probably requires microhomologies. In this review, we will focus on the current knowledge of the predominant NHEJ pathway in CSR and will also give a perspective on the A-EJ pathway.
Timing matters: error-prone gap filling and translesion synthesis in immunoglobulin gene hypermutation
Authors: Sale Julian E , Batters Christopher , Edmunds Charlotte E , Phillips Lara G , Simpson Laura J , Szüts Dávid
Published: November 2008

By temporarily deferring the repair of DNA lesions encountered during replication, the bypass of DNA damage is critical to the ability of cells to withstand genomic insults. Damage bypass can be achieved either by recombinational mechanisms that are generally accurate or by a process called translesion synthesis. Translesion synthesis involves replacing the stalled replicative polymerase with one of a number of specialized DNA polymerases whose active sites are able to tolerate a distorted or damaged DNA template. While this property allows the translesion polymerases to synthesize across damaged bases, it does so with the trade-off of an increased mutation rate. The deployment of these enzymes must therefore be carefully regulated. In addition to their important role in general DNA damage tolerance and mutagenesis, the translesion polymerases play a crucial role in converting the products of activation induced deaminase-catalysed cytidine deamination to mutations during immunoglobulin gene somatic hypermutation. In this paper, we specifically consider the control of translesion synthesis in the context of the timing of lesion bypass relative to replication fork progression and arrest at sites of DNA damage. We then examine how recent observations concerning the control of translesion synthesis might help refine our view of the mechanisms of immunoglobulin gene somatic hypermutation.
Somatic hypermutation of immunoglobulin genes: lessons from proliferating cell nuclear antigen
K164R
mutant mice
Authors: Langerak Petra , Krijger Peter H.L , Heideman Marinus R , van den Berk Paul C.M , Jacobs Heinz
Published: November 2008

Proliferating cell nuclear antigen (PCNA) encircles DNA as a ring-shaped homotrimer and, by tethering DNA polymerases to their template, PCNA serves as a critical replication factor. In contrast to high-fidelity DNA polymerases, the activation of low-fidelity translesion synthesis (TLS) DNA polymerases seems to require damage-inducible monoubiquitylation (Ub) of PCNA at lysine residue 164 (PCNA-Ub). TLS polymerases can tolerate DNA damage, i.e. they can replicate across DNA lesions. The lack of proofreading activity, however, renders TLS highly mutagenic. The advantage is that B cells use mutagenic TLS to introduce somatic mutations in immunoglobulin (Ig) genes to generate high-affinity antibodies. Given the critical role of PCNA-Ub in activating TLS and the role of TLS in establishing somatic mutations in immunoglobulin genes, we analysed the mutation spectrum of somatically mutated immunoglobulin genes in B cells from PCNA
K164R
knock-in mice. A 10-fold reduction in A/T mutations is associated with a compensatory increase in G/C mutations—a phenotype similar to Polη and mismatch repair-deficient B cells. Mismatch recognition, PCNA-Ub and Polη probably act within one pathway to establish the majority of mutations at template A/T. Equally relevant, the G/C mutator(s) seems largely independent of PCNA
K164
modification.
Transient cytochalasin-D treatment induces apically administered rAAV2 across tight junctions for transduction of enterocytes
Authors: Fu Ya-Yuan , Sibley Eric , Tang Shiue-Cheng
Published: November 2008

Enteropathogens are known to disrupt apical actin filaments and/or tight-junction barriers of intestinal epithelial cells to promote infection. In this study, we show that a controlled, cytochalasin-D (Cyto-D)-mediated disruption of actin filaments and tight junctions enhanced the apical delivery of the gene-therapy vector recombinant adeno-associated virus serotype 2 (rAAV2). This increase in transduction efficiency can be attributed to the enhanced delivery of rAAV2 across the Cyto-D disrupted tight junctions, allowing basolateral entry of rAAV2. Previously, we have shown that MG101 and doxorubicin are capable of overcoming proteasome-mediated transduction barriers of rAAV2 in enterocytes. In this study, when Cyto-D was combined with MG101 and doxorubicin in apical delivery of rAAV2 to transduce the differentiated Caco-2 enterocytes, a synergistic >2300-fold increase in transgene expression was achieved. We conclude that Cyto-D is capable of permeating the polarized enterocytes for rAAV2 transduction, which may potentially be a useful device to facilitate intestinal gene transfer via the gut lumen.
Dengue virus regulates type I interferon signalling in a strain-dependent manner in human cell lines
Authors: Umareddy Indira , Tang Kin Fai , Vasudevan Subhash G. , Devi Shamala , Hibberd Martin L. , Gu Feng
Published: November 2008

Outbreaks of dengue disease are constant threats to tropical and subtropical populations but range widely in severity, from mild to haemorrhagic fevers, for reasons that are still elusive. We investigated the interferon (IFN) response in infected human cell lines A549 and HepG2, using two strains (NGC and TSV01) of dengue serotype 2 (DEN2) and found that the two viruses exhibited a marked difference in inducing type I IFN response. While TSV01 infection led to activation of type I antiviral genes such as EIF2AK2 (PKR), OAS, ADAR and MX, these responses were absent in NGC-infected cells. Biochemical analysis revealed that NGC but not TSV01 suppressed STAT-1 and STAT-2 activation in response to type I IFN (αandβ). However, these two strains did not differ in their response to type II IFN (γ). Although unable to suppress IFN signalling, TSV01 infection caused a weaker IFN-βinduction compared with NGC, suggesting an alternative mechanism of innate immune escape. We extended our study to clinical isolates of various serotypes and found that while MY10245 (DEN2) and MY22713 (DEN4) could suppress the IFN response in a similar fashion to NGC, three other strains of dengue [EDEN167 (DEN1), MY02569 (DEN1) and MY10340 (DEN2)] were unable to suppress the IFN response, suggesting that this difference is strain-dependent but not serotype-specific. Our report indicates the existence of a strain-specific virulence factor that may impact on disease severity.
A short amino acid sequence containing tyrosine in the N-terminal region of G protein-coupled receptors is critical for their potential use as co-receptors for human and simian immunodeficiency viruses
Authors: Shimizu Nobuaki , Tanaka Atsushi , Oue Atsushi , Mori Takahisa , Apichartpiyakul Chatchawann , Hoshino Hiroo
Published: November 2008

Various G protein-coupled receptors (GPCRs) have the potential to work as co-receptors for human and simian immunodeficiency virus (HIV/SIV). HIV/SIV co-receptors have several tyrosines in their extracellular N-terminal region (NTR) as a common feature. However, the domain structure of the NTR that is critical for GPCRs to have co-receptor activity has not been identified. Comparative studies of different HIV/SIV co-receptors are an effective way to clarify the domain. These studies have been carried out only for the major co-receptors, CCR5 and CXCR4. A chemokine receptor, D6, has been shown to mediate infection of astrocytes with HIV-1. Recently, it was also found that an orphan GPCR, GPR1, and a formyl peptide receptor, FPRL1, work as potent HIV/SIV co-receptors in addition to CCR5 and CXCR4. To elucidate more about the domain of the NTR critical for HIV/SIV co-receptor activity, this study analysed the effects of mutations in the NTR on the co-receptor activity of D6, FPRL1 and GPR1 in addition to CCR5. The results identified a number of tyrosines that are indispensable for the activity of these co-receptors. The number and positions of those tyrosines varied among co-receptors and among HIV-1 strains. Moreover, it was found that a small domain of a few amino acids containing a tyrosine is critical for the co-receptor activity of GPR1. These findings will be useful in elucidating the mechanism that allows GPCRs to have the potential to act as HIV/SIV co-receptors.
Development of genetic markers in the non-structural protein 2 region of a US type 1 porcine reproductive and respiratory syndrome virus: implications for future recombinant marker vaccine development
Authors: Fang Ying , Christopher-Hennings Jane , Brown Elizabeth , Liu Haixia , Chen Zhenhai , Lawson Steven R. , Breen Rachael , Clement Travis , Gao Xiaofei , Bao Jingjing , Knudsen David , Daly Russell , Nelson Eric
Published: November 2008

Porcine reproductive and respiratory syndrome virus (PRRSV) continues to be a major problem in the pork industry worldwide. The limitations of current PRRSV vaccines require the development of a new generation of vaccines. One of the key steps in future vaccine development is to include markers for diagnostic differentiation of vaccinated animals from those naturally infected with wild-type virus. Using a cDNA infectious clone of type 1 PRRSV, this study constructed a recombinant green fluorescent protein (GFP)-tagged PRRSV containing a deletion of an immunogenic epitope, ES4, in the nsp2 region. In a nursery pig disease model, the recombinant virus was attenuated with a lower level of viraemia in comparison with that of the parental virus. To complement the marker identification, GFP and ES4 epitope-based ELISAs were developed. Pigs immunized with the recombinant virus lacked antibodies directed against the corresponding deleted epitope, but generated a high-level antibody response to GFP by 14 days post-infection. These results demonstrated that this recombinant marker virus, in conjunction with the diagnostic tests, enables serological differentiation between marker virus-infected animals and those infected with the wild-type virus. This rationally designed marker virus will provide a basis for further development of PRRSV marker vaccines to assist with the control of PRRS.
Examining the relative activity of several dicistrovirus intergenic internal ribosome entry site elements in uninfected insect and mammalian cell lines
Authors: Carter James R. , Fraser Tresa S. , Fraser Malcolm J.
Published: November 2008

Comparisons of the relative activities of 11 intergenic region (IGR) internal ribosome entry site (IRES) elements of insect dicistrovirus with 5′ IRES elements of the hepatitis C and encephalomyocarditis viruses were performed in insect and mammalian cells. Dual luciferase assays were performed to determine the most effective dicistrovirus IGR IRES in the lepidopteran cell lines Sf9 (Spodoptera frugiperda) and BmN (Bombyx mori), and the dipteran cell lines S2 (Drosophila melanogaster) and ATC-10 (Aedes aegypti). Evaluation of dual luciferase expression from DNA plasmids and in vitro-transcribed RNA revealed apparent splicing with certain IRES elements. Though IRES activity depended upon the cell line examined, the black queen cell and Drosophila C dicistrovirus intergenic IRES elements were most effective for coupled gene expression in the diverse insect cell lines examined.
The influenza A virus spliced messenger RNA M mRNA3 is not required for viral replication in tissue culture
Authors: Jackson David , Lamb Robert A.
Published: November 2008

Influenza A virus genome RNA segment 7 encodes three known mRNAs, two of which, M2 mRNA and M mRNA3, are derived by alternative splicing of the primary collinear mRNA transcript using alternative 5′ splice sites. The function of M mRNA3 is currently unknown, therefore we attempted to determine whether it is essential for virus replication. Recombinant viruses unable to produce M mRNA3 and/or M2 mRNA were created by mutating the shared 3′ splice site. Growth of the mutant viruses in M2-expressing MDCK cells was not significantly affected by the lack of M mRNA3. During the course of a wild-type virus infection, levels of M mRNA3 began to decrease while those of M2 mRNA increased, which may indicate a potential mechanism of alternative splicing control. These data suggest that neither M mRNA3 nor any potential protein product are essential for influenza virus replication in tissue culture.
A historical analysis of herpes simplex virus promoter activation in vivo reveals distinct populations of latently infected neurones
Authors: Proença João T. , Coleman Heather M. , Connor Viv , Winton Douglas J. , Efstathiou Stacey
Published: November 2008

Herpes simplex virus type 1 (HSV-1) has the capacity to establish a life-long latent infection in sensory neurones and also to periodically reactivate from these cells. Since mutant viruses defective for immediate-early (IE) expression retain the capacity for latency establishment it is widely assumed that latency is the consequence of a block in IE gene expression. However, it is not clear whether viral gene expression can precede latency establishment following wild-type virus infection. In order to address this question we have utilized a reporter mouse model system to facilitate a historical analysis of viral promoter activation in vivo. This system utilizes recombinant viruses expressing Cre recombinase under the control of different viral promoters and the Cre reporter mouse strain ROSA26R. In this model, viral promoter-driven Cre recombinase mediates a permanent genetic change, resulting in reporter gene activation and permanent marking of latently infected cells. The analyses of HSV-1 recombinants containing human cytomegalovirus major immediate-early, ICP0, gC or latency-associated transcript promoters linked to Cre recombinase in this system have revealed the existence of a population of neurones that have experienced IE promoter activation prior to the establishment of latency.
Identification of antibody neutralization epitopes on the fusion protein of human metapneumovirus
Authors: Ulbrandt Nancy D. , Ji Hong , Patel Nita K. , Barnes Arnita S. , Wilson Susan , Kiener Peter A. , Suzich JoAnn , McCarthy Michael P.
Published: November 2008

Human metapneumovirus (hMPV) is genetically related to respiratory syncytial virus (RSV); both cause respiratory tract illnesses ranging from a mild cough to bronchiolitis and pneumonia. The F protein-directed monoclonal antibody (mAb) palivizumab has been shown to prevent severe lower respiratory tract RSV infection in animals and humans. We have previously reported on a panel of mAbs against the hMPV F protein that neutralize hMPV in vitro and, in two cases, in vivo. Here we describe the generation of hMPV mAb-resistant mutants (MARMs) to these neutralizing antibodies. Sequencing the F proteins of the hMPV MARMs identified several neutralizing epitopes. Interestingly, some of the epitopes mapped on the hMPV F protein coincide with homologous regions mapped previously on the RSV F protein, including the site against which the broadly protective mAb palivizumab is directed. This suggests that these homologous regions play important, conserved functions in both viruses.
A Second Mechanism for Aluminum Resistance in Wheat Relies on the Constitutive Efflux of Citrate from Roots
Authors: Ryan Peter R. , Raman Harsh , Gupta Sanjay , Horst Walter J. , Delhaize Emmanuel
Published: November 2008

The first confirmed mechanism for aluminum (Al) resistance in plants is encoded by the wheat (Triticum aestivum) gene, TaALMT1, on chromosome 4DL. TaALMT1 controls the Al-activated efflux of malate from roots, and this mechanism is widespread among Al-resistant genotypes of diverse genetic origins. This study describes a second mechanism for Al resistance in wheat that relies on citrate efflux. Citrate efflux occurred constitutively from the roots of Brazilian cultivars Carazinho, Maringa, Toropi, and Trintecinco. Examination of two populations segregating for this trait showed that citrate efflux was controlled by a single locus. Whole-genome linkage mapping using an F2 population derived from a cross between Carazinho (citrate efflux) and the cultivar EGA-Burke (no citrate efflux) identified a major locus on chromosome 4BL, Xcec, which accounts for more than 50% of the phenotypic variation in citrate efflux. Mendelizing the quantitative variation in citrate efflux into qualitative data, the Xcec locus was mapped within 6.3 cM of the microsatellite marker Xgwm495 locus. This linkage was validated in a second population of F2:3 families derived from a cross between Carazinho and the cultivar Egret (no citrate efflux). We show that expression of an expressed sequence tag, belonging to the multidrug and toxin efflux (MATE) gene family, correlates with the citrate efflux phenotype. This study provides genetic and physiological evidence that citrate efflux is a second mechanism for Al resistance in wheat.
The elusive [Ni(H2O)2(15-crown-5)]2+ cation and related co-crystals of nickel(II) hydrates and 15-crown-5
Authors: Siegler Maxime A. , Parkin Sean , Selegue John P. , Brock Carolyn Pratt
Published: November 2008

Initial attempts to make [Ni(H2O)2(15-crown-5)](NO3)2, i.e. to insert the Ni2+ ion into the 15-crown-5 macrocycle, gave the mono- (two polymorphs) and dihydrate of a co-crystal of [Ni(H2O)6](NO3)2 and 15-crown-5 (1,4,7,10,13-pentaoxacyclopentadecane = 15C5). Synthetic routes designed to restrict the water available to the Ni2+ cation gave three additional compounds, [Ni(H2O)6](NO3)2-trans-[Ni(H2O)4(MeOH)2](NO3)2·2(15C5), cis-[Ni(H2O)4(NO3)2]-trans-[Ni(H2O)4(NO3)2]·2(15C5) and [Ni(H2O)2(MeCN)(NO3)2]·15C5·MeCN. All five compounds contain Ni2+ ions with two trans aqua ligands. In all six structures these aqua ligands make hydrogen bonds to the 15C5 molecules to form stacks in which the Ni complexes and 15C5 molecules alternate. The structures are surprisingly complicated: all are co-crystals, some are also solvates, and most have Z′ > 1. The target compound was finally prepared by heating pale green crystals of [Ni(H2O)6](NO3)2·15C5·2H2O to over 350 K and then cooling the resulting mixture of yellow crystals and solution to room temperature. Formation of the target compound seems to be favored at higher temperatures by a positive Δrxn
S
o and an increased rate of ligand exchange.
Quantifying the ‘hidden’ lactose in drugs used for the treatment of gastrointestinal conditions
Authors: EADALA P. , WAUD J. P. , MATTHEWS S. B. , GREEN J. T. , CAMPBELL A. K.
Published: November 2008

Background  Lactose intolerance affects 70% of the world population and may result in abdominal and systemic symptoms. Treatment focuses predominantly on the dietary restriction of food products containing lactose. Lactose is the most common form of excipient used in drug formulations and may be overlooked when advising these patients.

Aim  To identify and quantify the amount of lactose in medications used for the treatment of gastrointestinal disorders and to identify ‘lactose‐free’ preparations.

Methods  Medications used for the treatment of gastrointestinal disorders were identified from the British National Formulary (BNF). Their formulation including excipients was obtained from the Medicines Compendium. The lactose content and quantity in selected medications was measured using high‐performance liquid chromatography (HPLC).

Results  A wide range of medications prescribed for the treatment of gastrointestinal conditions contain lactose. We have quantified the lactose content in a selection of medications using HPLC. Lactose is present in amounts that may contribute towards symptoms. Lactose‐free alternatives were also identified.

Conclusions  Lactose is present in a range of medications and may contribute towards symptoms. This may not be recognized by the prescribing doctor as excipients are not listed in the BNF, and the quantity of lactose is not listed on the label or in the accompanying manufacturer’s leaflet.
Application of low frequency genetic marking at GPI‐3* and MDH‐B1,2* loci to assess supplementary stocking of Atlantic salmon, Salmo salar L., in a Northern Irish stream
Authors: CROZIER W. W. , MOFFETT I. J. J.
Published: November 2008

Abstract At the River Bush salmon station in Northern Ireland, a genetically marked strain of Atlantic salmon, Salmo salar L., was established, with a low frequency (0.194) of a glucose‐6‐phosphate isomerase genotype (GPI‐3* 100/93). As part of a salmon enhancement programme, 43500 of these fish were stocked as swim‐up fry into a tributary of the nearby Margy River in Spring 1990, following a baseline genetic survey which indicated an absence of the GPI–3*93 allele in the wild population. This survey also indicated a significant frequency difference of a malate dehydrogenase allele (MDH‐B1,2*85) present both in the stocked and wild fish. A post‐stocking electrofishing survey in summer 1990 indicated higher summerling densities in stocked sections compared with unstocked (control) sections, with an estimated survival of stocked fry to summerling ranging from 24% to 29%. Genetic analysis based on GPI‐3*100/93 and MDH‐B1,2*100/85 genotypes provided similar estimates of the overall contribution of stocked fish at 59.8% to 61.9%, respectively, although there was a disparity between markers in estimated contributions to stocked and control sections. A further genetic survey in 1991 estimated that 32.2% (MDH) to 69.1% (GPI) of the 1 + parr population consisted of stocked fish, the MDH‐based estimate having declined greatly between summerling and 1 + parr stages. Possible reasons for the disparity of marker results are outlined, and the implications for use of low‐frequency genetic marking discussed.
Population dynamics and management of culture‐based fisheries
Authors: LORENZEN K.
Published: November 2008

Abstract The population dynamics of culture‐based fisheries are studied by means of a mathematical model, which incorporates explicit sub‐models for density‐dependent individual growth and size‐dependent mortality. The model applies to populations of carps, i.e. common carp, Chinese carps, and Indian major carps, and coregonids.

The effects on production of stocking density and size of seed fish, fishing mortality, and size at harvesting are studied in a model population of carp. Management implications of the modelling results are emphasized. An adaptive approach to management, involving judicious experimentation with stocking and harvesting regimes, is proposed to gain information on the dynamics of actual fisheries, and to optimize their production.
Hydrological connectivity drives patterns of macroinvertebrate biodiversity in floodplain rivers of the Australian wet /dry tropics
Authors: LEIGH CATHERINE , SHELDON FRAN
Published: November 2008

1. Floodplain rivers in Australia’s wet/dry tropics are regarded as being among the most ecologically intact and bio‐diverse lotic ecosystems in the world, yet there have been relatively few community‐based studies of their aquatic fauna.

2. To investigate relationships between hydrological connectivity and biodiversity in the region, macroinvertebrates were collected from sites within two contrasting floodplain rivers, the ‘tropical’ Gregory River and ‘dryland’ Flinders River systems, during the dry season and analysed at various spatial scales. A subset of sites was re‐sampled in the following dry season to explore temporal variation. The fauna consisted of 124 morphotaxa, dominated by gatherers and the Insecta.

3. As predicted, hydrological connectivity (the lotic or lentic status of waterbodies) had a major influence on macroinvertebrate assemblage composition and diversity, both in space and time. Assemblages from waterbodies with similar connection histories were most alike, and beta‐diversity between assemblages was greatest between lotic and lentic waterbodies, tending to increase with increasing spatial separation.

4. At smaller spatial scales, a number of within‐waterbody, habitat and water quality characteristics were important for explaining variation (61%) in the taxonomic organization of assemblages, and characteristics associated with primary productivity and habitat diversity were important for explaining variation (45%) in the functional organization of assemblages. However, much of the small‐scale environmental variation across the study region appeared to be related to broad‐scale variation in hydrological connectivity, which had both direct and indirect effects on macroinvertebrate assemblages.

5. Conservation of the biodiversity in Australia’s wet/dry tropics may depend on conserving the natural variation in hydrological connectivity and the unregulated flow of floodplain rivers.
Plant behavioural ecology: dynamic plasticity in secondary metabolites
Authors: METLEN KERRY L. , ASCHEHOUG ERIK T. , CALLAWAY RAGAN M.
Published: November 2008

Behaviour is in part the ability to respond rapidly and reversibly in response to environmental stimuli during the lifetime of an individual. Plants and animals both exhibit behaviour, but plant behaviour is most often examined in the context of morphologically plastic growth. Rapid and reversible secondary metabolite production and release is also a key mechanism by which plants behave. Here, we review plant biochemical plasticity as plant behaviour, and explicitly focus on evidence for responses that display rapid induction, reversibility and ecological relevance. Rapid induction and attenuation of plant secondary metabolites occur as chemically mediated root foraging, plant defence, allelochemistry and to regulate mutualistic relationships. We describe a wealth of information on the induction of various plant biochemical responses to environmental stimuli but found a limited body of literature on the reversibility of induced biochemical responses. Understanding the full cycle of dynamic plasticity in secondary metabolites is an important niche for future research. Biochemical behaviours extend beyond the plant kingdom; however, they clearly illustrate the capacity for plants to behave in ways that closely mirror the classic definitions and research approaches applied to behaviour in animals.
Trends observed during a decade of paediatric sick visits to peripheral health facilities in rural western Kenya, 1997–2006
Authors: Van Hemelrijck Mieke J. J. , Lindblade Kim A. , Kubaje Adazu , Hamel Mary J. , Odhiambo Frank , Phillips‐Howard Penelope A. , Laserson Kayla F. , Slutsker Laurence , Feikin Daniel R.
Published: November 2008

Objectives  To assess whether longitudinal surveillance in peripheral health facilities could document trends in disease burden, healthcare practice and utilization resulting from large‐scale public health interventions made in the decade 1997–2006.

Methods  Data were collected from sick child visits (SCVs) among children <5 years attending 14 outpatient facilities in Asembo, rural western Kenya, during 1997–2006. Changes in proportions, and counts and rates were evaluated using chi‐square and Poisson regression respectively.

Results  During the decade, 64 394 SCVs were made, yielding an average rate of 0.70 SCVs per child‐year. The annual number of SCVs stayed constant during 1997–2003, then increased by 74% between 2003 and 2006 (P < 0.01). The time between symptom onset and SCV shortened from 5.6 days in 1997 to 4.4 days in 2006 (P < 0.01). Malaria and upper respiratory tract infection (URTI) were most commonly diagnosed (69% and 36% of SCVs respectively). Between 2003 and 2006, the proportion of SCVs with a malaria diagnosis fell from 77% to 48%, although the rate of malaria SCVs did not. URTI visits increased in 2004–2006. The most frequently prescribed antimalarials changed three times, lagging 1–2 years behind changes in national policy. Treatment of pneumonia with antibiotics varied by year, ranging from 19% to 89%.

Conclusion  Surveillance of paediatric SCVs at peripheral health facilities was useful in documenting the timing and penetration of changes in national policies and clinical patterns of drug use for common infections. The surveillance data suggested that improved access to care, rather than disease burden changes, likely led to greater healthcare utilization after 2003.
Pharmacy customers’ knowledge of side effects of purchased medicines in Mexico
Authors: Wirtz Veronika J. , Taxis Katja , Dreser Anahi
Published: November 2008

Objectives  To analyse pharmacy customers’ knowledge and information sources about side effects of medicines they purchased and factors associated with this knowledge.

Methods  Cross‐sectional survey and semi‐structured interviews with customers of 52 randomly selected community pharmacies in Morelos state, Mexico. Customers were included if they were older than 18 years, bought at least one drug either with or without medical prescription, and agreed to take part in the survey. Data were analysed using a multinomial logistic regression model.

Results  A total of 1445 customers buying 1946 drugs were surveyed (age 42.9 ± 15.7 years, 56.9% female); 627 (59%) of 1055 customers who purchased prescription‐only medicines (POM) did so without a prescription. Of all customers interviewed, 172 (11.9%) affirmed that the bought medicine(s) could cause harm. Only half of those (87 or 6%) were able to identify correctly at least one side effect of the purchased medicines. The majority received the information about side effects from a physician. Customers in semirural areas knew less about side effects (odds ratio: 0.26; 95% CI: 0.11–0.61; P = 0.00); whereas customers buying medicines for chronic pain, hypertension or diabetes knew more (odds ratio 2.63; 95% CI: 1.44–4.80; P = 0.00).

Conclusion  The overall majority of customers did not know that medicines they bought could be harmful. This is particularly alarming because they frequently used POM without consulting a physician.
Vegetation and seedbank response to Eragrostis lehmanniana removal in semi‐desert communities
Authors: CRIMMINS T M , McPHERSON G R
Published: November 2008

Eragrostis lehmanniana (Lehmann lovegrass) is an invasive perennial bunchgrass in semi‐desert grasslands in the USA. We removed E. lehmanniana using glyphosate at three locations in south‐eastern Arizona in 2003 and 2004 to evaluate the community response. We also sampled the seedbank five times during the course of the experiment to characterise viable seeds at the sites. Two of the sites with histories of livestock grazing responded similarly to the continued removal of E. lehmanniana, with significant increases in native cover and species richness, mainly attributable to herbaceous annual species. Over the course of the study, progressively fewer E. lehmanniana seeds and higher numbers of native annual herb seeds were germinated from seedbank samples of treated plots. At the third site, characterised by a history of intense agricultural use and drier conditions than the other sites, there was a large decrease in E. lehmanniana cover in all plots, followed by an increase in aggressive non‐native species as well as native grasses. The seedbank at this site suggested potential for restoration, with native perennial grass species present in increasing quantities. The results of this study have implications for site restoration, should a means of permanently removing E. lehmanniana be found.
Modelling within‐field spatial variability of crop biomass – weed density relationships using geographically weighted regression
Authors: BLANCO‐MORENO J M , CHAMORRO L , IZQUIERDO J , MASALLES R M , SANS F X
Published: November 2008

The objective of this study is to offer a new framework for exploring and modelling the spatial variation in crop biomass – weed density relationships, adapting geographically weighted regression (GWR) to include a non‐linear regression model. The relationship between crop biomass and weed density is usually modelled by non‐linear regression models, in which the spatial heterogeneity of the relationship is ignored, although the effect of weeds on crop can differ in relation to topographic and edaphic variability. GWR attempts to capture spatial variability by calibrating a regression model to each location in space. We show the application of the method in different cereal cropping systems, with one or two weed species. The results indicate that GWR can significantly improve model fitting over non‐linear least squares (NLS) in some situations. Furthermore, the parameter estimates can be mapped to illustrate local spatial variations in the regression relationship under study and eventually to relate the spatial variability of the model to the environmental heterogeneity. We discuss the value of the GWR for analysing the observed spatial variability and for improving model development and our understanding of spatial processes.
Liquid Storage of Goat Semen in Chemically Defined Extenders
Authors: Xu C‐L , Zhou J‐B , Zhao B‐T , Lan G‐C , Luo M‐J , Chang Z‐L , Sui H‐S , Tan J‐H
Published: November 2008

Contents

The suitability of certain commercial and self‐made chemically defined extenders for liquid storage of goat semen was tested and the effects of storage temperatures, dilution rates and sperm washing and pH of extenders on the goat sperm during liquid storage were observed. Semen was collected from nine goat bucks of the Lubei White and Boer breeds using an artificial vagina. Each ejaculate after initial evaluation was diluted with a specific extender, cooled and stored at a desired temperature. Stored semen was evaluated for sperm motility and other parameters every 24 or 48 h of storage. The ranking order of the existing milk‐ and yolk‐free extenders in sustaining goat sperm motility was Androhep > Zorlesco > Beltsville thawing solution > the Tris–glucose medium. The new extender (mZA) which was formulated based on Zorlesco and Androhep was more suitable for goat sperm than Androhep. The mZAP extender with Bovine Serum Albumin (BSA) replaced with polyvinyl alcohol (PVA) worked as efficiently as the mZA in maintaining sperm motility, membrane integrity, acrosome intactness and capacitation status. Goat sperm motility was best maintained at 5°C during liquid preservation, but decreased significantly as the temperature increased. When semen was sixfold diluted, sperm motility was maintained longer (p < 0.05) after centrifugation, but sperm motility did not differ between the centrifuged and non‐centrifuged groups when semen was 11‐fold diluted. When the extender pH was adjusted from 6.6 to 6.04, the efficiency increased significantly in both Androhep and mZAP. A forward sperm motility of 34% was maintained for 9 days when buck semen was 11‐fold diluted and stored at 5°C in mZAP, with pH adjusted to 6.04. It is concluded that for liquid storage of buck semen, the mZA extender was more suitable than other extenders; BSA can be replaced with PVA in mZA; centrifugation to remove seminal plasma can be omitted by adequate dilution; and the storage temperature and pH of extenders affected sperm motility significantly.
Serum growth factor analysis in dry eye syndrome
Authors: Bradley Jay C , Bradley Rachael H , McCartney David L , Mannis Mark J
Published: November 2008

Abstract

Background:  To perform a comprehensive serum growth factor analysis in dry eye syndrome patients and to compare this with matched controls.

Methods:  Six female dry eye syndrome patients and six age‐ and gender‐matched controls were recruited. Whole blood was collected, allowed to clot and then centrifuged. Serum was extracted by using sterile technique. Enzyme‐linked immunosorbent assays were performed to quantify serum growth factor levels.

Results:  Levels of transforming growth factor‐beta 1 and 2 (TGF‐β1 and β2), nerve growth factor (NGF), insulin‐like growth factor‐1 (IGF‐1), epidermal growth factor (EGF), acidic and basic fibroblast growth factor (FGF), keratinocyte growth factor (KGF), hepatocyte growth factor (HGF), vascular endothelial growth factor (VEGF), platelet‐derived growth factor‐AA, AB and BB (PDGF‐AA, AB and BB), brain‐derived neurotrophic factor (BDNF), neurotrophin‐3 (NT‐3) and glial cell line‐derived neurotrophic factor (GDNF) were quantified, and statistical analysis was performed by using the Mann–Whitney U‐test with the Bonferroni correction.

Conclusions:  No significant difference was found between serum growth factor levels in dry eye syndrome patients versus controls. Our study provides comprehensive analysis of serum growth factor levels in autologous serum eye drops produced from ocular surface disease patients. A knowledge of growth factor levels in serum may be important because of the increasing use of autologous serum eye drops in refractory ocular surface diseases and for an understanding of how topical serum may provide benefit.
Rapid visual recovery after penetrating keratoplasty for keratoconus
Authors: Sutton Gerard , Hodge Chris , McGhee Charles NJ
Published: November 2008

Abstract

Purpose:  To ascertain the level and speed of visual recovery after penetrating keratoplasty for keratoconus.

Method:  A retrospective review was performed of 100 consecutive cases of penetrating keratoplasty for keratoconus, performed between 1999 and 2005. Review assessed visual function and the speed at which patients achieved a functional best corrected visual acuity (BCVA) of ≥6/12 either with glasses or phoropter. Analysis of visual, refractive and keratometric results were made on 76 eyes that had reached 6 months after suture removal. Intraoperative and postoperative complications including graft rejections were recorded.

Results:  Post keratoplasty, 43.4%, 78.9% and 96.1% of patients achieved a BCVA of 6/12 or better by 1, 3 and 6 months, respectively. The mean time to achieve a BCVA of 6/12 was 9.6 weeks. Only 5.3% of patients required a rigid gas permeable contact lens. Overall 42.4% of patients had unaided visual acuity of 6/12 or better at 12 months. The mean refractive cylinder and standard deviation was 2.78 ± 1.6 D, and the mean spherical equivalent was −1.12 ± 2.9 D. There were no significant intraoperative complications, and although 3.9% of eyes had at least one graft rejection episode there were no graft failures.

Conclusion:  Penetrating keratoplasty is an effective method for treating advanced keratoconus. By 3 months almost all patients are able to achieve a BCVA of 6/12 or better with progressive improvement over time. This technique allows almost half of patients to achieve an unaided vision of 6/12 or better with sutures in situ.
Accident analysis: factors contributing to a ureteric injury during deep endometriosis surgery
Authors: Schonman R , De Cicco C , Corona R , Soriano D , Koninckx PR
Published: November 2008

Objective  To analyse factors associated with a ureteric injury.

Design  Retrospective accident analysis.

Setting  Deep endometriosis surgery in a tertiary referral centre.

Sample  Video recording of a surgical accident was analysed by six gynaecologists.

Methods  A 26‐year‐old woman underwent laparoscopy for deep endometriosis that involves the rectosigmoid and left ureter. Post operatively left ureter transection was identified and corrected by laparoscopy. Interventions were recorded and reviewed independently.

Main outcome measures  Changes in surgical behaviour that could be measured were identified using the video recording.

Results  During the intervention, the periods of uncontrolled bleeding (P < 0.0001) and the duration of laser activation (P = 0.013) increased progressively. Simultaneous laser activation and bipolar coagulation only occurred at the end of surgery (seven episodes). Fatigue could not be measured.

Conclusion  Unconscious acceleration of surgery, possibly as a consequence of fatigue, is suggested as a contributing factor for an error of judgement.
Somali women and their pregnancy outcomes postmigration: data from six receiving countries
Authors: Small R , Gagnon A , Gissler M , Zeitlin J , Bennis M , Glazier RH , Haelterman E , Martens G , McDermott S , Urquia M , Vangen S
Published: November 2008

Objective  This study aimed to investigate pregnancy outcomes in Somali‐born women compared with those women born in each of the six receiving countries: Australia, Belgium, Canada, Finland, Norway and Sweden.

Design  Meta‐analyses of routinely collected data on confinements and births.

Setting  National or regional perinatal datasets spanning 3–6 years between 1997 and 2004 from six countries.

Sample  A total of 10 431 Somali‐born women and 2 168 891 receiving country‐born women.

Methods  Meta‐analyses to compare outcomes for Somali‐born and receiving country‐born women across the six countries.

Main outcome measures  Events of labour (induction, epidural use and proportion of women using no analgesia), mode of birth (spontaneous vaginal birth, operative vaginal birth and caesarean section) and infant outcomes (preterm birth, birthweight, Apgar at 5 minutes, stillbirths and neonatal deaths).

Results  Compared with receiving country‐born women, Somali‐born women were less likely to give birth preterm (pooled OR 0.72, 95% CI 0.64–0.81) or to have infants of low birthweight (pooled OR 0.89, 95% CI 0.82–0.98), but there was an excess of caesarean sections, particularly in first births (pooled OR 1.41, 95% CI 1.25–1.59) and an excess of stillbirths (pooled OR 1.86, 95% CI 1.38–2.51).

Conclusions  This analysis has identified a number of disparities in outcomes between Somali‐born women and their receiving country counterparts. The disparities are not readily explained and they raise concerns about the provision of maternity care for Somali women postmigration. Review of maternity care practices followed by implementation and careful evaluation of strategies to improve both care and outcomes for Somali women is needed.
Transvaginal Burch operation for stress urinary incontinence: 5‐year results
Authors: Capar M , Balci O , Acar A , Karatayli R
Published: November 2008

Several techniques have been developed for the management of stress urinary incontinence (SUI). To establish 5‐year outcomes for women who underwent our previously described new retropubic suspension operation (transvaginal Burch operation) for SUI at the Meram Medicine Faculty, a prospective study was performed on 231 women who had been operated on for stress incontinence and who had completed 5 years of follow up. We observed complete remission during the follow‐up period in 215 women (93%). No major complication related to the procedure was reported, and results were found to be satisfactory and encouraging.
BOOK REVIEW
Authors: Furniss I. F.
Published: November 2008

Concepts of Productivity Measurement in Agriculture on a National Scale, by Prof. Dr. J. Honing, processed publication on E.P.A. project No. 6/16‐III, Directorate for Agriculture and Food, Division for Technical Action in Agriculture and Food, Organization for Economic Cooperation and Development, Paris, June 1962.