bluuebunny/crossref_metadata_2025 huggingface dataset:
Generation of optical solitons in the wavelength region 1.37–1.49 μm
Authors: Zysset B. , Beaud P. , Hodel W.
Published: July 2002

First-order soliton pulses of 77–250 fs duration have been generated in the wavelength region from 1.37 to 1.49 μm. These solitons are formed by transmitting dye laser pulses at 1.34 μm of 1 ps duration and peak intensity of ≊0.66 GW/cm2 through optical single mode fibers. Soliton narrowing and soliton self-frequency shift are the dominant shaping mechanisms.
Low-frequency magnetic field detection with a magnetostrictive amorphous metal ribbon
Authors: Mermelstein M. D. , Dandridge A.
Published: July 2002

A low-frequency magnetometer has been constructed by interfacing a transversely field-annealed amorphous metal ribbon to a resonating piezoelectric ceramic plate. Power spectrum measurements from 20 mHz to 1.0 Hz demonstrate a minimum detectable field of 8.7 pT/√Hz at 1.0 Hz with an approximate 1/f rise in the noise floor.
Nature of misfit dislocation sources in strained-layer semiconductor structures
Authors: Dodson Brian W.
Published: July 2002

It is currently possible to grow nearly perfect strained-layer semiconductor heterostructures. Experimental evidence shows that misfit dislocation sources become active almost immediately as the layer thickness exceeds the equilibrium critical thickness. These dislocation sources do not seem related to obvious causes, such as threading dislocations or homogeneous nucleation at surface structures. It is argued here that the dislocation sources are inhomogeneous in nature and result from local stress concentrations near the surface.
Targeting of both mouse neuropilin-1 and neuropilin-2 genes severely impairs developmental yolk sac and embryonic angiogenesis
Authors: Takashima Seiji , Kitakaze Masafumi , Asakura Masanori , Asanuma Hiroshi , Sanada Shoji , Tashiro Fumi , Niwa Hitoshi , Miyazaki Jun-ichi , Hirota Seiichi , Kitamura Yukihiko , Kitsukawa Takashi , Fujisawa Hajime , Klagsbrun Michael , Hori Masatsugu
Published: July 2002

Neuropilins (NP1 and NP2) are vascular endothelial growth factor (VEGF) receptors that mediate developmental and tumor angiogenesis. Transgenic mice, in which both NP1 and NP2 were targeted (NP1
−/−
NP2
−/−
) died
in utero
at E8.5. Their yolk sacs were totally avascular. Mice deficient for NP2 but heterozygous for NP1 (NP1
+/−
NP2
−/−
) or deficient for NP1 but heterozygous for NP2 (NP1
−/−
NP2
+/−
) were also embryonic lethal and survived to E10–E10.5. The E10 yolk sacs and embryos were easier to analyze for vascular phenotype than the fragile poorly formed 8.5 embryos. The vascular phenotypes of these E10 mice were very abnormal. The yolk sacs, although of normal size, lacked the larger collecting vessels and had less dense capillary networks. PECAM staining of yolk sac endothelial cells showed the absence of branching arteries and veins, the absence of a capillary bed, and the presence of large avascular spaces between the blood vessels. The embryos displayed blood vessels heterogeneous in size, large avascular regions in the head and trunk, and blood vessel sprouts that were unconnected. The embryos were about 50% the length of wild-type mice and had multiple hemorrhages. These double NP1/NP2 knockout mice had a more severe abnormal vascular phenotype than either NP1 or NP2 single knockouts. Their abnormal vascular phenotype resembled those of VEGF and VEGFR-2 knockouts. These results suggest that NRPs are early genes in embryonic vessel development and that both NP1 and NP2 are required.
Complete genome sequence of
Clostridium perfringens
, an anaerobic flesh-eater
Authors: Shimizu Tohru , Ohtani Kaori , Hirakawa Hideki , Ohshima Kenshiro , Yamashita Atsushi , Shiba Tadayoshi , Ogasawara Naotake , Hattori Masahira , Kuhara Satoru , Hayashi Hideo
Published: July 2002

Clostridium perfringens
is a Gram-positive anaerobic spore-forming bacterium that causes life-threatening gas gangrene and mild enterotoxaemia in humans, although it colonizes as normal intestinal flora of humans and animals. The organism is known to produce a variety of toxins and enzymes that are responsible for the severe myonecrotic lesions. Here we report the complete 3,031,430-bp sequence of
C. perfringens
strain 13 that comprises 2,660 protein coding regions and 10 rRNA genes, showing pronounced low overall G + C content (28.6%). The genome contains typical anaerobic fermentation enzymes leading to gas production but no enzymes for the tricarboxylic acid cycle or respiratory chain. Various saccharolytic enzymes were found, but many enzymes for amino acid biosynthesis were lacking in the genome. Twenty genes were newly identified as putative virulence factors of
C. perfringens
, and we found a total of five hyaluronidase genes that will also contribute to virulence. The genome analysis also proved an efficient method for finding four members of the two-component VirR/VirS regulon that coordinately regulates the pathogenicity of
C. perfringens
. Clearly,
C. perfringens
obtains various essential materials from the host by producing several degradative enzymes and toxins, resulting in massive destruction of the host tissues.
Atmospheric energy for subsurface life on Mars?
Authors: Weiss Benjamin P. , Yung Yuk L. , Nealson Kenneth H.
Published: July 2002

The location and density of biologically useful energy sources on Mars will limit the biomass, spatial distribution, and organism size of any biota. Subsurface Martian organisms could be supplied with a large energy flux from the oxidation of photochemically produced atmospheric H2and CO diffusing into the regolith. However, surface abundance measurements of these gases demonstrate that no more than a few percent of this available flux is actually being consumed, suggesting that biological activity driven by atmospheric H2and CO is limited in the top few hundred meters of the subsurface. This is significant because the available but unused energy is extremely large: for organisms at 30-m depth, it is 2,000 times previous estimates of hydrothermal and chemical weathering energy and far exceeds the energy derivable from other atmospheric gases. This also implies that the apparent scarcity of life on Mars is not attributable to lack of energy. Instead, the availability of liquid water may be a more important factor limiting biological activity because the photochemical energy flux can only penetrate to 100- to 1,000-m depth, where most H2O is probably frozen. Because both atmospheric and Viking lander soil data provide little evidence for biological activity, the detection of short-lived trace gases will probably be a better indicator of any extant Martian life.
Structural basis for the guanine nucleotide-binding activity of tissue transglutaminase and its regulation of transamidation activity
Authors: Liu Shenping , Cerione Richard A. , Clardy Jon
Published: July 2002

Tissue transglutaminase (TG) is a Ca
2+
-dependent acyltransferase with roles in cellular differentiation, apoptosis, and other biological functions. In addition to being a transamidase, TG undergoes a GTP-binding/GTPase cycle even though it lacks any obvious sequence similarity with canonical GTP-binding (G) proteins. Guanine nucleotide binding and Ca
2+
concentration reciprocally regulate TG's transamidation activity, with nucleotide binding being the negative regulator. Here we report the x-ray structure determined to 2.8-Å resolution of human TG complexed with GDP. Although the transamidation active site is similar to those of other known transglutaminases, the guanine nucleotide-binding site of TG differs markedly from other G proteins. The structure suggests a structural basis for the negative regulation of transamidation activity by bound nucleotide, and the positive regulation of transamidation by Ca
2+
.
Noncovalent self-assembly of a heterotetrameric diiron protein
Authors: Marsh E. Neil G. , DeGrado William F.
Published: July 2002

Diiron and dimanganese proteins catalyze a wide range of hydrolytic and oxygen-dependent reactions. To probe the mechanisms by which individual members of this class of proteins are able to catalyze such a wide range of reactions, we have prepared a model four-helix bundle with a diiron site located near the center of the bundle. The four-helix bundle is constructed by the noncovalent self-assembly of three different chains (A
a
, A
b
, and B) that self-assemble into the desired heterotetramer when mixed in a 1:1:2 molar ratio. On addition of ferrous ions and oxygen, the protein forms a complex with a UV-visible spectrum closely resembling that of peroxo-bridged diferric species in natural proteins and model compounds. By combining a small collection of
n
variants of these peptides, it should now be possible to prepare an
n
3
member library, which will allow systematic exploration of the features giving rise to the catalytic properties of this class of proteins.
Cross-clade inhibition of HIV-1 replication and cytopathology by using RNase P-associated external guide sequences
Authors: Kraus Günter , Geffin Rebeca , Spruill Gina , Young Andrea K. , Seivright Rachel , Cardona Diana , Burzawa Jennifer , Hnatyszyn H. James
Published: July 2002

RNase P complexes have been proposed as a novel RNA-based gene interference strategy to inhibit gene expression in human malignancies and infectious diseases. This approach is based on the sequence-specific design of an external guide sequence (EGS) RNA molecule that can specifically hybridize to almost any complementary target mRNA and facilitate its cleavage by the RNase P enzyme component. We designed a truncated RNase P-associated EGS molecule to specifically recognize the U5 region of HIV-1 mRNA and mediate cleavage of hybridized mRNA by the RNase P enzyme. Genes encoding for this U5-EGS (560) molecule, as well as a U5 EGS (560D) antisense control, were cloned into retroviral plasmids and transferred into a CD4
+
T cell line. Transfected cells were exposed to increasing concentrations of HIV-1 clinical isolates from clades A, B, C, and F. Heterogeneous cultures of CD4
+
T cells expressing the U5 EGS (560) molecule were observed to maintain CD4 levels, were devoid of cytopathology, and did not produce HIV p24 gag antigen through 30 days after exposure to all HIV-1 clades at a multiplicity of infection of 0.01. Identical cells expressing the U5 EGS (560D) antisense control molecule underwent a loss of CD4 expression, produced elevated levels of HIV-1, and formed large syncytia similar to untreated cells. When the viral inoculum was increased at the time of exposure (multiplicity of infection = 0.05), the inhibitory effect of the U5 EGS (560) molecule was overwhelmed, but viral-mediated cytopathology and particle production were delayed compared with control cell populations. Viral replication and cytopathology associated with infection of multiple HIV-1 clades can be effectively inhibited in CD4
+
cells expressing the RNase P-associated U5 EGS (560) molecule.
Thyroid hormone activates oligodendrocyte precursors and increases a myelin-forming protein and NGF content in the spinal cord during experimental allergic encephalomyelitis
Authors: Calza Laura , Fernandez Mercedes , Giuliani Alessandro , Aloe Luigi , Giardino Luciana
Published: July 2002

Remyelination in the adult central nervous system has been demonstrated in different experimental models of demyelinating diseases. However, there is no clear evidence that remyelination occurs in multiple sclerosis, the most diffuse demyelinating disease. In this article, we explore the possibility of promoting myelination in experimental allergic encephalomyelitis, a widely used experimental model of multiple sclerosis, by recruiting progenitors and channeling them into oligodendroglial lineage through administration of thyroid hormone (T4). A large number of proliferating cells (BrdUrd uptake and Ki67-IR) and the expression of markers for undifferentiated precursors (nestin) increased in the subventricular zone and spinal cord of experimental allergic encephalomyelitis animals. T4 administration reduces proliferation and nestin-immunoreactivity and up-regulates expression of markers for oligodendrocyte progenitors [polysialylated-neural cell adhesion molecule (PSA-NCAM), O4, A2B5] and mature oligodendrocytes (myelin basic protein) in the spinal cord, olfactory bulb, and subventricular zone.
Formation of temporal-feature maps by axonal propagation of synaptic learning
Authors: Kempter Richard , Leibold Christian , Wagner Hermann , van Hemmen J. Leo
Published: July 2002

Computational maps are of central importance to a neuronal
representation of the outside world. In a map, neighboring neurons
respond to similar sensory features. A well studied example is the
computational map of interaural time differences (ITDs), which is
essential to sound localization in a variety of species and allows
resolution of ITDs of the order of 10 μs. Nevertheless, it is unclear
how such an orderly representation of temporal features arises. We
address this problem by modeling the ontogenetic development of an ITD
map in the laminar nucleus of the barn owl. We show how the owl's ITD
map can emerge from a combined action of homosynaptic spike-based
Hebbian learning and its propagation along the presynaptic axon. In
spike-based Hebbian learning, synaptic strengths are modified according
to the timing of pre- and postsynaptic action potentials. In unspecific
axonal learning, a synapse's modification gives rise to a factor that
propagates along the presynaptic axon and affects the properties of
synapses at neighboring neurons. Our results indicate that both Hebbian
learning and its presynaptic propagation are necessary for map
formation in the laminar nucleus, but the latter can be orders of
magnitude weaker than the former. We argue that the algorithm is
important for the formation of computational maps, when, in particular,
time plays a key role.
Crystal structure of
cis
-prenyl chain elongating enzyme, undecaprenyl diphosphate synthase
Authors: Fujihashi Masahiro , Zhang Yuan-Wei , Higuchi Yoshiki , Li Xiao-Yuan , Koyama Tanetoshi , Miki Kunio
Published: July 2002

Undecaprenyl diphosphate synthase (UPS) catalyzes the
cis
-prenyl chain elongation onto
trans
,
trans
-farnesyl diphosphate (FPP) to produce undecaprenyl
diphosphate (UPP), which is indispensable for the biosynthesis of
bacterial cell walls. We report here the crystal structure of UPS as
the only three-dimensional structure among
cis
-prenyl
chain elongating enzymes. The structure is classified into a protein
fold family and is completely different from the so-called
“isoprenoid synthase fold” that is believed to be a common
structure for the enzymes relating to isoprenoid biosynthesis.
Conserved amino acid residues among
cis
-prenyl chain
elongating enzymes are located around a large hydrophobic cleft in the
UPS structure. A structural P-loop motif, which frequently appears in
the various kinds of phosphate binding site, is found at the entrance
of this cleft. The catalytic site is determined on the basis of these
structural features, from which a possible reaction mechanism is
proposed.
Tissue spreading on implantable substrates is a competitive outcome of cell–cell vs. cell–substratum adhesivity
Authors: Ryan Peter L. , Foty Ramsey A. , Kohn Joachim , Steinberg Malcolm S.
Published: July 2002

While the interactions of cells with polymeric substrata are widely
studied, the influence of cell–cell cohesivity on tissue spreading has
not been rigorously investigated. Here we demonstrate that the rate of
tissue spreading over a two-dimensional substratum reflects a
competition or “tug-of-war” between cell–cell and
cell–substratum adhesions. We have generated both a “library” of
structurally related copolymeric substrata varying in their adhesivity
to cells and a library of genetically engineered cell populations
varying only in cohesivity. Cell–substratum adhesivity was varied
through the poly(ethylene glycol) content of a series of copolymeric
substrata, whereas cell–cell cohesivity was varied through the
expression of the homophilic cohesion molecules N- and R-cadherin by
otherwise noncohesive L929 cells. In the key experiment, multicellular
aggregates containing about 600 cells were allowed to spread onto
copolymeric surfaces. We compared the spreading behavior of aggregates
having different levels of cell–cell cohesivity on a series of
copolymeric substrata having different levels of cell–substratum
adhesivity. In these experiments, cell–cell cohesivity was measured by
tissue surface tensiometry, and cell–substratum adhesivity was
assessed by a distractive method. Tissue spreading was assayed by
confocal microscopy as the rate of cell emigration from similar-sized,
fluorescence-labeled, multicellular aggregates deposited on each of the
substrata. We demonstrate that either decreasing substratum adhesivity
or increasing cell–cell cohesivity dramatically slowed the spreading
rate of cell aggregates.
The three-dimensional structure of halorhodopsin to 5 Å by electron crystallography: A new unbending procedure for two-dimensional crystals by using a global reference structure
Authors: Kunji Edmund R. S. , von Gronau Susanne , Oesterhelt Dieter , Henderson Richard
Published: July 2002

Electron microscopy does not, in principle, require highly ordered crystals to determine a high-resolution structure. Nevertheless, crystals of any type help to constrain the molecules into a more limited range of orientations and positions, from which it is easier to carry out structure determination. We describe an improved procedure for determination of crystalline disorder, which we have applied to poorly ordered two-dimensional crystals of the chloride pump halorhodopsin from
Halobacterium salinarum
. The new image analysis procedure involves the use of a reference projection calculated from a global three-dimensional map to carry out the initial cross-correlation analysis. Coupled with a greater number of images taken with field emission gun microscopes, this has allowed us to calculate a three-dimensional structure for halorhodopsin, in which the seven transmembrane helices and certain molecular features, such as the β-ionone ring of retinal, are now resolved.
Uncompensated polyuria in a mouse model of Bartter's syndrome
Authors: Takahashi Nobuyuki , Chernavvsky Daniel R. , Gomez R. Ariel , Igarashi Peter , Gitelman Hillel J. , Smithies Oliver
Published: July 2002

We have used homologous recombination to disrupt the mouse gene coding for the NaK2Cl cotransporter (NKCC2) expressed in kidney epithelial cells of the thick ascending limb and macula densa. This gene is one of several that when mutated causes Bartter's syndrome in humans, a syndrome characterized by severe polyuria and electrolyte imbalance. Homozygous NKCC2−/− pups were born in expected numbers and appeared normal. However, by day 1 they showed signs of extracellular volume depletion (hematocrit 51%; wild type 37%). They subsequently failed to thrive. By day 7, they were small and markedly dehydrated and exhibited renal insufficiency, high plasma potassium, metabolic acidosis, hydronephrosis of varying severity, and high plasma renin concentrations. None survived to weaning. Treatment of −/− pups with indomethacin from day 1 prevented growth retardation and 10% treated for 3 weeks survived, although as adults they exhibited severe polyuria (10 ml/day), extreme hydronephrosis, low plasma potassium, high blood pH, hypercalciuria, and proteinuria. Wild-type mice treated with furosemide, an inhibitor of NaK2Cl cotransporters, have a phenotype similar to the indomethacin-rescued −/− adults except that hydronephrosis was mild. The polyuria, hypercalciuria, and proteinuria of the −/− adults and furosemide-treated wild-type mice were unresponsive to inhibitors of the renin angiotensin system, vasopressin, and further indomethacin. Thus absence of NKCC2 in the mouse causes polyuria that is not compensated elsewhere in the nephron. The NKCC2 mutant animals should be valuable for uncovering new pathophysiologic and therapeutic aspects of genetic disturbances in water and electrolyte recovery by the kidney.
Differential activation of a
Candida albicans
virulence gene family during infection
Authors: Staib Peter , Kretschmar Marianne , Nichterlein Thomas , Hof Herbert , Morschhäuser Joachim
Published: July 2002

The yeast
Candida albicans
is a harmless commensal in most healthy people, but it causes superficial as well as life-threatening systemic infections in immunocompromised patients.
C. albicans
can colonize or infect virtually all body sites because of its high adaptability to different host niches, which involves the activation of appropriate sets of genes in response to complex environmental signals. We have used an
in vivo
expression technology that is based on genetic recombination as a reporter of gene expression to monitor the differential activation of individual members of a gene family encoding secreted aspartic proteinases (Saps), which have been implicated in
C. albicans
virulence, at various stages of the infection process. Our results demonstrate that
SAP
expression depends on the type of infection, with different
SAP
isogenes being activated during systemic disease as compared with mucosal infection. In addition, the activation of individual
SAP
genes depends on the progress of the infection, some members of the gene family being induced immediately after contact with the host, whereas others are expressed only after dissemination into deep organs. In the latter case, the number of invading organisms determines whether induction of a virulence gene is necessary for successful infection. The
in vivo
expression technology allows the elucidation of gene expression patterns at different stages of the fungus–host interaction, thereby revealing regulatory adaptation mechanisms that make
C. albicans
the most successful fungal pathogen of humans and, at the same time, identifying the stage of an infection at which certain virulence genes may play a role.
Oxytocin and its receptors are synthesized in the rat vasculature
Authors: Jankowski Marek , Wang Donghao , Hajjar Fadi , Mukaddam-Daher Suhayla , McCann Samuel M. , Gutkowska Jolanta
Published: July 2002

Produced and released by the heart, oxytocin (OT) acts on its cardiac receptors to decrease the cardiac rate and force of contraction. We hypothesized that it might also be produced in the vasculature and regulate vascular tone. Consequently, we prepared acid extracts of the pulmonary artery and vena cava of male rats. OT concentrations in dog and sheep aortae were equivalent to those of rat aorta (2745 ± 180 pg/mg protein), indicating that it is present in the vasculature of several mammalian species. Reverse-phase HPLC of aorta and vena cava extracts revealed a single peak corresponding to the amidated OT nonapeptide. Reverse-transcribed PCR confirmed OT synthesis in these tissues. Using the selective OT receptor ligand compound VI, we detected a high number of OT-binding sites in the rat vena cava and aorta. Furthermore, OT receptor (OTR) mRNA was found in the vena cava, pulmonary vein, and pulmonary artery with lower levels in the aorta, suggesting vessel-specific OTR distribution. The abundance of OTR mRNA in the vena cava and pulmonary vein was associated with high atrial natriuretic peptide mRNA. In addition, we have demonstrated that diethylstilbestrol treatment of immature female rats increased OT significantly in the vena cava but not in the aorta and augmented OTR mRNA in both the aorta (4-fold) and vena cava (2-fold), implying regulation by estrogen. Altogether, these data suggest that the vasculature contains an intrinsic OT system, which may be involved in the regulation of vascular tone as well as vascular regrowth and remodeling.
Hemispheric asymmetry in human lateral prefrontal cortex during cognitive set shifting
Authors: Konishi Seiki , Hayashi Toshihiro , Uchida Idai , Kikyo Hideyuki , Takahashi Emi , Miyashita Yasushi
Published: July 2002

Functional organization of human cerebral hemispheres is asymmetrically specialized, most typically along a verbal/nonverbal axis. In this event-related functional MRI study, we report another example of the asymmetrical specialization. Set-shifting paradigms derived from the Wisconsin card sorting test were used, where subjects update one behavior to another on the basis of environmental feedback. The cognitive requirements constituting the paradigms were decomposed into two components according to temporal stages of task events. Double dissociation of the component brain activity was found in the three bilateral pairs of regions in the lateral frontal cortex, the right regions being activated during exposure to negative feedback and the corresponding left regions being activated during updating of behavior, to suggest that both hemispheres contribute to cognitive set shifting but in different ways. The asymmetrical hemispheric specialization within the same paradigms further implies an interhemispheric interaction of these task components that achieve a common goal.
Demonstration of the extrinsic coagulation pathway in teleostei: Identification of zebrafish coagulation factor VII
Authors: Sheehan John , Templer Michael , Gregory Michael , Hanumanthaiah Ravikumar , Troyer Dean , Phan Thao , Thankavel Bharath , Jagadeeswaran Pudur
Published: July 2002

It is not known whether the mammalian mechanism of coagulation initiation is conserved in fish. Identification of factor VII is critical in providing evidence for such a mechanism. A cDNA was cloned from a zebrafish (teleost) library that predicted a protein with sequence similarity to human factor VII. Factor VII was shown to be present in zebrafish blood and liver by Western blot analysis and immunohistochemistry. Immunodepletion of factor VII from zebrafish plasma selectively inhibited thromboplastin-triggered thrombin generation. Heterologous expression of zebrafish factor VII demonstrated a secreted protein (50 kDa) that reconstituted thromboplastin-triggered thrombin generation in immunodepleted zebrafish plasma. These results suggest conservation of the extrinsic coagulation pathway between zebrafish and humans and add credence to the zebrafish as a model for mammalian hemostasis. The structure of zebrafish factor VIIa predicted by homology modeling was consistent with the overall three-dimensional structure of human factor VIIa. However, amino acid disparities were found in the epidermal growth factor-2/serine protease regions that are present in the human tissue factor–factor VIIa contact surface, suggesting a structural basis for the species specificity of this interaction. In addition, zebrafish factor VII demonstrates that the Gla-EGF-EGF-SP domain structure, which is common to coagulation factors VII, IX, X, and protein C, was present before the radiation of the teleosts from the tetrapods. Identification of zebrafish factor VII significantly narrows the evolutionary window for development of the vertebrate coagulation cascade and provides insight into the structural basis for species specificity in the tissue factor–factor VIIa interaction.
Omega 3 but not omega 6 fatty acids inhibit AP-1 activity and cell transformation in JB6 cells
Authors: Liu Guangming , Bibus Douglas M. , Bode Ann M. , Ma Wei-Ya , Holman Ralph T. , Dong Zigang
Published: July 2002

Epidemiological and animal-based investigations have indicated that the development of skin cancer is in part associated with poor dietary practices. Lipid content and subsequently the derived fatty acid composition of the diet are believed to play a major role in the development of tumorigenesis. Omega 3 (ω3) fatty acids, including docosahexaenoic acid (DHA) and eicosapentaenoic acid (EPA), can effectively reduce the risk of skin cancer whereas omega 6 (ω6) fatty acids such as arachidonic acid (AA) reportedly promote risk. To investigate the effects of fatty acids on tumorigenesis, we performed experiments to examine the effects of the ω3 fatty acids EPA and DHA and of the ω6 fatty acid AA on phorbol 12-tetradecanoate 13-acetate (TPA)-induced or epidermal growth factor (EGF)-induced transcription activator protein 1 (AP-1) transactivation and on the subsequent cellular transformation in a mouse epidermal JB6 cell model. DHA treatment resulted in marked inhibition of TPA- and EGF-induced cell transformation by inhibiting AP-1 transactivation. EPA treatment also inhibited TPA-induced AP-1 transactivation and cell transformation but had no effect on EGF-induced transformation. AA treatment had no effect on either TPA- or EGF-induced AP-1 transactivation or transformation, but did abrogate the inhibitory effects of DHA on TPA- or EGF-induced AP-1 transactivation and cell transformation in a dose-dependent manner. The results of this study demonstrate that the inhibitory effects of ω3 fatty acids on tumorigenesis are more significant for DHA than for EPA and are related to an inhibition of AP-1. Similarly, because AA abrogates the beneficial effects of DHA, the dietary ratio of ω6 to ω3 fatty acids may be a significant factor in mediating tumor development.
A growth-constrained environment drives tumor progression
in
vivo
Authors: Laconi S. , Pani P. , Pillai S. , Pasciu D. , Sarma D. S. R. , Laconi E.
Published: July 2002

We recently have shown that selective growth of transplanted normal hepatocytes can be achieved in a setting of cell cycle block of endogenous parenchymal cells. Thus, massive proliferation of donor-derived normal hepatocytes was observed in the liver of rats previously given retrorsine (RS), a naturally occurring alkaloid that blocks proliferation of resident liver cells. In the present study, the fate of nodular hepatocytes transplanted into RS-treated or normal syngeneic recipients was followed. The dipeptidyl peptidase type IV-deficient (DPPIV
−
) rat model for hepatocyte transplantation was used to distinguish donor-derived cells from recipient cells. Hepatocyte nodules were chemically induced in Fischer 344, DPPIV
+
rats; livers were then perfused and larger (>5 mm) nodules were separated from surrounding tissue. Cells isolated from either tissue were then injected into normal or RS-treated DPPIV
−
recipients. One month after transplantation, grossly visible nodules (2–3 mm) were seen in RS-treated recipients transplanted with nodular cells. They grew rapidly, occupying 80–90% of the host liver at 2 months, and progressed to hepatocellular carcinoma within 4 months. By contrast, no liver nodules developed within 6 months when nodular hepatocytes were injected into the liver of recipients not exposed to RS, although small clusters of donor-derived cells were present in these animals. Taken together, these results directly point to a fundamental role played by the host environment in modulating the growth and the progression rate of altered cells during carcinogenesis. In particular, they indicate that conditions associated with growth constraint of the host tissue can drive tumor progression
in vivo
.
The highly recombinogenic
bz
locus lies in an unusually gene-rich region of the maize genome
Authors: Fu Huihua , Park Wonkeun , Yan Xianghe , Zheng Zhenwei , Shen Binzhang , Dooner Hugo K.
Published: July 2002

The
bronze
(
bz
) locus exhibits the highest rate of recombination of any gene in higher plants. To investigate the possible basis of this high rate of recombination, we have analyzed the physical organization of the region around the
bz
locus. Two adjacent bacterial artificial chromosome clones, comprising a 240-kb contig centered around the
Bz-McC
allele, were isolated, and 60 kb of contiguous DNA spanning the two bacterial artificial chromosome clones was sequenced. We find that the
bz
locus lies in an unusually gene-rich region of the maize genome. Ten genes, at least eight of which are shown to be transcribed, are contained in a 32-kb stretch of DNA that is uninterrupted by retrotransposons. We have isolated nearly full length cDNAs corresponding to the five proximal genes in the cluster. The average intertranscript distance between them is just 1 kb, revealing a surprisingly compact packaging of adjacent genes in this part of the genome. At least 11 small insertions, including several previously described miniature inverted repeat transposable elements, were detected in the introns and 3′ untranslated regions of genes and between genes. The gene-rich region is flanked at the proximal and distal ends by retrotransposon blocks. Thus, the maize genome appears to have scattered regions of high gene density similar to those found in other plants. The unusually high rate of intragenic recombination seen in
bz
may be related to the very high gene density of the region.
The cysteine desulfurase, IscS, has a major role in
in vivo
Fe-S cluster formation in
Escherichia coli
Authors: Schwartz Christopher J. , Djaman Ouliana , Imlay James A. , Kiley Patricia J.
Published: July 2002

The cysteine desulfurase, IscS, provides sulfur for Fe-S cluster synthesis
in vitro
, but a role for IscS in
in vivo
Fe-S cluster formation has yet to be established. To study the
in vivo
function of IscS in
Escherichia coli
, a strain lacking IscS was constructed and characterized. Using this
iscS
deletion strain, we have observed decreased specific activities for proteins containing [4Fe-4S] clusters from soluble (aconitase B, 6-phosphogluconate dehydratase, glutamate synthase, fumarase A, and FNR) and membrane-bound proteins (NADH dehydrogenase I and succinate dehydrogenase). A specific role for IscS in
in vivo
Fe-S cluster assembly was demonstrated by showing that an Fe-S cluster independent mutant of FNR is unaffected by the lack of IscS. These data support the conclusion that, via its cysteine desulfurase activity, IscS provides the sulfur that subsequently becomes incorporated during
in vivo
Fe-S cluster synthesis. We also have characterized a growth phenotype associated with the loss of IscS. Under aerobic conditions the deletion of IscS caused an auxotrophy for thiamine and nicotinic acid, whereas under anaerobic conditions, only nicotinic acid was required. The lack of IscS also had a general effect on the growth of
E. coli
because the
iscS
deletion strain grew at half the rate of wild type in many types of media even when the auxotrophies were satisfied.
ATR inhibition selectively sensitizes G
1
checkpoint-deficient cells to lethal premature chromatin condensation
Authors: Nghiem Paul , Park Peter K. , Kim Yong-son , Vaziri Cyrus , Schreiber Stuart L.
Published: July 2002

Premature chromatin condensation (PCC) is a hallmark of mammalian cells that begin mitosis before completing DNA replication. This lethal event is prevented by a highly conserved checkpoint involving an unknown, caffeine-sensitive mediator. Here, we have examined the possible involvement of the caffeine-sensitive ATM and ATR protein kinases in this checkpoint. We show that caffeine's ability to inhibit ATR (but not ATM) causes PCC, that ATR (but not ATM) prevents PCC, and that ATR prevents PCC via Chk-1 regulation. Moreover, mimicking cancer cell phenotypes by disrupting normal G
1
checkpoints sensitizes cells to PCC by ATR inhibition plus low-dose DNA damage. Notably, loss of p53 function potently sensitizes cells to PCC caused by ATR inhibition by a small molecule. We present a molecular model for how ATR prevents PCC and suggest that ATR represents an attractive therapeutic target for selectively killing cancer cells by premature chromatin condensation.
Role of glutamate δ-2 receptors in activity-dependent competition between heterologous afferent fibers
Authors: Morando Laura , Cesa Roberta , Rasetti Roberta , Harvey Robin , Strata Piergiorgio
Published: July 2002

A principle that regulates detailed architecture in the brain is
that active terminals have a competitive advantage over less active
terminals in establishing synaptic connections. This principle is known
to apply to fibers within a single neuronal population competing for a
common target domain. Here we uncover an additional rule that applies
when two neuronal populations compete for two contiguous territories.
The cerebellar Purkinje cell dendrites have two different synaptic
domains with spines innervated by two separate excitatory inputs,
parallel fibers (PFs) and climbing fibers (CFs). Glutamate δ-2
receptors are normally present only on the PF spines where they are
important for their innervation. After block of activity by
tetrodotoxin, numerous new spines form in the CF domain and become
innervated mainly by PFs; all spines, including those still innervated
by the CFs, bear δ-2 receptors. Thus, in the absence of activity, PFs
gain a competitive advantage over CFs. The entire dendritic arbor
becomes a uniform territory with the molecular cues associated with the
PFs. To access their proper territory and maintain synaptic contacts,
CFs must be active and locally repress the cues of the competitor
afferents.
Human hepatitis C virus NS5A protein alters intracellular calcium levels, induces oxidative stress, and activates STAT-3 and NF-κB
Authors: Gong Guozhong , Waris Gulam , Tanveer Rasheeda , Siddiqui Aleem
Published: July 2002

The nonstructural protein 5A (NS5A) encoded by the human hepatitis C virus RNA genome is shown here to induce the activation of NF-κB and STAT-3 transcription factors from its cytoplasmic residence via oxidative stress. NS5A causes the disturbance of intracellular calcium. Ca2+signaling triggers the elevation of reactive oxygen species in mitochondria, leading to the translocation of NF-κB and STAT-3 into the nucleus. Evidence is presented for the constitutive activation of STAT-3 by NS5A. In the presence of antioxidants [pyrrolidine dithiocarbamate (PDTC), N-acetyll-cysteine (NAC)] or Ca2+chelators (EGTA-AM, TMB-8), NS5A-induced activation of NF-κB and STAT-3 was eliminated. These results provide an insight into the mechanism by which NS5A can alter intracellular events relevant to liver pathogenesis associated with the viral infection.
The murine β-globin locus control region regulates the rate of transcription but not the hyperacetylation of histones at the active genes
Authors: Schübeler Dirk , Groudine Mark , Bender M. A.
Published: July 2002

Locus control regions (LCRs) are defined by their ability to confer
high-level tissue-specific expression to linked genes in transgenic
assays. Previously, we reported that, at its native site, the murine
β-globin LCR is required for high-level β-globin gene expression,
but is not required to initiate an open chromatin conformation of the
locus. To further investigate the mechanism of LCR-mediated
transcriptional enhancement, we have analyzed allele-specific
β-globin expression and the pattern of histone acetylation in the
presence and absence of the LCR. In single cells from mice heterozygous
for a deletion of the LCR, β-globin expression from the LCR-deleted
allele is consistently low (≈1–4% of wild type). Thus, the
endogenous LCR enhances globin gene expression by
increasing the rate of transcription from each linked allele rather
than by increasing the probability of establishing transcription
per se
. Furthermore, in erythroid cells from mice
homozygous for the highly expressing wild-type β-globin locus,
hyperacetylation of histones H3 and H4 is localized to the LCR and
active genes. In mice homozygous for the LCR deletion reduced histone
hyperacetylation is observed in LCR proximal sequences; however,
deletion of the LCR has no effect on the localized hyperacetylation of
the genes. Together, our results suggest that, in its native genomic
context, the LCR follows the rate model of enhancer function, and that
the developmentally specific hyperacetylation of the globin genes is
independent of both the rate of transcription and the presence of the
LCR.
The case of medium-dependent dual mechanisms for photoisomerization: One-bond-flip and Hula-Twist
Authors: Liu Robert S. H. , Hammond George S.
Published: July 2002

This paper critically reviews examples in the literature of photochemical cis-trans isomerization paying particular attention to the medium effect and accompanied conformational changes. A case is made that the Hula-Twist mechanism, postulated in 1985 as a photochemical reaction pathway for a polyene chromophore imbedded in a protein binding cavity such as those of rhodopsin and bacteriorhodopsin, is also a dominant reaction pathway for a diene, or a longer polyene confined in a rigid (relative to isomerization rate) medium. The conventional one-bond-flip process is the preferred reaction pathway in a fluid medium. While defining experiments are proposed, this dual mechanistic approach successfully accounts for all examples in the literature on photoisomerization reactions whether involving conformational changes or not.
Stress-induced changes in cerebral metabolites, hippocampal volume, and cell proliferation are prevented by antidepressant treatment with tianeptine
Authors: Czéh Boldizsár , Michaelis Thomas , Watanabe Takashi , Frahm Jens , de Biurrun Gabriel , van Kampen Marja , Bartolomucci Alessandro , Fuchs Eberhard
Published: July 2002

Stress-induced structural remodeling in the adult hippocampus, involving debranching and shortening of dendrites and suppression of neurogenesis, provides a cellular basis for understanding the impairment of neural plasticity in the human hippocampus in depressive illness. Accordingly, reversal of structural remodeling may be a desirable goal for antidepressant therapy. The present study investigated the effect of tianeptine, a modified tricyclic antidepressant, in the chronic psychosocial stress model of adult male tree shrews (
Tupaia belangeri
), a model with high validity for research on the pathophysiology of major depression. Animals were subjected to a 7-day period of psychosocial stress to elicit stress-induced endocrine and central nervous alterations before the onset of daily oral administration of tianeptine (50 mg/kg). The psychosocial stress continued throughout the treatment period of 28 days. Brain metabolite concentrations were determined
in vivo
by proton magnetic resonance spectroscopy, cell proliferation in the dentate gyrus was quantified by using BrdUrd immunohistochemistry, and hippocampal volume was measured post mortem. Chronic psychosocial stress significantly decreased
in vivo
concentrations of
N
-acetyl-aspartate (−13%), creatine and phosphocreatine (−15%), and choline-containing compounds (−13%). The proliferation rate of the granule precursor cells in the dentate gyrus was reduced (−33%). These stress effects were prevented by the simultaneous administration of tianeptine yielding normal values. In stressed animals treated with tianeptine, hippocampal volume increased above the small decrease produced by stress alone. These findings provide a cellular and neurochemical basis for evaluating antidepressant treatments with regard to possible reversal of structural changes in brain that have been reported in depressive disorders.
Nuclear relocation of a transactivator subunit precedes target gene activation
Authors: Francastel Claire , Magis Wendy , Groudine Mark
Published: July 2002

Murine erythroleukemia (MEL) cells are a model system to study reorganization of the eukaryotic nucleus during terminal differentiation. Upon chemical induction, MEL cells undergo erythroid differentiation, leading to activation of globin gene expression. Both processes strongly depend on the transcriptional activator NF-E2. Before induction of differentiation, both subunits of the NF-E2 heterodimer are present, but little DNA-binding activity is detectable. Using immunofluorescence microscopy, we show that the two NF-E2 subunits occupy distinct nuclear compartments in uninduced MEL cells; the smaller subunit NF-E2p18 is found primarily in the centromeric heterochromatin compartment, whereas the larger subunit NF-E2p45 occupies the euchromatin compartment. Concomitant with the commitment period of differentiation that precedes globin gene activation, NF-E2p18, along with other transcriptional repressors, relocates to the euchromatin compartment. Thus, relocation of NF-E2 p18 may be a rate-limiting step in formation of an active NF-E2 complex. To understand the mechanisms of NF-E2 localization, we show that centromeric targeting of NF-E2p18 requires dimerization, but not with an erythroid-specific partner, and that the transactivation domain of NF-E2p45 may be necessary and sufficient to prevent its localization in centromeric heterochromatin. Finally, using fluorescence
in situ
hybridization, we show that, upon differentiation, the β-globin gene loci relocate away from heterochromatin compartments to euchromatin. This relocation correlates with both transcriptional activation of the globin locus and relocation of NF-E2p18 away from heterochromatin, suggesting that these processes are linked.
Neisseria gonorrhoeae
PilV, a type IV pilus-associated protein essential to human epithelial cell adherence
Authors: Winther-Larsen Hanne C. , Hegge Finn Terje , Wolfgang Matthew , Hayes Stanley F. , van Putten Jos P. M. , Koomey Michael
Published: July 2002

Type IV pili (Tfp) of
Neisseria gonorrhoeae
, the
Gram-negative etiologic agent of gonorrhea, facilitate colonization of
the human host. Tfp are assumed to play a key role in the initial
adherence to human epithelial cells by virtue of the associated adhesin
protein PilC. To examine the structural and functional basis for
adherence in more detail, we identified potential genes encoding
polypeptides sharing structural similarities to PilE (the Tfp subunit)
within the
N. gonorrhoeae
genome sequence database. We
show here that a fiber subunit-like protein, termed PilV, is essential
to organelle-associated adherence but dispensable for Tfp biogenesis
and other pilus-related phenotypes, including autoagglutination,
competence for natural transformation, and twitching motility. The
adherence defect in
pilV
mutants cannot be attributed to
reduced levels of piliation, defects in fiber anchoring to the
bacterial cell surface, or to unstable pilus expression related to
organelle retraction. PilV is expressed at low levels relative to PilE
and copurifies with Tfp fibers in a PilC-dependent fashion. Purified
Tfp from
pilV
mutants contain PilC adhesin at reduced
levels. Taken together, these data support a model in which PilV
functions in adherence by promoting the functional display of PilC in
the context of the pilus fiber.
Ancient single origin for Malagasy primates.
Authors: Yoder A D , Cartmill M , Ruvolo M , Smith K , Vilgalys R
Published: July 2002

We report new evidence that bears decisively on a long-standing controversy in primate systematics. DNA sequence data for the complete cytochrome b gene, combined with an expanded morphological data set, confirm the results of a previous study and again indicate that all extant Malagasy lemurs originated from a single common ancestor. These results, as well as those from other genetic studies, call for a revision of primate classifications in which the dwarf and mouse lemurs are placed within the Afro-Asian lorisiforms. The phylogenetic results, in agreement with paleocontinental data, indicate an African origin for the common ancestor of lemurs and lorises (the Strepsirrhini). The molecular data further suggest the surprising conclusion that lemurs began evolving independently by the early Eocene at the latest. This indicates that the Malagasy primate lineage is more ancient than generally thought and places the split between the two strepsirrhine lineages well before the appearance of known Eocene fossil primates. We conclude that primate origins were marked by rapid speciation and diversification sometime before the late Paleocene.