bluuebunny/crossref_metadata_2025 huggingface dataset:
The CNA1 Histone of the CiliateTetrahymena thermophilaIs Essential for Chromosome Segregation in the Germline Micronucleus
Authors: Cervantes Marcella D. , Xi Xiaohui , Vermaak Danielle , Yao Meng-Chao , Malik Harmit S.
Published: October 2005

Ciliated protozoans present several features of chromosome segregation that are unique among eukaryotes, including their maintenance of two nuclei: a germline micronucleus, which undergoes conventional mitosis and meiosis, and a somatic macronucleus that divides by an amitotic process. To study ciliate chromosome segregation, we have identified the centromeric histone gene in the Tetrahymena thermophila genome (CNA1). CNA1p specifically localizes to peripheral centromeres in the micronucleus but is absent in the macronucleus during vegetative growth. During meiotic prophase of the micronucleus, when chromosomes are stretched to twice the length of the cell, CNA1p is found localized in punctate spots throughout the length of the chromosomes. As conjugation proceeds, CNA1p appears initially diffuse, but quickly reverts to discrete dots in those nuclei destined to become micronuclei, whereas it remains diffuse and is gradually lost in developing macronuclei. In progeny of germline CNA1 knockouts, we see no defects in macronuclear division or viability of the progeny cells immediately following the knockout. However, within a few divisions, progeny show abnormal mitotic segregation of their micronucleus, with most cells eventually losing their micronucleus entirely. This study reveals a strong dependence of the germline micronucleus on centromeric histones for proper chromosome segregation.
Mitochondrial AKAP121 Links cAMP and src Signaling to Oxidative Metabolism
Authors: Livigni Alessandra , Scorziello Antonella , Agnese Savina , Adornetto Annagrazia , Carlucci Annalisa , Garbi Corrado , Castaldo Imma , Annunziato Lucio , Avvedimento Enrico V. , Feliciello Antonio
Published: October 2005

AKAP121 focuses distinct signaling events from membrane to mitochondria by binding and targeting cAMP-dependent protein kinase (PKA), protein tyrosine phosphatase (PTPD1), and mRNA. We find that AKAP121 also targets src tyrosine kinase to mitochondria via PTPD1. AKAP121 increased src-dependent phosphorylation of mitochondrial substrates and enhanced the activity of cytochrome c oxidase, a component of the mitochondrial respiratory chain. Mitochondrial membrane potential and ATP oxidative synthesis were enhanced by AKAP121 in an src- and PKA-dependent manner. Finally, siRNA-mediated silencing of endogenous AKAP121 drastically impaired synthesis and accumulation of mitochondrial ATP. These findings indicate that AKAP121, through its role in enhancing cAMP and tyrosine kinase signaling to distal organelles, is an important regulator in mitochondrial metabolism.
The Homologous Putative GTPases Grn1p from Fission Yeast and the Human GNL3L Are Required for Growth and Play a Role in Processing of Nucleolar Pre-rRNA
Authors: Du Xianming , Rao Malireddi R.K. Subba , Chen Xue Qin , Wu Wei , Mahalingam Sundarasamy , Balasundaram David
Published: October 2005

Grn1p from fission yeast and GNL3L from human cells, two putative GTPases from the novel HSR1_MMR1 GTP-binding protein subfamily with circularly permuted G-motifs play a critical role in maintaining normal cell growth. Deletion of Grn1 resulted in a severe growth defect, a marked reduction in mature rRNA species with a concomitant accumulation of the 35S pre-rRNA transcript, and failure to export the ribosomal protein Rpl25a from the nucleolus. Deleting any of the Grn1p G-domain motifs resulted in a null phenotype and nuclear/nucleolar localization consistent with the lack of nucleolar export of preribosomes accompanied by a distortion of nucleolar structure. Heterologous expression of GNL3L in a Δgrn1 mutant restored processing of 35S pre-rRNA, nuclear export of Rpl25a and cell growth to wild-type levels. Genetic complementation in yeast and siRNA knockdown in HeLa cells confirmed the homologous proteins Grn1p and GNL3L are required for growth. Failure of two similar HSR1_MMR1 putative nucleolar GTPases, Nucleostemin (NS), or the dose-dependent response of breast tumor autoantigen NGP-1, to rescue Δgrn1 implied the highly specific roles of Grn1p or GNL3L in nucleolar events. Our analysis uncovers an important role for Grn1p/GNL3L within this unique group of nucleolar GTPases.
Type I Collagen Structure Regulates Cell Morphology and EGF Signaling in Primary Rat Hepatocytes through cAMP-dependent Protein Kinase A
Authors: Fassett John , Tobolt Diane , Hansen Linda K.
Published: October 2005

Adhesion to type 1 collagen elicits different responses dependent on whether the collagen is in fibrillar (gel) or monomeric form (film). Hepatocytes adherent to collagen film spread and proliferate, whereas those adherent to collagen gel remain rounded and growth arrested. To explore the role of potential intracellular inhibitory signals responsible for collagen gel-mediated growth arrest, cAMP-dependent protein kinase A (PKA) was examined in hepatocytes adherent to collagen film or gel. PKA activity was higher in hepatocytes on collagen gel than on film during G1 of the hepatocyte cell cycle. Inhibition of PKA using H89 increased cell spreading on collagen gel in an EGF-dependent manner, whereas activation of PKA using 8-Br-cAMP decreased cell spreading on collagen film. PKA inhibition also restored ERK activation, cyclin D1 expression and G1-S progression on collagen gel, but had no effect on cells adherent to collagen film. Analysis of EGF receptor phosphorylation revealed that adhesion to collagen gel alters tyrosine phosphorylation of the EGF receptor, leading to reduced phosphorylation of tyrosine residue 845, which was increased by inhibition of PKA. These results demonstrate that fibrillar type 1 collagen can actively disrupt cell cycle progression by inhibiting specific signals from the EGF receptor through a PKA-dependent pathway.
Integrating time-course microarray gene expression profiles with cytotoxicity for identification of biomarkers in primary rat hepatocytes exposed to cadmium
Authors: Tan Yongxi , Shi Leming , Hussain Saber M. , Xu Jun , Tong Weida , Frazier John M. , Wang Charles
Published: October 2005

Motivation: DNA microarrays can provide information about the expression levels of thousands of genes simultaneously at the transcriptomic level, while conventional cell viability and cytotoxicity measurement methods provide information about the biological functions at the cellular level. Integrating these data at different levels provides a promising approach for evaluating or predicting how cells respond to chemical exposure. It is important to investigate the multi-scale biological system in a systematic way to better understand the gene regulation networks and signal transduction pathways involved in the cellular responses to environmental factors.

Results: Primary rat hepatocytes were exposed to cadmium acetate at 0, 1.25 and 2 μM. mRNA expression profiles at 0, 3, 6, 12 and 24 h were measured using the Affymetrix RatTox U34 GeneChip® arrays. Simultaneously, cytotoxicity was assessed by lactase dehydrogenase leakage assay. Gene expression profiles at different time points were used to evaluate cytotoxicity at subsequent time points using partial least squares, and it was found that gene expression profiles at 0 h had the best prediction accuracy for the cytotoxicity observed at 12 h. Some biomarkers whose expression profiles showed strong relationship with cytotoxicity were identified and the underlying pathways were reconstructed to illustrate how hepatocytes respond to cadmium exposure. Permutation studies were also applied to assess the reliability of the predictive models.

Availability: Matlab source code is available upon request and DNA microarray data are available at GEO ().

Contact: cwang61@ucla.edu

Supplementary information: Supplementary data are available at Bioinformatics online.
Gene C atchr—Gene Cloning And Tagging for Caenorhabditis elegans using yeast Homologous Recombination: a novel approach for the analysis of gene expression
Authors: Sassi Holly E. , Renihan Stephanie , Spence Andrew M. , Cooperstock Ramona L.
Published: October 2005

Expression patterns of gene products provide important insights into gene function. Reporter constructs are frequently used to analyze gene expression in Caenorhabditis elegans, but the sequence context of a given gene is inevitably altered in such constructs. As a result, these transgenes may lack regulatory elements required for proper gene expression. We developed Gene Catchr, a novel method of generating reporter constructs that exploits yeast homologous recombination (YHR) to subclone and tag worm genes while preserving their local sequence context. YHR facilitates the cloning of large genomic regions, allowing the isolation of regulatory sequences in promoters, introns, untranslated regions and flanking DNA. The endogenous regulatory context of a given gene is thus preserved, producing expression patterns that are as accurate as possible. Gene Catchr is flexible: any tag can be inserted at any position without introducing extra sequence. Each step is simple and can be adapted to process multiple genes in parallel. We show that expression patterns derived from Gene Catchr transgenes are consistent with previous reports and also describe novel expression data. Mutant rescue assays demonstrate that Gene Catchr-generated transgenes are functional. Our results validate the use of Gene Catchr as a valuable tool to study spatiotemporal gene expression.
Colonic Chicken‐Skin Mucosa in Children with Polyps is not a Preneoplastic Lesion
Authors: Nowicki Michael J , Bishop Phyllis R , Subramony Charu , Wyatt‐Ashmead Josephine , May Warren , Crawford Maxine
Published: October 2005

Colonic polyps are common both in adults and children; however, the malignant potential varies according to the type of polyp. Most childhood polyps are solitary juvenile polyps, which have negligible malignant potential. Chicken‐skin mucosa (CSM) is an endoscopic finding initially described associated with adenomatous polyps and adenocarcinoma, suggesting a preneoplastic lesion. Subsequently, CSM was described in association with juvenile polyps, suggesting that this mucosal finding is not a precursor to dysplasia. To determine whether CSM represents a preneoplastic lesion, we studied endoscopic colonic mucosal biopsies for markers of cell replication (Ki‐67) and malignant transformation (p53) in mucosal biopsies of CSM, normal colonic tissue, tubular adenomas, and adenocarcinomas. Samples were subjected to immunostaining for the presence of Ki‐67 and p53. The degree of Ki‐67‐positive staining cells was similar for CSM and normal colonic tissue, whereas there was significantly increased staining for both tubular adenomas and adenocarcinomas. There was no evidence of p53 staining in CSM and normal colonic mucosa, whereas there was varying degrees of staining in tubular adenomas and adenocarcinomas. The association of CSM with benign juvenile polyps and the absence of histologic markers for increased replication and malignant transformation support the notion that this endoscopic finding is not preneoplastic. Rather, CSM arises in proximity to polyps of all histologic types because of local mucosal damage.
Clinical Features of Pathologic Childhood Aerophagia: Early Recognition and Essential Diagnostic Criteria
Authors: Hwang Jin‐Bok , Choi Won Joung , Kim Jun Sik , Lee Sang Yun , Jung Chul‐Ho , Lee Young Hwan , Kam Sin
Published: October 2005

Objective:

This study investigated the early recognition and diagnosis of pathologic childhood aerophagia to avoid unnecessary diagnostic approaches and serious complications.

Methods:

Between 1995 and 2003, data from 42 consecutive patients with pathologic childhood aerophagia, aged 2 to 16 years, were reviewed. An esophageal air sign was defined as an abnormal air shadow on the proximal esophagus adjacent to the trachea on a full‐inflated chest radiograph.

Results:

Of the 42 patients, the chief complaints were abdominal distention (52.4%), recurrent abdominal pain syndrome (21.4%), chronic diarrhea (11.9%), acute abdominal pain (7.1%) and others (7.2%). Mean symptom duration before diagnosis was 10.6 months (range, 1 to 60 months), and it exceeded 12 months for 16 (38.1%) patients. The clinical features common to all patients were abdominal distention that increased progressively during the day, increased flatus on sleep, increased bowel sound on auscultation and an air‐distended stomach with increased gas in the small and large bowel by radiography. Visible or audible air swallowing (26.2%) and repetitive belching (9.5%) were also noted. Esophageal air sign was observed in 76.2% of the patients and in 9.7% of the controls (P = 0.0001). The subgroups of pathologic childhood aerophagia divided by underlying associations were pathologic childhood aerophagia without severe mental retardation (76.2%), which consisted of psychological stresses and uncertain condition, and pathologic childhood aerophagia with severe mental retardation (23.8%).

Conclusions:

The common manifestations of pathologic childhood aerophagia may be its essential diagnostic criteria, and esophageal air sign may be useful for the early recognition of pathologic childhood aerophagia. Our observations show that the diagnostic clinical profiles suggested by Rome II criteria should be detailed and made clearer if they are to serve as diagnostic criteria for pathologic childhood aerophagia.
Does Increased Duration of Exclusive Breastfeeding Protect Against Helicobacter pylori Infection? The Newcastle Thousand Families Cohort Study at Age 49‐51 Years
Authors: Pearce Mark S , Thomas Julian E , Campbell David I , Parker Louise
Published: October 2005

Objective:

Helicobacter pylori acquired in childhood is an important risk factor for gastric carcinoma. Once colonization is established, infection may be carried for life. This study used prospectively recorded, detailed information on infant feeding and investigated the potential link between duration of exclusive breastfeeding in infancy and seropositivity at age 50 years, as measured by enzyme‐linked immunosorbent assay.

Methods:

H. pylori seropositivity at age 50 years was investigated among 407 individuals born in Newcastle in May and June 1947 and related to the duration of exclusive breastfeeding after adjusting for measures of socioeconomic status and adverse housing conditions at birth.

Results:

Duration of exclusive breastfeeding in infancy was significantly associated with H. pylori seropositivity (odds ratio per 30 days, 0.88; 95% confidence interval, 0.78 to 0.98). The significant protective trend was only seen among men (odds ratio per 30 days, 0.78; 95% confidence interval, 0.65 to 0.95), with no significant effect seen among women.

Conclusion:

Increased duration of exclusive breastfeeding in infancy may have a long‐term protective effect against chronic H. pylori infection and hence the risk of gastric carcinoma. Although further research is required, particularly as to why a significant effect was only seen among men, the results provide additional support for the concept that breastfeeding may have long‐term influences on health and that human milk is the ideal complete first diet for human infants.
Widespread Use of Soy‐Based Formula Without Clinical Indications
Authors: Berger‐Achituv Sivan , Shohat Tamar , Romano‐Zelekha Orly , Ophir Einat , Rachmani Sarit , Malovizky Drora , Garty Ben‐Zion
Published: October 2005

Objectives:

In view of reports of the growing popularity of soy‐based formula for infants, we examined soy consumption and its possible overuse during early infancy in central Israel.

Methods:

Mothers of 1803 infants aged 2, 4, 6 and 12 months attending well‐baby clinics participated in a telephone survey covering background data, rate, duration, and pattern of soy‐based formula use and the reasons for its initiation. The reasons were grouped into those based on the recommendations of the medical personnel and those based on mothers' initiative, and evaluated according to infants' age at soy‐based formula initiation (0 to 1, 2 to 4 and 5 to 12 months). The symptoms that prompted soy‐based formula use were assessed quantitatively.

Results:

The rate of soy‐based formula use was 10.4% at 2 months and 31.5% at 12 months (P < 0.001); 70.6% ± 2.7% of the infants were given soy for >6 months. Regardless of infants' age, the role of the mothers in the decision to use soy‐based formula was greater than that of the medical personnel, and increased significantly with age (χ2 for trend = 0.018). A suspicion of cow's milk allergy was responsible for only 10.9% (7/64) of all soy initiations in infants aged 5 to 12 months. In all ages, occasional symptoms, mainly diarrhea (33.3%) and colic (19.8%), were the leading cause for recommending soy‐based formula by medical personnel, whereas the personal preference without clinical justification was the leading cause among mothers.

Conclusions:

The use of soy‐based formula in central Israel is extensive and continues for long periods, with rates far beyond clinical indications. Mothers play a greater role than medical personnel in the decision to initiate soy‐based formula.
Serum Ghrelin Concentration and Weight Gain in Healthy Term Infants in the First Year of Life
Authors: Savino F , Liguori S A , Fissore M F , Oggero R , Silvestro L , Miniero R
Published: October 2005

Objectives:

Ghrelin, a recently discovered hormone mainly secreted by the stomach, has several metabolic functions including regulation of food intake, energy homeostasis and body weight. There are few studies on this hormone in healthy infants during the first year of life. The aim of this study was to examine the correlations between ghrelin and weight gain in healthy term infants in the first year of life.

Methods:

104 healthy term infants aged 0 to 12 months were included in a cross‐sectional study. Anthropometric measurements were assessed and mean weight gain was calculated. Serum ghrelin concentrations have been determined at least 3 hours after feeding by radioimmunoassay test.

Results:

Ghrelin concentrations were correlated negatively to weight gain (r = −0.302; P = 0.003) and positively to age (r = 0.412; P < 0.001), weight (r = 0.374; P < 0.001) and length (r = 0.387; P < 0.001). In breastfed infants a statistically significant negative correlation between ghrelin concentration and infant weight gain (r = −0.407; P = 0.001) was observed, whereas in formula‐fed infants this correlation was not statistically significant (r = −0.067; P = 0.719).

Conclusions:

The negative correlation observed between ghrelin concentration and infant weight gain suggests that ghrelin might also play a role in the regulation of body weight in healthy infants with a physiologic energy balance. Further studies are needed to clarify how ghrelin might be involved in both short‐term and long‐term energy balance.
The Effect of Ribavirin on Bone Density in Patients with Chronic Hepatitis C Treated with Interferon‐Ribavirin Therapy
Authors: Urganci Nafiye , Gulec Seda Geylani , Arapoglu Mujde , Vural Sema , Nuhoğ Asiye
Published: October 2005

Objective:

The objective of this study was to investigate the effects of ribavirin on bone mineral metabolism in patients with chronic hepatitis C who had been treated with interferon and ribavirin.

Methods:

Twenty patients (3 female, 17 male) with chronic hepatitis C were enrolled. Age range was 6 to 15 years (mean ± SD, 11.15 ± 2.3 years). Thirteen patients received combined interferon alpha‐2b and ribavirin therapy (Group 1), and 7 patients received only interferon alpha‐2b (Group 2). Both groups were treated for 12 months. Bone mineral density,z‐scores and biochemical bone markers were evaluated in both groups before and after treatment.

Results:

There were no significant differences between the groups in age or gender. Mean lumbar vertebral bone mineral density and meanz‐scores in groups 1 and 2 before and after treatment were not significantly different. In both groups, serum and urinary biochemical values and bone markers were all normal and there were no differences between the pretreatment and post‐treatment values.

Conclusion:

Contrary to studies in adults, we did not find any ribavirin‐dependent changes related to bone mineral metabolism in our pediatric study groups. Further studies are needed to obtain more detailed information about the effects of ribavirin on bone mineral density.
Pancreatic Development in Newborn Guinea Pigs Fed Intact or Low‐Hydrolyzed Protein Formulas
Authors: Colombo Carla , Biffi Arianna , Agosti Massimo , Crosignani Andrea , Bennato Veronica , Marini Antonio
Published: October 2005

Aim:

To evaluate pancreatic development in newborn guinea pigs fed since birth intact or low‐hydrolyzed protein formulas compared with breast milk.

Methods:

Forty‐five newborn guinea pigs were allocated to three feeding regimens: breast milk (n = 15) and two isocaloric isonitrogen milk formulas containing intact (n = 15) or low‐hydrolyzed proteins (n = 15). Body weight and food consumption were recorded every day. After 8 days, one third of pups from each group was killed, and the remaining animals were weaned. Another third was killed on day 14, and the remainders were killed on day 20. Zymogen storage was evaluated on pancreatic sections, whereas DNA and RNA concentrations were measured by a fluorometric method.

Results:

Compared with breast fed pups, both groups of artificially fed animals showed lower weight gain during the first 2 weeks of life but not after weaning. Both formulas fed groups had significantly lower amount of zymogen granules in pancreatic acinar cells at 8 and 14 days of life. This reduction was still present at day 20 in intact protein formula but not in low‐hydrolyzed protein formula fed animals in which higher RNA/DNA ratio was also observed compared with breast fed pups.

Conclusion:

In newborn guinea pigs, artificial feeding is associated with reduced zymogen storage at days 8 and 14 of life. After weaning, cellular content of zymogen granules is comparable with breast fed pups only in low‐hydrolyzed protein formula fed animals, even in the presence of some evidence of pancreatic hypoplasia.
Global Standard for the Composition of Infant Formula: Recommendations of an ESPGHAN Coordinated International Expert Group
Authors: Koletzko Berthold , Baker Susan , Cleghorn Geoff , Neto Ulysses Fagundes , Gopalan Sarath , Hernell Olle , Hock Quak Seng , Jirapinyo Pipop , Lonnerdal Bo , Pencharz Paul , Pzyrembel Hildegard , Ramirez‐Mayans Jaime , Shamir Raanan , Turck Dominique , Yamashiro Yuichiro , Zong‐Yi Ding
Published: October 2005

The Codex Alimentarius Commission of the Food and Agriculture Organization of the United Nations (FAO) and the World Health Organization (WHO) develops food standards, guidelines and related texts for protecting consumer health and ensuring fair trade practices globally. The major part of the world's population lives in more than 160 countries that are members of the Codex Alimentarius. The Codex Standard on Infant Formula was adopted in 1981 based on scientific knowledge available in the 1970s and is currently being revised. As part of this process, the Codex Committee on Nutrition and Foods for Special Dietary Uses asked the ESPGHAN Committee on Nutrition to initiate a consultation process with the international scientific community to provide a proposal on nutrient levels in infant formulae, based on scientific analysis and taking into account existing scientific reports on the subject. ESPGHAN accepted the request and, in collaboration with its sister societies in the Federation of International Societies on Pediatric Gastroenterology, Hepatology and Nutrition, invited highly qualified experts in the area of infant nutrition to form an International Expert Group (IEG) to review the issues raised. The group arrived at recommendations on the compositional requirements for a global infant formula standard which are reported here.
Ageing and the evolution of female resistance to remating in seed beetles
Authors: Maklakov Alexei A , Kremer Natacha , Arnqvist Göran
Published: October 2005

Female remating behaviour is a key mating system parameter that is predicted to evolve according to the net effect of remating on female fitness. In many taxa, females commonly resist male remating attempts because of the costs of mating. Here, we use replicated populations of the seed beetle
Acanthoscelides obtectus
selected for either early or late life reproduction and show that ‘Early’ and ‘Late’ females evolved different age-specific rates of remating. Early females were more likely to remate with control males as they aged, while Late females were more resistant to remating later in life. Thus, female remating rate decreases with age when direct selection on late-life fitness is operating and increases when such selection is relaxed. Our findings not only demonstrate that female resistance to remating can evolve rapidly, but also that such evolution is in accordance with the genetic interests of females.
Structural or pigmentary? Origin of the distinctive white stripe on the blue wing of a
Morpho
butterfly
Authors: Yoshioka Shinya , Kinoshita Shuichi
Published: October 2005

A few species of
Morpho
butterflies have a distinctive white stripe pattern on their structurally coloured blue wings. Since the colour pattern of a butterfly wing is formed as a mosaic of differently coloured scales, several questions naturally arise: are the microstructures the same between the blue and white scales? How is the distinctive whiteness produced, structurally or by means of pigmentation? To answer these questions, we have performed structural and optical investigations of the stripe pattern of a butterfly,
Morpho cypris
. It is found that besides the dorsal and ventral scale layers, the wing substrate also has the corresponding stripe pattern. Quantitative optical measurements and analysis using a simple model for the wing structure reveal the origin of the higher reflectance which makes the white stripe brighter.
The kaleidoscope ocean
Authors: Martin Adrian
Published: October 2005

Oceanic plant life is dominated by the microscopic phytoplankton. Regardless of the scale at which they are observed, they display striking heterogeneity in their distribution. At their most dramatic they paint colourful swathes across whole seas. A short history of observations of phytoplankton ‘patchiness’ is presented, illustrated with some of the many ideas put forward to explain it. Focus is then turned to the mesoscale, covering scales of roughly 1–500 km. It is argued that the spatial variability seen in phytoplankton at these scales gives important information on the biogeochemistry of the ocean. In particular, interplay between the physical circulation and biological processes results in constantly shifting patterns that are strongly related to changes induced in phytoplankton production. It is thought that this physical influence may play a major role in controlling the rate at which new plant material (primary production) is generated in much of the world's oceans. Major questions yet to be addressed are also discussed including the difficulty of quantifying processes on the very limit of what we can model or observe and how these processes may change in response to and exert a feedback on future climate change.
Integrated approaches to climate–crop modelling: needs and challenges
Authors: A. Betts Richard
Published: October 2005

This paper discusses the need for a more integrated approach to modelling changes in climate and crops, and some of the challenges posed by this. While changes in atmospheric composition are expected to exert an increasing radiative forcing of climate change leading to further warming of global mean temperatures and shifts in precipitation patterns, these are not the only climatic processes which may influence crop production. Changes in the physical characteristics of the land cover may also affect climate; these may arise directly from land use activities and may also result from the large-scale responses of crops to seasonal, interannual and decadal changes in the atmospheric state. Climate models used to drive crop models may, therefore, need to consider changes in the land surface, either as imposed boundary conditions or as feedbacks from an interactive climate–vegetation model. Crops may also respond directly to changes in atmospheric composition, such as the concentrations of carbon dioxide (CO2), ozone (O3) and compounds of sulphur and nitrogen, so crop models should consider these processes as well as climate change. Changes in these, and the responses of the crops, may be intimately linked with meteorological processes so crop and climate models should consider synergies between climate and atmospheric chemistry. Some crop responses may occur at scales too small to significantly influence meteorology, so may not need to be included as feedbacks within climate models. However, the volume of data required to drive the appropriate crop models may be very large, especially if short-time-scale variability is important. Implementation of crop models within climate models would minimize the need to transfer large quantities of data between separate modelling systems. It should also be noted that crop responses to climate change may interact with other impacts of climate change, such as hydrological changes. For example, the availability of water for irrigation may be affected by changes in runoff as a direct consequence of climate change, and may also be affected by climate-related changes in demand for water for other uses. It is, therefore, necessary to consider the interactions between the responses of several impacts sectors to climate change. Overall, there is a strong case for a much closer coupling between models of climate, crops and hydrology, but this in itself poses challenges arising from issues of scale and errors in the models. A strategy is proposed whereby the pursuit of a fully coupled climate–chemistry–crop–hydrology model is paralleled by continued use of separate climate and land surface models but with a focus on consistency between the models.
Quantification of physical and biological uncertainty in the simulation of the yield of a tropical crop using present-day and doubled CO
2
climates
Authors: Challinor A.J , Wheeler T.R , Slingo J.M , Hemming D
Published: October 2005

The impacts of climate change on crop productivity are often assessed using simulations from a numerical climate model as an input to a crop simulation model. The precision of these predictions reflects the uncertainty in both models. We examined how uncertainty in a climate (HadAM3) and crop General Large-Area Model (GLAM) for annual crops model affects the mean and standard deviation of crop yield simulations in present and doubled carbon dioxide (CO
2
) climates by perturbation of parameters in each model. The climate sensitivity parameter (
λ
, the equilibrium response of global mean surface temperature to doubled CO
2
) was used to define the control climate. Observed 1966–1989 mean yields of groundnut (
Arachis hypogaea
L.) in India were simulated well by the crop model using the control climate and climates with values of
λ
near the control value.

The simulations were used to measure the contribution to uncertainty of key crop and climate model parameters. The standard deviation of yield was more affected by perturbation of climate parameters than crop model parameters in both the present-day and doubled CO
2
climates. Climate uncertainty was higher in the doubled CO
2
climate than in the present-day climate. Crop transpiration efficiency was key to crop model uncertainty in both present-day and doubled CO
2
climates. The response of crop development to mean temperature contributed little uncertainty in the present-day simulations but was among the largest contributors under doubled CO
2
. The ensemble methods used here to quantify physical and biological uncertainty offer a method to improve model estimates of the impacts of climate change.
Multi-agent modelling of climate outlooks and food security on a community garden scheme in Limpopo, South Africa
Authors: Bharwani Sukaina , Bithell Mike , Downing Thomas E , New Mark , Washington Richard , Ziervogel Gina
Published: October 2005

Seasonal climate outlooks provide one tool to help decision-makers allocate resources in anticipation of poor, fair or good seasons. The aim of the ‘Climate Outlooks and Agent-Based Simulation of Adaptation in South Africa’ project has been to investigate whether individuals, who adapt gradually to annual climate variability, are better equipped to respond to longer-term climate variability and change in a sustainable manner. Seasonal climate outlooks provide information on expected annual rainfall and thus can be used to adjust seasonal agricultural strategies to respond to expected climate conditions. A case study of smallholder farmers in a village in Vhembe district, Limpopo Province, South Africa has been used to examine how such climate outlooks might influence agricultural strategies and how this climate information can be improved to be more useful to farmers. Empirical field data has been collected using surveys, participatory approaches and computer-based knowledge elicitation tools to investigate the drivers of decision-making with a focus on the role of climate, market and livelihood needs. This data is used in an agent-based social simulation which incorporates household agents with varying adaptation options which result in differing impacts on crop yields and thus food security, as a result of using or ignoring the seasonal outlook. Key variables are the skill of the forecast, the social communication of the forecast and the range of available household and community-based risk coping strategies. This research provides a novel approach for exploring adaptation within the context of climate change.
Climate change and food security
Authors: Gregory P.J , Ingram J.S.I , Brklacich M
Published: October 2005

Dynamic interactions between and within the biogeophysical and human environments lead to the production, processing, distribution, preparation and consumption of food, resulting in food systems that underpin food security. Food systems encompass food availability (production, distribution and exchange), food access (affordability, allocation and preference) and food utilization (nutritional and societal values and safety), so that food security is, therefore, diminished when food systems are stressed. Such stresses may be induced by a range of factors in addition to climate change and/or other agents of environmental change (e.g. conflict, HIV/AIDS) and may be particularly severe when these factors act in combination. Urbanization and globalization are causing rapid changes to food systems.

Climate change may affect food systems in several ways ranging from direct effects on crop production (e.g. changes in rainfall leading to drought or flooding, or warmer or cooler temperatures leading to changes in the length of growing season), to changes in markets, food prices and supply chain infrastructure. The relative importance of climate change for food security differs between regions. For example, in southern Africa, climate is among the most frequently cited drivers of food insecurity because it acts both as an underlying, ongoing issue and as a short-lived shock. The low ability to cope with shocks and to mitigate long-term stresses means that coping strategies that might be available in other regions are unavailable or inappropriate. In other regions, though, such as parts of the Indo-Gangetic Plain of India, other drivers, such as labour issues and the availability and quality of ground water for irrigation, rank higher than the direct effects of climate change as factors influencing food security.

Because of the multiple socio-economic and bio-physical factors affecting food systems and hence food security, the capacity to adapt food systems to reduce their vulnerability to climate change is not uniform. Improved systems of food production, food distribution and economic access may all contribute to food systems adapted to cope with climate change, but in adopting such changes it will be important to ensure that they contribute to sustainability. Agriculture is a major contributor of the greenhouse gases methane (CH
4
) and nitrous oxide (N
2
O), so that regionally derived policies promoting adapted food systems need to mitigate further climate change.
Climate science and famine early warning
Authors: Verdin James , Funk Chris , Senay Gabriel , Choularton Richard
Published: October 2005

Food security assessment in sub-Saharan Africa requires simultaneous consideration of multiple socio-economic and environmental variables. Early identification of populations at risk enables timely and appropriate action. Since large and widely dispersed populations depend on rainfed agriculture and pastoralism, climate monitoring and forecasting are important inputs to food security analysis. Satellite rainfall estimates (RFE) fill in gaps in station observations, and serve as input to drought index maps and crop water balance models. Gridded rainfall time-series give historical context, and provide a basis for quantitative interpretation of seasonal precipitation forecasts. RFE are also used to characterize flood hazards, in both simple indices and stream flow models. In the future, many African countries are likely to see negative impacts on subsistence agriculture due to the effects of global warming. Increased climate variability is forecast, with more frequent extreme events. Ethiopia requires special attention. Already facing a food security emergency, troubling persistent dryness has been observed in some areas, associated with a positive trend in Indian Ocean sea surface temperatures. Increased African capacity for rainfall observation, forecasting, data management and modelling applications is urgently needed. Managing climate change and increased climate variability require these fundamental technical capacities if creative coping strategies are to be devised.
Genetically indistinguishable SNPs and their influence on inferring the location of disease-associated variants
Authors: Lawrence Robert , Evans David M. , Morris Andrew P. , Ke Xiayi , Hunt Sarah , Paolucci Marta , Ragoussis Jiannis , Deloukas Panos , Bentley David , Cardon Lon R.
Published: October 2005

As part of a recent high-density linkage disequilibrium (LD) study of chromosome 20, we obtained genotypes for ∼30,000 SNPs at a density of 1 SNP/2 kb on four different population samples (47 CEPH founders; 91 UK unrelateds [unrelated white individuals of western European ancestry]; 97 African Americans; 42 East Asians). We observed that ∼50% of SNPs had at least one genetically indistinguishable partner; i.e., for every individual considered, their genotype at the first locus was identical to their genotype at the second locus, or in LD terms, the SNPs were in “perfect” LD (r2 = 1.0). These “genetically indistinguishable SNPs” (giSNPs) formed into clusters of varying size. The larger the cluster, the greater the tendency to be located within genes and to overlap with giSNP clusters in other population samples. As might be expected for this map density, many giSNPs were located close to one another, thus reflecting local regions of undetected recombination or haplotype blocks. However, ∼1/3 of giSNP clusters had intermingled, non-indistinguishable SNPs with incomplete LD (D′ and r2 <1), sometimes spanning hundreds of kilobases, comprising up to 70 indistinguishable markers and overlapping multiple haplotype blocks. These long-range, nonconsecutive giSNPs have implications for disease gene localization by allelic association as evidence for association at one locus will be indistinguishable from that at another locus, even though both loci may be situated far apart. We describe the distribution of giSNPs on this map of chromosome 20 and illustrate the potential impact they can have on association mapping.
Sequence features in regions of weak and strong linkage disequilibrium
Authors: Smith Albert V. , Thomas Daryl J. , Munro Heather M. , Abecasis Gonçalo R.
Published: October 2005

We use genotype data generated by the International HapMap Project to dissect the relationship between sequence features and the degree of linkage disequilibrium in the genome. We show that variation in linkage disequilibrium is broadly similar across populations and examine sequence landscape in regions of strong and weak disequilibrium. Linkage disequilibrium is generally low within ∼15 Mb of the telomeres of each chromosome and noticeably elevated in large, duplicated regions of the genome as well as within ∼5 Mb of centromeres and other heterochromatic regions. At a broad scale (100–1000 kb resolution), our results show that regions of strong linkage disequilibrium are typically GC poor and have reduced polymorphism. In addition, these regions are enriched for LINE repeats, but have fewer SINE, DNA, and simple repeats than the rest of the genome. At a fine scale, we examine the sequence composition of “hotspots” for the rapid breakdown of linkage disequilibrium and show that they are enriched in SINEs, in simple repeats, and in sequences that are conserved between species. Regions of high and low linkage disequilibrium (the top and bottom quartiles of the genome) have a higher density of genes and coding bases than the rest of the genome. Closer examination of the data shows that whereas some types of genes (including genes involved in immune response and sensory perception) are typically located in regions of low linkage disequilibrium, other genes (including those involved in DNA and RNA metabolism, response to DNA damage, and the cell cycle) are preferentially located in regions of strong linkage disequilibrium. Our results provide a detailed analysis of the relationship between sequence features and linkage disequilibrium and suggest an evolutionary justification for the heterogeneity in linkage disequilibrium in the genome.
Cryptochrome 1 Contributes to Blue-Light Sensing in Pea
Authors: Platten J. Damien , Foo Eloise , Elliott Robert C. , Hecht Valérie , Reid James B. , Weller James L.
Published: October 2005

Cryptochromes are widespread in higher plants but their physiological roles as blue-light photoreceptors have been examined in relatively few species. Screening in a phyA null mutant background has identified several blue-light response mutants in pea (Pisum sativum), including one that carries a substitution of a highly conserved glycine residue in the N-terminal photolyase-homologous domain of the pea CRY1 gene. Analyses of cry1, phyA, and phyB mutants show that all three photoreceptors contribute to seedling photomorphogenesis under high-irradiance blue light, whereas phyA is the main photoreceptor active under low irradiances. Triple phyA phyB cry1 mutants grown under high-irradiance blue light are indistinguishable from dark-grown wild-type plants in length and leaf expansion but show a small residual response to higher-irradiance white light. Monogenic cry1 mutants have little discernable phenotype at the seedling stage, but later in development are more elongated than wild-type plants. In addition, the loss of cry1 moderates the short-internode phenotype of older phyA mutants, suggesting an antagonism between phyA and cry1 under some conditions. Pea cry1 has a small inhibitory effect on flowering under long and short days. However, the phyA cry1 double mutant retains a clear promotion of flowering in response to blue-light photoperiod extensions, indicating a role for one or more additional blue-light photoreceptors in the control of flowering in pea.
The Dynamic Changes of Tonoplasts in Guard Cells Are Important for Stomatal Movement inVicia faba
Authors: Gao Xin-Qi , Li Chun-Guang , Wei Peng-Cheng , Zhang Xin-Yan , Chen Jia , Wang Xue-Chen
Published: October 2005

Stomatal movement is important for plants to exchange gas with environment. The regulation of stomatal movement allows optimizing photosynthesis and transpiration. Changes in vacuolar volume in guard cells are known to participate in this regulation. However, little has been known about the mechanism underlying the regulation of rapid changes in guard cell vacuolar volume. Here, we report that dynamic changes in the complex vacuolar membrane system play a role in the rapid changes of vacuolar volume in Vicia faba guard cells. The guard cells contained a great number of small vacuoles and various vacuolar membrane structures when stomata closed. The small vacuoles and complex membrane systems fused with each other or with the bigger vacuoles to generate large vacuoles during stomatal opening. Conversely, the large vacuoles split into smaller vacuoles and generated many complex membrane structures in the closing stomata. Vacuole fusion inhibitor, (2s,3s)-trans-epoxy-succinyl-l-leucylamido-3-methylbutane ethyl ester, inhibited stomatal opening significantly. Furthermore, an Arabidopsis (Arabidopsis thaliana) mutation of the SGR3 gene, which has a defect in vacuolar fusion, also led to retardation of stomatal opening. All these results suggest that the dynamic changes of the tonoplast are essential for enhancing stomatal movement.
Evidence That Bicarbonate Is Not the Substrate in Photosynthetic Oxygen Evolution
Authors: Clausen Juergen , Beckmann Katrin , Junge Wolfgang , Messinger Johannes
Published: October 2005

It is widely accepted that the oxygen produced by photosystem II of cyanobacteria, algae, and plants is derived from water. Earlier proposals that bicarbonate may serve as substrate or catalytic intermediate are almost forgotten, though not rigorously disproved. These latter proposals imply that CO2 is an intermediate product of oxygen production in addition to O2. In this work, we investigated this possible role of exchangeable HCO3− in oxygen evolution in two independent ways. (1) We studied a possible product inhibition of the electron transfer into the catalytic Mn4Ca complex during the oxygen-evolving reaction by greatly increasing the pressure of CO2. This was monitored by absorption transients in the near UV. We found that a 3,000-fold increase of the CO2 pressure over ambient conditions did not affect the UV transient, whereas the S3 → S4 → S0 transition was half-inhibited by raising the O2 pressure only 10-fold over ambient, as previously established. (2) The flash-induced O2 and CO2 production by photosystem II was followed simultaneously with membrane inlet mass spectrometry under approximately 15% H218O enrichment. Light flashes that revealed the known oscillatory O2 release failed to produce any oscillatory CO2 signal. Both types of results exclude that exchangeable bicarbonate is the substrate for (and CO2 an intermediate product of) oxygen evolution by photosynthesis. The possibility that a tightly bound carbonate or bicarbonate is a cofactor of photosynthetic water oxidation has remained.