bluuebunny/crossref_metadata_2025 huggingface dataset:
p38 MAPK enhances STAT1-dependent transcription independently of Ser-727 phosphorylation
Authors: Ramsauer Katrin , Sadzak Iwona , Porras Almudena , Pilz Andreas , Nebreda Angel R. , Decker Thomas , Kovarik Pavel
Published: October 2002

The transcription factor signal transducer and activator of transcription 1 (STAT1) requires phosphorylation at both Tyr-701 and Ser-727 for full activation. IFN-γ induces phosphorylation of both residues, whereas stress signals like UV or lipopolysaccharide stimulate phosphorylation of Ser-727 only. Using p38α mitogen-activated protein kinase (MAPK)-deficient cells, we show that the stress-induced phosphorylation of Ser-727 requires p38α MAPK activity, whereas IFN-γ-stimulated Ser-727 phosphorylation occurs independently of the p38α pathway. Consistently, IFN-γ stimulated expression of the STAT1 target gene IRF1 to a similar extent in both wild-type and p38α-deficient cells. However, stress-induced activation of the p38 MAPK pathway considerably enhanced the IFN-γ-induced expression of both the endogenous IRF1 gene and a reporter driven by the IFN-γ-activated sequence element of the IRF1 promoter. This enhancement occurred independently of increased phosphorylation of Ser-727 by the p38 pathway. Taken together, these results demonstrate an interaction between IFN-γ signaling and the p38 pathway that leads to increased transcriptional activation by STAT1 independently of phosphorylation at Ser-727.
The
Brucella
suis
genome reveals fundamental similarities between animal and plant pathogens and symbionts
Authors: Paulsen Ian T. , Seshadri Rekha , Nelson Karen E. , Eisen Jonathan A. , Heidelberg John F. , Read Timothy D. , Dodson Robert J. , Umayam Lowell , Brinkac Lauren M. , Beanan Maureen J. , Daugherty Sean C. , Deboy Robert T. , Durkin A. Scott , Kolonay James F. , Madupu Ramana , Nelson William C. , Ayodeji Bola , Kraul Margaret , Shetty Jyoti , Malek Joel , Van Aken Susan E. , Riedmuller Steven , Tettelin Herve , Gill Steven R. , White Owen , Salzberg Steven L. , Hoover David L. , Lindler Luther E. , Halling Shirley M. , Boyle Stephen M. , Fraser Claire M.
Published: October 2002

The 3.31-Mb genome sequence of the intracellular pathogen and potential bioterrorism agent,
Brucella
suis
, was determined. Comparison of
B.
suis
with
Brucella
melitensis
has defined a finite set of differences that could be responsible for the differences in virulence and host preference between these organisms, and indicates that phage have played a significant role in their divergence. Analysis of the
B.
suis
genome reveals transport and metabolic capabilities akin to soil/plant-associated bacteria. Extensive gene synteny between
B.
suis
chromosome 1 and the genome of the plant symbiont
Mesorhizobium
loti
emphasizes the similarity between this animal pathogen and plant pathogens and symbionts. A limited repertoire of genes homologous to known bacterial virulence factors were identified.
Cell transplantation after oxidative hepatic preconditioning with radiation and ischemia–reperfusion leads to extensive liver repopulation
Authors: Malhi Harmeet , Gorla Giridhar R. , Irani Adil N. , Annamaneni Pallavi , Gupta Sanjeev
Published: October 2002

The inability of transplanted cells to proliferate in the normal liver hampers cell therapy. We considered that oxidative hepatic DNA damage would impair the survival of native cells and promote proliferation in transplanted cells. Dipeptidyl peptidase-deficient F344 rats were preconditioned with whole liver radiation and warm ischemia–reperfusion followed by intrasplenic transplantation of syngeneic F344 rat hepatocytes. The preconditioning was well tolerated, although serum aminotransferase levels rose transiently and hepatic injury was observed histologically, along with decreased catalase activity and 8-hydroxy adducts of guanine, indicating oxidative DNA damage. Transplanted cells did not proliferate in the liver over 3 months in control animals and animals preconditioned with ischemia–reperfusion alone. Animals treated with radiation alone showed some transplanted cell proliferation. In contrast, the liver of animals preconditioned with radiation plus ischemia–reperfusion was replaced virtually completely over 3 months. Transplanted cells integrated in the liver parenchyma and liver architecture were preserved normally. These findings offer a paradigm for repopulating the liver with transplanted cells. Progressive loss of cells experiencing oxidative DNA damage after radiation and ischemia–reperfusion injury could be of significance for epithelial renewal in additional organs.
Expression of functional neurotransmitter receptors in
Xenopus
oocytes after injection of human brain membranes
Authors: Miledi Ricardo , Eusebi Fabrizio , Martínez-Torres Ataúlfo , Palma Eleonora , Trettel Flavia
Published: October 2002

The
Xenopus
oocyte is a very powerful tool for studies of the structure and function of membrane proteins, e.g., messenger RNA extracted from the brain and injected into oocytes leads to the synthesis and membrane incorporation of many types of functional receptors and ion channels, and membrane vesicles from
Torpedo
electroplaques injected into oocytes fuse with the oocyte membrane and cause the appearance of functional
Torpedo
acetylcholine receptors and Cl
−
channels. This approach was developed further to transplant already assembled neurotransmitter receptors from human brain cells to the plasma membrane of
Xenopus
oocytes. Membranes isolated from the temporal neocortex of a patient, operated for intractable epilepsy, were injected into oocytes and, within a few hours, the oocyte membrane acquired functional neurotransmitter receptors to γ-aminobutyric acid, α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid, kainate, and glycine. These receptors were also expressed in the plasma membrane of oocytes injected with mRNA extracted from the temporal neocortex of the same patient. All of this makes the
Xenopus
oocyte a more useful model than it already is for studies of the structure and function of many human membrane proteins and opens the way to novel pathophysiological investigations of some human brain disorders.
Two degrees of separation in complex food webs
Authors: Williams Richard J. , Berlow Eric L. , Dunne Jennifer A. , Barabási Albert-László , Martinez Neo D.
Published: October 2002

Feeding relationships can cause invasions, extirpations, and population fluctuations of a species to dramatically affect other species within a variety of natural habitats. Empirical evidence suggests that such strong effects rarely propagate through food webs more than three links away from the initial perturbation. However, the size of these spheres of potential influence within complex communities is generally unknown. Here, we show for that species within large communities from a variety of aquatic and terrestrial ecosystems are on average two links apart, with >95% of species typically within three links of each other. Species are drawn even closer as network complexity and, more unexpectedly, species richness increase. Our findings are based on seven of the largest and most complex food webs available as well as a food-web model that extends the generality of the empirical results. These results indicate that the dynamics of species within ecosystems may be more highly interconnected and that biodiversity loss and species invasions may affect more species than previously thought.
Delayed onset of brain edema and mislocalization of aquaporin-4 in dystrophin-null transgenic mice
Authors: Vajda Zsolt , Pedersen Michael , Füchtbauer Ernst-Martin , Wertz Karin , Stødkilde-Jørgensen Hans , Sulyok Endre , Dóczi Tamás , Neely John D. , Agre Peter , Frøkiær Jørgen , Nielsen Søren
Published: October 2002

Cerebral water accumulation was studied during induction of brain edema in dystrophin-null transgenic mice (
mdx-
β
geo
) and control mice. Immunofluorescence and immunoelectron microscopic analyses of dystrophin-null brains revealed a dramatic reduction of AQP4 (aquaporin-4) in astroglial end-feet surrounding capillaries (blood–brain barrier) and at the glia limitans (cerebrospinal fluid–brain interface). The AQP4 protein is mislocalized, because immunoblotting showed that the total AQP4 protein abundance was unaltered. Brain edema was induced by i.p. injection of distilled water and 8-deamino-arginine vasopressin. Changes in cerebral water compartments were assessed by diffusion-weighted MRI with determination of the apparent diffusion coefficient (ADC). In dystrophin-null mice and control mice, ADC gradually decreased by 5–6% from baseline levels during the first 35 min, indicating the initial phase of intracellular water accumulation is similar in the two groups. At this point, the control mice sustained an abrupt, rapid decline in ADC to 58% ± 2.2% of the baseline at 52.5 min, and all of the animals were dead by 56 min. After a consistent delay, the dystrophin-null mice sustained a similar decline in ADC to 55% ± 3.4% at 66.5 min, when all of the mice were dead. These results demonstrate that dystrophin is necessary for polarized distribution of AQP4 protein in brain where facilitated movements of water occur across the blood–brain barrier and cerebrospinal fluid–brain interface. Moreover, these results predict that interference with the subcellular localization of AQP4 may have therapeutic potential for delaying the onset of impending brain edema.
Gradients of substrate-bound laminin orient axonal specification of neurons
Authors: Dertinger Stephan K. W. , Jiang Xingyu , Li Zhiying , Murthy Venkatesh N. , Whitesides George M.
Published: October 2002

Little is known about the influence of substrate-bound gradients on neuronal development, since it has been difficult to fabricate gradients over the distances typically required for biological studies (a few hundred micrometers). This article demonstrates a generally applicable technique for the fabrication of substrate-bound gradients of proteins with complex shapes, using laminar flows in microchannels. Gradients that range from pure laminin to pure BSA were formed in solution by using a network of microchannels, and these proteins were allowed to adsorb onto a homogeneous layer of poly-
l
-lysine. Rat hippocampal neurons were cultivated on these substrate-bound gradients. Analysis of optical images of these neurons showed that axon specification is oriented in the direction of increasing surface density of laminin. Linear gradients in laminin adsorbed from a gradient in solution having a slope of ∇[laminin] > about 0.06 μg (ml⋅μm)
−1
(defined by dividing the change of concentration of laminin in solution over the distance of the gradient) orient axon specification, whereas those with ∇[laminin] < about 0.06 μg (ml⋅μm)
−1
have no effect.
External control of Her2 expression and cancer cell growth by targeting a Ras-linked coactivator
Authors: Asada Shinichi , Choi Yongmun , Yamada Masaki , Wang Shao-Chun , Hung Mien-Chie , Qin Jun , Uesugi Motonari
Published: October 2002

Overproduction of the Her2 oncoprotein has been found in ≈30% of breast tumors, and patients who have Her2 excesses typically have more aggressive disease. Here we show that the expression of the
Her2
gene can be decreased by inhibiting the interaction of the two cancer-linked proteins, DRIP130/CRSP130/Sur-2 (a Ras-linked subunit of human mediator complexes) and ESX (an epithelial-restricted transcription factor). Disruption of the interaction by a short cell-permeable peptide reduced the expression of the
Her2
gene and specifically impaired the growth and viability of Her2-overexpressing breast cancer cells. The association of ESX with DRIP130 is mediated by a small hydrophobic face of an 8-aa helix in ESX, suggesting a therapeutic approach to incapacitating the
Her2
gene by small organic molecules.
Corridors affect plants, animals, and their interactions in fragmented landscapes
Authors: Tewksbury Joshua J. , Levey Douglas J. , Haddad Nick M. , Sargent Sarah , Orrock John L. , Weldon Aimee , Danielson Brent J. , Brinkerhoff Jory , Damschen Ellen I. , Townsend Patricia
Published: October 2002

Among the most popular strategies for maintaining populations of both plants and animals in fragmented landscapes is to connect isolated patches with thin strips of habitat, called corridors. Corridors are thought to increase the exchange of individuals between habitat patches, promoting genetic exchange and reducing population fluctuations. Empirical studies addressing the effects of corridors have either been small in scale or have ignored confounding effects of increased habitat area created by the presence of a corridor. These methodological difficulties, coupled with a paucity of studies examining the effects of corridors on plants and plant–animal interactions, have sparked debate over the purported value of corridors in conservation planning. We report results of a large-scale experiment that directly address this debate. In eight large-scale experimental landscapes that control for patch area and test alternative mechanisms of corridor function, we demonstrate that corridors not only increase the exchange of animals between patches, but also facilitate two key plant–animal interactions: pollination and seed dispersal. Our results show that the beneficial effects of corridors extend beyond the area they add, and suggest that increased plant and animal movement through corridors will have positive impacts on plant populations and community interactions in fragmented landscapes.
Fluid flow increases mineralized matrix deposition in 3D perfusion culture of marrow stromal osteoblasts in a dose-dependent manner
Authors: Bancroft Gregory N. , Sikavitsas Vassilios I. , van den Dolder Juliette , Sheffield Tiffany L. , Ambrose Catherine G. , Jansen John A. , Mikos Antonios G.
Published: October 2002

Bone is a complex highly structured mechanically active 3D tissue composed of cellular and matrix elements. The true biological environment of a bone cell is thus derived from a dynamic interaction between responsively active cells experiencing mechanical forces and a continuously changing 3D matrix architecture. To investigate this phenomenon
in vitro
, marrow stromal osteoblasts were cultured on 3D scaffolds under flow perfusion with different rates of flow for an extended period to permit osteoblast differentiation and significant matrix production and mineralization. With all flow conditions, mineralized matrix production was dramatically increased over statically cultured constructs with the total calcium content of the cultured scaffolds increasing with increasing flow rate. Flow perfusion induced
de novo
tissue modeling with the formation of pore-like structures in the scaffolds and enhanced the distribution of cells and matrix throughout the scaffolds. These results represent reporting of the long-term effects of fluid flow on primary differentiating osteoblasts and indicate that fluid flow has far-reaching effects on osteoblast differentiation and phenotypic expression
in vitro
. Flow perfusion culture permits the generation and study of a 3D, actively modeled, mineralized matrix and can therefore be a valuable tool for both bone biology and tissue engineering.
An optical marker based on the UV-induced green-to-red photoconversion of a fluorescent protein
Authors: Ando Ryoko , Hama Hiroshi , Yamamoto-Hino Miki , Mizuno Hideaki , Miyawaki Atsushi
Published: October 2002

We have cloned a gene encoding a fluorescent protein from a stony coral,
Trachyphyllia geoffroyi
, which emits green, yellow, and red light. The protein, named Kaede, includes a tripeptide, His-Tyr-Gly, that acts as a green chromophore that can be converted to red. The red fluorescence is comparable in intensity to the green and is stable under usual aerobic conditions. We found that the green-red conversion is highly sensitive to irradiation with UV or violet light (350–400 nm), which excites the protonated form of the chromophore. The excitation lights used to elicit red and green fluorescence do not induce photoconversion. Under a conventional epifluorescence microscope, Kaede protein expressed in HeLa cells turned red in a graded fashion in response to UV illumination; maximal illumination resulted in a 2,000-fold increase in the ratio of red-to-green signal. These color-changing properties provide a simple and powerful technique for regional optical marking. A focused UV pulse creates an instantaneous plane source of red Kaede within the cytosol. The red spot spreads rapidly throughout the cytosol, indicating its free diffusibility in the compartment. The extensive diffusion allows us to delineate a single neuron in a dense culture, where processes originating from many different somata are present. Illumination of a focused UV pulse onto the soma of a Kaede-expressing neuron resulted in filling of all processes with red fluorescence, allowing visualization of contact sites between the red and green neurons of interest.
Trace fossils and substrates of the terminal Proterozoic–Cambrian transition: Implications for the record of early bilaterians and sediment mixing
Authors: Droser Mary L. , Jensen Sören , Gehling James G.
Published: October 2002

The trace fossil record is important in determining the timing of the appearance of bilaterian animals. A conservative estimate puts this time at ≈555 million years ago. The preservational potential of traces made close to the sediment–water interface is crucial to detecting early benthic activity. Our studies on earliest Cambrian sediments suggest that shallow tiers were preserved to a greater extent than typical for most of the Phanerozoic, which can be attributed both directly and indirectly to the low levels of sediment mixing. The low levels of sediment mixing meant that thin event beds were preserved. The shallow depth of sediment mixing also meant that muddy sediments were firm close to the sediment–water interface, increasing the likelihood of recording shallow-tier trace fossils in muddy sediments. Overall, trace fossils can provide a sound record of the onset of bilaterian benthic activity.
Functional coadaptation between cytochrome
c
and cytochrome
c
oxidase within allopatric populations of a marine copepod
Authors: Rawson Paul D. , Burton Ronald S.
Published: October 2002

Geographically isolated populations may accumulate alleles that function well on their own genetic backgrounds but poorly on the genetic backgrounds of other populations. Consequently, interpopulation hybridization may produce offspring of low fitness as a result of incompatibilities arising in allopatry. Genes participating in these epistatic incompatibility systems remain largely unknown. In fact, despite the widely recognized importance of epistatic interactions among gene products, few data directly address the functional consequences of such interactions among natural genetic variants. In the marine copepod,
Tigriopus californicus
, we found that the cytochrome
c
variants isolated from two different populations each had significantly higher activity with the cytochrome
c
oxidase derived from their respective source population. Three amino acid substitutions in the cytochrome
c
protein appear to be sufficient to confer population specificity. These results suggest that electron transport system (ETS) proteins form coadapted sets of alleles within populations and that disruption of the coadapted ETS gene complex leads to functional incompatibilities that may lower hybrid fitness.
Hitchhiking mapping: A population-based fine-mapping strategy for adaptive mutations inDrosophilamelanogaster
Authors: Harr Bettina , Kauer Max , Schlötterer Christian
Published: October 2002

The identification of genes contributing to the adaptation of local populations is of great biological interest. In an attempt to characterize functionally important differences among African and non-AfricanDrosophila melanogasterpopulations, we surveyed neutral microsatellite variation in an 850-kb genomic sequence. Three genomic regions were identified that putatively bear an adaptive mutation associated with the habitat expansion ofD. melanogaster. A further inspection of two regions by sequence analysis of multiple fragments confirmed the presence of a recent beneficial mutation in the non-African populations. Our study suggests that hitchhiking mapping is a universal approach for the identification of ecologically important mutations.
A heterotrimeric death domain complex in Toll signaling
Authors: Sun Huaiyu , Bristow Benjamin N. , Qu Guowei , Wasserman Steven A.
Published: October 2002

Signaling from the transmembrane receptor Toll to Rel-related transcription factors regulates dorsoventral patterning of the
Drosophila
embryo, as well as larval and adult immunity. To identify additional pathway components, we have used double-stranded RNA interference to investigate
Drosophila
counterparts of genes that regulate the mammalian Rel family member NF-κB. Experiments in cultured cells reveal that the fly orthologue of the adaptor protein MyD88 is essential for signal transduction from Toll to a second adaptor protein, Tube. By using coimmunoprecipitation studies, we find a heterotrimeric association of the death domains of MyD88, Tube, and the protein kinase Pelle. Site-directed mutational analyses of interaction sites defined by crystallographic studies demonstrate that Tube recruits MyD88 and Pelle into the heterotrimer by two distinct binding surfaces on the Tube death domain. Furthermore, functional assays confirm that the formation of this heterotrimer is critical for signal transduction by the Toll pathway.
Circuits and programmable self-assembling DNA structures
Authors: Carbone Alessandra , Seeman Nadrian C.
Published: October 2002

Self-assembly is beginning to be seen as a practical vehicle for computation. We investigate how basic ideas on tiling can be applied to the assembly and evaluation of circuits. We suggest that these procedures can be realized on the molecular scale through the medium of self-assembled DNA tiles. One layer of self-assembled DNA tiles will be used as the program or circuit that leads to the computation of a particular Boolean expression. This layer templates the assembly of tiles, and their associations then lead to the actual evaluation involving the input data. We describe DNA motifs that can be used for this purpose; we show how the template layer can be programmed, in much the way that a general-purpose computer can run programs for a variety of applications. The molecular system that we describe is fundamentally a pair of two-dimensional layers, but it seems possible to extend this system to multiple layers.
Hypoxia and acidosis activate cardiac myocyte death through the Bcl-2 family protein BNIP3
Authors: Kubasiak Lori A. , Hernandez Olga M. , Bishopric Nanette H. , Webster Keith A.
Published: October 2002

Coronary artery disease leads to injury and loss of myocardial tissue by deprivation of blood flow (ischemia) and is a major underlying cause of heart failure. Prolonged ischemia causes necrosis and apoptosis of cardiac myocytes and vascular cells; however, the mechanisms of ischemia-mediated cell death are poorly understood. Ischemia is associated with both hypoxia and acidosis due to increased glycolysis and lactic acid production. We recently reported that hypoxia does not induce cardiac myocyte apoptosis in the absence of acidosis. We now report that hypoxia-acidosis-associated cell death is mediated by BNIP3, a member of the Bcl-2 family of apoptosis-regulating proteins. Chronic hypoxia induced the expression and accumulation of BNIP3 mRNA and protein in cardiac myocytes, but acidosis was required to activate the death pathway. Acidosis stabilized BNIP3 protein and increased the association with mitochondria. Cell death by hypoxia-acidosis was blocked by pretreatment with antisense BNIP3 oligonucleotides. The pathway included extensive DNA fragmentation and opening of the mitochondrial permeability transition pore, but no apparent caspase activation. Overexpression of wild-type BNIP3, but not a translocation-defective mutant, activated cardiac myocyte death only when the myocytes were acidic. This pathway may figure significantly in muscle loss during myocardial ischemia.
Rice phosphate transporters include an evolutionarily divergent gene specifically activated in arbuscular mycorrhizal symbiosis
Authors: Paszkowski Uta , Kroken Scott , Roux Christophe , Briggs Steven P.
Published: October 2002

Using a genome-wide approach, we asked how many transporter genes contribute to symbiotic phosphate uptake and analyzed their evolutionary conservation. Considering the sequenced rice genome at hand, only the
Oryza sativa
phosphate transporter (
OsPT
) gene
OsPT11
was specifically induced during the arbuscular mycorrhizal symbiosis. This induction was confined to the root system and was tightly correlated with the degree of root colonization by
Glomus intraradices. OsPT11
activation was independent of the nutritional status of the plant and phosphate availability in the rhizosphere. Moreover, infection of roots with the fungal pathogens
Rhizoctonia solani
and
Fusarium moniliforme
did not activate
OsPT11
, corroborating the high signal specificity for
OsPT11
activation in the arbuscular mycorrhizal symbiosis.
OsPT11
expression complemented a defect in phosphate uptake in a yeast strain mutated in its high-affinity P
i
transporter (
pho84
), thereby confirming its function. Recently, a phosphate transporter gene in potato was shown to be induced during arbuscular mycorrhizal symbiosis. Assessment of the phylogenetic relationship of the rice and potato protein revealed that the rice is nonorthologous to the potato protein. Further, there are no structural commonalities in the promoter regions. Thus, although cytological and physiological features of the arbuscular mycorrhizal symbiosis seem to be conserved, the molecular components may differ significantly between distantly related plant species.
Investigation of Overhauser effects between pseudouridine and water protons in RNA helices
Authors: Newby Meredith I. , Greenbaum Nancy L.
Published: October 2002

The inherent chemical properties of RNA molecules are expanded by posttranscriptional modification of specific nucleotides. Pseudouridine (ψ), the most abundant of the modified bases, features an additional imino group, NH1, as compared with uridine. When ψ forms a Watson–Crick base pair with adenine in an RNA helix, NH1 is positioned within the major groove. The presence of ψ often increases thermal stability of the helix or loop in which it is found [Hall, K. B. & McLaughlin, L. (1992)Nucleic Acids Res.20, 1883–1889]. X-ray crystal structures of transfer RNAs [e.g., Arnez, J. & Steitz, T. (1994)Biochemistry33, 7560–7567] have depicted water molecules bridging ψNH1 groups and nearby phosphate oxygen atoms, but direct evidence for this interaction in solution has not been acquired. Toward this end, we have used a rotating-frame Overhauser effect spectroscopy-type NMR pulse sequence with a CLEAN chemical-exchange spectroscopy spin-lock pulse train [Hwang, T.-L., Mori, S., Shaka, A. J. & van Zijl, P. C. M. (1997)J. Am. Chem. Soc.119, 6203–6204] to test for ψNH1–water cross-relaxation effects within two RNA helices: (i) a complementary duplex, in which ψ is not associated with structural change, and (ii) an RNA duplex representing the eukaryotic pre-mRNA branch-site helix fromSaccharomyces cerevisiae, in which a conserved ψ extrudes the branch-site adenosine from the helix. Our data implicate a water–ψNH1 hydrogen bond both in stabilizing the complementary helix and in favoring formation of the unique structure of the branch-site helix.
T cells from the tumor microenvironment of patients with progressive myeloma can generate strong, tumor-specific cytolytic responses to autologous, tumor-loaded dendritic cells
Authors: Dhodapkar Madhav V. , Krasovsky Joseph , Olson Kara
Published: October 2002

Most untreated cancer patients develop progressive tumors. We tested the capacity of T lymphocytes from patients with clinically progressive, multiple myeloma to develop killer function against fresh autologous tumor. In this malignancy, it is feasible to reproducibly evaluate freshly isolated tumor cells and T cells from the marrow tumor environment. When we did this with seven consecutive patients, with all clinical stages of disease, we did not detect reactivity to autologous cancer cells. However, both cytolytic and IFN-γ-producing responses to autologous myeloma were generated in six of seven patients after stimulation
ex vivo
with dendritic cells that had processed autologous tumor cells. The antitumor effectors recognized fresh autologous tumor but not nontumor cells in the bone marrow, myeloma cell lines, dendritic cells loaded with tumor-derived Ig, or allogeneic tumor. Importantly, these CD8
+
effectors developed with similar efficiency by using T cells from both the blood and the bone marrow tumor environment. Therefore, even in the setting of clinical tumor progression, the tumor bed of myeloma patients contains T cells that can be activated readily by dendritic cells to kill primary autologous tumor.
Aberrant accumulation of EFEMP1 underlies drusen formation in Malattia Leventinese and age-related macular degeneration
Authors: Marmorstein Lihua Y. , Munier Francis L. , Arsenijevic Yvan , Schorderet Daniel F. , McLaughlin Precious J. , Chung Daniel , Traboulsi Elias , Marmorstein Alan D.
Published: October 2002

Malattia Leventinese (ML), an inherited macular degenerative disease, is closely reminiscent of age-related macular degeneration (AMD), the most common cause of incurable blindness. Both ML and AMD are characterized by extracellular deposits known as drusen between the retinal pigment epithelium (RPE) and Bruch's membrane. The mechanism underlying drusen formation is unknown. An Arg to Trp mutation in a gene of unknown function,
EFEMP1
, is responsible for ML, indicating EFEMP1 may be important in drusen formation. Here, we show that wild-type EFEMP1 is a secreted protein whereas mutant EFEMP1 is misfolded, secreted inefficiently, and retained within cells. In normal eyes, EFEMP1 is not present at the site of drusen formation. However, in ML eyes, EFEMP1 accumulates within the RPE cells and between the RPE and drusen, but does not appear to be a major component of drusen. Furthermore, in AMD eyes, EFEMP1 is found to accumulate beneath the RPE immediately overlaying drusen, but not in the region where there is no apparent retinal pathology observed. These data present evidence that misfolding and aberrant accumulation of EFEMP1 may cause drusen formation and cellular degeneration and play an important role in the etiology of both ML and AMD.
Myristoylation as a target for inhibiting HIV assembly: Unsaturated fatty acids block viral budding
Authors: Lindwasser O. Wolf , Resh Marilyn D.
Published: October 2002

Modification of HIV-1 Gag with myristic acid, a saturated 14-carbon fatty acid (14:0), is essential for HIV-1 assembly. We recently showed that exogenous treatment of cells with unsaturated 14-carbon fatty acids, 5-
cis
-tetradecenoic acid (14:1
n
-9) and 5-
cis
,8-
cis
-tetradecadienoic acid (14:2
n
-6), reduces the affinity of some myristoylated proteins for plasma membrane rafts, membrane subdomains that have been shown to be required for efficient assembly of HIV. Here we demonstrate that treatment of cells with 14:1
n
-9 and 14:2
n
-6 fatty acids reduced the affinity of Gag for rafts but not membranes in general. Furthermore, treatment of cells with 14-carbon unsaturated fatty acids inhibited Gag-driven particle assembly. These effects most likely reflect covalent modification of Gag with unsaturated fatty acids. Treatment with 14:1
n
-9 and 14:2
n
-6 fatty acids did not alter intracellular protein trafficking, nor did it reduce cell viability. These studies suggest a strategy to attack HIV assembly by selectively altering the patterns of fatty acid modification.
The grafting map of Teichmüller space
Authors: Scannell Kevin , Wolf Michael
Published: October 2002

Grafting is a method of obtaining new projective structures from a hyperbolic structure, basically by gluing a flat cylinder into a surface along a closed geodesic in the hyperbolic structure, or by limits of that procedure. This induces a map of Teichmüller space to itself. We prove that this map is a homeomorphism by analyzing harmonic maps between pairs of grafted surfaces. As a corollary we obtain bending coordinates for the Bers embedding of Teichmüller space.
Evolutionary pattern of intra–host pathogen antigenic drift: effect of cross–reactivity in immune response
Authors: Haraguchi Yoshihiro , Sasaki Akira
Published: October 2002

Several viruses are known to change their surface antigen types after infecting a host, thereby escaping the immune defence and ensuring persistent infection. In this paper, we theoretically study the pattern of intra-ndash;host micro-ndash;evolution of pathogen antigen variants under the antigen specific immune response. We assume that the antigen types of the pathogen can be indexed in one-ndash;dimensional space, and that a mutation can produce a new antigen variant that is one step distant from the parental type. We also assume that antibodies directed to a specific antigen can also neutralize similar antigen types with a decreased efficiency (cross-ndash;reactivity). The model reveals that the pattern of intra-ndash;host antigen evolution critically depends on the width of cross-ndash;reactivity. If the width of cross-ndash;reactivity is narrower than a certain threshold, antigen variants gradually evolve in antigen space as a travelling wave with a constant wave speed, and the total pathogen density approaches a constant. In contrast, if the width of cross-ndash;reactivity exceeds the threshold, the travelling wave loses stability and the distribution of antigen variants fluctuates both in time and in genotype space. In the latter case, the expected episodes after infection are a series of intermittent outbreaks of pathodgen density, caused by distantly separated antigen types. The implication of the model to intra-ndash;host evolution of equine infectious anaemia virus and human immunodeficiency virus is discussed.
The phylogeny of varanoid lizards and the affinities of snakes
Authors: Lee Michael S. Y.
Published: October 2002

Evidence that platynotan squamates (living varanoid lizards, snakes and their fossil relatives) are monophyletic is presented. Evolutionary relationships within this group are then ascertained through a cladistic analysis of 144 osteological characters. Mosasauroids (aigialosaurs and mosasaurs), a group of large marine lizards, are identified as the nearest relatives of snakes, thus resolving the long-standing problem of snake affinities. The mosasauroid–snake clade (Pythonomorpha) is corroborated by 40 derived characters, including recumbent replacement teeth, thecodonty, four or fewer premaxillary teeth, supratemporal–prootic contact, free mandibular tips, crista circumfenestralis, straight vertical splenio-angular joint, loss of posterior ramus of the coronoid, reduced basipterygoid processes, reduced interpterygoid vacuity, zygosphene–zygantral articulations, and absence of epiphyses on the axial skeleton and skull. After mosasauroids, the next closest relatives of snakes are varanids (Varanus,SaniwaandSaniwides) and lanthanotids (LanthanotusandCherminotus). Derived features uniting varanids and lanthanotids include nine cervical vertebrae and three or fewer pairs of sternal ribs. The varanid–lanthanotid–pythonomorph clade, here termed Thecoglossa, is supported by features such as the anteriorly positioned basal tubera, and the loss of the second epibranchial. Successive outgroups to thecoglossans areTelmasaurus, an unresolved polytomy (Estesia, Gobidermatidae and Helodermatidae),ParavaranusandProplatynota. The ‘necrosaurs’ are demonstrated to be an artificial (polyphyletic) assemblage of primitive platynotans that are not particularly closely related to each other. Snakes are presumed to have evolved from small, limbless, burrowing lizards and the inability of previous analyses to resolve the affinities of snakes has been attributed to extensive convergence among the numerous lineages of such lizards. The present study contradicts this claim, demonstrating that the problem is due instead to omission of critical fossil taxa. No modern phylogenetic analysis of squamate relationships has simultaneously includedbothmosasauroids and snakes: previous studies have therefore failed to identify the mosasauroid–snake association and the suite of derived characters supporting it. Mosasauroids are large aquatic animals with well-developed appendages, and none of the derived characters uniting mosasauroids and snakes is obviously correlated with miniaturization, limb reduction or fossoriality. Recognition that mosasauroids, followed by varanids and lanthanotids, are the nearest relatives of snakes will also facilitate studies of relationships within snakes, which until now have been hampered by uncertainty over the most appropriate (closely–related) lizard outgroups.
The vortex wake of a ‘hovering’ model hawkmoth
Authors: van den Berg Coen , Ellington Charles P.
Published: October 2002

Visualization experiments with
Manduca sexta
have revealed the presence of a leading–edge vortex and a highly three–dimensional flow pattern. To further investigate this important discovery, a scaled–up robotic insect was built (the ‘flapper’) which could mimic the complex movements of the wings of a hovering hawkmoth. Smoke released from the leading edge of the flapper wing revealed a small but strong leading–edge vortex on the downstroke. This vortex had a high axial flow velocity and was stable, separating from the wing at approximately 75 % of the wing length. It connected to a large, tangled tip vortex, extending back to a combining stopping and starting vortex from pronation. At the end of the downstroke, the wake could be approximated as one vortex ring per wing. Based on the size and velocity of the vortex rings, the mean lift force during the downstroke was estimated to be about 1.5 times the body weight of a hawkmoth, confirming that the downstroke is the main provider of lift force.
Flightlessness and phylogeny amongst endemic rails (Aves: Rallidae) of the New Zealand region
Authors: Trewick S. A.
Published: October 2002

The phylogenetic relationships of a number of flightless and volant rails have been investigated using mtDNA sequence data. The third domain of the small ribosomal subunit (12S) has been sequenced for 22 taxa, and part of the 5′ end of the cytochrome–bgene has been sequenced for 12 taxa. Additional sequences were obtained from outgroup taxa, two species of jacana, sarus crane, spur–winged plover and kagu. Extinct rails were investigated using DNA extracted from subfossil bones, and in cases where fresh material could not be obtained from other extant taxa, feathers and museum skins were used as sources of DNA.

Phylogenetic trees produced from these data have topologies that are, in general, consistent with data from DNA–DNA hybridization studies and recent interpretations based on morphology.Gallinula chloropus(moorhen) groups basally withFulica(coots),Amaurornis(=Megacrex)ineptusfalls within theGallirallus/Rallusgroup, andGallinula(=Porphyrula)martinicais basal toPorphyrio(swamphens) and should probably be placed in that genus. Subspecies ofPorphyrio porphyrioare paraphyletic with respect toPorphyrio mantelli(takahe). The Northern HemisphereRallus aquaticusis basal to the south–western PacificRallus(orGallirallus) group. The flightlessRallus philippensis dieffenbachiiis close toRallus modestusand distinct from the volantRallus philippensis, and is evidently a seperate species.Porzana(crakes) appears to be more closely associated withPorphyriothanRallus. Deep relationships among the rails remain poorly resolved.Rhynochetos jubatus(kagu) is closer to the cranes than the rails in this analysis.

Genetic distances between flightless rails and their volant counterparts varied considerably with observed 12S sequence distances, ranging from 0.3 % (Porphyrio porphyrio melanotusandP. mantelli mantelli) to 7.6 % (Rallus modestusandRallus philippensis). This may be taken as an indication of the rapidity with which flightlessness can evolve, and of the persistence of flightless taxa. Genetic data supported the notion that flightless taxa were independently derived, sometimes from similar colonizing ancestors. The morphology of flightless rails is apparently frequently dominated by evolutionary parallelism although similarity of external appearance is not an indication of the extent of genetic divergence. In some cases, taxa that are genetically close are morphologically distinct from one another (e.g.Rallus (philippensis) dieffenbachiiandR. modestus), whilst some morphologically similar taxa are evidently independently derived (e.g.Porphyio mantelli hochstetteriandP. m. mantelli).
Regulation and control of intracellular algae (= zooxanthellae) in hard corals
Authors: Jones Ross J. , Yellowlees D.
Published: October 2002

To examine algal (= zooxanthellae) regulation and control, and the factors determining algal densities in hard corals, the zooxanthellae mitotic index and release rates were regularly determined in branch tips from a colony of a staghorn coral,Acropora formosa, recovering from a coral ‘bleaching’ event (the stress–related dissociation of the coral–algal symbiosis). Mathematical models based upon density–dependent decreases in the algal division frequency and increases in algal release rates during the post–bleaching recovery period accurately predict the observed recovery period (≈ 20 weeks). The models suggest that (i) the colony recovered its algal population from the division of the remaining zooxanthellae, and (ii) the continual loss of zooxanthellae significantly slowed the recovery of the coral. Possible reasons for the ‘paradoxical’ loss of healthy zooxanthellae from the bleached coral are discussed in terms of endodermal processes occurring in the recovering coral and the redistribution of newly formed zooxanthellae to aposymbiotic host cells. At a steady–state algal density of 2.1 × 106zooxanthellae cm−2at the end of the recovery period, the zooxanthellae would have to form a double layer of cells in the coral tissues, consistent with microscopic observations. Neighbouring colonies ofA. formosawith inherently higher algal densities possess proportionately smaller zooxanthellae. Results suggest that space availability and the size of the algal symbionts determines the algal densities in the coral colonies. The large increases in the algal densities reported in corals exposed to elevated nutrient concentrations (i.e between a two– and five–fold increase in the algal standing stock) are not consistent with this theory. We suggest that increases of this magnitude are a product of the experimental conditions: reasons for this statement are discussed. We propose that the stability of the coral–algal symbiosis under non–stress conditions, and the constancy of zooxanthellae densities in corals reported across growth form, depth and geographic range, are related to space availability limiting algal densities. However, at these densities, zooxanthellae have attributes consistent with nutrient limitation.
Functional design of tentacles in squid: linking sarcomere ultrastructure to gross morphological dynamics
Authors: Van Leeuwen J. L. , Kier W. M.
Published: October 2002

This paper offers a quantitative analysis of tentacle extension in squid that integrates several levels of structural organization. The muscular stalks of the two tentacles of squid are rapidly elongated by 70 per cent of resting length during prey capture. A typical duration of the extension is 30 ms inLoligo pealei(with a contracted tentacle length of 93 mm and a strike distance of about 37 mm). In a successful strike, the terminal clubs hit the prey and attach to it via arrays of suckers. A forward dynamics model is proposed for the extension of the tentacular stalk and the forward motion of the terminal club. The stalk is modelled as a longitudinal array of thin muscular discs with extensor muscle fibres oriented parallel to the disc planes. As a disc contracts radially, it lengthens because its volume is constant. The equations of motion for the linked system of discs were formulated and solved numerically. The inputs of the model are the dimensions of the tentacle, passive and active muscle properties such as Hill's force–velocity relationship, myofilament lengths and activation of the muscle fibres. The model predicts the changing geometry of the tentacle, the pressure and stress distribution inside the tentacle and the velocity and kinetic energy distribution of the stalk and club. These predictions are in agreement with kinematic observations from high–speed films of prey capture. The model demonstrates also that the unusually short myosin filaments (reported range 0.5–0.9 micrometre) that characterize the extensor muscles are necessary for the observed extension performance. Myosin filament lengths typical for vertebrate sarcomeres (1.58 micrometre) would lead to a significant reduction in performance. In addition, the model predicts that, to maximize peak velocity of the terminal club, the myosin filaments should be longer at the base and shorter at the tip of the stalk (0.97 micrometre at the base and 0.50 micrometre at the tip for the tentacle size above). This results from differences in dynamic loading along the stalk. Finally, the model allows exploration of the effects of changes in the dimensions and mass of the tentacle and intrinsic speed of the myofilaments on the optimum myosin filament lengths.
Quantification in tissue near–infrared spectroscopy
Authors: Delpy D. T. , Cope M.
Published: October 2002

In near–infrared spectroscopy (NIRS) of tissue, light attenuation is due to: (i) absorption from chromophores of fixed concentration, (ii) absorption from chromophores of variable concentration, and (iii) light scatter. NIRS is usually concerned with trying to quantify the concentrations of chromophores in category (ii), in particular oxy– and deoxyhaemoglobin (HbO2and Hb) and cytochrome oxidase.

In the absence of scatter the total light absorption in the medium is a linear sum of that due to each chromophore. In a scattering medium like tissue, this linear summation is distorted because the optical path length at each wavelength may differ. This distorted spectrum is then superimposed upon a further wavelength–dependent attenuation arising from light loss due to scatter, which is a complex function of the tissue absorption and scattering coefficients (μaandμs), scattering phase function, and tissue and measurement geometry. Consequently, quantification of NIRS data is difficult.

Over the past 20 years many differing approaches to quantification have been tried. The development of methods for measuring optical path length in tissue initially enabled changes in concentration to be quantified, and subsequently methods for absolute quantification of HbO2and Hb were developed by correlating NIRS changes with an independent measurement of arterial haemoglobin saturation. Absolute determination of tissue optical properties, however, requires additional information over and above the detected intensity at the tissue surface, which must then be combined with a model of light transport to deriveμaandμs. The additional data can take many forms, e.g. the change in intensity with distance, the temporal dispersion of light from an ultrashort input light pulse, or phase, and modulation depth changes of intensity–modulated light. All these approaches are now being actively pursued with considerable success. However, all the approaches are limited by the accuracy of the light transport models, especially in inhomogeneous media.