bluuebunny/crossref_metadata_2025 huggingface dataset:
Mounting Live Cells onto Microscope Slides
Authors: Chazotte Brad
Published: January 2011

INTRODUCTION

This protocol describes the mounting of cells which have been grown on cleaned coverslips in cell culture dishes containing the appropriate medium and supplements. Labeling is performed with the coverslips placed in culture dishes. After cells are labeled, the coverslips can be mounted onto microscope slides to be viewed for short-term observation of live cells or longer-term observation of fixed cells. For viewing live cells for longer periods of time, specialized chambers should be used in which suitable growth conditions can be maintained.
Labeling Nuclear DNA Using DAPI
Authors: Chazotte Brad
Published: January 2011

INTRODUCTION

A number of fluorescent stains are available that label DNA and allow easy visualization of the nucleus in interphase cells and chromosomes in mitotic cells, including Hoechst, 4′,6-diamidino-2-phenylindole (DAPI), ethidium bromide, propidium iodide, and acridine orange. Although not as bright as the vital Hoechst stains for DNA, DAPI has greater photostability. It is believed that DAPI associates with the minor groove of double-stranded DNA, with a preference for the adenine-thymine clusters. Cells must be permeabilized and/or fixed for DAPI to enter the cell and to bind DNA. Fluorescence increases approximately 20-fold when DAPI is bound to double-stranded DNA. This protocol describes the use of DAPI to label nuclear DNA of cells grown in culture.
Labeling Nuclear DNA with Hoechst 33342
Authors: Chazotte Brad
Published: January 2011

INTRODUCTION

A number of fluorescent stains are available that label DNA and allow easy visualization of the nucleus in interphase cells and chromosomes in mitotic cells. One advantage of Hoechst 33342 is that it is membrane permeant and, thus, can stain live cells. Hoechst 33342 binds to adenine-thymine-rich regions of DNA in the minor groove. On binding to DNA, the fluorescence greatly increases. This protocol describes the use of Hoechst 33342 to label nuclear DNA of cells grown in culture.
Correlated Live Cell Light and Electron Microscopy Using Tetracysteine Tags and Biarsenicals
Authors: Gaietta Guido M. , Deerinck Thomas J. , Ellisman Mark H.
Published: January 2011

INTRODUCTION

Fundamental to obtaining a more complete understanding of the roles played by macromolecular complexes in cells is the ability to map their location, movement, and transient interactions at high temporal and high spatial resolution. Unfortunately, probes capable of allowing direct correlation of real-time or time-lapse light microscopy (LM) with electron microscopic observations are relatively few. Genetically encoded fluorescent reporters such as green fluorescent protein (GFP) have revolutionized live cell imaging studies but are not directly visible by electron microscopy (EM). Fluorescent nanoparticles or quantum dots are a type of label for LM that can also be visualized directly by EM, but targeting these to cytoplasmic proteins in living cells remains difficult. One method that does allow for highly correlated LM and EM with excellent preservation of cellular ultrastructure is fluorescence photoconversion, in which a fluorescent compound causes the deposition of a reaction product that can be rendered electron-dense and directly visualized by EM. We have used this method in combination with a class of genetically encoded peptide tags that can be labeled in living cells by fluorophores bearing two appropriately spaced arsenic atoms (biarsenicals). The tetracysteine motif is short, easily inserted into or attached to the termini of the host protein, and can be used in combination with other molecular tags such as GFP and its derivatives. This article presents methods to label cells with biarsenicals, conduct live cell imaging recording sessions, and generate specimens that can be evaluated by EM for a correlated LM/EM analysis.
Combining Enhanced Root and Shoot Growth Reveals Cross Talk between Pathways That Control Plant Organ Size in Arabidopsis
Authors: Vercruyssen Liesbeth , Gonzalez Nathalie , Werner Tomá¡ , Schmülling Thomas , Inzé Dirk
Published: January 2011

Functionally distinct Arabidopsis (Arabidopsis thaliana) genes that positively affect root or shoot growth when ectopically expressed were combined to explore the feasibility of enhanced biomass production. Enhanced root growth resulting from cytokinin deficiency was obtained by overexpressing CYTOKININ OXIDASE/DEHYDROGENASE3 (CKX3) under the control of the root-specific PYK10 promoter. Plants harboring the PYK10-CKX3 construct were crossed with four different transgenic lines showing enhanced leaf growth. For all combinations, the phenotypic traits of the individual lines could be combined, resulting in an overall growth increase. Unexpectedly, three out of four combinations had more than additive effects. Both leaf and root growth were synergistically enhanced in plants ectopically expressing CKX3 and BRASSINOSTEROID INSENSITIVE1, indicating cross talk between cytokinins and brassinosteroids. In agreement, treatment of PYK10-CKX3 plants with brassinolide resulted in a dramatic increase in lateral root growth that could not be observed in wild-type plants. Coexpression of CKX3 and the GROWTH-REGULATING FACTOR5 (GRF5) antagonized the effects of GRF5 overexpression, revealing an interplay between cytokinins and GRF5 during leaf cell proliferation. The combined overexpression of CKX3 and GIBBERELLIN 20-OXIDASE1 led to a synergistic increase in leaf growth, suggesting an antagonistic growth control by cytokinins and gibberellins. Only additive effects on root and shoot growth were visible in plants ectopically expressing both CKX3 and ARABIDOPSIS VACUOLAR PYROPHOSPHATASE1, hinting at an independent action mode. Our results show new interactions and contribute to the molecular and physiological understanding of biomass production at the whole plant level.
Deficiency of the Erc/mesothelin gene ameliorates renal carcinogenesis in Tsc2 knockout mice
Authors: Zhang Danqing , Kobayashi Toshiyuki , Kojima Tetsuo , Kanenishi Kenji , Hagiwara Yoshiaki , Abe Masaaki , Okura Hidehiro , Hamano Yoshitomo , Sun Guodong , Maeda Masahiro , Jishage Kou‐ichi , Noda Tetsuo , Hino Okio
Published: January 2011

Genetic crossing experiments were performed between tuberous sclerosis‐2 (Tsc2) KO and expressed in renal carcinoma (Erc) KO mice to analyze the function of the Erc/mesothelin gene in renal carcinogenesis. We found the number and size of renal tumors were significantly less in Tsc2+/−;Erc−/− mice than in Tsc2+/−;Erc+/+ and Tsc2+/−;Erc+/− mice. Tumors from Tsc2+/−;Erc−/− mice exhibited reduced cell proliferation and increased apoptosis, as determined by proliferating cell nuclear antigen (Ki67) and TUNEL analysis, respectively. Adhesion to collagen‐coated plates in vitro was enhanced in Erc‐restored cells and decreased in Erc‐suppressed cells with siRNA. Tumor formation by Tsc2‐deficient cells in nude mice was remarkably suppressed by stable knockdown of Erc with shRNA. Western blot analysis showed that the phosphorylation of focal adhesion kinase, Akt and signal transducer and activator of transcription protein 3 were weaker in Erc‐deficient/suppressed cells compared with Erc‐expressed cells. These results indicate that deficiency of the Erc/mesothelin gene ameliorates renal carcinogenesis in Tsc2 KO mice and inhibits the phosphorylation of several kinases of cell adhesion mechanism. This suggests that Erc/mesothelin may have an important role in the promotion and/or maintenance of carcinogenesis by influencing cell‐substrate adhesion via the integrin‐related signal pathway. (Cancer Sci 2011; 102: 720–727)
Cancer detection using infrared hyperspectral imaging
Authors: Akbari Hamed , Uto Kuniaki , Kosugi Yukio , Kojima Kazuyuki , Tanaka Naofumi
Published: January 2011

During the last few decades, many studies have been performed on the early detection of cancer using noninvasive or minimally invasive techniques in lieu of traditional excisional biopsy. Early detection can make an immense difference because cancer treatment is often simpler and more effective when diagnosed at an early stage. Cancer detecting methods may help physicians to diagnose cancer, to dissect the malignant region with a safe margin, and to evaluate the tumor bed after resection. In this paper, the advanced hyperspectral imaging system has been assessed using infrared wavelengths region for tumor detection. We were able to identify an appropriate wavelength region for cancer detection, spatially resolved images, and highlight the differences in reflectance properties of cancerous versus non‐cancerous tissues. The capability of this instrument was demonstrated by observing gastric tumors in 10 human subjects. The spectral signatures were extracted and evaluated in cancerous and non‐cancerous tissues. Processing means with the standard deviation of the spectral diagram, support vector machine, and first derivatives and integral of in spectral diagram were proposed to enhance and detect the cancerous regions. The first derivatives in spectral region between 1226–1251 nm and 1288–1370 nm were proposed as criteria that successfully distinguish between non‐cancerous and cancerous tissue. The results of this study will lead to advances in the optical diagnosis of cancer. (Cancer Sci 2011; 102: 852–857)
Interdecadal declines in flood frequency increase primary production in lakes of a northern river delta
Authors: McGOWAN SUZANNE , LEAVITT PETER R. , HALL ROLAND I. , WOLFE BRENT B. , EDWARDS THOMAS W. D. , KARST‐RIDDOCH TAMMY , VARDY SHEILA R.
Published: January 2011

Human activities and climate change have greatly altered flooding regimes in many of the world's river deltas, but the impact of such changes remains poorly quantified on decadal to multidecadal timescales. This study identified the response of delta lake primary production (measured as the concentration of sedimentary pigments) to variations in flood frequency using spatial surveys and paleolimnological analyses of lakes in the Peace‐Athabasca Delta (PAD), Canada. Surveys of 61 lakes spanning a range of hydrological conditions showed that those lakes that received flood waters less frequently were associated with elevated algal production (surface sedimentary pigments) and, in some lakes, increased growth of emergent macrophytes and epiphytic diatoms. Paleolimnological analyses of five lakes corroborated the contemporary spatial survey results by showing that production of pigments from most algal groups increased during recent periods of lower flood frequency in the 20th century as determined from increases in cellulose‐inferred lake‐water oxygen isotope composition and plant macrofossils, but remained stable in a ‘reference’ basin. In general, past periods of elevated algal production coincided with the increased abundance of submerged macrophytes or emergent vegetation that provide habitat for attached algae. These results suggest that interdecadal declines in river discharge arising from increased aridity, hydrologic regulation or consumptive water use will cause long‐term increases in primary production and alter ecosystem processes (carbon sequestration, biological diversity) in aquatic delta ecosystems similar to the PAD where lakes become nutrient‐rich in the absence of flooding.
Training emotional intelligence related to treatment skills of staff working with clients with intellectual disabilities and challenging behaviour
Authors: Zijlmans L. J. M. , Embregts P. J. C. M. , Gerits L. , Bosman A. M. T. , Derksen J. J. L.
Published: January 2011

Background  Staff working with clients with intellectual disabilities (ID) who display challenging behaviour may contribute to the continuation of this behaviour, because it causes emotional reactions such as anxiety, anger and annoyance, which may prohibit adequate response behaviour. To enhance staff behaviour and treatment skills a training that aimed at improving emotional intelligence (EQ) was developed.

Aim  The goal of this study was to assess whether an EQ training in combination with a video‐feedback training programme improves emotional intelligence of staff working with clients with ID and challenging behaviour.

Methods  Participants were 60 staff members working with individuals with ID and challenging behaviour. Thirty‐four staff members participated in a 4‐month training programme and 26 constituted the control group. A pretest–posttest control group design was used. Effectiveness was assessed by using the Dutch version of the Bar‐On EQ‐i and the judgments of experts on emotional intelligence.

Results  Emotional intelligence of the experimental group changed significantly more than that of the control group. Judgments of experts on emotional intelligence indicated that the change of emotional intelligence of the experimental group improved positively.

Conclusions  The positive effect of the training programme on emotional intelligence is consistent with previous research on emotional intelligence and suggests that emotional intelligence of staff working with clients with ID and challenging behaviour can be influenced by training.
The relationship between specific cognitive impairment and behaviour in Prader–Willi syndrome
Authors: Woodcock K. A. , Oliver C. , Humphreys G. W.
Published: January 2011

Background  Individuals with Prader–Willi syndrome (PWS) have been shown to demonstrate a particular cognitive deficit in attention switching and high levels of preference for routine and temper outbursts. This study assesses whether a specific pathway between a cognitive deficit and behaviour via environmental interaction can exist in individuals with PWS.

Methods  Four individuals with PWS participated in a series of three single‐case experiments including laboratory‐based and natural environment designs. Cognitive (computer‐based) challenges placed varying demands on attention switching or controlled for the cognitive demands of the tasks while placing no demands on switching. Unexpected changes to routines or expectations were presented in controlled games, or imposed on participants' natural environments and compared with control conditions during which no unexpected changes occurred. Behaviour was observed and heart rate was measured.

Results  Participants showed significantly increased temper outburst related behaviours during cognitive challenges that placed demands on attention switching, relative to the control cognitive challenges. Participants showed significantly increased temper outburst related behaviours when unexpected changes occurred in an experimental or the natural environment compared with when no changes occurred.

Conclusions  Difficult behaviours that could be triggered reliably in an individual by a specific cognitive demand could also be triggered via manipulation of the environment. Results suggest that a directional relationship between a specific cognitive deficit and behaviour, via environmental interaction, can exist in individuals with PWS.
A pilot study of social competence group training for adolescents with borderline intellectual functioning and emotional and behavioural problems (SCT‐ABI)
Authors: Nestler J. , Goldbeck L.
Published: January 2011

Background  Emotional and behavioural problems as well as a lack of social competence are common in adolescents with borderline intellectual functioning and impair their social and vocational integration. Group interventions specifically developed for this target group are scarce and controlled evaluation studies are absent.

Methods  A cognitive–behavioural group training (Social Competence Training for Adolescents with Borderline Intelligence) was developed and its effectiveness was examined in students attending special vocational schools. A total of 77 adolescents with borderline intelligence were randomised either to the intervention (n = 40) or to the control group (n = 37). Outcome measures at post‐treatment and at a 6‐month follow‐up comprised self‐reports, caregiver reports and behavioural observations.

Results  The adolescents in the intervention group showed temporally stable improvement in their social competence, especially in social problem solving (F = 17.6, P < 0.001) and attainment of individual behavioural goals in everyday life (self‐reports: F = 15.9, P < 0.001; caregiver reports: F = 87.9, P < 0.001). Effects of the intervention on other outcomes such as problem‐solving competence and skills performed in standardised role plays were weak or absent.

Conclusions  Social Competence Training for Adolescents with Borderline Intelligence is a promising treatment for adolescents with borderline intellectual functioning and associated emotional/behavioural symptoms. Further studies examining long‐term effects on the participants’ social and vocational integration are needed.
Stereotyped behaviour in children with autism and intellectual disability: an examination of the executive dysfunction hypothesis
Authors: Sayers N. , Oliver C. , Ruddick L. , Wallis B.
Published: January 2011

Background  Increasing attention has been paid to the executive dysfunction hypothesis argued to underpin stereotyped behaviour in autism. The aim of this study is to investigate one component of this model, that stereotyped behaviours are related to impaired generativity and compromised behavioural inhibition, by examining whether episodes of these behaviours terminate naturally without external intervention.

Methods  Using a naturalistic observational methodology the stereotyped behaviours of six participants with autism were recorded in real time over periods ranging from 3.59 to 9.20 h. Data were also recorded for teaching staff interactions with participants and environmental settings (one‐to‐one, group and freetime).

Results  In comparison with one‐to‐one settings stereotyped behaviours were more frequent when participants were in freetime settings with the exception of one participant. For the termination of stereotyped behaviours these behaviours stopped with no ongoing physical or verbal adult contact being evident for a median of 73.25% of the time. Additionally, for a median of 89.40% of the time stereotyped behaviour stopped without the initiation of adult contact.

Discussion  The termination of bouts of stereotyped behaviour was frequently not associated with any adult contact and thus this form of external intervention. This finding warrants explanation by extending the hypothesis that compromised impaired generativity and behavioural inhibition offers a complete explanation of stereotyped behaviours.
Prevalence, phenomenology, aetiology and predictors of challenging behaviour in Smith‐Magenis syndrome
Authors: Sloneem J. , Oliver C. , Udwin O. , Woodcock K. A.
Published: January 2011

Background The prevalence, phenomenology aetiology and correlates of four forms of challenging behaviour in 32 children and adults with Smith‐Magenis syndrome (SMS) were investigated.

Methods Cognitive assessments, questionnaires and semi‐structured interviews were used to gather data on intellectual disability, verbal and physical aggression, destructive behaviour and self‐injury and on characteristics known to be associated with aggression.

Results Aggression in SMS was more prevalent (87%), but not more severe than aggression in contrast groups. Aggressive behaviour was more frequently associated with environmental contingencies (e.g. attention, escape and access to tangibles) than self‐injury and destructive behaviours. Severity of challenging behaviours was associated with high impulsivity.

Conclusion Aggression is seen in the majority of people with SMS. Results suggest that behavioural disinhibition and operant social reinforcement are associated with the manifestation of aggression.
Association between selected folate pathway polymorphisms and nonsyndromic limb reduction defects: a case–parental analysis
Authors: Cleves Mario A. , Hobbs Charlotte A. , Zhao Weizhi , Krakowiak Patrycja A. , MacLeod Stewart L. ,   the National Birth Defects Prevention Study
Published: January 2011

Cleves MA, Hobbs CA, Zhao W, Krakowiak PA, MacLeod SL, the National Birth Defects Prevention Study. Association between selected folate pathway polymorphisms and nonsyndromic limb reduction defects: a case–parental analysis. Paediatric and Perinatal Epidemiology 2011.

Inadequate folate status resulting from either genetic variation or nutritional deficiencies has been associated with an increased risk of congenital malformations including orofacial clefting, limb, cardiac and neural tube defects. Few epidemiological studies have examined the association between limb reduction defects (LRDs) and folate‐related genetic polymorphisms other than MTHFR 677C→T. We conducted a case–parental analysis of 148 families who participated in the National Birth Defects Prevention Study to examine the association between nonsyndromic transverse and longitudinal LRDs with five single nucleotide polymorphisms (SNPs) in genes encoding enzymes in folate and methionine pathways. Log‐linear Poisson regression, adapted for analysis of case–parental data assuming an additive genetic model, was used to estimate genetic relative risks and 95% confidence intervals for the association between LRDs and each SNP. Among women who did not take multivitamin supplements, the MTHFR 677T variant acts via the offspring's genome to increase the risk of LRDs. No association between LRDs and any fetal SNP was found among women who used multivitamin supplements. These results suggest the possibility that initiating folic acid supplementation prior to pregnancy may reduce the risk of having a LRD‐affected pregnancy, especially in women whose offspring inherit one or two copies of the MTHFR 677T variant.
Age at diagnosis and disease progression of cystic fibrosis in an area without newborn screening
Authors: de Monestrol Isabelle , Klint Åsa , Sparén Pär , Hjelte Lena
Published: January 2011

de Monestrol I, Klint Å, Sparén P, Hjelte L. Age at diagnosis and disease progression of cystic fibrosis in an area without newborn screening. Paediatric and Perinatal Epidemiology 2011; 25: 298–305.

We studied age at diagnosis and disease progression of cystic fibrosis (CF) patients with a new study design, using data of 119 patients extracted from Stockholm CF Centre registry. Risk factors for overall morbidity and for lung, liver and nutritional morbidity were investigated separately using time to event methodology (Kaplan‐Meier curves, proportional hazards regression). The patients were followed from: (i) healthy at diagnosis to morbidity, (ii) diagnosis with symptoms of morbidity to being free of morbidity, and (iii) free of morbidity to relapse of morbidity.

Median age at diagnosis was 5.0 months. Of the patients with overall morbidity at diagnosis 50% became free of morbidity after 4.8 years; however, the patients above the age of 24 months at diagnosis had a reduced chance of becoming free of morbidity (crude hazard ratio 0.14 [95 % confidence interval 0.04, 0.45]) compared with those with diagnosis between the ages of 2 and 12 months (P < 0.01).

Of the healthy at diagnosis, 50% experienced overall morbidity after 1.4 years. They had a slow decline to the endpoint of the specific morbidities; 50% experienced lung morbidity after 3.4 years and liver morbidity after 4.8 years, while 50% never reached nutritional morbidity during the 10 years follow‐up.

We conclude that there was a disadvantage for the CF patients diagnosed after the age of 24 months with symptoms of overall morbidity at diagnosis in an area without newborn screening.
Diversity of Killer Cell Immunoglobulin‐like Receptor Genes in the Bai Ethnic Minority of Yunnan, China
Authors: Zhu B.‐F. , Wang H.‐D. , Shen C.‐M. , Fan A.‐Y. , Yang G. , Qin H.‐X. , Jin T.‐B. , Xie T. , Deng L. , Lucas R. , Lian Z.‐M.
Published: January 2011

Killer cell immunoglobulin‐like receptors (KIRs), expressed in both natural killer (NK) cells and a subset of T cells, represent a family of both inhibitory and activating receptors that can regulate NK and T cells upon interacting with human leucocyte antigen (HLA) class I molecules on target cells. The number and distribution of KIR genes vary between individuals and populations from different geographical regions and ethnic origins. In this study, we investigated KIR gene frequencies and genotype diversities of 13 KIR genes, 2 pseudogenes, expressed and non‐expressed forms of KIR2DL5 and the two subtypes, full‐length and deleted forms, of KIR2DS4 in 100 unrelated healthy individuals of the Bai population, living in the Dali Bai autonomous prefecture in the Yunnan province. All individuals were typed positive for the three framework loci KIR3DL3, 2DL4 and 3DL2, as well as for three non‐framework genes KIR2DL1, 2DL3 and the pseudogene KIR2DP1. The gene frequencies of the other KIR genes ranged from 7%‐95%. The results of tested linkage disequilibrium (LD) among KIR genes demonstrated that they display a wide range of LD. χ2 analysis among non‐ubiquitous genes, using the KIR gene frequency data from our study population, as well as from previously published population data, was conducted and revealed significant differences in the KIR2DL1, 2DL2, 3DL1 and KIR2DS1 genes. The results of the present study can be valuable for enriching the Chinese ethnical gene information resources of the KIR gene pool, for anthropological studies, as well as for KIR‐related disease research.
Linking invertebrate burrow distributions (neoichnology) to physicochemical stresses on a sandy tidal flat: implications for the rock record
Authors: DASHTGARD SHAHIN E.
Published: January 2011

Invertebrate burrow distributions (neoichnology) across a modern tidal flat are presented as an analogue for interpreting the ichnology of palaeo‐tidal‐flat successions. Burrow distributions are linked to physical and chemical (physicochemical) stresses to establish the main controls on the distribution of biosedimentary structures. Across the tidal flat, there is clear heterogeneity in both the diversity of traces and the intensity of burrowing. This heterogeneity reflects a myriad of physicochemical stresses, with the sedimentation rate dominating burrow distributions. Across all substrates, the total area occupied by organisms rarely exceeds 3% of the tidal‐flat surface, and is commonly <1%; this equates to a bioturbation index value of one. To reach bioturbation index values of two to six, sediments must be available to biogenic reworking and/or recolonization. With an increasing sedimentation rate, substrates are rapidly buried and re‐exposed, which limits the time when a substrate is available to colonization. For palaeo‐ichnological studies, this research presents several key results. (i) Burrow cross‐cutting relationships in tidal‐flat successions commonly reflect natural heterogeneities in the areal distribution of infaunal communities, rather than infaunal tiering. (ii) Ichnofabric analysis of palaeo‐tidal flats with a high sedimentation rate would yield fabrics that reflect heterogeneities in the areal distribution of infaunal communities rather than variability in the physicochemical stresses of the environment. (iii) The composite trace‐fossil assemblage of tidal flats cannot be attributed to a single ichnofacies, but instead comprises elements typical of multiple ichnofacies. (iv) The main controls on trace assemblages across tidal flats in fully marine settings are sedimentological and include the sedimentation rate and, to a lesser extent, grain size.
Artificial infection of Cirsium arvense with the rust pathogen Puccinia punctiformis by imitation of natural spore transfer by the weevil Ceratapion onopordi
Authors: MÜLLER E , JUD P , NENTWIG W
Published: January 2011

Müller E, Jud P & Nentwig W (2011). Artificial infection of Cirsium arvense with the rust pathogen Puccinia punctiformis by imitation of natural spore transfer of the weevil Ceratapion onopordi. Weed Research51, 209–213.

Cirsium arvense is a noxious perennial weed. Because of the limited possibilities of chemical and physical control of this weed, many studies have been performed on biological methods. Successful control of C. arvense using the rust fungus Puccinia punctiformis needs the establishment of systemic infection, often connected with the weevil Ceratapion onopordi as a spore vector. To analyse whether an artificial infection of C. arvense with P. punctiformis through the plant stem is possible without the weevil, different infection tests were performed. Urediniospore solutions with different kinds of additives of weevil origin were applied. All treatments with infectious material led to an infection. Injection of pure urediniospores into the plant stem resulted in the highest infection rate (50%). Even though the infection‐via‐the‐stem‐method used in this study was successful in principle, this method is not practicable in the field. Therefore, further studies of infection techniques are needed, particularly to examine the spore stages that cause systemic infections.
Impact of the quality of organic amendments on size and composition of the weed seed bank
Authors: DE CAUWER B , D’HOSE T , COUGNON M , LEROY B , BULCKE R , REHEUL D
Published: January 2011

De Cauwer B, D’Hose T, Cougnon M, Leroy B, Bulcke R & Reheul D (2011). Impact of the quality of organic amendments on size and composition of the weed seed bank. Weed Research51, 250–260.

In addition to improving the soil quality, organic amendments of soils may affect weed seed survival, emergence, growth and reproduction. This study evaluated the effects of applications of different qualities of organic amendments on size and composition of the weed seed bank in a field under sequential cropping over 4 years. Fertilisation systems tested included farmyard manure, vegetable fruit and garden waste compost, two types of farm compost differing in carbon:nitrogen (C:N) ratio, cattle slurry and mineral fertiliser. All organically amended plots received equal amounts of C. Crop growth was equalised on all plots by applying supplemental mineral N. Seed bank sampling took place in May 2009 to a depth of 10 cm. The weed seed bank was analysed using the seedling emergence method. Despite equal crop growth in fertilised plots, total seed bank density was lowest in plots amended with compost with low C:N ratio and highest in slurry‐amended plots. Observed differences in seed bank densities reflected differences in soil organic carbon content and microbial biomass. At plot level, hard‐coated seeds in the seed bank (e.g. Chenopodium spp.) were inversely related to soil microbial activity. Observed differential responses of species to applied fertilisers might be attributed to interspecific differences in resistance against microbial seed degradation. Compost‐based fertilisation systems could be sustainable tools for incorporation into integrated weed control strategies aiming at depleting the weed seed bank.
Effect of incremental levels of fish oil supplementation on specific bacterial populations in bovine ruminal fluid
Authors: Liu S. J. , Bu D. P. , Wang J. Q. , Liu L. , Liang S. , Wei H. Y. , Zhou L. Y. , Li D. , Loor J. J.
Published: January 2011

The objective of this study was to determine the effects of incremental replacement of dietary linoleic acid by >20‐carbon polyunsaturated fatty acids (PUFA) on changes in population of ruminal micro‐organisms associated with fibre digestion and biohydrogenation using real‐time PCR of bacterial 16S rRNA sequences. Four beef steers with ruminal cannulas were randomly assigned to control (CK, 65:35 forage to concentrate), CK with 3% sunflower oil plus 1% fish oil (S3F1), 2.5% sunflower oil plus 1.5% fish oil (S2.5F1.5) or 2% sunflower oil plus 2% fish oil (S2F2) in a 4 × 4 Latin square design with 21‐day periods. Ruminal fluid was collected on day 15 of each period. Compared with CK, oil addition led to lower ruminal acetate and butyrate but greater propionate concentration. DNA copy number of Anaerovibrio lipolytica in ruminal fluid was greater with oil (average 5.38 vs. 3.62 × 105 DNA copy number), particularly with S2F2 relative to CK. Fibrobacter succinogenes and Butyrivibrio fibrisolvens DNA copy number decreased by 74% (1.06 vs. 4.01 × 105) and 39% (5.16 vs. 8.42 × 107) in response to S2F2 compared with CK. DNA copy numbers of Ruminococcus flavefaciens and Ruminococcus albus were not affected by incremental fish oil. Results suggest that greater availability of PUFA with >20 carbons (i.e. eicosapentaenoic acid and docosahexaenoic acid) promoted changes in bacterial populations that are relevant for fibre digestion and biohydrogenation.
Fat source affects growth of weanling rats fed high‐fat diets low in zinc
Authors: Weigand E.
Published: January 2011

In two 3‐week experiments with a 2‐factorial design, weanling rats were fed semi‐purified diets in which the zinc concentration was either suboptimal or adequate for maximum growth. In experiment 1, one low‐fat diet and four diets enriched with 26% beef tallow (BT), butterfat (BF), coconut oil or sunflower oil (SF) were compared. The low‐Zn SF diet did not support growth. The animals fed the high‐Zn SF diet had the lowest final weights among all other groups, and their serum and femur Zn concentrations were markedly depressed. In experiment 2, the low‐ and high‐Zn diets were enriched with 18% BT, SF, BT + SF (1:1 w/w), or olive oil (OL). Final live weights showed a Zn × fat source interaction. The low‐Zn SF and OL groups consumed less food and weighed less than the low‐Zn BT group. At the high‐Zn level, final weights were comparable among groups. Serum and femur Zn concentrations did not significantly vary among groups fed diets with the same Zn level. Possibilities for the growth‐retarding effect of the diets rich in unsaturated fatty acids (SF and OL) are discussed. Metabolic studies are needed to clarify the observed zinc × fat source interaction.
Gastroesophageal Reflux Disease in Asia: A historical perspective and present challenges
Authors: Goh Khean‐Lee
Published: January 2011

Gastroesophageal reflux disease (GERD), previously uncommon in Asia, has now become an important disease in the region. Although much variability exists between studies, most endoscopy‐based studies show a prevalence of erosive esophagitis of more than 10%. Symptom‐based studies also show a prevalence of 6–10%. Two longitudinal follow‐up studies on GERD symptoms have shown an increase with time, and several endoscopy‐based time trend studies have also shown a significant increase in erosive reflux esophagitis. Studies on Barrett's esophagus have been confounded by the description of short (SSBE) and long segment (LSBE) Barrett's esophagus. Great variation in prevalence rates has been reported. SSBE vary from 0.1% to more than 20% while LSBE vary from 1–2%. Of the putative causative factors, obesity has been the most important. Many studies have linked GERD‐esophagitis as well as occurrence of reflux symptoms with an increase in body mass index (BMI), obesity, especially visceral or central obesity, and metabolic syndrome. A decline in Helicobacter pylori infection with growing affluence in Asia has been broadly thought to result in healthier stomachs and a higher gastric acid output resulting in reflux disease. However, variable results have been obtained from association and H. pylori eradication studies.
Barrett's esophagus: A historical perspective, an update on core practicalities and predictions on future evolutions of management
Authors: Dent John
Published: January 2011

Interpretation of exploding knowledge about Barrett's esophagus is impaired by use of several conflicting definitions. Because any histological type of esophageal columnar metaplasia carries risk for esophageal adenocarcinoma, the diagnosis of Barrett's esophagus should no longer require demonstration of intestinal‐type metaplasia. Endoscopic recognition and grading of Barrett's esophagus remains a significant source of ambiguity.

Reflux disease is a key factor for development of Barrett's esophagus, but other factors must underlie its development, since it occurs in only a minority of reflux disease patients. Neither antireflux surgery nor proton pump inhibitor (PPI) therapy has major impacts on cancer risk. Within a year, a major trial should indicate whether low‐dose aspirin usefully reduces cancer risk.

The best referral centers have transformed the accuracy of screening and surveillance for early curable esophageal adenocarcinoma by use of enhanced and novel endoscopic imaging, visually‐guided, rather than blind biopsies and by partnership with expert pathologists. General endoscopists now need to upgrade their skills and equipment so that they can rely mainly on visual targeting of biopsies on mucosal areas of concern in their surveillance practice. General pathologists need to greatly improve their interpretation of biopsies.

Endoscopic therapy now achieves very high rates of cure of high‐grade dysplasia and esophageal adenocarcinoma with minimal morbidity and risk. Such results will only be achieved by skilled interventional endoscopists. Esophagectomy should now be mainly restricted to patients whose cancer has extended into and beyond the submucosa.

Weighing risks and benefits in the management of Barrett's esophagus is difficult, as is the process of adequately informing patients about their specific cancer risk.
The Sydney System for classification of gastritis 20 years ago
Authors: Sipponen Pentti , Price Ashley B
Published: January 2011

The roots of research into gastritis go back into the early decades of the 20th century. Modern aspects of its classification and knowledge of its biological course and consequences were relatively well known even at the time that Helicobcter pylori was discovered by Robin Warren and Barry Marshall in 1982. This discovery, however, significantly changed the field, establishing that the commonest form of gastritis is simply an infectious disease, a finding that raised enormous interest in the subject amongst gastroenterologists, microbiologists, pathologists and basic researchers. However, many of these “new” players in the field often had a limited knowledge of the morphological aspects of gastric inflammations and chronic gastritis. As a consequence in the late 1980's a Working Party was set up to review the biology and natural course of chronic gastritis, to propose a new classification for gastritis, and to provide simple guidelines for reporting the pathology of gastritis in endoscopic biopsies in an attempt to bring uniformity to the subject and facilitate comparative studies in what was to be an era of high research activity. These guidelines, The Sydney System: A New Classification of Gastritis was presented to the World Congress of Gastroenterology in Sydney in 1990, and was later published as six papers in the Journal of Gastroenterology and Hepatology. Now, twenty years on, this review looks back on the birth of Sydney System and why it is still important and successful.
The ulcer sleuths: The search for the cause of peptic ulcers
Authors: Yeomans Neville D
Published: January 2011

The search for the cause or causes of peptic ulcers has been a long one. It was recognised as early as the 19th Century that damage to the stomach or duodenal bulb was likely to result if the resistance of their mucosae to luminal acid was for some reason impaired. An early theory suggested microscopic vascular occlusion leading to local infarction could be the initiating event but evidence was lacking. Excessive acid secretion is seen in some patients but not in many so is implausible as the main factor in most ulcers. Cigarette smoking is a risk factor and chronic life difficulties has been shown to sometimes play a part, but we would now think that they play only minor roles to possibly tip the balance when a major etiologic factor is already present. The overwhelming evidence now is that the major etiologic factors in chronic peptic ulcer are ingestion of nonsteroidal anti‐inflammatory drugs (NSAIDs) and infection with Helicobacter pylori. Understanding the mechanism of the first, and the discovery and demonstration of Koch's postulates for the second, have been instrumental in the award of two Nobel prizes.
New concepts in liver regeneration
Authors: Riehle Kimberly J , Dan Yock Y , Campbell Jean S , Fausto Nelson
Published: January 2011

The unique ability of the liver to regenerate itself has fascinated biologists for years and has made it the prototype for mammalian organ regeneration. Harnessing this process has great potential benefit in the treatment of liver failure and has been the focus of intense research over the past 50 years. Not only will detailed understanding of cell proliferation in response to injury be applicable to other dysfunction of organs, it may also shed light on how cancer develops in a cirrhotic liver, in which there is intense pressure on cells to regenerate. Advances in molecular techniques over the past few decades have led to the identification of many regulatory intermediates, and pushed us onto the verge of an explosive era in regenerative medicine. To date, more than 10 clinical trials have been reported in which augmented regeneration using progenitor cell therapy has been attempted in human patients. This review traces the path that has been taken over the last few decades in the study of liver regeneration, highlights new concepts in the field, and discusses the challenges that still stand between us and clinical therapy.
Hepatitis E: Historical, contemporary and future perspectives
Authors: Aggarwal Rakesh
Published: January 2011

Hepatitis E was suspected for the first time in 1980 during a waterborne epidemic of acute hepatitis in Kashmir, India. In the 30 years since then, a small virus with single‐stranded RNA genome has been identified as the cause of this disease and named as hepatitis E virus (HEV). The virus has four genotypes; of these, genotypes 1 and 2 are known to infect only humans, whereas genotypes 3 and 4 primarily infect other mammals, particularly pigs, but occasionally cause human disease. In highly‐endemic areas, the disease occurs in epidemic and sporadic forms, caused mainly by infection with genotype 1 or 2 virus, acquired through the fecal‐oral route, usually through contaminated water supplies. The disease is characterized by particularly severe course and high mortality among pregnant women. In persons with pre‐existing chronic liver disease, HEV superinfection can present as acute‐on‐chronic liver disease. In low‐endemic regions, sporadic cases of locally‐acquired HEV infection are reported; these are caused mainly by genotype 3 or 4 HEV acquired possibly through zoonotic transmission from pigs, wild boars or deer. In these areas, chronic infection with genotype 3 HEV, which may progress to liver cirrhosis, has been reported among immunosuppressed persons. Two subunit vaccines containing recombinant truncated capsid proteins of HEV have been shown to be highly effective in preventing the disease; however, these are not yet commercially available. These vaccines should be of particular use in groups that are at high risk of HEV infection and/or of poor outcome.
Hepatic steatosis and hepatitis C: Still unhappy bedfellows?
Authors: Hwang Shinn‐Jang , Lee Shou‐Dong
Published: January 2011

Hepatic steatosis is commonly seen in patients with chronic hepatitis C virus (HCV) infection, and the prevalence is much higher prevalence than in the general population or in patients with chronic hepatitis B. Hepatic steatosis in patients with chronic hepatitis C can be due to alcohol consumption and host metabolic factors such as high body mass index (BMI), obesity, hyperlipidemia, metabolic syndrome and diabetes mellitus in which insulin resistance plays an important role. However, in genotype 3 HCV infection, hepatic steatosis can result from direct viral cytopathic effect. Demographic and clinical characteristics associated with hepatic steatosis in patients with chronic hepatitis C including older age, higher BMI, more genotype 3 infection, and higher mean serum levels of triglyceride, alanine aminotransferase and γ‐glutamyl transpeptidase. The clinical relevance of hepatic steatosis in patients with chronic hepatitis C includes a close correlation with hepatic fibrosis, and a poor response to combination peginterferon and ribavirin treatment. In addition, hepatic steatosis has been reported to associate with increased frequency of hepatocellular carcinoma in patients with chronic HCV infection. Whether life style modification such as weight reduction or adding an insulin resistance reducing agent such as metformin or thiazolidinediones combined with current standard peginterferon plus ribavirin treatment will benefit to the chronic hepatitis C patients with hepatic steatosis deserves further evaluation.
Recent advances of radiofrequency ablation for early hepatocellular carcinoma
Authors: Izumi Namiki
Published: January 2011

Hepatocellular carcinoma (HCC) is the third leading cause of death in the malignant neoplastic diseases in the world. Surgical operation is sometimes not indicated because of complicated liver cirrhosis and extrahepatic disorders. Radiofrequency ablation has been developed as a less invasive treatment for HCC since 1999, and long‐term outcome has been shown. There are several complications which should be paid attention, and to improve the prognosis, combination treatment with transarterial chemoembolization should be discussed. Overall survival after between RFA and surgical resection should be compared prospectively. Establishment of staging system for treatment allocation of HCC and prevention of HCC recurrence is important issue to be examined.
Chronic hepatitis B in Asia—new insights from the past decade
Authors: Chan Henry Lik‐Yuen , Jia Jidong
Published: January 2011

Chronic hepatitis B virus (HBV) infection is a major health problem in the Asia‐Pacific region. In the past decade, much progress has been made in the understanding and management of this disease. The introduction of universal vaccination has significantly reduced the incidence of perinatal infection in most Asia‐Pacific countries. As the majority of the adult population have not been immunized at birth, we are still facing a large population of young HBV‐infected patients in the coming two decades. The study of long‐term longitudinal databases has provided deeper insight into the clinical significance of HBV DNA suppression, hepatitis B e antigen (HBeAg) seroconversion and hepatitis B surface antigen (HBsAg) seroclearance in chronic hepatitis B. With a better understanding on the natural history of HBV infection, one can now stratify the risk of chronic hepatitis B patients for adverse clinical outcomes and use this to individualize management. The introduction of non‐invasive assessment of liver fibrosis can potentially reduce the necessity of liver biopsy. There have also been great advances in the development of antiviral therapy in the past decade. However, the high cost of HBV antiviral drugs poses major challenges to health authorities in many Asia‐Pacific countries. Properly performed cost‐effective analysis and understanding on the best timing of stopping antiviral drugs will be important to facilitate the most appropriate allocation of resources.