bluuebunny/crossref_metadata_2025 huggingface dataset:
Experimental eye enlargement in mature animals changes the
retinal pigment epithelium
Authors: HARMAN ALISON M. , HOSKINS ROBERT , BEAZLEY LYN D.
Published: July 2002

Form deprivation has been shown to result in myopia
in a number of species such that the eye enlarges if one
eye is permanently closed at the time of eye opening. In
the quokka wallaby, the eye grows slowly throughout life.
After form deprivation, the eye enlarges by 1–1.5
years of age to the size of that in a 4–6-year-old
animal and the number of multinucleated retinal pigment
epithelial (RPE) cells in the enlarged retina remains much
lower than would be expected in eyes of comparable size.
Here we have repeated the experiment but examined animals
at 4 years of age. The sutured eye grew significantly larger
than did its partner. Numbers of RPE cells were comparable
between sutured and partner eyes but were lower than in
normal animals of similar age. Reductions in RPE cell density
were greater in nasal than in dorsal or ventral retina
and were not seen in temporal retina. The distribution
of multinucleated cells was quite different in the sutured
and open eyes. As in normal eyes, partner eyes had most
multinucleated cells in ventral retina, while in the sutured
eyes such cells were located mainly in the far periphery.
In conclusion, the RPE is significantly changed by the
eye enlargement process. However, it is not known whether
this change results from an active part played by the RPE
in the retinal expansion process or whether the changes
are simply a result of a passive increase in area of the
RPE.
Visual cortical simple cells: Who inhibits whom
Authors: SAUL ALAN B.
Published: July 2002

Simple cells display a specific adaptation aftereffect
when tested with drifting gratings. The onset of the response
to each cycle of the grating is delayed after adapting,
but the offset is unaffected. Testing with stationary bars
whose luminance was modulated in time revealed that aftereffects
occur only at certain points in both space and time. The
aftereffects seen with moving stimuli were predicted from
those seen with stationary stimuli. These adaptation experiments
suggest a model that consists of mutually inhibitory simple
cells that are in spatiotemporal quadrature. The inhibition
is appropriately localized in space and time to create
the observed aftereffects. In this model, inhibition onto
direction-selective simple cells arises from simple cells
with the same preferred direction.
The contributions of voltage- and time-dependent potassium
conductances to the electroretinogram in rabbits
Authors: LEI B. , PERLMAN I.
Published: July 2002

The electroretinogram (ERG) is generated by light-induced
electrical activity in retinal cells. Since potassium ions
and potassium conductances play a major role in determining
the membrane potential of cells, changes in these are expected
to affect the amplitude and pattern of the ERG. We recorded
the ERG responses and the isolated P-III waves of rabbits
after intraocular injections of specific blockers for potassium
channels. 4-aminopyridine (4-AP) did not cause any noticeable
changes in the ERG while tetraethylammonium chloride (TEA)
induced time-dependent effects. Short-term (1–2 h)
effects were expressed as significant augmentation of the
b-wave with little change in the a-wave.
At longer periods of follow-up, the a-wave increased
in amplitude while the b-wave decreased. TEA augmented
the amplitude of the isolated P-III wave. These effects
of TEA can be explained by TEA-induced depolarization of
the photoreceptors. Cesium ions and barium ions induced
substantial augmentation of the b-wave. Barium
but not cesium ions reduced the isolated P-III component
of the ERG probably by blocking the potassium channels
in the Müller cells. The augmentation of the b-wave
by both barium or cesium ions is inconsistent with the
Müller cells hypothesis for the ERG b-wave.
Electroretinogram of the parietal eye of lizards: Photoreceptor,
glial, and lens cell contributions
Authors: SOLESSIO EDUARDO , ENGBRETSON GUSTAV A.
Published: July 2002

Local electroretinograms (ERGs) were recorded in
the parietal eye of Xantusia vigilis. The responses
to monochromatic light under dark- and light-adapted conditions
were studied. We found that two antagonistic chromatic
mechanisms dominate the overall response. With the electrode
tip in the lumen of the eye, light stimulation under dark-adapted
conditions evoked responses of negative polarity with maximum
sensitivity to green light. Intense green background illumination
saturated the green-sensitive mechanism, and superposition
of a blue stimulus then elicited responses of opposite
polarity, driving the potentials back toward the dark resting
level. The spectral sensitivities of the two chromatic
mechanisms were determined using chromatic adaptation.
The lower threshold, green-sensitive mechanism has a maximum
sensitivity at 495 nm while the antagonistic mechanism,
with its maximal spectral sensitivity at 430 nm, is at
least 2 log units less sensitive. The polarity of the ERG
recording inverts as the electrode traverses the photoreceptor
layer, suggesting that the photoreceptors are the major
source of the ERG. This result was confirmed with intracellular
recordings from photoreceptors, glial, and lens cells.
The glial and lens cells of the parietal eye respond to
local changes in [K+]o.
Intracellular recordings of the responses of these cells
to light stimuli follow time courses similar to changes
in extracellular potassium concentrations measured with
K+-specific electrodes. These results suggest
that the glial and lens cell membranes are highly permeable
to potassium and, therefore, the electrical responses of
these cells are evoked by changes in [K+]o
elicited by light stimulation of the photoreceptors. Nevertheless,
the major component of the parietal eye ERG is the photoreceptor
signal. A circuit model of the ERG sources is presented.
GABAA receptor immunoreactivity is transiently
expressed in the developing outer retina
Authors: MITCHELL CHERYL K. , HUANG BO , REDBURN-JOHNSON DIANNA A.
Published: July 2002

Extensive evidence has suggested a trophic role
of γ-aminobutyric acid (GABA) on developing cone photoreceptors
in postnatal retina. In a previous study, we showed that
GABA raises intracellular calcium levels in the developing
cones via activation of GABAA receptors.
Using confocal microscopy in conjunction with immunocytochemistry,
we have now demonstrated that (1) GABAA receptor
subunits are localized on cone cell bodies as well as on
cone pedicles, indicating that GABA has a direct, rather
than indirect, effect on cones and (2) the temporal expression
of GABAA receptor subunits coincides with the
developmental effects of GABA on cone synaptogenesis. An
antibody against the β 2/3 subunits of the GABAA
receptor and a specific cone marker peanut-agglutinin lectin
(PNA) were used to double-label wholemount neonatal retinal
preparations. Results show that GABAA receptors
are transiently expressed on cone photoreceptors in the
early stages of postnatal retinal development. GABAA
receptor immunoreactivity is clearly present on cone cell
bodies and their processes and on other—as yet
unidentified—elements (horizontal cells?) in the outer
plexiform layer. Immunoreactivity decreases within cone
photoreceptor somata after postnatal day 5, but persists
in the processes of the outer plexiform layer until day
7. Our results provide support for the hypothesis that
GABA acts as an important developmental regulator of cone
photoreceptor maturation.
Neurochemical changes following postmortem ischemia in the
rat retina
Authors: NAPPER GENEVIEVE A. , KALLONIATIS MICHAEL
Published: July 2002

Glutamate and γ-aminobutyric acid (GABA) are the
dominant amino acids in the retina and brain. The manufacturing
and degradation pathways of both of these amino acids are
intricately linked with the tricarboxylic acid cycle leading
to rapid redistribution of these amino acids after metabolic
insult. Postmortem ischemia in mammalian retina predominantly
results in a loss of glutamate and GABA from neurons and
accumulation of these amino acids within Müller cells.
This accumulation of glutamate and GABA in Müller
cells may occur as a result of increased release of these
neurotransmitters from neurons, and decreased degradation.
Quantification of the semisaturation value (half-maximal
response) for glutamate and GABA Müller cell loading
during postmortem ischemia indicated a shorter semisaturation
value for GABA than glutamate. Such changes are consistent
with a single aerobically dependent GABA-degradation pathway,
and the existence of multiple glutamate-degradation pathways.
Comparison with the in vitro ischemic model showed
similar qualitative characteristics, but a markedly increased
semisaturation time for glutamate and GABA Müller
cell loading (a factor of 5–10) in the postmortem
ischemia model. We interpret these differences to indicate
that the in vitro condition provides a more immediate
and/or severe ischemic insult. In the postmortem ischemia
model, the delayed glial cell loading implies the availability
of internal stores of both glucose and/or oxygen. Increased
glial and neuronal immunoreactivity for the amino acids
involved in transamination reactions, aspartate, alanine,
leucine, and ornithine was observed, indicating a potential
shift in the equilibrium of transamination reactions associated
with glutamate production. These findings provide evidence
that, in the rat retina, there are multiple pathways subserving
glutamate production/degradation that include a multitude
of transamination reactions. Further evidence is therefore
provided to support a role for all four amino acids in
glutamate metabolism within a variety of retinal neurons
and glia.
Gap junctions between AII amacrine cells and calbindin-positive
bipolar cells in the rabbit retina
Authors: MASSEY STEPHEN C. , MILLS STEPHEN L.
Published: July 2002

Electrical synapses or gap junctions occur between
many retinal neurons. However, in most cases, the gap junctions
have not been visualized directly. Instead, their presence
has been inferred from tracer spread throughout the network
of cells. Thus, tracer coupling is taken as a marker for
the presence of gap junctions between coupled cells. AII
amacrine cells are critical interneurons in the rod pathway
of the mammalian retina. Rod bipolar cell output passes
to AII amacrine cells, which in turn make conventional
synapses with OFF cone bipolar cells and gap junctions
with ON cone bipolar cells. Injections of biotinylated
tracers into AII amacrine cells reveals coupling between
the AII amacrine cell network and heterologous coupling
with a variety of ON cone bipolar cells, including the
calbindin-positive cone bipolar cell. To directly visualize
gap junctions in this network, we prepared material for
electron microscopy that was double labeled with antibodies
to calretinin and calbindin to label AII amacrine cells
and calbindin-positive cone bipolar cells, respectively.
AII amacrine cells were postsynaptic to large vesicle-laden
rod bipolar terminals, as previously reported. Gap junctions
were identified between AII amacrine cells and calbindin-positive
cone bipolar cell terminals identified by the presence
of immunostaining and ribbon synapses. This represents
direct confirmation of gap junctions between two different
yet positively identified cells, which are tracer coupled,
and provides additional evidence that tracer coupling with
Neurobiotin indicates the presence of gap junctions. These
results also definitively establish the presence of gap
junctions between AII amacrine cells and calbindin bipolar
cells which can therefore carry rod signals to the ON alpha
ganglion cell.
The grasping behaviour, locomotion and substrate use of the tree shrews Tupaia minor and T. tana (Mammalia, Scandentia)
Authors: Sargis Eric J.
Published: July 2002

The grasping behaviour, locomotion and substrate use of the tree shrews Tupaia minor and T. tana were investigated in the Department of Zoological Research at the National Zoological Park in Washington, DC. Seven arboreal T. minor and five terrestrial T. tana were observed and videotaped for 10‐min focal animal samples totalling 77 h of observation. Locomotion and substrate use were scored and images of grasping behaviour were captured from videotapes. Tupaia minor individuals were videotaped crossing dowels and the number of dowel crossings that included grasps were scored. In 84% of dowel crossings, T. minor individuals used either their hallux or their pollex to grasp the dowels. Tupaia minor was also more active, moved more quickly, was more arboreal, rooted less, reversed its feet more, flexed its forelimbs more and was more semi‐plantigrade than T. tana. It is proposed that arboreal tupaiids, such as Ptilocercus lowii and T. minor, may represent better models for early primates than didelphid marsupials because they are capable of grasping and are more closely related to primates.
Severe maternal psychopathology and infant–mother attachment
Authors: HIPWELL A. E. , GOOSSENS F. A. , MELHUISH E. C. , KUMAR R.
Published: July 2002

Eighty-two mother–infant dyads, comprising women with psychiatric disorder and
individually matched controls, were followed up over the children's 1st year of life. The
mothers with mental illness consisted of two subgroups: first, 25 severely mentally ill mothers
who had been admitted to a psychiatric unit with their infants; and second, 16 mothers from a
community sample meeting research diagnostic criteria for unipolar, nonpsychotic depression.
With the exception of six dyads in the in-patient group, observations were made of the
mother–infant interaction and the quality of the infant–mother attachment
relationship at 12 months. The nature and course of the mothers' illness was also
documented. Although few residual symptoms of maternal mental illness were detected at 1 year
postpartum, interactional disturbances were evident among the case group dyads. A strong
association was revealed between infant–mother attachment quality and maternal
diagnosis: a manic episode of illness in the postpartum period was related to security in the
attachment relationship, and psychotic or nonpsychotic depression was related to insecurity.
Concurrent patterns of mother–infant interaction provided support for this finding.
Multiple risk factors in the development of externalizing behavior problems: Group and
individual differences
Authors: DEATER–DECKARD KIRBY , DODGE KENNETH A. , BATES JOHN E. , PETTIT GREGORY S.
Published: July 2002

The aim of this study was to test whether individual risk factors as well as the number of risk
factors (cumulative risk) predicted children's externalizing behaviors over middle
childhood. A sample of 466 European American and 100 African American boys and girls from
a broad range of socioeconomic levels was followed from age 5 to 10 years. Twenty risk
variables from four domains (child, sociocultural, parenting, and peer-related) were measured
using in-home interviews at the beginning of the study, and annual assessments of externalizing
behaviors were conducted. Consistent with past research, individual differences in externalizing
behavior problems were stable over time and were related to individual risk factors as well as the
number of risk factors present. Particular risks accounted for 36% to 45% of the variance, and the
number of risks present (cumulative risk status) accounted for 19% to 32% of the variance, in
externalizing outcomes. Cumulative risk was related to subsequent externalizing even after initial
levels of externalizing had been statistically controlled. All four domains of risk variables made
significant unique contributions to this statistical prediction, and there were multiple clusters of
risks that led to similar outcomes. There was also evidence that this prediction was moderated by
ethnic group status, most of the prediction of externalizing being found for European American
children. However, this moderation effect varied depending on the predictor and outcome
variables included in the model.
Properties of steady states for thin film equations
Authors: LAUGESEN R. S. , PUGH M. C.
Published: July 2002

We consider nonnegative steady-state solutions of the evolution equation

formula here

Our class of coefficients f, g allows degeneracies at h = 0,
such as f(0) = 0, as well as divergences like g(0) = ±∞. We first construct steady states and study their regularity. For
f, g > 0 we construct positive periodic steady states, and non-negative steady states with either
zero or nonzero contact angles. For f > 0 and g < 0, we prove there are no non-constant
positive periodic steady states or steady states with zero contact angle, but we do construct
non-negative steady states with nonzero contact angle. In considering the volume, length (or
period) and contact angle of the steady states, we find a rescaling identity that enables us to
answer questions such as whether a steady state is uniquely determined by its volume and
contact angle. Our tools include an improved monotonicity result for the period function of
the nonlinear oscillator. We also relate the steady states and their scaling properties to a
recent blow-up conjecture of Bertozzi and Pugh.
Zygotic and embryonic gene expression in cow: a review of timing and mechanisms of early gene expression as compared with other species
Authors: Memili Erdogan , First Neal L.
Published: July 2002

Early embryonic development is largely dependent on maternal RNAs and proteins synthesised during oogenesis. Zygotic transcription is an essential event that occurs at a species-specific time after fertilisation. In the absence of zygotic transcription the embryo dies since it can no longer support requirements for successful embryo development. Molecular genetics of gene expression during early embryogenesis, especially in the bovine species, remain one of the unsolved questions in modern biology. Earlier studies suggested that embryonic transcription in cattle begins at the late 4-cell or 8-cell stage. However, more recent studies suggest that bovine zygotes and 2-cell embryos are both transcriptionally and translationally active. Moreover, changes in chromatin structure due to acetylation of core histones and DNA replication play important roles in the regulation of zygotic/embryonic gene expression. This review will summarise results of recent studies about the timing and mechanisms of zygotic/embryonic gene expression in cattle. In addition, terminology in the literature regarding gene expression during early embryogenesis will be clarified. These terminologies include: ‘zygotic/embryonic gene expression’, ‘maternal to embryonic transition in control of development (MET)’ and ‘zygotic/embryonic genome activation (ZEGA)’.
Xenopus laevis fertilisation: analysis of sperm motility in egg jelly using video light microscopy
Authors: Reinhart Donnie , Ridgway James , Chandler Douglas E.
Published: July 2002

Xenopus laevis eggs are surrounded by an extracellular matrix consisting of a vitelline envelope, and three jelly layers, J1, J2, and J3 (from egg surface outward). The jelly layers vary in thickness (about 150, 15 and 200 μm for J1, J2 and J3 respectively) but all are translucent allowing observation of sperm penetration. Video microscopy demonstrated that sperm are able to penetrate and traverse J3 at velocities approaching 30 μm/s. Sperm swim through jelly in a corkscrew-like manner with their rotational and forward velocities being tightly coupled at about 30°/μm forward travel. They are propelled by whip-like power strokes involving hairpin bends in the flagellum that are generated every 180° of rotation and which are propagated from base to tip. The overall trajectories of individual sperm are quite variable. Many sperm head directly for J2 but some do not, these swimming circumferentially, or even away from the egg surface. Most sperm (over 97%) that enter the jelly do not get to the egg surface but are stopped at a variety of positions within J3 or at the outer surface of J2. Efficient sperm penetration and passage through the jelly layers requires a low electrolyte concentration in the surrounding medium, and is inhibited by the lectin wheat germ agglutin (WGA) in a dose-dependent manner. WGA does not block sperm penetration of J3 but does block further progression towards the egg surface. This observation suggests that sperm motility within the jelly is dependent on the carbohydrate moieties of the large glycoconjugates present, and that their alteration by WGA binding accounts for the inability of sperm to reach the egg surface and fertilise the egg.
Numerical simulation of monsoon depressions over India with a high‐resolution nested regional model
Authors: Potty K V J , Mohanty U C , Raman S
Published: July 2002

The structure and track of monsoon depressions over India during the summer monsoon have been simulated using a double‐nested limited‐area numerical weather prediction model. Four distinct cases of monsoon depressions that formed over the Bay of Bengal and adjoining areas have been studied. Initial conditions for the simulations are from either the European Centre for Medium Range Weather Forecasts, Reading, UK or the National Centre for Medium Range Weather Forecasting, New Delhi, India. The model is integrated for up to 48 hours for each case and the results are compared with verification fields. Forecasts of mean sea level pressure and low‐level wind indicate that the location of the centres of the depressions and their track could be predicted satisfactorily even though the magnitude of the central pressure is slightly too high. Temperature forecasts show close agreement with the verification analyses and the distribution of precipitation is well simulated. The vertical cross‐sections of temperature and wind forecasts show the correct vertical structure. RMS errors of the mean sea level pressure, wind and temperature indicate that the model could simulate the large‐scale fields reasonably well. RMS errors of the tracks of the depressions confirm the fact that the high‐resolution nested grid model can predict the tracks of the depressions with reasonable accuracy. Copyright © 2000 Royal Meteorological Society
Carbon emissions and economic development: future trajectories based on historical experience
Authors: HEIL MARK T. , SELDEN THOMAS M.
Published: July 2002

This paper estimates the historic relationship between carbon emissions and GDP using data across countries and across time. We combine this relationship with plausible projections for GDP and population growth to construct a model that offers insights into the likely path of global emissions in the next century. In addition, we experiment with a method for incorporating oil prices into the model. Our analysis provides independent confirmation of the business-as-usual forecasts generated by the larger structural models.
Resilience in natural and socioeconomic systems
Authors: LEVIN SIMON A. , BARRETT SCOTT , ANIYAR SARA , BAUMOL WILLIAM , BLISS CHRISTOPHER , BOLIN BERT , DASGUPTA PARTHA , EHRLICH PAUL , FOLKE CARL , GREN ING-MARIE , HOLLING C.S. , JANSSON ANNMARI , JANSSON BENGT-OWE , MÄLER KARL-GÖRAN , MARTIN DAN , PERRINGS CHARLES , SHESHINSKI EYTAN
Published: July 2002

We, as a society, find ourselves confronted with a spectrum of potentially catastrophic and irreversible environmental problems, for which conventional approaches will not suffice in providing solutions. These problems are characterized, above all, by their unpredictability. This means that surprise is to be expected, and that sudden qualitative shifts in dynamics present serious problems for management. In general, it is difficult to detect strong signals of change early enough to motivate effective solutions, or even to develop scientific consensus on a time scale rapid enough to allow effective solution. Furthermore, such signals, even when detected, are likely to be displaced in space or sector from the source, so that the motivation for action is small. Conventional market mechanisms thus will be inadequate to address these challenges.
The Arabidopsis PILZ group genes encode tubulin-folding cofactor orthologs required for cell division but not cell growth
Authors: Steinborn Katharina , Maulbetsch Christoph , Priester Bianca , Trautmann Susanne , Pacher Tobias , Geiges Bernd , Küttner Frank , Lepiniec Loic , Stierhof York-Dieter , Schwarz Heinz , Jürgens Gerd , Mayer Ulrike
Published: July 2002

Plant microtubules are organized into specific cell cycle-dependent arrays that have been implicated in diverse cellular processes, including cell division and organized cell expansion. Mutations in fourArabidopsis genes collectively called the PILZ group result in lethal embryos that consist of one or a few grossly enlarged cells. The mutant embryos lack microtubules but not actin filaments. Whereas the cytokinesis-specific syntaxin KNOLLE is not localized properly, trafficking of the putative auxin efflux carrier PIN1 to the plasma membrane is normal. The four PILZ group genes were isolated by map-based cloning and are shown to encode orthologs of mammalian tubulin-folding cofactors (TFCs) C, D, and E, and associated small G-protein Arl2 that mediate the formation of α/β-tubulin heterodimers in vitro. The TFC C ortholog, PORCINO, was detected in cytosolic protein complexes and did not colocalize with microtubules. Another gene with a related, although weaker, embryo-lethal phenotype,KIESEL, was shown to encode a TFC A ortholog. Our genetic ablation of microtubules shows their requirement in cell division and vesicle trafficking during cytokinesis, whereas cell growth is mediated by microtubule-independent vesicle trafficking to the plasma membrane during interphase.
Requirement for Atr in phosphorylation of Chk1 and cell cycle regulation in response to DNA replication blocks and UV-damaged DNA in Xenopus egg extracts
Authors: Guo Zijian , Kumagai Akiko , Wang Sophie X. , Dunphy William G.
Published: July 2002

The checkpoint kinase Xchk1 becomes phosphorylated inXenopus egg extracts in response to DNA replication blocks or UV-damaged DNA. Xchk1 is also required for the cell cycle delay that is induced by unreplicated or UV-damaged DNA. In this report, we have removed the Xenopus homolog of ATR (Xatr) from egg extracts by immunodepletion. In Xatr-depleted extracts, the checkpoint-associated phosphorylation of Xchk1 is abolished, and the cell cycle delay induced by replication blocks is strongly compromised. Xatr from egg extracts phosphorylated recombinant Xchk1 in vitro, but not a mutant form of Xchk1 (Xchk1-4AQ) containing nonphosphorylatable residues in its four conserved SQ/TQ motifs. Recombinant human ATR, but not a kinase-inactive mutant, phosphorylated the same sites in Xchk1. Furthermore, the Xchk1-4AQ mutant was found to be defective in mediating a checkpoint response in egg extracts. These findings suggest that Xchk1 is a functionally important target of Xatr during a checkpoint response to unreplicated or UV-damaged DNA.
The NPK1 mitogen-activated protein kinase kinase kinase is a regulator of cell-plate formation in plant cytokinesis
Authors: Nishihama Ryuichi , Ishikawa Masaki , Araki Satoshi , Soyano Takashi , Asada Tetsuhiro , Machida Yasunori
Published: July 2002

Mitogen-activated protein kinase (MAPK) cascades play important roles not only in the transduction of extracellular signals but in the progression of the cell cycle. However, evidence for their role in cytokinesis is limited. Here, we show that a tobacco MAPK kinase kinase (MAPKKK), designated NPK1, is required for cytokinesis. The activity of NPK1 increases in the late M phase of the tobacco cell cycle. During expansion of a new cross-wall (cell plate) toward the cell cortex, NPK1 is consistently localized to the equatorial zone of the phragmoplast, the cytokinetic apparatus where the cell plate is formed. Expression of a kinase-negative mutant of NPK1 results in the generation of multinucleate cells with incomplete cell plates. Phragmoplasts can be formed, but its expansion toward the cell cortex is also blocked. Thus, our results indicate that the NPK1 MAPKKK is essential for the formation of the cell plate, especially for its lateral growth.
Control of axillary bud initiation and shoot architecture in Arabidopsis through the SUPERSHOOT gene
Authors: Tantikanjana Titima , Yong Jean W.H. , Letham D. Stuart , Griffith Megan , Hussain Mumtaz , Ljung Karin , Sandberg Göran , Sundaresan Venkatesan
Published: July 2002

The aerial architecture of flowering plants is determined to a large extent by shoot growth and shoot branching arising from the initiation and growth of axillary meristems. We have identified anArabidopsis mutant, supershoot (sps), which is characterized by a massive overproliferation of shoots, such that a single plant can generate 500 or more inflorescences. Analysis of the mutant plants shows that the primary defect is because of an increase in the number of meristems formed in leaf axils, together with release of bud arrest, resulting in reiterative branch formation from rosette and cauline leaves. The SPS gene is shown here to encode a cytochrome P450, and together with a 3- to 9-fold increase in levels of Z-type cytokinins in sps mutant plants, indicate a role forSPS in modulating hormone levels. The expression pattern ofSPS, with strong expression at the leaf axils, correlates well with the phenotypic defects. Our results indicate that control of shoot branching in Arabidopsis may be accomplished in part by suppression of axillary meristem initiation and growth through the localized attenuation of cytokinin levels at sites of bud initiation.
Computational Inference of Homologous Gene Structures in the Human Genome
Authors: Yeh Ru-Fang , Lim Lee P. , Burge Christopher B.
Published: July 2002

With the human genome sequence approaching completion, a major challenge is to identify the locations and encoded protein sequences of all human genes. To address this problem we have developed a new gene identification algorithm, GenomeScan, which combines exon–intron and splice signal models with similarity to known protein sequences in an integrated model. Extensive testing shows thatGenomeScan can accurately identify the exon–intron structures of genes in finished or draft human genome sequence with a low rate of false-positives. Application of GenomeScan to 2.7 billion bases of human genomic DNA identified at least 20,000–25,000 human genes out of an estimated 30,000–40,000 present in the genome. The results show an accurate and efficient automated approach for identifying genes in higher eukaryotic genomes and provide a first-level annotation of the draft human genome.
Exploring Expression Data: Identification and Analysis of Coexpressed Genes
Authors: Heyer Laurie J. , Kruglyak Semyon , Yooseph Shibu
Published: July 2002

Analysis procedures are needed to extract useful information from the large amount of gene expression data that is becoming available. This work describes a set of analytical tools and their application to yeast cell cycle data. The components of our approach are (1) a similarity measure that reduces the number of false positives, (2) a new clustering algorithm designed specifically for grouping gene expression patterns, and (3) an interactive graphical cluster analysis tool that allows user feedback and validation. We use the clusters generated by our algorithm to summarize genome-wide expression and to initiate supervised clustering of genes into biologically meaningful groups.
Localization of mariner DNA Transposons in the Human Genome by PRINS
Authors: Reiter Lawrence T. , Liehr Thomas , Rautenstrauss Bernd , Robertson Hugh M. , Lupski James R.
Published: July 2002

Homologous recombination occurring among misaligned repeated sequences is a significant source of the molecular rearrangements resulting in human genetic disease. Studies of the Charcot-Marie-Tooth disease locus on chromosome 17 have implicated the involvement of an ancient DNA transposon of the mariner family (Hsmar2) in the initiation of double-strand break events leading to homologous recombination. In this study, the genomic locations of 109 Hsmar2 elements were determined by primed in situ labeling (PRINS) using primers designed to match the right and left inverted terminal repeats (ITRs) of the transposon. Although the resolution of the PRINS technique is ∼400 chromosomal Giemsa bands, the data presented here provide the first large-scale mapping study of these elements, which may be involved in initiation of homologous recombination events in the human genome.
CAP3: A DNA Sequence Assembly Program
Authors: Huang Xiaoqiu , Madan Anup
Published: July 2002

We describe the third generation of the CAP sequence assembly program. The CAP3 program includes a number of improvements and new features. The program has a capability to clip 5′ and 3′ low-quality regions of reads. It uses base quality values in computation of overlaps between reads, construction of multiple sequence alignments of reads, and generation of consensus sequences. The program also uses forward–reverse constraints to correct assembly errors and link contigs. Results of CAP3 on four BAC data sets are presented. The performance of CAP3 was compared with that of PHRAP on a number of BAC data sets. PHRAP often produces longer contigs than CAP3 whereas CAP3 often produces fewer errors in consensus sequences than PHRAP. It is easier to construct scaffolds with CAP3 than with PHRAP on low-pass data with forward–reverse constraints.
Role of Hippocampal Signaling Pathways in Long-Term Memory Formation of a Nonassociative Learning Task in the Rat
Authors: Vianna Monica R.M. , Alonso Mariana , Viola Haydee , Quevedo Joao , de Paris Fernanda , Furman Melina , de Stein Miguelina Levi , Medina Jorge H. , Izquierdo Ivan
Published: July 2002

Long-term habituation to a novel environment is one of the most elementary forms of nonassociative learning. Here we studied the effect of pre- or posttraining intrahippocampal administration of drugs acting on specific molecular targets on the retention of habituation to a 5-min exposure to an open field measured 24 h later. We also determined whether the exposure to a novel environment resulted in the activation of the same intracellular signaling cascades previously shown to be activated during hippocampal-dependent associative learning. The immediate posttraining bilateral infusion of CNQX (1 μg/side), an AMPA/kainate glutamate receptor antagonist, or of muscimol (0.03 μg/side), a GABAA receptor agonist, into the CA1 region of the dorsal hippocampus impaired long-term memory of habituation. The NMDA receptor antagonist AP5 (5 μg/side) impaired habituation when infused 15 min before, but not when infused immediately after, the 5-min training session. In addition, KN-62 (3.6 ng/side), an inhibitor of calcium calmodulin-dependent protein kinase II (CaMKII), was amnesic when infused 15 min before or immediately and 3 h after training. In contrast, the cAMP-dependent protein kinase (PKA) inhibitor Rp-cAMPS, the mitogen-activated protein kinase kinase (MAPKK) inhibitor PD098059, and the protein synthesis inhibitor anisomycin, at doses that fully block memory formation of inhibitory avoidance learning, did not affect habituation to a novel environment. The detection of spatial novelty is associated with a sequential activation of PKA, ERKs (p44 and p42 MAPKs) and CaMKII and the phosphorylation of c-AMP responsive element-binding protein (CREB) in the hippocampus. These findings suggest that memory formation of spatial habituation depends on the functional integrity of NMDA and AMPA/kainate receptors and CaMKII activity in the CA1 region of the hippocampus and that the detection of spatial novelty is accompanied by the activation of at least three different hippocampal protein kinase signaling cascades.
Lesions of Periaqueductal Gray Dissociate-Conditioned Freezing From Conditioned Suppression Behavior in Rats
Authors: Amorapanth Prin , Nader Karim , LeDoux Joseph E.
Published: July 2002

It is commonly assumed that suppression of an ongoing behavior is an indirect measure of freezing behavior. We tested whether conditioned suppression and freezing are the same or distinct conditioned responses. Rats were trained to press a bar for food and then given fear-conditioning sessions in which a tone was paired with a foot shock (two pairings a day for 2 days). They then received either sham or electrolytic lesions of the periaqueductal gray (PAG). Post-training PAG lesions blocked freezing to the conditioned stimulus (CS), but had no effect on the suppression of operant behavior to the same CS. Thus, conditioned suppression and freezing, which both cause a cessation in activity, appear to be mediated by separate processes.
The α-Amylase Induction in Endosperm during Rice Seed Germination Is Caused by Gibberellin Synthesized in Epithelium
Authors: Kaneko Miyuki , Itoh Hironori , Ueguchi-Tanaka Miyako , Ashikari Motoyuki , Matsuoka Makoto
Published: July 2002

We recently isolated two genes (OsGA3ox1 andOsGA3ox2) from rice (Oryza sativa) encoding 3β-hydroxylase, which catalyzes the final step of active gibberellin (GA) biosynthesis (H. Itoh, M. Ueguchi-Tanaka, N. Sentoku, H. Kitano, M. Matsuoka, M. Kobayashi [2001] Proc Natl Acad Sci USA 98: 8909–8914). Using these cloned cDNAs, we analyzed the temporal and spatial expression patterns of the 3β-hydroxylase genes and also an α-amylase gene (RAmy1A) during rice seed germination to investigate the relationship between GA biosynthesis and α-amylase expression. Northern-blot analyses revealed that RAmy1Aexpression in the embryo occurs before the induction of 3β-hydroxylase expression, whereas in the endosperm, a high level ofRAmy1A expression occurs 1 to 2 d after the peak ofOsGA3ox2 expression and only in the absence of uniconazol. Based on the analysis of an OsGA3ox2 null mutant (d18-Akibare dwarf), we determined that 3β-hydroxylase produced by OsGA3ox2 is important for the induction of RAmy1A expression and that the OsGA3ox1 product is not essential for α-amylase induction. The expression ofOsGA3ox2 was localized to the shoot region and epithelium of the embryo, strongly suggesting that active GA biosynthesis occurs in these two regions. The synthesis of active GA in the epithelium is important for α-amylase expression in the endosperm, because an embryonic mutant defective in shoot formation, but which developed epithelium cells, induced α-amylase expression in the endosperm, whereas a mutant defective in epithelium development did not.
Phosphorylation by a Cyclin-Dependent Kinase Modulates DNA Binding of the Arabidopsis Heat-Shock Transcription Factor HSF1 in Vitro
Authors: Reindl A. , Schoffl F. , Schell J. , Koncz C. , Bako L.
Published: July 2002

Phosphorylation is one of the mechanisms controlling the activity of heat-shock transcription factors in yeast and mammalian cells. Here we describe partial purification, identification, and characterization of a protein kinase that phosphorylates the Arabidopsis heat-shock factor AtHSF1 at multiple serine residues. The HSF1 kinase forms a stable complex with AtHSF1, which can be detected by kinase pull-down assays using a histidine-tagged AtHSF1 substrate. The HSF1 kinase interacts with the cell-cycle control protein Suc1p and is immunoprecipitated by an antibody specific for the Arabidopsis cyclin-dependent CDC2a kinase. Phosphorylation by CDC2a in vitro inhibits DNA binding of AtHSF1 to the cognate heat-shock elements, suggesting a possible regulatory interaction between heat-shock response and cell-cycle control in plants.
A Ubiquitous Plant Housekeeping Gene, PAP, Encodes a Major Protein Component of Bell Pepper Chromoplasts
Authors: Pozueta-Romero J. , Rafia F. , Houlne G. , Cheniclet C. , Carde J. P. , Schantz M. L. , Schantz R.
Published: July 2002

We have isolated a cDNA (PAP) corresponding to a single nuclear gene that encodes an approximately 30-kD major protein of bell pepper (Capsicum annuum L.) fruit chromoplasts. RNA and protein analyses revealed that, although at a low level, this gene is also expressed in every organ of the plant, the amount of the corresponding transcript and protein dramatically increasing in the latter stages of fruit development. Western-blot and immunocytochemical analyses of purified chloroplasts from leaves and fruits and of chromoplasts from red fruits showed that the encoded protein is the major component of plastoglobules and fibrils and is localized on the outer surface of these lipid structures. Analyses of PAP in plants belonging to different taxa revealed that it is expressed and highly conserved in both monocotyledonous and dicotyledonous plants. The presence of the protein in plastids not differentiating into chromoplasts indicates that PAP is expressed irrespective of the ontogeny of various plastid lines. In light of our results and since the encoded protein, identical to that previously named ChrB or fibrillin, is present in plastoglobules from several species and accumulates in the fibrils of bell pepper chromoplast, we propose to designate it as a plastid-lipid-associated protein.
Effects of Short- and Long-Term Elevated CO2 on the Expression of Ribulose-1,5-Bisphosphate Carboxylase/Oxygenase Genes and Carbohydrate Accumulation in Leaves of Arabidopsis thaliana (L.) Heynh.1
Authors: Cheng Shu-Hua , Moore Brandon d. , Seemann Jeffrey R.
Published: July 2002

To investigate the proposed molecular characteristics of sugar-mediated repression of photosynthetic genes during plant acclimation to elevated CO2, we examined the relationship between the accumulation and metabolism of nonstructural carbohydrates and changes in ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) gene expression in leaves of Arabidopsis thaliana exposed to elevated CO2. Long-term growth of Arabidopsis at high CO2 (1000 μL L−1) resulted in a 2-fold increase in nonstructural carbohydrates, a large decrease in the expression of Rubisco protein and in the transcript ofrbcL, the gene encoding the large subunit of Rubisco (approximately 35–40%), and an even greater decline in mRNA ofrbcS, the gene encoding the small subunit (approximately 60%). This differential response of protein and mRNAs suggests that transcriptional/posttranscriptional processes and protein turnover may determine the final amount of leaf Rubisco protein at high CO2. Analysis of mRNA levels of individualrbcS genes indicated that reduction in totalrbcS transcripts was caused by decreased expression of all four rbcS genes. Short-term transfer of Arabidopsis plants grown at ambient CO2 to high CO2resulted in a decrease in total rbcS mRNA by d 6, whereas Rubisco content and rbcL mRNA decreased by d 9. Transfer to high CO2 reduced the maximum expression level of the primary rbcS genes (1A and, particularly, 3B) by limiting their normal pattern of accumulation through the night period. The decreased nighttime levels of rbcS mRNA were associated with a nocturnal increase in leaf hexoses. We suggest that prolonged nighttime hexose metabolism resulting from exposure to elevated CO2 affects rbcS transcript accumulation and, ultimately, the level of Rubisco protein.
Drought-Induced Effects on Nitrate Reductase Activity and mRNA and on the Coordination of Nitrogen and Carbon Metabolism in Maize Leaves1
Authors: Foyer Christine H. , Valadier Marie-Hélène , Migge Andrea , Becker Thomas W.
Published: July 2002

Maize (Zea mays L.) plants were grown to the nine-leaf stage. Despite a saturating N supply, the youngest mature leaves (seventh position on the stem) contained little NO3− reserve. Droughted plants (deprived of nutrient solution) showed changes in foliar enzyme activities, mRNA accumulation, photosynthesis, and carbohydrate and amino acid contents. Total leaf water potential and CO2assimilation rates, measured 3 h into the photoperiod, decreased 3 d after the onset of drought. Starch, glucose, fructose, and amino acids, but not sucrose (Suc), accumulated in the leaves of droughted plants. Maximal extractable phosphoenolpyruvate carboxylase activities increased slightly during water deficit, whereas the sensitivity of this enzyme to the inhibitor malate decreased. Maximal extractable Suc phosphate synthase activities decreased as a result of water stress, and there was an increase in the sensitivity to the inhibitor orthophosphate. A correlation between maximal extractable foliar nitrate reductase (NR) activity and the rate of CO2 assimilation was observed. The NR activation state and maximal extractable NR activity declined rapidly in response to drought. Photosynthesis and NR activity recovered rapidly when nutrient solution was restored at this point. The decrease in maximal extractable NR activity was accompanied by a decrease in NR transcripts, whereas Suc phosphate synthase and phosphoenolpyruvate carboxylase mRNAs were much less affected. The coordination of N and C metabolism is retained during drought conditions via modulation of the activities of Suc phosphate synthase and NR commensurate with the prevailing rate of photosynthesis.
Polygalacturonase Gene Expression in Ripe Melon Fruit Supports a Role for Polygalacturonase in Ripening-Associated Pectin Disassembly
Authors: Hadfield Kristen A. , Rose Jocelyn K.C. , Yaver Debbie S. , Berka Randy M. , Bennett Alan B.
Published: July 2002

Ripening-associated pectin disassembly in melon is characterized by a decrease in molecular mass and an increase in the solubilization of polyuronide, modifications that in other fruit have been attributed to the activity of polygalacturonase (PG). Although it has been reported that PG activity is absent during melon fruit ripening, a mechanism for PG-independent pectin disassembly has not been positively identified. Here we provide evidence that pectin disassembly in melon (Cucumis melo) may be PG mediated. Three melon cDNA clones with significant homology to other cloned PGs were isolated from the rapidly ripening cultivar Charentais (C. melo cv Reticulatus F1 Alpha) and were expressed at high levels during fruit ripening. The expression pattern correlated temporally with an increase in pectin-degrading activity and a decrease in the molecular mass of cell wall pectins, suggesting that these genes encode functional PGs. MPG1 and MPG2 were closely related to peach fruit and tomato abscission zone PGs, and MPG3 was closely related to tomato fruit PG. MPG1, the most abundant melon PG mRNA, was expressed in Aspergillus oryzae. The culture filtrate exponentially decreased the viscosity of a pectin solution and catalyzed the linear release of reducing groups, suggesting that MPG1 encodes an endo-PG with the potential to depolymerize melon fruit cell wall pectin. Because MPG1 belongs to a group of PGs divergent from the well-characterized tomato fruit PG, this supports the involvement of a second class of PGs in fruit ripening-associated pectin disassembly.
Manipulation of Glutathione and Amino Acid Biosynthesis in the Chloroplast
Authors: Noctor Graham , Arisi Ana-Carolina M. , Jouanin Lise , Foyer Christine H.
Published: July 2002

Poplars (Populus tremula × Populus alba) were transformed to overexpress Escherichia coliγ-glutamylcysteine synthetase (γ-ECS) or glutathione synthetase in the chloroplast. Five independent lines of each transformant strongly expressed the introduced gene and possessed markedly enhanced activity of the gene product. Glutathione (GSH) contents were unaffected by high chloroplastic glutathione synthetase activity. Enhanced chloroplastic γ-ECS activity markedly increased γ-glutamylcysteine and GSH levels. These effects are similar to those previously observed in poplars overexpressing these enzymes in the cytosol. Similar to cytosolic γ-ECS overexpression, chloroplastic overexpression did not deplete foliar cysteine or methionine pools and did not lead to morphological changes. Light was required for maximal accumulation of GSH in poplars overexpressing γ-ECS in the chloroplast. High chloroplastic, but not cytosolic, γ-ECS activities were accompanied by increases in amino acids synthesized in the chloroplast. We conclude that (a) GSH synthesis can occur in the chloroplast and the cytosol and may be up-regulated in both compartments by increased γ-ECS activity, (b) interactions between GSH synthesis and the pathways supplying the necessary substrates are similar in both compartments, and (c) chloroplastic up-regulation of GSH synthesis is associated with an activating effect on the synthesis of specific amino acids formed in the chloroplast.