bluuebunny/crossref_metadata_2025 huggingface dataset:
Nutrition Society Medal Lecture: The role of the skeleton in acid—base homeostasis
Authors: New Susan A.
Published: February 2003

Nutritional strategies for optimising bone health throughout the life cycle are extremely important, since a dietary approach is more popular amongst osteoporosis sufferers than drug intervention, and long-term drug treatment compliance is relatively poor. As an exogenous factor, nutrition is amenable to change and has relevant public health implications. With the growing increase in life expectancy, hip fractures are predicted to rise dramatically in the next decade, and hence there is an urgent need for the implementation of public health strategies to target prevention of poor skeletal health on a population-wide basis. The role that the skeleton plays in acid-base homeostasis has been gaining increasing prominence in the literature; with theoretical considerations of the role alkaline bone mineral may play in the defence against acidosis dating as far back as the late 19th century. Natural, pathological and experimental states of acid loading and/or acidosis have been associated with hypercalciuria and negative Ca balance and, more recently, the detrimental effects of ‘acid’ from the diet on bone mineral have been demonstrated. At the cellular level, a reduction in extracellular pH has been shown to have a direct enhancement on osteoclastic activity, with the result of increased resorption pit formation in bone. A number of observational, experimental, clinical and intervention studies over the last decade have suggested a positive link between fruit and vegetable consumption and the skeleton. Further research is required, particularly with regard to the influence of dietary manipulation using alkali-forming foods on fracture prevention. Should the findings prove conclusive, a “fruit and vegetable” approach to bone health maintenance may provide a very sensible (and natural) alternative therapy for osteoporosis treatment, which is likely to have numerous additional health-related benefits.
Plenary Lecture: Strategies for skeletal health in the elderly
Authors: Eastell Richard , Lambert Helen
Published: February 2003

Osteoporosis is a common disease in the elderly, and the fractures that result from this disorder affect 40 % of women and 14 % of men over the age of 50 years. The risk of fracture relates to bone mineral density and the risk of falling, among other factors. Low bone mineral density in the elderly can result from either low peak bone mass or accelerated bone loss, or a combination of the two. Nutritional factors play a role in both the attainment of peak bone mass and in the rate of age-related bone loss. The main determinants of peak bone mass are genetic factors, early-life nutrition, diet and exercise. Of the nutritional factors Ca, and particularly milk, are the most important contributors to peak bone mass. Some of these factors may interact; for example, a low dietary Ca in addition to an unfavourable vitamin D receptor gene polymorphism may result in low peak bone mass. The age-related changes in bone mass may also have a genetic basis, but deficiency of oestrogen is a major contributor. In addition, undernutrition is common in the elderly, and lack of dietary protein contributes both to impaired bone mineral conservation and increased propensity to fall. There is a decreased ability of the intestine to adapt to a low-Ca diet with increasing age. Other dietary factors include vitamin K, Zn and fruit and vegetables. Adequate nutritional status, particularly of Ca and vitamin D, is essential for the successful pharmaceutical treatment of osteoporosis. Thus, strategies for enhancing skeletal health in the elderly must begin in early childhood, and continue throughout life.
Erratum
Authors: Schutz Yves
Published: February 2003

Role of substrate utilization and thermogenesis on body-weight control with particular reference to alcohol By Yves Schutz Volume 59 (2000), Number 4 Figure 1, page 513
Nutritional improvement of plant foods by non-thermal processing
Authors: Knorr D. , Ade-Omowaye B. I. O. , Heinz V.
Published: February 2003

As a result of the increasing consumer demand for minimally-processed fresh-like food products with high sensory and nutritional qualities, there is a growing interest in non-thermal processes for food processing and preservation. Key advanced technologies such as high-pressure processing, pulsed electric fields, dense gases and ultrasound are being applied to develop gentle but targeted processes to further improve the quality and safety of processed foods. These technologies also offer the potential for improving existing processes as well as for developing new process options. Furthermore, by adding new process dimensions (such as hydrostatic pressure, electric fields, ultrasonics, supercritical CO2) to the conventional process variables of temperature and time, they facilitate enlargement of the availability of unit operations. These operations might be applied effectively in unique combination processes, or as subsequent processing tools in more-targeted and subsequently less-intensive processes for food preservation and modification than the currently-applied processes.
Can supplements help meet the micronutrient needs of the developing world?
Authors: Shrimpton Roger , Schultink Werner
Published: February 2003

Supplementation has many potential advantages over fortification and dietary approaches for improving micronutrient intake. Pregnant and lactating women and infants are most likely to benefit from supplementation. Recent experience with vitamin A supplementation in young children has proved to be remarkably successful. Demonstrated efficacy of vitamin A supplements for improved child survival in many settings and a technical consensus on how to implement interventions were major factors in achieving this success. Bilateral and UN agencies worked together so that in 1999 80 % of children under 5 years of age in the least-developed countries received a vitamin A capsule in the last 6 months. At least one million child lives saved were associated with the increase in coverage in the last 2 years of the 1990s. Experience with Fe-folate supplements has not been as successful. Whilst a technical consensus has been reached on how to implement programmes to control Fe deficiency, the lack of convincing evidence of efficacy of Fe-folate supplements in terms of maternal and child survival outcomes has undoubtedly contributed to the limited pursuit of effective action. A new multiple micronutrient supplement for se amongst women of reproductive age in developing countries has been formulated. UNICEF is employing the supplement in programmes aimed at helping to prevent low birth weight. The new supplement is likely to be more efficacious than Fe-folate supplements for both maternal and child survival and development outcomes. Successful completion of rigorous efficacy trials will be critical for creating the political support needed to achieve universal coverage.
Understanding chronic malnutrition in childhood and old age: role of energy balance research
Authors: Reilly John J.
Published: February 2003

Undernutrition is commonly associated with chronic disease in children and the elderly. Overnutrition is also, but less commonly, associated with chronic illness. In most diseases malnutrition arises because energy intake does not match energy output. Traditionally, the focus of research has been on abnormalities in energy expenditure, in the belief that these factors were the main determinants of energy imbalance. Recent studies using the doubly-labelled-water method to measure total energy expenditure, combined with more complex study design, have suggested an alternative conclusion. In many chronic diseases patient behaviour, and particularly energy intake, is responsible for energy imbalance and malnutrition. Energy balance studies have therefore provided a useful foundation for the design of strategies aimed at preventing or managing chronic malnutrition. However, modifying patient behaviour is an ambitious undertaking which may not be within the scope of existing clinical nutrition services. A number of non-traditional models of managing chronic malnutrition in children and the elderly are promising. Increasing recognition of the value of systematic review will also provide improved strategies for prevention and management of chronic malnutrition.
Scottish Home Parenteral Nutrition Managed Clinical Network: coordination and standards
Authors: Baxter Janet P. , Tait Jan M.
Published: February 2003

Home parenteral nutrition is required by patients with intestinal disease such that they are unable to maintain nutritional status or fluid volume without this treatment. A Managed Clinical Network has been established in Scotland. The aims of this multi-professional group are to ensure equity of access and that patients are managed according to nationally-agreed evidence-based procedures and protocols. The Clinical Standards Board for Scotland has provided support in preparing a quality-assurance framework to which the network must adhere.
Dietary modification of inflammation with lipids
Authors: Calder Philip C.
Published: February 2003

Then-3 polyunsaturated fatty acids (PUFA) eicosapentaenoic acid (EPA) and docosahexaenoicacid (DHA) are found in high proportions in oily fish and fish oils. Then-3 PUFA are structurally and functionally distinct from then-6 PUFA. Typically, human inflammatory cells contain high proportions of then-6 PUFA arachidonic acid and low proportions ofn-3 PUFA. The significance of this difference is that arachidonic acid is the precursor of 2-series prostaglandins and 4-series leukotrienes, which are highly-active mediators of inflammation. Feeding fish oil results in partial replacement of arachidonic acid in inflammatory cell membranes by EPA. This change leads to decreased production of arachidonic acid-derived mediators. This response alone is a potentially beneficial anti-inflammatory effect of n-3 PUFA. However,n-3 PUFA have a number of other effects which might occur downstream of altered eicosanoid production or might be independent of this activity. For example, animal and human studies have shown that dietary fish oil results in suppressed production of pro-inflammatory cytokines and can decrease adhesion molecule expression. These effects occur at the level of altered gene expression. This action might come about through antagonism of the effects of arachidonic acid-derived mediators or through more direct actions on the intracellular signalling pathways which lead to activation of transcription factors such as nuclear factor kappa B (NFêB). Recent studies have shown thatn-3 PUFA can down regulate the activity of the nuclear transcription factor NFêB. Fish oil feeding has been shown to ameliorate the symptoms in some animal models of chronic inflammatory disease and to protect against the effects of endotoxin and similar inflammatory challenges. Clinical studies have reported that oral fish oil supplementation has beneficial effects in rheumatoid arthritis and among some patients with asthma, supporting the idea that then-3 PUFA in fish oil are antiinflammatory. There are indications that inclusion ofn-3 PUFA in enteral and parenteral formulas might be beneficial to patients in intensive care or post-surgery.
Effects of fatty acids on gene expression: role of peroxisome proliferator-activated receptor α, liver X receptor α and sterol regulatory element-binding protein-1c
Authors: Kersten Sander
Published: February 2003

Dietary fatty acids have numerous effects on cellular function, many of which are achieved by altering the expression of genes. The present paper reviews recent data on the mechanisms by which fatty acids influence DNA transcription, and focus specifically on the importance of three transcription factors: peroxisome proliferator-activated receptor α; liver X receptor α; sterol regulatory element-binding protein 1c. These data indicate that fatty acids induce or inhibit the mRNA expression of a variety of different genes by acting both as agonists and as antagonists for nuclear hormone receptors.
n-3 Fatty acids for the treatment of inflammatory bowel diseases
Authors: Belluzzi Andrea
Published: February 2003

The aim of the present paper is to briefly review the literature relating to clinical studies of the use of polyunsaturated long-chain fatty acids in the treatment of inflammatory bowel diseases (
IBD) such as ulcerative colitis and Crohn's disease. The reasons for the discrepancies in the findings could be related to the different study designs, different treatments, overlapping of treatment effects, as well as the variety of treatment formulations and doses used, which have led to results that are, in certain instances, very difficult to explain. Emphasis on a treatment formulation which reduces the incidence of side effects, together with careful selection of patients and experimental design, seems to be associated with benefits, and these studies point to the therapeutic potential for these lipids in the therapy of IBD. It is possible that these fatty acids act by reducing low-grade active inflammation rather than by preventing reinitiation of the inflammatory process from a truly quiescent state. Whether this treatment is applicable to all IBD patients has not been fully elucidated. Nevertheless, taken together, all these studies suggest the effectiveness of these new therapeutic approaches, not only when conventional treatment fails or when it is not possible to treat chronically, but also, in some instances, as first choice.
Vitamin A as an anti-inflammatory agent
Authors: Reifen Ram
Published: February 2003

Vitamin A is necessary for normal differentiation of epithelial tissues, the visual process and reproduction, and is vital for the optimal maintenance and functioning of the innate and adaptive immune system. Vitamin A deficiency is one of the most profuse nutritional deficiencies worldwide. It is associated with increased susceptibility to infectious diseases in both man and animal models. Vitamin A also has a role as an anti-inflammatory agent. Supplementation with vitamin A has been found to be beneficial in a number of inflammatory conditions, including skin disorders such as acne vulgaris, broncho-pulmonary dysplasia and some forms of precancerous and cancer states. The present review suggests that vitamin A deficiency induces inflammation and aggravates existing inflammatory states. Supplementation with vitamin A in selected cases could ameliorate inflammation. The two main mechanisms which appear to be involved in the prevention of disease are the effects of vitamin A on the immune system and the effect on epithelial integrity.
A role for the peroxisome proliferator-activated receptor α in T-cell physiology and ageing immunobiology
Authors: Jones Dallas C. , Manning Bernadette M. , Daynes Raymond A.
Published: February 2003

Peroxisome proliferator-activated receptor (PPAR) α represents an important member of the nuclear hormone receptor superfamily that can be activated by a variety of natural fatty acids, some of their metabolites and by commonly-used anti-lipidaemic drugs. We recently demonstrated PPARα expression in T lymphocytes, where it controls the initiation of transcription of T-box expressed in T-cells (T-bet) independent of added agonist. T-bet is an activation-inducible transcription factor regulator of interleukin 2 (suppression) and interferon γ (stimulation) synthesis. A suppressed ability to produce interleukin 2 and an enhanced production of interferon γ occurs in activated T-cells from PPARα-/- mice, as well as in T-cells from wild-type aged animals whose lymphocytes express lowered basal levels of PPARα. The dysregulated expression and/or function of cytokines, glucocorticoids or leptin that occurs with advanced age could all be responsible for the reduced expression of PPARα. Dietary supplementation of aged mice with vitamin E, or supplementation with known agonists of PPARα, was associated with elevation of lymphocyte expression of this nuclear hormone receptor, restoration of control over T-bet expression and elimination of the dysregulated production of interleukin 2 and interferon γ following lymphocyte activation. Interleukin 2 and interferon γ play very important roles in the initiation and/or regulation of immune, inflammatory and autoimmune disease states. Thus, the mechanisms that control the timing, magnitude and duration of specific cytokine production by activated T lymphocytes need clarification before appropriate nutritional or therapeutic strategies can be devised to treat disease conditions where cytokine expression and/or activities are deemed to be dysregulated and responsible.
Peri-operative amino acid administration and the metabolic response to surgery
Authors: Selldén Eva
Published: February 2003

General anaesthesia causes hypothermia due to decreased metabolic rate and impaired thermoregulation. Many warming devices are in use to prevent heat loss, but little attention has been paid to stimulating the body's own heat generation. All nutrients raise energy expenditure, and the highest thermic effect is ascribed to amino acids and proteins, 30–40% in the awake state. Amino acids infused during general anaesthesia exert a thermic effect that is enhanced compared with that in the awake state. At awakening from anaesthesia, post-operative hypothermia may be prevented without shivering. The tissues involved and the mechanisms by which nutrients stimulate heat production are still not completely understood. However, these findings support the existence of an inhibitory action normally exerted by central thermosensors, in order to maintain oxidative metabolism within certain limits, to prevent hyperthermia. During anaesthesia central thermosensors are silenced and, hence, amino acid thermogenesis is exaggerated. The amino acid-induced heat generation during anaesthesia predominantly occurs in extra-splanchnic tissues, most probably in skeletal muscle. It may reflect an increased protein turnover, as both protein breakdown and synthesis are energy-consuming processes known to generate heat. Possibly, amino acid infusion provides substrates, otherwise mobilized from the body's own tissues, needed for wound healing and immunological function. However, other cellular mechanisms may also contribute to this non-shivering thermogenesis.
Seed genomics: germinating opportunities
Authors: (Lonneke) A. , van der Geest H.M.
Published: February 2003

With the sequencing of theArabidopsis thalianagenome, the field of plant biology has made a quantum leap. The sequence information available to the community has greatly facilitated the identification of genes responsible for mutant phenotypes and the large-scale analysis of gene expression inArabidopsis. High-throughput laboratory tools for DNA sequencing (genomics), mutant analysis (functional genomics), mRNA quantification (transcriptomics) and protein analysis (proteomics) are being used to scrutinize this model plant. For seed physiologists, the challenge lies in translating this information into physiological processes in seeds from other plant species. Combining more traditional seed biology with the new high-throughput molecular tools should yield breakthroughs in seed science.
Effect of low water potential on phytochrome-induced germination, endosperm softening and cell-wall mannan degradation in Datura ferox seeds
Authors: Sánchez Rodolfo A. , Miguel Lucila de , Lima Carlos , M. de Lederkremer Rosa
Published: February 2003

Phytochrome-induced softening of the micropylar endosperm ofDatura feroxseeds is followed by radicle protrusion and preceded by a significant increase in the extractable activity of β-mannanase and β-mannosidase (6 and 3 times over the far-red light controls, respectively) and a decrease in the mannan content of the micropylar endosperm cell walls. This relationship between phytochrome-induced germination, endosperm softening and mannan degradation was studied inDatura feroxseeds subjected to a range of water potentials during the presence of Pfr. Low water potential inhibited the decrease in mannose-rich cell-wall insoluble polysaccharides, the increase in activity of β-mannosidase and endosperm softening. A good correlation was found between activity of β-mannosidase measured at 45 h after exposure to a red light pulse and germination counted 24 h later when, with different external water potentials, germination varied between 0 and 90%. In contrast, no inhibitory effect of low water potential onin vitroβ-mannanase activity was detected. We suggest that thein vivoaction of β-mannanase might be limited by accumulation of manno-oligosaccharides caused by inhibition of β-mannosidase. These data are consistent with the concept of a link between mannan mobilization and endosperm softening. Part of the effect of low water potential on Pfr-induced germination may be mediated by inhibition of β-mannosidase activity, with consequences for mannan hydrolysis and endosperm softening.
Comparison of the seed germination and early seedling growth of soybean in saline conditions
Authors: Hosseini Mohammad Khajeh , Powell Alison A. , Bingham Ian J.
Published: February 2003

Germination and seedling growth of soybean (Glycine maxL.) cv. Williams were examined on paper towels pre-moistened with a range of saline solutions (germination: 0–500 mMolal NaCl; seedling growth: 0–330 mMolal NaCl). The Na+, K+and Ca2+concentrations in the embryonic axis immediately before germination and in the seedling 3.5 d after germination were measured. Germination decreased at NaCl concentrations of 330 mMolal (81% germination) and above. At 420 mMolal NaCl, only 40% of seeds germinated, and at 500 mMolal NaCl there was no germination. Seedling growth rate decreased drastically with increasing salinity. At 220 mMolal NaCl, seedling growth rate had declined to 5% of the control, whereas at 330 mMolal NaCl seedling growth was almost zero 3–4 d after germination. Thus, soybean seeds were more tolerant of salinity in the germination than in the seedling phase. The results suggest that the greater tolerance of salinity during the germination phase might, in part, be the result of a lower sensitivity to high tissue Na+concentrations. Germination (40%) was possible at a tissue Na+concentration in the embryonic axis of 9.3 mg g FW-1, whereas seedling growth was completely inhibited at a tissue Na+concentration of 6.1 mg g FW-1. Germination at higher tissue Na+concentrations was associated with higher K+and Ca2+concentrations in the embryo axis, compared with growing seedlings, suggesting that these ions may protect the seeds in the pre-germination phase against salinity.
Lipid concentration in the embryo–endosperm fraction of seeds of Australian tropical lowland rainforest trees: relevance to defence and dispersal
Authors: Finkelstein Sarah , Grubb Peter J.
Published: February 2003

The lipid concentration (LC) of the embryo–endosperm fraction was determined for the seeds of 60 species in 22 families from an Australian tropical lowland rainforest. It was negatively related to the mass of the embryo–endosperm across all species, but the relationship was not significant atP< 0.05. LC was significantly and positively correlated with N concentration when all species were considered, but not within the families represented by the most species (Lauraceae, 13;Sapindaceae, 9;Proteaceae, 6). LC was significantly and markedly higher in more heavily defended seeds (medians: 27 and 6.9%); there is evidence for the view that seeds rich in either lipid or nitrogen are markedly defended. Lipid concentration was also markedly higher, on average, in seeds taken by the scatter-hoardingUromys caudimaculatus(white-tailed rat) than in seeds of comparable size not taken byUromys, but not known to be protected by any toxin or irritant (medians: 35 and 3.7%, respectively). However, LC was not notably high in one major group of seeds taken byUromys– the largest-seeded species ofBeilschmiediaandEndiandra(Lauraceae). The comparisons mostly involved different phyletic lines, and were not consistently supported by contrasts within phyletic lines.
Embryo dormancy responses to temperature in capeweed (Arctotheca calendula) seeds
Authors: Ellery Amanda J.
Published: February 2003

Changes in embryo dormancy of capeweed [Arctotheca calendula (L.) Levyns.] seeds in response to temperature were investigated to determine the nature of seasonal dormancy cycles. Primary embryo dormancy persisted for 2–3 months after seed collection and was then rapidly relieved when seeds were maintained at temperatures simulating summer soil surface temperatures. Embryo dormancy was also rapidly relieved in seeds maintained at constant temperatures, indicating that a daily temperature fluctuation was not necessary for the relief of embryo dormancy in capeweed. Dormancy relief was maximal at 40°C. Secondary dormancy was induced when seeds were maintained at low temperatures and a water potential of –1.5 MPa, suggesting that the onset of winter may postpone germination until a subsequent autumn. These results indicate that the dormancy cycles observed in capeweed seeds maintained on the soil surface are probably driven by seasonal changes in soil temperature.
Ecophysiology of seed germination in Mediterranean geophytes. 1. Muscari spp
Authors: Doussi Maria A. , Thanos Costas A.
Published: February 2003

Ecophysiological aspects of seed germination were investigated in four Mediterranean geophytes of the genus Muscari (Liliaceae): M. comosum (tassel hyacinth), M. neglectum (common grape hyacinth), M. commutatum and M. weissii. Experiments were performed at constant temperatures in the dark and under temperature and light conditions simulating those prevailing in nature during November–January, i.e. well into the rainy season of the Mediterranean climate. In all species, no primary dormancy was revealed, and germination occurred in a rather narrow range of cool temperatures (optimum at 10 or 15°C) and at a remarkably slow rate; both germination characteristics seem to be associated with autumn/winter seed germination and seedling establishment. Such a postulated strategy is ecologically advantageous within an unpredictable rainfall regime, known to prevail during the start of the rainy period of the Mediterranean climate. This strategy may also explain the spread of germination of M. comosum seeds over two consecutive years, observed by Theophrastus. Far-red light, simulating light conditions under a dense canopy, resulted in only a slight delay of germination compared to dark controls. Diurnal white light, qualitatively simulating natural daylight, caused a significant decrease of the germination rate in all four species studied. Moreover, white light was found to suppress considerably final seed germination (photoinhibition) in M. weissii and M. neglectum; in the latter species, prolonged imbibition under white light also led to the induction of secondary dormancy.
Sacred lotus, the long-living fruits of China Antique
Authors: Shen-Miller J.
Published: February 2003

In the West, lotus (Nelumbo nuciferaGaertn.) is relatively little known. However, for more than 3000 years, lotus plants have been cultivated as a crop in Far-East Asia, where they are used for food, medicine and play a significant role in religious and cultural activities. Holder of the world’s record for long-term seed viability (1300 years) is a lotus fruit (China Antique) from Xipaozi, Liaoning Province, China. Five offspring of this variety, from 200–500-year-old fruits (14C dates) collected at Xipaozi, have recently been germinated, and are the first such seedlings to be raised from directly dated fruits. The fruits at Xipaozi, preserved in a dry ancient lakebed, have been exposed to low-dose γ-radiation for hundreds of years (having an accumulated soil irradiation of 0.1–1.0 Gy). Offspring from these old fruits show abnormalities that resemble those in various modern seedlings irradiated at much higher doses. Although these lotus offspring are phenotypically abnormal, the viability of old seeds was evidently not affected by accumulated doses of up to 3 Gy. Growth characteristics of first- and second-year lotus offspring of these fruits, products of the longest-term radiobiological experiment on record, are summarized here (rapid early growth, phenotypic abnormalities, lack of vigour, poor rhizome development and low photosynthetic activity during second-year growth). Aspects of their chromosomal organization, phenotype and physiology (rapid recovery from stress, heat-stable proteins, protein-repair enzyme) are discussed. Important unsolved problems are suggested to elicit interest among members of the seed science community to the study of old fruits recently collected at Xipaozi, with particular emphasis on aspects of ageing and repair.
Direct activation of PDE5 by cGMP
Authors: Mullershausen Florian , Friebe Andreas , Feil Robert , Thompson W. Joseph , Hofmann Franz , Koesling Doris
Published: March 2003

In platelets, the nitric oxide (NO)–induced cGMP response is indicative of a highly regulated interplay of cGMP formation and cGMP degradation. Recently, we showed that within the NO-induced cGMP response in human platelets, activation and phosphorylation of phosphodiesterase type 5 (PDE5) occurred. Here, we identify cyclic GMP-dependent protein kinase I as the kinase responsible for the NO-induced PDE5 phosphorylation. However, we demonstrate that cGMP can directly activate PDE5 without phosphorylation in platelet cytosol, most likely via binding to the regulatory GAF domains. The reversal of activation was slow, and was not completed after 60 min. Phosphorylation enhanced the cGMP-induced activation, allowing it to occur at lower cGMP concentrations. Also, in intact platelets, a sustained NO-induced activation of PDE5 for as long as 60 min was detected. Finally, the long-term desensitization of the cGMP response induced by a low NO concentration reveals the physiological relevance of the PDE5 activation within NO/cGMP signaling. In sum, we suggest NO-induced activation and phosphorylation of PDE5 as the mechanism for a long-lasting negative feedback loop shaping the cGMP response in human platelets in order to adapt to the amount of NO available.
Large-Scale Variation Among Human and Great Ape Genomes Determined by Array Comparative Genomic Hybridization
Authors: Locke Devin P. , Segraves Richard , Carbone Lucia , Archidiacono Nicoletta , Albertson Donna G. , Pinkel Daniel , Eichler Evan E.
Published: March 2003

Large-scale genomic rearrangements are a major force of evolutionary change and the ascertainment of such events between the human and great ape genomes is fundamental to a complete understanding of the genetic history and evolution of our species. Here, we present the results of an evolutionary analysis utilizing array comparative genomic hybridization (array CGH), measuring copy-number gains and losses among these species. Using an array of 2460 human bacterial artificial chromosomes (BACs) (12% of the genome), we identified a total of 63 sites of putative DNA copy-number variation between humans and the great apes (chimpanzee, bonobo, gorilla, and orangutan). Detailed molecular characterization of a subset of these sites confirmed rearrangements ranging from 40 to at least 175 kb in size. Surprisingly, the majority of variant sites differentiating great ape and human genomes were found within interstitial euchromatin. These data suggest that such large-scale events are not restricted solely to subtelomeric or pericentromeric regions, but also occur within genic regions. In addition, 5/9 of the verified variant sites localized to areas of intrachromosomal segmental duplication within the human genome. On the basis of the frequency of duplication in humans, this represents a 14-fold positional bias. In contrast to previous cytogenetic and comparative mapping studies, these results indicate extensive local repatterning of hominoid chromosomes in euchromatic regions through a duplication-driven mechanism of genome evolution.

[Supplemental material is available online at www.genome.org. The following individuals kindly provided reagents, samples, or unpublished information as indicated in the paper: O. Ryder, L. Faust, and E. Adams.]
A Global Search Reveals Epistatic Interaction Between QTL for Early Growth in the Chicken
Authors: Carlborg Örjan , Kerje Susanne , Schütz Karin , Jacobsson Lina , Jensen Per , Andersson Leif
Published: March 2003

We have identified quantitative trait loci (QTL) explaining a large proportion of the variation in body weights at different ages and growth between chronological ages in an F2 intercross between red junglefowl and White Leghorn chickens. QTL were mapped using forward selection for loci with significant marginal genetic effects and with a simultaneous search for epistatic QTL pairs. We found 22 significant loci contributing to these traits, nine of these were only found by the simultaneous two-dimensional search, which demonstrates the power of this approach for detecting loci affecting complex traits. We have also estimated the relative contribution of additive, dominance, and epistasis effects to growth and the contribution of epistasis was more pronounced prior to 46 days of age, whereas additive genetic effects explained the major portion of the genetic variance later in life. Several of the detected loci affected either early or late growth but not both. Very few loci affected the entire growth process, which points out that early and late growth, at least to some extent, have different genetic regulation.

[Supplemental material is available online at www.genome.org.]
Schizosaccharomyces pombe Essential Genes: A Pilot Study
Authors: Decottignies Anabelle , Sanchez-Perez Isabel , Nurse Paul
Published: March 2003

After completion of the Schizosaccharomyces pombe genome sequence, we have carried out a pilot gene deletion project to assess the feasibility of a genome-wide deletion project and to estimate the percentage of essential genes. Using a PCR-based gene deletion procedure, we investigated 100 genes within a 253-kb region of chromosome II. Eight of nine genes located within a region of 18 kb could not be deleted, suggesting that systematic deletion of all fission yeast genes may be difficult to achieve using this PCR approach. The percentage of essential genes was found to be 17.5%. Further deletion of selected S. pombe genes revealed that whether a gene is essential or not is correlated with the timing of its appearance on the tree of life and its conservation within all branches of the tree. None of the investigated ancient genes in fission yeast that have been lost in the Saccharomyces cerevisiae lineage are essential. In agreement with S. cerevisiae andCaenorhabditis elegans genome analyses, our data suggest that natural selection has preferentially kept the genes required for vital functions. We propose that many of the essential eukaryotic genes appeared with the first eukaryotic cell and have remained conserved in all species.
Disruption Mutations of ADA2b and GCN5 Transcriptional Adaptor Genes Dramatically Affect Arabidopsis Growth, Development, and Gene Expression[W]
Authors: Vlachonasios Konstantinos E. , Thomashow Michael F. , Triezenberg Steven J.
Published: March 2003

We previously identified Arabidopsis genes homologous with the yeast ADA2 and GCN5 genes that encode components of the ADA and SAGA histone acetyltransferase complexes. In this report, we explore the biological roles of the Arabidopsis ADA2b and GCN5 genes. T-DNA insertion mutations in ADA2b and GCN5 were found to have pleiotropic effects on plant growth and development, including dwarf size, aberrant root development, and short petals and stamens in flowers. Approximately 5% of the 8200 genes assayed by DNA microarray analysis showed changes of expression in the mutants, three-fourths of which were upregulated and only half of which were altered similarly in the two mutant strains. In cold acclimation experiments, C-repeat binding factors (CBFs) were induced in the mutants as in wild-type plants, but subsequent transcription of cold-regulated (COR) genes was reduced in both mutants. Remarkably, nonacclimated ada2b-1 (but not gcn5-1) mutant plants were more freezing tolerant than nonacclimated wild-type plants, suggesting that ADA2b may directly or indirectly repress a freezing tolerance mechanism that does not require the expression of CBF or COR genes. We conclude that the Arabidopsis ADA2b and GCN5 proteins have both similar and distinct functions in plant growth, development, and gene expression and may be components of both a common coactivator complex and separate complexes with distinct biological activities.
The future of reference: point‐of‐need reference service: no longer an afterthought
Authors: Grodzins Lipow Anne
Published: March 2003

Makes a strong case for reference librarians to invent their futures, urging them to promulgate new images of the work they perform. "Looks back" at reference librarianship from the year 2020, commenting on the world‐wide alliances of librarians, the library building, and the virtual environment.
The future of reference: get real!
Authors: LaGuardia Cheryl
Published: March 2003

This paper takes a pragmatic practitioner’s view of the future of reference. It discusses five issues that need to be addressed for reference to advance logically: designing the right systems; keeping a local focus on user needs; getting a realistic perspective on library instruction; acknowledging the paradigm shift in reference question complexity; and the public relations aspects of reference services. Emphasis is placed on using technology as a tool to gain our ends, rather than employing it simply as a new toy and an end in itself.
The future of reference: the intersection of information resources, technology and users
Authors: Richardson John V.
Published: March 2003

Provides a reflective essay on the five papers, and notes that the authors each address the intersection of three concepts: information resources, technology, and users. Points out that the social aspect is one of the most important drivers in the provision of reference services.
Surviving and thriving in academia: a selective bibliography for new faculty members
Authors: Lee Deborah
Published: March 2003

The transition from graduate student to new faculty member can be an exciting and challenging period in an academic career. New faculty members must successfully balance service obligations, research demands, and teaching responsibilities. Numerous guides have been developed to assist new faculty members in developing their careers. This selective bibliography identifies sources that can assist both graduate students and new faculty members as they develop their academic career.
Alkaline Phosphatase Reporter Transposon for Identification of Genes Encoding Secreted Proteins in Gram-Positive Microorganisms
Authors: Gibson Carmela M. , Caparon Michael G.
Published: February 2003

We describe the construction of TnFuZ, a genetic tool for the discovery and mutagenesis of proteins exported from gram-positive bacteria. This tool combines a transposable element (Tn
4001
) of broad host range in gram-positive bacteria and an alkaline phosphatase gene (
phoZ
) derived from a gram-positive bacterium that has been modified by removal of the region encoding its export signal. Mutagenesis of
Streptococcus pyogenes
with TnFuZ (“FuZ” stands for fusions to
phoZ
) identified genes encoding secreted proteins whose expression was enhanced during growth in an aerobic environment. Thus, TnFuZ should be valuable for analysis of protein secretion, gene regulation, and virulence in gram-positive bacteria.
Tolerance and Metabolic Response of Acetogenic Bacteria toward Oxygen
Authors: Karnholz Arno , Küsel Kirsten , Gößner Anita , Schramm Andreas , Drake Harold L.
Published: February 2003

The acetogens
Sporomusa silvacetica
,
Moorella thermoacetica
,
Clostridium magnum
,
Acetobacterium woodii
, and
Thermoanaerobacter kivui
(i) grew in both semisolid and liquid cultivation media containing O
2
and (ii) consumed small amounts of O
2
. Low concentrations of O
2
caused a lag phase in growth but did not alter the ability of these acetogens to synthesize acetate via the acetyl coenzyme A pathway. Cell extracts of
S. silvacetica
,
M. thermoacetica
, and
C. magnum
contained peroxidase and NADH oxidase activities; catalase and superoxide dismutase activities were not detected.
Quantitation of DNA Sequences in Environmental PCR Products by a Multiplexed, Bead-Based Method
Authors: Spiro Alexander , Lowe Mary
Published: February 2003

A first application of a multiplexed, bead-based method is described for determining the abundances of target sequences in an environmental PCR product. Target sequences as little as 0.3% of the total amount of DNA can be quantified. Tests were conducted on 16S ribosomal DNA sequences from microorganisms collected from contaminated groundwater.
Multiple Alternate Transcripts Direct the Biosynthesis of Microcystin, a Cyanobacterial
Authors: Kaebernick Melanie , Dittmann Elke , Börner Thomas , Neilan Brett A.
Published: February 2003

The
mcyABCDEFGHIJ
gene cluster of
Microcystis aeruginosa
encodes the mixed polyketide synthase/nonribosomal peptide synthetase (microcystin synthetase) which is responsible for biosynthesis of the potent liver toxin microcystin. The sequence and orientation of the
mcy
genes have previously been reported, but no transcriptional analysis had been performed prior to this study. The
mcyABCDEFGHIJ
genes are transcribed as two polycistronic operons,
mcyABC
and
mcyDEFGHIJ
, from a central bidirectional promoter between
mcyA
and
mcyD
. Two transcription start sites were detected for both
mcyA
and
mcyD
when cells were exposed to light intensities of 68 and 16 μmol of photons m
−2
s
−1
. The start sites, located 206 and 254 bp upstream of the translational start for
mcyD
under high and low light conditions, respectively, indicate long untranslated leader regions. Putative transcription start sites were also identified for
mcyE
,
mcyF
,
mcyG
,
mcyH
,
mcyI
, and
mcyJ
but not for
mcyB
and
mcyC
. A combination of reverse transcription-PCR and rapid amplification of cDNA ends was employed throughout this work, which may have been one of the first transcriptional analyses of a large nonribosomal polyketide gene cluster.
Enhanced Levels of Cold Shock Proteins in
Listeria monocytogenes
LO28 upon Exposure to Low Temperature and High Hydrostatic Pressure
Authors: Wemekamp-Kamphuis Henrike H. , Karatzas Andreas K. , Wouters Jeroen A. , Abee Tjakko
Published: February 2003

Listeria monocytogenes
is a psychrotrophic food-borne pathogen that is problematic for the food industry because of its ubiquitous distribution in nature and its ability to grow at low temperatures and in the presence of high salt concentrations. Here we demonstrate that the process of adaptation to low temperature after cold shock includes elevated levels of cold shock proteins (CSPs) and that the levels of CSPs are also elevated after treatment with high hydrostatic pressure (HHP). Two-dimensional gel electrophoresis combined with Western blotting performed with anti-CspB of
Bacillus subtilis
was used to identify four 7-kDa proteins, designated Csp1, Csp2, Csp3, and Csp4. In addition, Southern blotting revealed four chromosomal DNA fragments that reacted with a
csp
probe, which also indicated that a CSP family is present in
L. monocytogenes
LO28. After a cold shock in which the temperature was decreased from 37°C to 10°C the levels of Csp1 and Csp3 increased 10- and 3.5-fold, respectively, but the levels of Csp2 and Csp4 were not elevated. Pressurization of
L. monocytogenes
LO28 cells resulted in 3.5- and 2-fold increases in the levels of Csp1 and Csp2, respectively. Strikingly, the level of survival after pressurization of cold-shocked cells was 100-fold higher than that of cells growing exponentially at 37°C. These findings imply that cold-shocked cells are protected from HHP treatment, which may affect the efficiency of combined preservation techniques.
FK506 Binding Protein from the Hyperthermophilic Archaeon
Pyrococcus horikoshii
Suppresses the Aggregation of Proteins in
Escherichia coli
Authors: Ideno Akira , Furutani Masahiro , Iba Yoshitaka , Kurosawa Yoshikazu , Maruyama Tadashi
Published: February 2003

The 29-kDa FK506 binding protein (FKBP) gene is the only peptidyl-prolyl
cis-trans
isomerase (PPIase) gene in the genome of
Pyrococcus horikoshii
. We characterized the function of this FKBP (PhFKBP29) and used it to increase the production yield of soluble recombinant protein in
Escherichia coli
. The PPIase activity (
k
cat
/

K
m

) of PhFKBP29 was found to be much lower than that of other archaeal 16- to 18-kDa FKBPs by a chymotrypsin-coupled assay of the oligo-peptidyl substrate at 15°C. Besides this low PPIase activity, PhFKBP29 showed chaperone-like protein folding activity which enhanced the refolding yield of chemically unfolded rhodanese in vitro. In addition, it suppressed thermal protein aggregation in a temperature range of 45 to 100°C. When the PhFKBP29 gene was coexpressed with the recombinant Fab fragment gene of the anti-hen egg lysozyme antibody in the cytoplasm of
E. coli
, whose expressed product tended to form an inactive aggregate in
E. coli
, it improved the yield of the soluble Fab fragments with antibody specificity. PhFKBP29 exerted protein folding and aggregation suppression in
E. coli
cells.
Occurrence and Phenotypic Characterization of
Yersinia ruckeri
Strains with Biofilm-Forming Capacity in a Rainbow Trout Farm
Authors: Coquet L. , Cosette P. , Quillet L. , Petit F. , Junter G.-A. , Jouenne T.
Published: February 2003

The presence of
Yersinia ruckeri
in a French fish farm was investigated.
Y. ruckeri
was isolated mainly from algae and sediment samples rather than from water. Twenty-two
Y. ruckeri
isolates were obtained, and three strains were distinguished by enterobacterial repetitive intergenic consensus PCR amplification. These strains were able to adhere to solid supports. This characteristic was correlated with flagellum-mediated motility. Killing experiments showed that sessile cells were more resistant to oxolinic acid than their planktonic counterparts. Our results demonstrate that surface colonization of fish farm tanks by
Y. ruckeri
biofilms is a potential source of recurrent infection for extended periods of time.