bluuebunny/crossref_metadata_2025 huggingface dataset:
Interactions between plant nutrients, water and carbon dioxide as factors limiting crop yields
Authors: Gregory P. J. , Simmonds L. P. , Warren G. P.
Published: October 2002

Biomass production of annual crops is often directly proportional to the amounts of radiation intercepted, water transpired and nutrients taken up. In many places the amount of rainfall during the period of rapid crop growth is less than the potential rate of evaporation, so that depletion of stored soil water is commonplace. The rate of mineralization of nitrogen (N) from organic matter and the processes of nutrient loss are closely related to the availability of soil water. Results from Kenya indicate the rapid changes in nitrate availability following rain.

Nutrient supply has a large effect on the quantity of radiation intercepted and hence, biomass production. There is considerable scope for encouraging canopy expansion to conserve water by reducing evaporation from the soil surface in environments where it is frequently rewetted, and where the unsaturated hydraulic conductivity of the soil is sufficient to supply water at the energy limited rate (e.g. northern Syria). In regions with high evaporative demand and coarse–textured soils (e.g. Niger), transpiration may be increased by management techniques that reduce drainage.

Increases in atmospheric [CO
2
] are likely to have only a small impact on crop yields when allowance is made for the interacting effects of temperature, and water and nutrient supply.
Genetic testing, life insurance, and adverse selection
Authors: Harper P. S.
Published: October 2002

Life insurance is a key element of the UK social structure in terms of family protection and house purchase; it thus needs to be viewed in this broad context, rather that solely as a commercial activity. Insurers have not so far actively requested genetic tests for life insurance, but have insisted on knowing of and being able to act on existing genetic test information. The main reason given for this has been to avoid servious adverse selection; however, this has never been adequately estimated. Review of the different major categories of Medelian genetic disorders suggests that the scope for adverse selection is extremely limited and that insurers would lose little, and possibly gain more, by foregoing the disclosure and use of this information in relation to life insurance policies of ‘normal’ size and nature. The likely future use in service of genetic tests based on susceptibility or population screening makes it especially important that the issue is rapidly resolved for Menelian disorders; so far there is no sign that insurers are willing to achieve this.
A model of visual recognition and categorization
Authors: Edelman Shimon , Duvdevani-Bar Sharon
Published: October 2002

To recognize a previously seen object, the visual system must overcome the variability in the object's appearance caused by factors such as illumination and pose. Developments in computer vision suggest that it may be possible to counter the influence of these factors, by learning to interpolate between stored views of the target object, taken under representative combinations of viewing conditions. Daily life situations, however, typically require categorization, rather than recognition, of objects. Due to the open–ended character of both natural and artificial categories, categorization cannot rely on interpolation between stored examples. Nonetheless, knowledge of several representative members, or prototypes, of each of the categories of interest can still provide the necessary computational substrate for the categorization of new instances. The resulting representational scheme based on similarities to prototypes appears to be computationally viable, and is readily mapped onto the mechanisms of biological vision revealed by recent psychophysical and physiological studies.
The knowledge base of the oculomotor system
Authors: Land Michael F. , Furneaux Sophie
Published: October 2002

In everyday life, eye movements enable the eyes to gather the information required for motor actions. They are thus proactive, anticipating actions rather than just responding to stimuli. This means that the oculomotor system needs to know where to look and what to look for. Using examples from table tennis, driving and music reading we show that the information the eye movement system requires is very varied in origin and highly task specific, and it is suggested that the control program orschemafor a particular action must include directions for the oculomotor and visual processing systems. In many activities (reading text and music, typing, steering) processed information is held in a memory buffer for a period of about a second. This permits a match between the discontinuous input from the eyes and continuous motor output, and in particular allows the eyes to be involved in more than one task.
Vision without knowledge
Authors: Milner A. D.
Published: October 2002

A brain–damaged patient (D.F.) with visual form agnosia is described and discussed. D.F. has a profound inability to recognize objects, places and people, in large part because of her inability to make perceptual discriminations of size, shape or orientation, despite having good visual acuity. Yet she is able to perform skilled actions that depend on that very same size, shape and orientation information that is missing from her perceptual awareness. It is suggested that her intact vision can best be understood within the framework of a dual processing model, according to which there are two cortical processing streams operating on different coding principles, for perception and for action, respectively. These may be expected to have different degrees of dependence on top–down information. One possibility is that D.F.'s lack of explicit awareness of the visual cues that guide her behaviour may result from her having to rely on a processing system which is not knowledge–based in a broad sense. Conversely, it may be that the perceptual system can provide conscious awareness of its products in normal individuals by virtue of the fact that it does interact with a stored base of visual knowledge.
Content-based indexing of images and video
Authors: Pentland Alex
Published: October 2002

By representing image content using probabilistic models of an object's appearance we can obtain semantics–preserving compression of the image data. Such compact representations of an image's salient features allow rapid computer searches of even large image databases. Examples are shown for databases of face images, a video of American sign language (ASL), and a video of facial expressions.
Genetic analysis of host–parasite coevolution in human malaria
Authors: Hill Adrian V. S. , Jepson Annette , Plebanski Magdalena , Gilbert Sarah C.
Published: October 2002

Recent twin studies of clinical malaria and immune responses to malaria antigens have underscored the importance of both MHC and non–MHC genes in determining variable susceptibility and immune responsiveness. By using a combination of whole genome genetic linkage studies of families and candidate gene analysis, non–MHC genes are being mapped and identified. HLA genotype was found to affect susceptibility to severe malaria in a large study of West African children. T lymphocytes that may mediate such resistance have been identified and their target antigens and epitopes characterized. Some of these epitopes show substantial polymorphism, which appears to result from immune selection pressure. Natural variant epitopes have been found to escape T–cell recognition in cytolytic and other T–cell assays. More recently a novel immune escape mechanism has been described in viral infections, altered peptide ligand antagonism, whereby variants of a T–cell epitope can downregulate or ablate a T cell response to the index peptide. The likely implications of such immune escape mechanisms for the population structure of malaria parasites, for HLA associations with malaria infection and disease, and for the design of new malaria vaccines, are discussed. The evolutionary consequences of such molecular interactions can be assessed by using mathematical models that capture the dynamic interplay of variable host and parasite molecules. Combined genetic, immunological and mathematical analysis of host and parasite variants in natural populations can identify some mechanisms driving host–parasite coevolution.
Mechanisms of innate resistance toToxoplasma gondiiinfection
Authors: Alexander J. , Scharton-Kersten T. M. , Yap G. , Roberts C. W. , Liew F. Y. , Sher A.
Published: October 2002

The interaction of protozoan parasites with innate host defences is critical in determining the character of the subsequent infection. The initial steps in the encounter ofToxoplasma gondiiwith the vertebrate immune system provide a striking example of this important aspect of the host–parasite relationship. In immunocompetent individuals this intracellular protozoan produces an asymptomatic chronic infection as part of its strategy for transmission. Nevertheless,T. gondiiis inherently a highly virulent pathogen. The rapid induction by the parasite of a potent cell–mediated immune response that both limits its growth and drives conversion to a dormant cyst stage explains this apparent paradox. Studies with gene–deficient mice have demonstrated the interleukin–12 (IL–12)–dependent production of interferon gamma (IFN–gamma) to be of paramount importance in controlling early parasite growth. However, this seems to be independent of nitric oxide production as mice deficient in inducible nitric oxide synthase (iNOS) and tumour necrosis factor receptor were able to control early growth ofT. gondii, although they later succumbed to infection. Nitric oxide does, however, seem to be important in controlling persistent infection; treating chronic infection with iNOS metabolic inhibitors results in disease reactivation. Preliminary evidence implicates neutrophils in effector pathways against this parasite distinct from that described for macrophages. Once initiated, IL–12–dependent IFN–gamma production in synergy with other proinflammatory cytokines can positively feed back on itself to induce ‘cytokine shock’. Regulatory cytokines, particularly IL–10, are essential to down–regulate inflammation and limit host pathology.
Pre–erythrocytic–stage immune effector mechanisms inPlasmodiumspp. infections
Authors: Doolan Denise L. , Hoffman Stephen L.
Published: October 2002

The potent protective immunity against malaria induced by immunization of mice and humans with radiation–attenuatedPlasmodiumspp. sporozoites is thought to be mediated primarily by T–cell responses directed against infected hepatocytes. This has led to considerable efforts to develop subunit vaccines that duplicate this protective immunity, but a universally effective vaccine is still not available andin vitrocorrelates of protective immunity have not been established. Contributing to this delay has been a lack of understanding of the mechanisms responsible for the protection. There are now data indicating that CD8+ T cells, CD4+ T cells, cytokines, and nitric oxide can all mediate the elimination of infected hepatocytesin vitroandin vivo. By dissecting the protection induced by immunization with irradiated sporozoite, DNA and synthetic peptide–adjuvant vaccines, we have demonstrated that different T–cell–dependent immune responses mediate protective immunity in the same inbred strain of mouse, depending on the method of immunization. Furthermore, the mechanism of protection induced by a single method of immunization may vary among different strains of mice. These data have important implications for the development of pre–erythrocytic–stage vaccines designed to protect a heterogeneous human population, and of assays that predict protective immunity.
Multimodal integration for the representation of space in the posterior parietal cortex
Authors: Andersen Richard A.
Published: October 2002

The posterior parietal cortex has long been considered an ‘association’ area that combines information from different sensory modalities to form a cognitive representation of space. However, until recently little has been known about the neural mechanisms responsible for this important cognitive process. Recent experiments from the author's laboratory indicate that visual, somatosensory, auditory and vestibular signals are combined in areas LIP and 7a of the posterior parietal cortex.The integration of these signals can represent the locations of stimuli with respect to the observer and within the environment. Area MSTd combines visual motion signals, similar to those generated during an observer's movement through the environment, with eye–movement and vestibular signals. This integration appears to play a role in specifying the path on which the observer is moving. All three cortical areas combine different modalities into common spatial frames by using a gain–field mechanism. The spatial representations in areas LIP and 7a appear to be important for specifying the locations of targets for actions such as eye movements or reaching; the spatial representation within area MSTd appears to be important for navigation and the perceptual stability of motion signals.
Memory reprocessing in corticocortical and hippocampocortical neuronal ensembles
Authors: Qin Yu-Lin , Mcnaughton Bruce L. , Skaggs William E. , Barnes Carol A.
Published: October 2002

Hippocampal cells that fire together during behaviour exhibit enhanced activity correlations during subsequent sleep, with some preservation of temporal order information. Thus, information reflecting experiences during behaviour is re–expressed in hippocampal circuits during subsequent ‘offline’ periods, as postulated by some theories of memory consolidation. If the hippocampus orchestrates the reinstatement of experience–specific activity patterns in the neocortex, as also postulated by such theories, then correlation patterns both within the neocortex and between hippocampus and neocortex should also re–emerge during sleep. Ensemble recordings were made in the posterior parietal neocortex, in CA1, and simultaneously in both areas, in seven rats. Each session involved an initial sleep episode (S1), behaviour on a simple maze (M), and subsequent sleep (S2). The ensemble activity–correlation structure within and between areas during S2 resembled that of M more closely than did the correlation pattern of S1. Temporal order (i.e. the asymmetry of the cross–correlogram) was also preserved within, but not between, structures. Thus, traces of recent experience are re–expressed in both hippocampal and neocortical circuits during sleep, and the representations in the two areas tend to correspond to the same experience. The poorer preservation of temporal firing biases between neurons in the different regions may reflect the less direct synaptic coupling between regions than within them. Alternatively, it could result from a shift, between behavioural states, in the relative dominance relations in the corticohippocampal dialogue. Between–structure order will be disrupted, for example, if, during behaviour, neocortical patterns tend to drive corresponding hippocampal patterns, whereas during sleep the reverse occurs. This possibility remains to be investigated.
Architecture and functional morphology of the skeletal apparatus of ozarkodinid conodonts
Authors: Purnell Mark A. , Donoghue Philip C. J.
Published: October 2002

Ozarkodinid conodonts were one of the most successful groups of agnathan vertebrates. Only the oropharyngeal feeding apparatus of conodonts was mineralized, and the skeletal elements were generally disarticulated on the death and decay of the body. Occasionally, however, they were preserved in association as ‘natural assemblages’, fossilized
in situ
after post–mortem collapse of the apparatus. From analysis of element arrangement in natural assemblages of
Idiognathodus
from the Pennsylvanian of Illinois we have produced a precise scale model of the feeding apparatus of ozarkodinid conodonts. At the front lay an axial Sa element, flanked by two groups of four close-set elongate Sb and Sc elements which were inclined obliquely inwards and forwards; above these elements lay a pair of arched and inward pointing M elements. Behind the S-M array lay transversely oriented and bilaterally opposed Pb and Pa elements.

Our model sheds new light on food acquisition in conodonts. We propose that the anterior S and M elements of ozarkodinid conodonts were attached to cartilaginous plates. In order for the animal to feed, these plates were first everted, and then drawn back and upward over the anterior edge of an underlying cartilage. These movements produced a highly effective grasping action, the cusps and denticles of the elements converging to grab and impale any food item that lay anterior to the open array. According to this hypothesis, the anterior part of the conodont apparatus is comparable to, and possibly homologous with, the lingual apparatus of extant agnathans; the elements themselves, however, have no direct homologues.
Characteristic length scales of spatial models in ecology via fluctuation analysis
Authors: Keeling M. J. , Mezić I. , Hendry R. J. , McGlade J. , Rand D. A.
Published: October 2002

A technique of fluctuation analysis is introduced for the identification of characteristic length scales in spatial models, with similarities to the recently introduced methods using correlations. The identified length scale provides the optimal size to extract non-trivial large-scale behaviour in such models. The method is demonstrated for three biological models: genetic selection, plant competition and a complex marine system; the first two are coupled map lattices and the last one is a cellular automaton. These cover the three possibilities for asymptotic (long time) dynamics: fixation (the system converges to a fixed point); statistical fixation (the spatial statistics converge to fixed values); and complex statistical structure (the statistics do not converge to fixed values). The technique is shown to have an additional use in the identification of aggregation or dispersal at various scales. The method is rigorously justifiable in the cases when the system under analysis satisfies the FKG (Fortuin-Kasteleyn-Ginibre) property and has a fast decay of correlations. We also discuss the connection between the fluctuation analysis length scale and hydrodynamic limits methods to derive large scale equations for ecological models.
Hypnosis, memory and amnesia
Authors:   The American Association for Research into Nervous and Mental Diseases, Kihlstrom John F.
Published: October 2002

Hypnotized subjects respond to suggestions from the hypnotist for imaginative experiences involving alterations in perception and memory. Individual differences in hypnotizability are only weakly related to other forms of suggestibility. Neuropsychological speculations about hypnosis focus on the right hemisphere and/or the frontal lobes. Posthypnotic amnesia refers to subjects' difiiculty in remembering, after hypnosis, the events and experiences that transpired while they were hypnotized. Posthypnotic amnesia is not an instance of state-dependent memory, but it does seem to involve a disruption of retrieval processes similar to the functional amnesias observed in clinical dissociative disorders. Implicit memory, however, is largely spared, and may underlie subjects' ability to recognize events that they cannot recall. Hypnotic hypermnesia refers to improved memory for past events. However, such improvements are illusory: hypermnesia suggestions increase false recollection, as well as subjects' confidence in both true and false memories. Hypnotic age regression can be subjectively compelling, but does not involve the ablation of adult memory, or the reinstatement of childlike modes of mental functioning, or the revivification of memory. The clinical and forensic use of hypermnesia and age regression to enhance memory in patients, victims and witnesses (e.g. recovered memory therapy for child sexual abuse) should be discouraged.
The remarkable improvements in survival at older ages
Authors: Vaupel James W.
Published: October 2002

The belief that old–age mortality is intractable remains deeply held by many people. Remarkable progress, however, has been made since 1950, and especially since 1970, in substantially improving survival at older ages, even the most advanced ages. The pace of mortality improvement at older ages continues to be particularly rapid in Japan, even though mortality levels in Japan are lower than elsewhere. The progress in improving survival has accelerated the growth of the population of older people and has advanced the frontier of human survival substantially beyond the extremes of longevity attained in pre–industrial times. Little, however, is known about why mortality among the oldest–old has been so plastic since 1950. The little that is known has largely been learned within the past few years. New findings, especially concerning genetic factors that influence longevity, are emerging at accelerating rate.
Interpreting the demographic changes
Authors: Laslett Peter
Published: October 2002

The paper sets out the novel shape of current Western populations as to age composition, and demonstrates that their drastic ageing has been virtually instantaneous. European populations are described as uniquely old, with no precedent whatever in human history. Moreover, all the world's populations are undergoing the same process, including those of the developing societies, at an even faster pace. The general failure of people at large to recognize the process, and their persistent, entirely anachronistic attitudes to the older members of their societies, is described as cultural lag. The development now beginning of the so–called bean–pole family, vertical kin links between contemporary relatives stretching over four generations or more, with progressively fewer lateral linkages, is sketched out. The necessity of all persons having to live in the presence of their future selves is insisted on, with its corollary about having to pay personally in lowered subsistence levels for the doubled life span. The emergence of what is termed a third age is run over, and it is suggested that its presence might create a new civilization, one of the features of which might be the absence of enforced idleness due to unemployment.
Epidemiological aspects of ageing
Authors: Khaw Kay-Tee
Published: October 2002

A major societal challenge is to improve quality of life and prevent or reduce disability and dependency in an ageing population. Increasing age is associated with increasing risk of disability and loss of independence, due to functional impairments such as loss of mobility, hearing and vision; a major issue must be how far disability can be prevented. Ageing is associated with loss of bone tissue, reduction in muscle mass, reduced respiratory function, decline in cognitive function, rise in blood pressure and macular degeneration which predispose to disabling conditions such as osteoporosis, heart disease, dementia and blindness. However, there are considerable variations in different communities in terms of the rate of age–related decline. Large geographic and secular variations in the age–adjusted incidence of major chronic diseases such as stroke, hip fracture, coronary heart disease, cancer, visual loss from cataract, glaucoma and macular degeneration suggest strong environmental determinants in diet, physical activity and smoking habit. The evidence suggests that a substantial proportion of chronic disabling conditions associated with ageing are preventable, or at least postponable and not an inevitable accompaniment of growing old. Postponement or prevention of these conditions may not only increase longevity, but, more importantly, reduce the period of illnesses such that the majority of older persons may live high–quality lives, free of disability, until very shortly before death. We need to understand better the factors influencing the onset of age–related disability in the population, so that we have appropriate strategies to maintain optimal health in an ageing population.
The three pillars of the new family
Authors: Young Michael
Published: October 2002

Children are the chief sufferers from the growing fragility of marriages and partnerships. They may also suffer from their mothers going out to paid work unless satisfactory alternative arrangements are made for their care, for instance, by bringing in grandparents to look after their grandchildren when the mothers are not at home. Grandparents may also have an important role when parents separate. There is a dearth of facts about what actually happens. The part played by grandparents has been touched on, but nothing more, in the course of studies in baby care and baby–sitting and the repercussions of the illness of the mother.

A Grandparent Commission is proposed to set in motion some of the necessary research and to review official policy as it affects grandparents. If grandparents already do a lot for children, and could do more, a measure of optimism about the future of the family could succeed the prevailing pessimism.
Measuring the quality of later life
Authors: O'boyle Ciaran A.
Published: October 2002

This paper examines quality of life as a scientific construct with a wide range of applications. The assessment of patients' quality of life is assuming increasing importance in medicine and health care. Illnesses, diseases and their treatments can have significant impacts on such areas of functioning as mobility, mood, life satisfaction, sexuality, cognition and ability to fulfill occupational, social and family roles. The emerging quality of life construct may be viewed as a paradigm shift in outcome measurement since it shifts the focus of attention from symptoms to functioning. This holistic approach more clearly establishes the patient as the centre of attention and subsumes many of the traditional measures of outcome. Quality of life assessment is particularly relevant to ageing populations both for healthy elderly and for those who develop chronic diseases where maintenance of quality of life rather than cure may be the primary goal of treatment. This paper introduces the concept of quality of life and describes the significant difficulties in definition, measurement and interpretation that must be addressed before such measures can be used as reliable and valid indicators of disease impact and treatment outcomes. It is argued that approaches to quality of life assessment in the elderly should incorporate advances in knowledge about the psychological adaptation to ageing. Consequently, the unique perspective of the individual on his or her own quality of life must be incorporated into outcome assessments aimed at improving the quality of health care. Incorporating measures of subjective outcome such as quality of life into policy decisions on resource allocation in health care will prove one of the major challenges for health services over the next decade.
Implications for health services
Authors: Evans John Grimley
Published: October 2002

Health services for older people in the NHS have developed pragmatically, and reflect the nature of disease in later life and the need to agree objectives of care with patients. Although services are likely to be able to cope with the immediate future, the growth of the elderly population anticipated from 2030 calls for long–term planning and research. The issue of funding requires immediate political thought and action. Scientifically the focus needs to be on maximizing the efficiency of services by health services research and reducing the incidence of disability in later life through research on its biological and social determinants. Senescence is a progressive loss of adaptability due to an interaction between intrinsic (genetic) processes with extrinsic factors in environment and lifestyle. There are grounds for postulating that a policy of postponement of the onset of disability, by modifications of lifestyle and environment, could reduce the average duration of disability before death. The new political structures of Europe offer underexploited–unexploited opportunities for the necessary research.
Aggregation and collapse of fungal wall vesicles in hyphal tips: a model for the origin of the Spitzenkörper
Authors: Regalado Carlos M. , Sleeman Brian D. , Ritz Karl
Published: October 2002

The intracellular origins of polarity and branch initiation in fungi centre upon a localization in the supply of fungal wall constituents to specific regions on the hyphal wall. Polarity is achieved and maintained by accumulating secretory vesicles, prior to incorporation into the wall, in the form of an apical body or Spitzenkörper. However, neither the mechanisms leading to this accumulation nor the initiation of branching, are as yet understood. We propose a mechanism, based on experimental evidence, which considers the mechanical properties of the cytoskeleton in order to explain these phenomena. Cytoskeletal viscoelastic forces are hypothesized to be responsible for biasing vesicles in their motion, and a mathematical model is derived to take these considerations into account. We find that, as a natural consequence of the assumed interactions between vesicles and cytoskeleton, wall vesicles aggregate in a localized region close to the tip apex. These results are used to interpret the origin of the Spitzenkörper. The model also shows that an aggregation peak can collapse and give rise to two new centres of aggregation coexisting near the tip. We interpret this as a mechanism for apical branching, in agreement with published observations. We also investigate the consequences and presumptive role of vesicle—cytoskeleton interactions in the migration of satellite Spitzenkörper. The results of this work strongly suggest that the formation of the Spitzenkörper and the series of dynamical events leading to hyphal branching arise as a consequence of the bias in vesicle motion resulting from interactions with the cytoskeleton.
YaeL (EcfE) activates the ςE pathway of stress response through a site-2 cleavage of anti-ςE, RseA
Authors: Kanehara Kazue , Ito Koreaki , Akiyama Yoshinori
Published: October 2002

Escherichia coli YaeL (EcfE) is a homolog of human site-2 protease (S2P), a membrane-bound zinc metalloprotease involved in regulated intramembrane proteolysis. We have shown previously that YaeL, having essential metalloprotease active site motifs in the cytoplasmic domain, is indispensable for viability. Here, we obtainedrpoE, encoding an extracytoplasmic stress response ς factor (ςE), as a multicopy suppressor against the yaeLdisruption. Whereas ςE is thought to be activated by regulated cleavage of RseA on the periplasmic side by the DegS protease, we found that a degradation intermediate of RseA consisting of the transmembrane and the cytoplasmic domains accumulated in the YaeL-depleted cells. This intermediate was degraded on expression of YaeL but not of its metalloprotease motif mutants. Cells depleted of YaeL were incapable of activating a ςE-dependent promoter in response to an envelope stress. It is suggested that ςEactivation involves two successive proteolytic cleavages: first, at a periplasmic site by DegS; second, at a cytoplasmic or intramembrane site by YaeL. Thus, YaeL is positively required for the ςEextracytoplasmic stress response.
Phytochrome mediates the external light signal to repress FT orthologs in photoperiodic flowering of rice
Authors: Izawa Takeshi , Oikawa Tetsuo , Sugiyama Nobuko , Tanisaka Takatoshi , Yano Masahiro , Shimamoto Ko
Published: October 2002

Phytochromes confer the photoperiodic control of flowering in rice (Oryza sativa), a short-day plant. To better understand the molecular mechanisms of day-length recognition, we examined the interaction between phytochrome signals and circadian clocks in photoperiodic-flowering mutants of rice. Monitoring behaviors of circadian clocks revealed that phase setting of circadian clocks is not affected either under short-day (SD) or under long-day (LD) conditions in a phytochrome-deficient mutant that shows an early-flowering phenotype with no photoperiodic response. Non-24-hr-light/dark-cycle experiments revealed that a rice counterpart gene of Arabidopsis CONSTANS (CO), named PHOTOPERIOD SENSITIVITY 1(Heading date 1) [SE1 (Hd1)], functions as an output of circadian clocks. In addition, the phytochrome deficiency does not affect the diurnal mRNA expression of SE1 upon floral transition. Downstream floral switch genes were further identified with rice orthologs of Arabidopsis FLOWERING LOCUS T (FT). Our RT-PCR data indicate that phytochrome signals repress mRNA expression of FT orthologs, whereas SE1 can function to promote and suppress mRNA expression of the FT orthologs under SD and LD, respectively. This SE1 transcriptional activity may be posttranscriptionally regulated and may depend on the coincidence with Pfr phytochromes. We propose a model to explain how a short-day plant recognizes the day length in photoperiodic flowering.
Functional Cloning, Sorting, and Expression Profiling of Nucleic Acid-Binding Proteins
Authors: Ramanathan Y. , Zhang Haibo , Aris Virginie , Soteropoulos Patricia , Aaronson Stuart A. , Tolias Peter P.
Published: October 2002

A major challenge in the post-sequencing era is to elucidate the activity and biological function of genes that reside in the human genome. An important subset includes genes that encode proteins that regulate gene expression or maintain the structural integrity of the genome. Using a novel oligonucleotide-binding substrate as bait, we show the feasibility of a modified functional expression-cloning strategy to identify human cDNAs that encode a spectrum of nucleic acid-binding proteins (NBPs). Approximately 170 cDNAs were identified from screening phage libraries derived from a human colorectal adenocarcinoma cell line and from noncancerous fetal lung tissue. Sequence analysis confirmed that virtually every clone contained a known DNA- or RNA-binding motif. We also report on a complementary sorting strategy that, in the absence of subcloning and protein purification, can distinguish different classes of NBPs according to their particular binding properties. To extend our functional annotation of NBPs, we have used GeneChip expression profiling of 14 different breast-derived cell lines to examine the relative transcriptional activity of genes identified in our screen and cluster analysis to discover other genes that have similar expression patterns. Finally, we present strategies to analyze the upstream regulatory region of each gene within a cluster group and select unique combinations of transcription factor binding sites that may be responsible for dictating the observed synexpression.

[The following individual kindly provided reagents, samples, or unpublished information as indicated in the paper: M. Stempher.]
Parallel Identification of New Genes in Saccharomyces cerevisiae
Authors: Oshiro Guy , Wodicka Lisa M. , Washburn Michael P. , Yates John R. , Lockhart David J. , Winzeler Elizabeth A.
Published: October 2002

Short open reading frames (ORFs) occur frequently in primary genome sequence. Distinguishing bona fide small genes from the tens of thousands of short ORFs is one of the most challenging aspects of genome annotation. Direct experimental evidence is often required. Here we use a combination of expression profiling and mass spectrometry to verify the independent transcription of 138 and the translation of 50 previously nonannotated genes in the Saccharomyces cerevisiae genome. Through combined evidence, we propose the addition of 62 new genes to the genome and provide experimental support for the inclusion of 10 previously identified genes.

[The following individuals kindly provided reagents, samples, or unpublished information as indicated in the paper: V. Velculescu. Supplementary material is available online at http://www.genome.org.]
The Drosophila Gene Collection: Identification of Putative Full-Length cDNAs for 70% of D. melanogaster Genes
Authors: Stapleton Mark , Liao Guochun , Brokstein Peter , Hong Ling , Carninci Piero , Shiraki Toshiyuki , Hayashizaki Yoshihide , Champe Mark , Pacleb Joanne , Wan Ken , Yu Charles , Carlson Joe , George Reed , Celniker Susan , Rubin Gerald M.
Published: October 2002

Collections of full-length nonredundant cDNA clones are critical reagents for functional genomics. The first step toward these resources is the generation and single-pass sequencing of cDNA libraries that contain a high proportion of full-length clones. The first release of the Drosophila Gene Collection Release 1 (DGCr1) was produced from six libraries representing various tissues, developmental stages, and the cultured S2 cell line. Nearly 80,000 random 5′ expressed sequence tags (5′ expressed sequence tags [ESTs]from these libraries were collapsed into a nonredundant set of 5849 cDNAs, corresponding to ∼40% of the 13,474 predicted genes in Drosophila. To obtain cDNA clones representing the remaining genes, we have generated an additional 157,835 5′ ESTs from two previously existing and three new libraries. One new library is derived from adult testis, a tissue we previously did not exploit for gene discovery; two new cap-trapped normalized libraries are derived from 0–22-h embryos and adult heads. Taking advantage of the annotated D. melanogaster genome sequence, we clustered the ESTs by aligning them to the genome. Clusters that overlap genes not already represented by cDNA clones in the DGCr1 were analyzed further, and putative full-length clones were selected for inclusion in the new DGC. This second release of the DGC (DGCr2) contains 5061 additional clones, extending the collection to 10,910 cDNAs representing >70% of the predicted genes inDrosophila.

[The sequence data described in this paper have been submitted to the GenBank data library under accession nos. BF485518-BF503517, BF503521-BF506780, BG631888-BG631996,BG633696-BG637540, BG640063-BG641469, BI141709-BI142246,BI161485-BI173971, BI212109-BI216987, BI227448-BI233322,BI234009-BI243989, BI351612-BI354228, BI354231-BI355901,BI355935-BI358751, BI361285-BI376197, BI481532-BI487261,BI563331-BI593695, BI604243-BI620155, BI620158-BI635012,BI635064-BI638027, and BI638030-BI642053. The following individuals kindly provided reagents, samples, or unpublished information as indicated in the paper: J. Pringle and M. Fuller.]
“Silent” Metaplasticity of the Late Phase of Long-Term Potentiation Requires Protein Phosphatases
Authors: Woo Newton H. , Nguyen Peter V.
Published: October 2002

The late phase of long-term potentiation (L-LTP) is correlated with some types of long-term memory, but the mechanisms by which L-LTP is modulated by prior synaptic activity are undefined. Activation of protein phosphatases by low-frequency stimulation (LFS) given before induction of L-LTP may significantly modify L-LTP. Using cellular electrophysiological recording methods in mouse hippocampal slices, we show that LFS given before induction of L-LTP inhibited L-LTP in an activity-dependent manner without affecting either basal synaptic strength or the early phase of LTP (E-LTP). This anterograde inhibitory effect of LFS was persistent, required N-methyl-D-aspartate (NMDA) receptor activation, and was blocked by inhibitors of protein phosphatase 1 (PP1) and protein phosphatase 2A (PP2A). These data indicate that certain patterns of LFS can activate PP1 and/or PP2A, and that long-lasting activation of these phosphatases by prior LFS can suppress the subsequent expression of L-LTP without affecting E-LTP. Because this inhibition of L-LTP is caused by prior synaptic activity that, alone, produced no net effect on synaptic efficacy, we suggest that this is a “silent” form of metaplasticity that may influence long-term information storage by modulating the capacity of synapses to express L-LTP after repeated bouts of activity.
Intrahippocampal Wortmannin Infusion Enhances Long-Term Spatial and Contextual Memories
Authors: Dash Pramod K. , Mach Sara A. , Blum Sonja , Moore Anthony N.
Published: October 2002

The transition from short- to long-term memory involves several biochemical cascades, some of which act in an antagonistic manner. Post-training intrahippocampal administration of wortmannin, a pharmacological inhibitor of phosphatidylinositol 3-kinase, had no effect on memory tested 3 h later, but improved long-term memory tested 48 h following the completion of training. This effect was seen in two hippocampus-dependent tasks: the Morris water maze, using both massed and distributed training paradigms, and contextual fear conditioning. The improvement of long-term memory appears to be the result of enhanced consolidation, as wortmannin had no effect on memory recall. These results are consistent with the hypothesis that memory consolidation involves competing processes, and that blockade of an inhibitory constraint facilitates the consolidation process.
Deficits in Trace Cued Fear Conditioning in Galanin-Treated Rats and Galanin-Overexpressing Transgenic Mice
Authors: Kinney Jefferson W. , Starosta Grzegorz , Holmes Andrew , Wrenn Craige C. , Yang Rebecca J. , Harris Ashley P. , Long Katharine C. , Crawley Jacqueline N.
Published: October 2002

Galanin inhibits the release of several neurotransmitters and produces performance deficits in a variety of spatial and aversive learning and memory tasks. The experiments in this study investigated the role galanin has in emotional learning and memory using a standard delay cued and contextual fear conditioning task. Rats were administered galanin into the lateral ventricles before training, and scored for freezing behavior in the same context and in a novel context with and without an auditory cue (CS) that had been paired previously with an aversive stimulus (US). Galanin-overexpressing transgenic mice were tested in an identical behavioral protocol. The galanin-administered rats and the transgenic mice were not significantly different from their respective controls on this task. A more challenging trace cued and contextual fear conditioning procedure was administered to separate groups of galanin-treated rats and galanin-overexpressing transgenic mice. Subjects were trained with the same CS and US, however, a 2.5-sec delay was inserted between CS offset and US onset. Following the trace conditioning, rats administered galanin and mice overexpressing galanin both exhibited significantly less freezing to the CS in the novel context as compared with their control groups. These results indicate that the observed disruption of cued fear conditioning was specific to the more difficult trace conditioning task. These findings are the first demonstration that galanin impairs performance on an emotional memory task and support the hypothesis that galanin-induced deficits are specific to more difficult cognitive tasks.
In Vivo Interactions between Photosynthesis, Mitorespiration, and Chlororespiration in Chlamydomonas reinhardtii
Authors: Cournac Laurent , Latouche Gwendal , Cerovic Zoran , Redding Kevin , Ravenel Jacques , Peltier Gilles
Published: October 2002

Interactions between photosynthesis, mitochondrial respiration (mitorespiration), and chlororespiration have been investigated in the green alga Chlamydomonas reinhardtiiusing flash illumination and a bare platinum electrode. Depending on the physiological status of algae, flash illumination was found to induce either a fast (t1/2 ≈ 300 ms) or slow (t1/2 ≈ 3 s) transient inhibition of oxygen uptake. Based on the effects of the mitorespiratory inhibitors myxothiazol and salicyl hydroxamic acid (SHAM), and of propyl gallate, an inhibitor of the chlororespiratory oxidase, we conclude that the fast transient is due to the flash-induced inhibition of chlororespiration and that the slow transient is due to the flash-induced inhibition of mitorespiration. By measuring blue-green fluorescence changes, related to the redox status of the pyridine nucleotide pool, and chlorophyll fluorescence, related to the redox status of plastoquinones (PQs) in C.  reinhardtii wild type and in a photosystem I-deficient mutant, we show that interactions between photosynthesis and chlororespiration are favored when PQ and pyridine nucleotide pools are reduced, whereas interactions between photosynthesis and mitorespiration are favored at more oxidized states. We conclude that the plastid oxidase, similar to the mitochondrial alternative oxidase, becomes significantly engaged when the PQ pool becomes highly reduced, and thereby prevents its over-reduction.
High-Stearic and High-Oleic Cottonseed Oils Produced by Hairpin RNA-Mediated Post-Transcriptional Gene Silencing
Authors: Liu Qing , Singh Surinder P. , Green Allan G.
Published: October 2002

We have genetically modified the fatty acid composition of cottonseed oil using the recently developed technique of hairpin RNA-mediated gene silencing to down-regulate the seed expression of two key fatty acid desaturase genes, ghSAD-1-encoding stearoyl-acyl-carrier protein Δ9-desaturase andghFAD2-1-encoding oleoyl-phosphatidylcholine ω6-desaturase. Hairpin RNA-encoding gene constructs (HP) targeted against either ghSAD-1 or ghFAD2-1 were transformed into cotton (Gossypium hirsutum cv Coker 315). The resulting down-regulation of the ghSAD-1 gene substantially increased stearic acid from the normal levels of 2% to 3% up to as high as 40%, and silencing of the ghFAD2-1gene resulted in greatly elevated oleic acid content, up to 77% compared with about 15% in seeds of untransformed plants. In addition, palmitic acid was significantly lowered in both high-stearic and high-oleic lines. Similar fatty acid composition phenotypes were also achieved by transformation with conventional antisense constructs targeted against the same genes, but at much lower frequencies than were achieved with the HP constructs. By intercrossing the high-stearic and high-oleic genotypes, it was possible to simultaneously down-regulate both ghSAD-1 and ghFAD2-1to the same degree as observed in the individually silenced parental lines, demonstrating for the first time, to our knowledge, that duplex RNA-induced posttranslational gene silencing in independent genes can be stacked without any diminution in the degree of silencing. The silencing of ghSAD-1 and/or ghFAD2-1 to various degrees enables the development of cottonseed oils having novel combinations of palmitic, stearic, oleic, and linoleic contents that can be used in margarines and deep frying without hydrogenation and also potentially in high-value confectionery applications.
Inhibition of Phospholipase Dα byN-Acylethanolamines
Authors: Austin-Brown Shea L. , Chapman Kent D.
Published: October 2002

N-Acylethanolamines (NAEs) are endogenous lipids in plants produced from the phospholipid precursor,N-acylphosphatidylethanolamine, by phospholipase D (PLD). Here, we show that seven types of plant NAEs differing in acyl chain length and degree of unsaturation were potent inhibitors of the well-characterized, plant-specific isoform of PLD—PLDα. It is notable that PLDα, unlike other PLD isoforms, has been shown not to catalyze the formation of NAEs fromN-acylphosphatidylethanolamine. In general, inhibition of PLDα activity by NAEs increased with decreasing acyl chain length and decreasing degree of unsaturation, such thatN-lauroylethanolamine andN-myristoylethanolamine were most potent with IC50s at submicromolar concentrations for the recombinant castor bean (Ricinus communis) PLDα expressed inEscherichia coli and for partially purified cabbage (Brassica oleracea) PLDα. NAEs did not inhibit PLD from Streptomyces chromofuscus, and exhibited only moderate, mixed effects for two other recombinant plant PLD isoforms. Consistent with the inhibitory biochemical effects on PLDα in vitro,N-lauroylethanolamine, but not lauric acid, selectively inhibited abscisic acid-induced closure of stomata in epidermal peels of tobacco (Nicotiana tabacum cv Xanthi) andCommelina communis at low micromolar concentrations. Together, these results provide a new class of biochemical inhibitors to assist in the evaluation of PLDα physiological function(s), and they suggest a novel, lipid mediator role for endogenously produced NAEs in plant cells.