bluuebunny/crossref_metadata_2025 huggingface dataset:
Presenilin-1 binds cytoplasmic epithelial cadherin, inhibits cadherin/p120 association, and regulates stability and function of the cadherin/catenin adhesion complex
Authors: Baki Lia , Marambaud Philippe , Efthimiopoulos Spiros , Georgakopoulos Anastasios , Wen Paul , Cui Wen , Shioi Junichi , Koo Eduard , Ozawa Masayuki , Friedrich Victor L. , Robakis Nikolaos K.
Published: July 2002

Here we show that presenilin-1 (PS1), a protein involved in
Alzheimer's disease, binds directly to epithelial cadherin
(E-cadherin). This binding is mediated by the large cytoplasmic loop of
PS1 and requires the membrane-proximal cytoplasmic sequence 604–615 of
mature E-cadherin. This sequence is also required for E-cadherin
binding of protein p120, a known regulator of cadherin-mediated cell
adhesion. Using wild-type and PS1 knockout cells, we found that
increasing PS1 levels suppresses p120/E-cadherin binding, and
increasing p120 levels suppresses PS1/E-cadherin binding. Thus
PS1 and p120 bind to and mutually compete for cellular E-cadherin.
Furthermore, PS1 stimulates E-cadherin binding to β- and γ-catenin,
promotes cytoskeletal association of the cadherin/catenin
complexes, and increases Ca
2+
-dependent cell–cell
aggregation. Remarkably, PS1 familial Alzheimer disease mutant ΔE9
increased neither the levels of cadherin/catenin complexes nor
cell aggregation, suggesting that this familial Alzheimer disease
mutation interferes with cadherin-based cell–cell adhesion. These data
identify PS1 as an E-cadherin-binding protein and a regulator of
E-cadherin function
in vivo
.
FKBP12, the 12-kDa FK506-binding protein, is a physiologic regulator of the cell cycle
Authors: Aghdasi Bahman , Ye Keqiang , Resnick Adam , Huang Alex , Ha Hyo Chol , Guo Xin , Dawson Ted M. , Dawson Valina L. , Snyder Solomon H.
Published: July 2002

FKBP12, the 12-kDa FK506-binding protein, is a ubiquitous abundant
protein that acts as a receptor for the immunosuppressant drug FK506,
binds tightly to intracellular calcium release channels and to the
transforming growth factor β (TGF-β) type I receptor. We now
demonstrate that cells from FKBP12-deficient (FKBP12
−/−
)
mice manifest cell cycle arrest in G
1
phase and that these
cells can be rescued by FKBP12 transfection. This arrest is mediated by
marked augmentation of p21(WAF1/CIP1) levels, which cannot be
further augmented by TGF-β1. The p21 up-regulation and cell cycle
arrest derive from the overactivity of TGF-β receptor signaling,
which is normally inhibited by FKBP12. Cell cycle arrest is prevented
by transfection with a dominant-negative TGF-β receptor construct.
TGF-β receptor signaling to gene expression can be mediated by SMAD,
p38, and ERK/MAP kinase (extracellular signal-regulated
kinase/mitogen-activated protein kinase) pathways. SMAD
signaling is down-regulated in FKBP12
−/−
cells.
Inhibition of ERK/MAP kinase fails to affect p21 up-regulation.
By contrast, activated phosphorylated p38 is markedly augmented in
FKBP12
−/−
cells and the p21 up-regulation is prevented by
an inhibitor of p38. Thus, FKBP12 is a physiologic regulator of cell
cycle acting by normally down-regulating TGF-β receptor signaling.
Topping off: A mechanism of first-male sperm precedence in a vertebrate
Authors: Jones Adam G. , Adams Erika M. , Arnold Stevan J.
Published: July 2002

Competition among the sperm of rival males is an important evolutionary phenomenon in many organisms. Yet, despite extensive research on sperm competition in some vertebrate taxa, very little progress has been made on this topic in amphibians. Urodele amphibians (newts and salamanders) are of particular interest to theories of sperm competition because most urodele females—in contrast to other vertebrate females—control the transfer of sperm from the male. Here we present a molecular study of sperm precedence and storage patterns in the rough-skinned newt (
Taricha granulosa
). First, we used microsatellite markers to show that female newts typically use sperm from 1–3 males under natural and seminatural conditions. Second, we mated experimental females sequentially to two males and collected fertilized eggs in a temporal series. Patterns of paternity were consistent with first-male sperm precedence and complete mixing of sperm within the female. This simple pattern of sperm usage, best described as “topping off,” is consistent with the expectation from sexual conflict theory that free female choice before insemination eliminates selective pressures for the evolution of complex patterns of paternity manipulation involving cryptic female choice.
UBE1L is a retinoid target that triggers PML/RARα degradation and apoptosis in acute promyelocytic leukemia
Authors: Kitareewan Sutisak , Pitha-Rowe Ian , Sekula David , Lowrey Christopher H. , Nemeth Michael J. , Golub Todd R. , Freemantle Sarah J. , Dmitrovsky Ethan
Published: July 2002

All
-
trans
-retinoic acid (RA) treatment induces remissions in acute promyelocytic leukemia (APL) cases expressing the t(15;17) product, promyelocytic leukemia (PML)/RA receptor α (RARα). Microarray analyses previously revealed induction of UBE1L (ubiquitin-activating enzyme E1-like) after RA treatment of NB4 APL cells. We report here that this occurs within 3 h in RA-sensitive but not RA-resistant APL cells, implicating UBE1L as a direct retinoid target. A 1.3-kb fragment of the UBE1L promoter was capable of mediating transcriptional response to RA in a retinoid receptor-selective manner. PML/RARα, a repressor of RA target genes, abolished this UBE1L promoter activity. A hallmark of retinoid response in APL is the proteasome-dependent PML/RARα degradation. UBE1L transfection triggered PML/RARα degradation, but transfection of a truncated UBE1L or E1 did not cause this degradation. A tight link was shown between UBE1L induction and PML/RARα degradation. Notably, retroviral expression of UBE1L rapidly induced apoptosis in NB4 APL cells, but not in cells lacking PML/RARα expression. UBE1L has been implicated directly in retinoid effects in APL and may be targeted for repression by PML/RARα. UBE1L is proposed as a direct pharmacological target that overcomes oncogenic effects of PML/RARα by triggering its degradation and signaling apoptosis in APL cells.
Ionic dependence of Ca
2+
channel modulation by syntaxin 1A
Authors: Wiser Ofer , Cohen Roy , Atlas Daphne
Published: July 2002

Alteration of the kinetic properties of voltage-gated Ca
2+
channels, Ca
v
1.2 (Lc-type), Ca
v
2.2 (N type), and Ca
v
2.3 (R type), by syntaxin 1A (Syn1A) and synaptotagmin could modulate exocytosis. We tested how switching divalent charge carriers from Ca
2+
to Sr
2+
and Ba
2+
affected Syn1A and synaptotagmin modulation of Ca
2+
-channel activation. Syn1A accelerated Ca
v
1.2 activation if Ca
2+
was the charge carrier; and by substituting for Ba
2+
, Syn1A slowed Ca
v
1.2 activation. Syn1A also significantly accelerated Ca
v
2.3 activation in Ca
2+
and marginally in Ba
2+
. Synaptotagmin, on the other hand, increased the rate of activation of Ca
v
2.3 and Ca
v
2.2 in all permeating ions tested. The Syn1A-channel interaction, unlike the synaptotagmin-channel interaction, proved significantly more sensitive to the type of permeating ion. It is well established that exocytosis is affected by switching the charge carriers. Based on the present results, we suggest that the channel-Syn1A interaction could respond to the conformational changes induced within the channel during membrane depolarization and divalent ion binding. These changes could partially account for the charge specificity of synaptic transmission as well as for the fast signaling between the Ca
2+
source and the fusion apparatus of
c
hannel-
a
ssociated-
v
esicles (CAV). Furthermore, propagation of conformational changes induced by the divalent ions appear to affect the concerted interaction of the channel with the fusion/docking machinery upstream to free Ca
2+
buildup and/or binding to a cytosolic Ca
2+
sensor. These results raise the intriguing possibility that the channel is the Ca
2+
sensor in the process of fast neurotransmitter release.
Microcin E492, a channel-forming bacteriocin from
Klebsiella pneumoniae
, induces apoptosis in some human cell lines
Authors: Hetz Claudio , Bono María Rosa , Barros Luis Felipe , Lagos Rosalba
Published: July 2002

The cytotoxic effect of microcin E492, a low-molecular-mass channel-forming bacteriocin (7,887 Da) produced by a strain of
Klebsiella pneumoniae
, was characterized in HeLa cells. At low (5 μg/ml) and intermediate (10 μg/ml) concentrations, microcin E492 induced biochemical and morphological changes typical of apoptosis, such as cell shrinkage, DNA fragmentation, extracellular exposure of phosphatidylserine, caspase activation, and loss of mitochondrial membrane potential. Treatment with zVAD-fmk, a general caspase inhibitor, completely blocked the cytotoxic effect of this bacteriocin. At higher microcin concentrations (>20 μg/ml) a necrotic phenotype was observed. Induction of apoptosis by microcin E492 was associated with the release of calcium from intracellular stores, probably after microcin-triggered ion channel formation. Microcin E492 also presented a cytotoxic effect on Jurkat and RJ2.25 cells, but had no effect on KG-1 cells nor on a primary culture of human tonsil endothelial cells, suggesting that there is a specific interaction of the bacteriocin with components of the target cell surface. This report describes a bacteriocin that has the capacity to induce apoptosis in human cell lines.
Impaired endochondral ossification and angiogenesis in mice deficient in membrane-type matrix metalloproteinase I
Authors: Zhou Zhongjun , Apte Suneel S. , Soininen Raija , Cao Renhai , Baaklini George Y. , Rauser Richard W. , Wang Jianming , Cao Yihai , Tryggvason Karl
Published: July 2002

Membrane-type matrix metalloproteinase I (MT1-MMP)-deficient mice were found to have severe defects in skeletal development and angiogenesis. The craniofacial, axial, and appendicular skeletons were severely affected, leading to a short and domed skull, marked deceleration of postnatal growth, and death by 3 wk of age. Shortening of bones is a consequence of decreased chondrocyte proliferation in the proliferative zone of the growth plates. Defective vascular invasion of cartilage leads to enlargement of hypertrophic zones of growth plates and delayed formation of secondary ossification centers in long bones. In an
in vivo
corneal angiogenesis assay, null mice did not have angiogenic response to implanted FGF-2, suggesting that the defect in angiogenesis is not restricted to cartilage alone. In tissues from null mice, activation of latent matrix metalloproteinase 2 was deficient, suggesting that MT1-MMP is essential for its activation
in vivo
.
Retroviral RNA identified in the cerebrospinal fluids and brains of individuals with schizophrenia
Authors: Karlsson Håkan , Bachmann Silke , Schröder Johannes , McArthur Justin , Torrey E. Fuller , Yolken Robert H.
Published: July 2002

Schizophrenia is a serious brain disease of uncertain etiology. A
role for retroviruses in the etiopathogenesis of some cases of
schizophrenia has been postulated on the basis of clinical and
epidemiological observations. We found sequences homologous to
retroviral
pol
genes in the cell-free cerebrospinal
fluids (CSFs) of 10 of 35 (29%) individuals with recent-onset
schizophrenia or schizoaffective disorder. Retroviral sequences also
were identified in the CSFs of 1 of 20 individuals with chronic
schizophrenia. However, retroviral sequences were not identified in any
of the CSFs obtained from 22 individuals with noninflammatory
neurological diseases or from 30 individuals without evidence of
neurological or psychiatric diseases (χ
2
= 19.25,
P
< 0.001). The nucleotide sequences identified in
the CSFs of the individuals with schizophrenia or schizoaffective
disorder were related to those of the human endogenous
retroviral (HERV)-W family of endogenous retroviruses and
to other retroviruses in the murine leukemia virus genus. Transcription
of RNA homologous to members of the HERV-W family of retroviruses also
was found to be up-regulated differentially in the frontal cortex
regions of brains obtained postmortem from individuals with
schizophrenia, as compared with corresponding tissue from individuals
without psychiatric diseases. The transcriptional activation of certain
retroviral elements within the central nervous system may be associated
with the development of schizophrenia in at least some individuals. The
further characterization of retroviral elements within the central
nervous system of individuals with schizophrenia might lead to improved
methods for the diagnosis and management of this disorder.
Short day lengths augment stress-induced leukocyte trafficking and stress-induced enhancement of skin immune function
Authors: Bilbo Staci D. , Dhabhar Firdaus S. , Viswanathan Kavitha , Saul Alison , Yellon Steven M. , Nelson Randy J.
Published: July 2002

Environmental conditions influence the onset and severity of infection and disease. Stressful conditions during winter may weaken immune function and further compromise survival by means of hypothermia, starvation, or shock. To test the hypothesis that animals may use photoperiod to anticipate the onset of seasonal stressors and adjust immune function, we evaluated glucocorticoids and the distribution of blood leukocytes in Siberian hamsters (Phodopus sungorus) exposed to long day lengths (i.e., summer) or short day (SD) lengths (i.e., winter) at baseline and during acute stress. We also investigated the influence of photoperiod and acute stress on a delayed-type hypersensitivity response in the skin. SDs increased glucocorticoid concentrations and the absolute number of circulating blood leukocytes, lymphocytes, T cells, and natural killer cells at baseline in hamsters. During stressful challenges, it appears beneficial for immune cells to exit the blood and move to primary immune defense areas such as the skin, in preparation for potential injury or infection. Acute (2 h) restraint stress induced trafficking of lymphocytes and monocytes out of the blood. This trafficking occurred more rapidly in SDs compared to long days. Baseline delayed-type hypersensitivity responses were enhanced during SDs; this effect was augmented by acute stress and likely reflected more rapid redistribution of leukocytes out of the blood and into the skin. These results suggest that photoperiod may provide a useful cue by which stressors in the environment may be anticipated to adjust the repertoire of available immune cells and increase survival likelihood.
Deletion of the thyroid hormone receptor α1 prevents the structural alterations of the cerebellum induced by hypothyroidism
Authors: Morte Beatriz , Manzano Jimena , Scanlan Thomas , Vennström Björn , Bernal Juan
Published: July 2002

Thyroid hormone (T3) controls critical aspects of cerebellar development, such as migration of postmitotic granule cells and terminal differentiation of Purkinje cells. T3 acts through nuclear receptors (TR) of two types, TRα1 and TRβ, that either repress or activate gene expression. We have analyzed the cerebellar structure of developing mice lacking the TRα1 isoform, which normally accounts for about 80% of T3 receptors in the cerebellum. Contrary to what was expected, granule cell migration and Purkinje cell differentiation were normal in the mutant mice. Even more striking was the fact that when neonatal hypothyroidism was induced, no alterations in cerebellar structure were observed in the mutant mice, whereas the wild-type mice showed delayed granule cell migration and arrested Purkinje cell growth. The results support the idea that repression by the TRα1 aporeceptor, and not the lack of thyroid hormone, is responsible for the hypothyroid phenotype. This conclusion was supported by experiments with the TRβ-selective compound GC-1. Treatment of hypothyroid animals with T3, which binds to TRα1 and TRβ, prevents any defect in cerebellar structure. In contrast, treatment with GC-1, which binds to TRβ but not TRα1, partially corrects Purkinje cell differentiation but has no effect on granule cell migration. Our data indicate that thyroid hormone has a permissive effect on cerebellar granule cell migration through derepression by the TRα1 isoform.
Attention deficit/hyperactivity disorder children with a 7-repeat allele of the dopamine receptor D4 gene have extreme behavior but normal performance on critical neuropsychological tests of attention
Authors: Swanson James , Oosterlaan Jaap , Murias Michael , Schuck Sabrina , Flodman Pamela , Spence M. Anne , Wasdell Michael , Ding Yuanchun , Chi Han-Chang , Smith Moyra , Mann Miranda , Carlson Caryn , Kennedy James L. , Sergeant Joseph A. , Leung Patrick , Zhang Ya-Ping , Sadeh Avi , Chen Chuansheng , Whalen Carol K. , Babb Kimberley A. , Moyzis Robert , Posner Michael I.
Published: July 2002

An association of the dopamine receptor D4 (DRD4) gene located on chromosome 11p15.5 and attention deficit/hyperactivity disorder (ADHD) has been demonstrated and replicated by multiple investigators. A specific allele [the 7-repeat of a 48-bp variable number of tandem repeats (VNTR) in exon 3] has been proposed as an etiological factor in attentional deficits manifested in some children diagnosed with this disorder. In the current study, we evaluated ADHD subgroups defined by the presence or absence of the 7-repeat allele of the DRD4 gene, using neuropsychological tests with reaction time measures designed to probe attentional networks with neuroanatomical foci in D4-rich brain regions. Despite the same severity of symptoms on parent and teacher ratings for the ADHD subgroups, the average reaction times of the 7-present subgroup showed normal speed and variability of response whereas the average reaction times of the 7-absent subgroup showed the expected abnormalities (slow and variable responses). This was opposite the primary prediction of the study. The 7-present subgroup seemed to be free of some of the neuropsychological abnormalities thought to characterize ADHD.
Multicopy plasmids are clustered and localized in
Escherichia coli
Authors: Pogliano Joe , Ho Thanh Quoc , Zhong Zhenping , Helinski Donald R.
Published: July 2002

We localized the multicopy plasmid RK2 in
Escherichia
coli
and found that the number of fluorescent foci observed in
each cell was substantially less than the copy number of the plasmid,
suggesting that many copies of RK2 are grouped into a few multiplasmid
clusters. In minimal glucose media, the majority of cells had one or
two foci, with a single focus localized near midcell, and two foci near
the 1/4 and 3/4 cell positions. The number of foci per cell
increased with cell length and with growth rate, and decreased upon
entering stationary phase, suggesting a coordination of RK2 replication
or segregation with the bacterial cell cycle. Time-lapse microscopy
demonstrated that partitioning of RK2 foci is achieved by the splitting
of a single focus into two or three smaller foci, which are capable of
separating with rapid kinetics. A derivative of the high-copy-number
plasmid pUC19 containing the
lacO
array was also
localized by tagging with GFP-LacI. Whereas many of the cells contained
numerous, randomly diffusing foci, most cells exhibited one or two
plasmid clusters located at midcell or the cell quarter positions. Our
results suggest a model in which multicopy plasmids are not always
randomly diffusing throughout the cell as previously thought, but can
be replicated and partitioned in clusters targeted to specific
locations.
The global phylogeny of glycolytic enzymes
Authors: Canback B. , Andersson S. G. E. , Kurland C. G.
Published: July 2002

Genes encoding the glycolytic enzymes of the facultative endocellular parasite
Bartonella henselae
have been analyzed phylogenetically within a very large cohort of homologues from bacteria and eukaryotes. We focus on this relative of
Rickettsia prowazekii
along with homologues from other α-proteobacteria to determine whether there have been systematic transfers of glycolytic genes from the presumed α-proteobacterial ancestor of the mitochondrion to the nucleus of the early eukaryote. The α-proteobacterial homologues representing the eight glycolytic enzymes studied here tend to cluster in well-supported nodes. Nevertheless, not one of these α-proteobacterial enzymes is related as a sister clade to the corresponding eukaryotic homologues. Nor is there a close phylogenetic relationship between glycolytic genes from Eucarya and any other bacterial phylum. In contrast, several of the reconstructions suggest that there may have been systematic transfer of sequences encoding glycolytic enzymes from cyanobacteria to some green plants. Otherwise, surprisingly little exchange between the bacterial and eukaryotic domains is observed. The descent of eukaryotic genes encoding enzymes of intermediary metabolism is reevaluated.
Animal antibiotic use has an early but important impact on the emergence of antibiotic resistance in human commensal bacteria
Authors: Smith David L. , Harris Anthony D. , Johnson Judith A. , Silbergeld Ellen K. , Morris J. Glenn
Published: July 2002

Antibiotic use is known to promote the development of antibiotic resistance, but substantial controversy exists about the impact of agricultural antibiotic use (AAU) on the subsequent emergence of antibiotic-resistant bacteria among humans. AAU for animal growth promotion or for treatment or control of animal diseases generates reservoirs of antibiotic-resistant (AR) bacteria that contaminate animal food products. Mathematical models are an important tool for understanding the potential medical consequences of this increased exposure. We have developed a mathematical model to evaluate factors affecting the prevalence of human commensal AR bacteria that cause opportunistic infections (e.g., enterococci). Our analysis suggests that AAU hastens the appearance of AR bacteria in humans. Our model indicates that the greatest impact occurs very early in the emergence of resistance, when AR bacteria are rare, possibly below the detection limits of current surveillance methods.
Methylation of histone H3 Lys 4 in coding regions of active genes
Authors: Bernstein Bradley E. , Humphrey Emily L. , Erlich Rachel L. , Schneider Robert , Bouman Peter , Liu Jun S. , Kouzarides Tony , Schreiber Stuart L.
Published: July 2002

Posttranslational modifications of histone tails regulate chromatin structure and transcription. Here we present global analyses of histone acetylation and histone H3 Lys 4 methylation patterns in yeast. We observe a significant correlation between acetylation of histones H3 and H4 in promoter regions and transcriptional activity. In contrast, we find that dimethylation of histone H3 Lys 4 in
coding regions
correlates with transcriptional activity. The histone methyltransferase Set1 is required to maintain expression of these active, promoter-acetylated, and coding region-methylated genes. Global comparisons reveal that genomic regions deacetylated by the yeast enzymes Rpd3 and Hda1 overlap extensively with Lys 4 hypo- but not hypermethylated regions. In the context of recent studies showing that Lys 4 methylation precludes histone deacetylase recruitment, we conclude that Set1 facilitates transcription, in part, by protecting active coding regions from deacetylation.
Polyglutamine aggregates alter protein folding homeostasis in
Caenorhabditis elegans
Authors: Satyal Sanjeev H. , Schmidt Enrico , Kitagawa Kazunori , Sondheimer Neal , Lindquist Susan , Kramer James M. , Morimoto Richard I.
Published: July 2002

Expansion of polyglutamine repeats in several unrelated proteins causes neurodegenerative diseases with distinct but related pathologies. To provide a model system for investigating common pathogenic features, we have examined the behavior of polyglutamine expansions expressed in
Caenorhabditis elegans
. The expression of polyglutamine repeats as green fluorescent protein (GFP)-fusion proteins in body wall muscle cells causes discrete cytoplasmic aggregates that appear early in embryogenesis and correlates with a delay in larval to adult development. The heat shock response is activated idiosyncratically in individual cells in a polyglutamine length-dependent fashion. The toxic effect of polyglutamine expression and the formation of aggregates can be reversed by coexpression of the yeast chaperone Hsp104. The altered homeostasis associated with polyglutamine aggregates causes both the sequestration of an otherwise soluble protein with shorter arrays of glutamine repeats and the relocalization of a nuclear glutamine-rich protein. These observations of induced aggregation and relocalization have implications for disorders involving protein aggregation.
Evidence in support of a four transmembrane-pore-transmembrane topology model for the
Arabidopsis thaliana
Na
+
/K
+
translocating AtHKT1 protein, a member of the superfamily of K
+
transporters
Authors: Kato Yasuhiro , Sakaguchi Masao , Mori Yasuo , Saito Kumiko , Nakamura Tatsunosuke , Bakker Evert P. , Sato Yoko , Goshima Shinobu , Uozumi Nobuyuki
Published: July 2002

The
Arabidopsis thaliana
AtHKT1 protein, a
Na
+
/K
+
transporter, is capable of mediating
inward Na
+
currents in
Xenopus laevis
oocytes and K
+
uptake in
Escherichia coli
.
HKT1 proteins are members of a superfamily of K
+
transporters. These proteins have been proposed to contain eight
transmembrane segments and four pore-forming regions arranged in a mode
similar to that of a K
+
channel tetramer. However, computer
analysis of the AtHKT1 sequence identified eleven potential
transmembrane segments. We have investigated the membrane topology of
AtHKT1 with three different techniques. First, a gene fusion alkaline
phosphatase study in
E. coli
clearly defined the
topology of the N-terminal and middle region of AtHKT1, but the model
for membrane folding of the C-terminal region had to be refined.
Second, with a reticulocyte-lysate supplemented with dog-pancreas
microsomes, we demonstrated that
N
-glycosylation occurs
at position 429 of AtHKT1. An engineered unglycosylated protein
variant, N429Q, mediated Na
+
currents in
X.
laevis
oocytes with the same characteristics as the wild-type
protein, indicating that
N
-glycosylation is not
essential for the functional expression and membrane targeting of
AtHKT1. Five potential glycosylation sites were introduced into the
N429Q. Their pattern of glycosylation supported the model based on the
E. coli
-alkaline phosphatase data. Third,
immunocytochemical experiments with FLAG-tagged AtHKT1 in HEK293 cells
revealed that the N and C termini of AtHKT1, and the regions containing
residues 135–142 and 377–384, face the cytosol, whereas the region of
residues 55–62 is exposed to the outside. Taken together, our results
show that AtHKT1 contains eight transmembrane-spanning segments.
Museum specimen data predict crop damage by tropical rodents
Authors: Sánchez-Cordero Víctor , Martínez-Meyer Enrique
Published: July 2002

Museum collections constitute a massive store of information on biological diversity. We used museum specimen data to generate ecological niche models that provide predictions of geographic distributions of native rodent pest species and agricultural census data that summarize the geographic distribution of nine crops in the state of Veracruz, Mexico, as well as crop losses between planting and harvest. Herein, we show that crop damage is related significantly to the predicted presence of rodent species for seven of nine crops. Museum collections may thus provide important baseline information for designing land-use and agricultural pest-management programs.
Enhanced resistance in STAT6-deficient mice to infection with ectromelia virus
Authors: Mahalingam Surendran , Karupiah Gunasegaran , Takeda Kiyoshi , Akira Shizuo , Matthaei Klaus I. , Foster Paul S.
Published: July 2002

We inoculated BALB/c mice deficient in STAT6 (STAT6−/−) and their wild-type (wt) littermates (STAT6+/+) with the natural mouse pathogen, ectromelia virus (EV). STAT6−/−mice exhibited increased resistance to generalized infection with EV when compared with STAT6+/+mice. In the spleens and lymph nodes of STAT6−/−mice, T helper 1 (Th1) cytokines were induced at earlier time points and at higher levels postinfection when compared with those in STAT6+/+mice. Elevated levels of NO were evident in plasma and splenocyte cultures of EV-infected STAT6−/−mice in comparison with STAT6+/+mice. The induction of high levels of Th1 cytokines in the mutant mice correlated with a strong natural killer cell response. We demonstrate in genetically susceptible BALB/c mice that the STAT6 locus is critical for progression of EV infection. Furthermore, in the absence of this transcription factor, the immune system defaults toward a protective Th1-like response, conferring pronounced resistance to EV infection and disease progression.
Crystal structures of the vitamin D-binding protein and its complex with actin: Structural basis of the actin-scavenger system
Authors: Otterbein Ludovic R. , Cosio Christophe , Graceffa Philip , Dominguez Roberto
Published: July 2002

Actin is the most abundant protein in eukaryotic cells, but its release from cells into blood vessels can be lethal, being associated with clinical situations including hepatic necrosis and septic shock. A homeostatic mechanism, termed the actin-scavenger system, is responsible for the depolymerization and removal of actin from the circulation. During the first phase of this mechanism, gelsolin severs the actin filaments. In the second phase, the vitamin D-binding protein (DBP) traps the actin monomers, which accelerates their clearance. We have determined the crystal structures of DBP by itself and complexed with actin to 2.1 Å resolution. Similar to its homologue serum albumin, DBP consists of three related domains. Yet, in DBP a strikingly different organization of the domains gives rise to a large actin-binding cavity. After complex formation the three domains of DBP move slightly to “clamp” onto actin subdomain 3 and to a lesser extent subdomain 1. Contacts between actin and DBP throughout their extensive 3,454-Å2intermolecular interface involve a mixture of hydrophobic, electrostatic, and solvent-mediated interactions. The area of actin covered by DBP within the complex approximately equals the sum of those covered by gelsolin and profilin. Moreover, certain interactions of DBP with actin mirror those observed in the actin-gelsolin complex, which may explain how DBP can compete effectively with gelsolin for actin binding. Formation of the strong actin–DBP complex proceeds with limited conformational changes to both proteins, demonstrating how DBP has evolved to become an effective actin-scavenger protein.
Role of the
iroquois3
homeobox gene in organizer formation
Authors: Kudoh Tetsuhiro , Dawid Igor B.
Published: July 2002

In zebrafish, the organizer is thought to consist of two regions, the yolk syncytial layer (YSL) and the shield. The dorsal YSL appears to send signals that affect formation of the shield in the overlying mesendoderm. We show here that a domain of dorsal deep cells located between the YSL and the shield is marked by expression of the
iro3
gene. As gastrulation proceeds, the
iro3
positive domain involutes and migrates to the animal pole.
Iro3
expression is regulated by Nodal and bone morphogenic protein antagonists. Overexpression of
iro3
induced ectopic expression of shield-specific genes. This effect was mimicked by an Iro3-Engrailed transcriptional repressor domain fusion, whereas an Iro3-VP16 activator domain fusion behaved as a dominant negative or antimorphic form. These results suggest that Iro3 acts as a transcriptional repressor and further implicate the
iro3
gene in regulating organizer formation. We propose that the
iro3
-expressing dorsal deep cells represent a distinct organizer domain that receives signals from the YSL and in turn sends signals to the forming shield, thereby influencing its expansion and differentiation.
Fundamental patterns underlying gene expression profiles: Simplicity from complexity
Authors: Holter Neal S. , Mitra Madhusmita , Maritan Amos , Cieplak Marek , Banavar Jayanth R. , Fedoroff Nina V.
Published: July 2002

Analysis of previously published sets of DNA microarray gene expression data by singular value decomposition has uncovered underlying patterns or “characteristic modes” in their temporal profiles. These patterns contribute unequally to the structure of the expression profiles. Moreover, the essential features of a given set of expression profiles are captured using just a small number of characteristic modes. This leads to the striking conclusion that the transcriptional response of a genome is orchestrated in a few fundamental patterns of gene expression change. These patterns are both simple and robust, dominating the alterations in expression of genes throughout the genome. Moreover, the characteristic modes of gene expression change in response to environmental perturbations are similar in such distant organisms as yeast and human cells. This analysis reveals simple regularities in the seemingly complex transcriptional transitions of diverse cells to new states, and these provide insights into the operation of the underlying genetic networks.
Tuning DNA “strings”: Modulating the rate of DNA replication with mechanical tension
Authors: Goel Anita , Frank-Kamenetskii Maxim D. , Ellenberger Tom , Herschbach Dudley
Published: July 2002

Recent experiments have measured the rate of replication of DNA catalyzed by a single enzyme moving along a stretched template strand. The dependence on tension was interpreted as evidence that T7 and related DNA polymerases convert two (
n
= 2) or more single-stranded template bases to double helix geometry in the polymerization site during each catalytic cycle. However, we find structural data on the T7 enzyme–template complex indicate
n
= 1. We also present a model for the “tuning” of replication rate by mechanical tension. This model considers only local interactions in the neighborhood of the enzyme, unlike previous models that use stretching curves for the entire polymer chain. Our results, with
n
= 1, reconcile force-dependent replication rate studies with structural data on DNA polymerase complexes.
Connexin expression in electrically coupled postnatal rat brain neurons
Authors: Venance Laurent , Rozov Andrei , Blatow Maria , Burnashev Nail , Feldmeyer Dirk , Monyer Hannah
Published: July 2002

Electrical coupling by gap junctions is an important form of cell-to-cell communication in early brain development. Whereas glial cells remain electrically coupled at postnatal stages, adult vertebrate neurons were thought to communicate mainly via chemical synapses. There is now accumulating evidence that in certain neuronal cell populations the capacity for electrical signaling by gap junction channels is still present in the adult. Here we identified electrically coupled pairs of neurons between postnatal days 12 and 18 in rat visual cortex, somatosensory cortex, and hippocampus. Notably, coupling was found both between pairs of inhibitory neurons and between inhibitory and excitatory neurons. Molecular analysis by single-cell reverse transcription–PCR revealed a differential expression pattern of connexins in these identified neurons.
Exploring the transcriptome of the malaria sporozoite stage
Authors: Kappe Stefan H. I. , Gardner Malcolm J. , Brown Stuart M. , Ross Jessica , Matuschewski Kai , Ribeiro Jose M. , Adams John H. , Quackenbush John , Cho Jennifer , Carucci Daniel J. , Hoffman Stephen L. , Nussenzweig Victor
Published: July 2002

Most studies of gene expression inPlasmodiumhave been concerned with asexual and/or sexual erythrocytic stages. Identification and cloning of genes expressed in the preerythrocytic stages lag far behind. We have constructed a high quality cDNA library of thePlasmodiumsporozoite stage by using the rodent malaria parasiteP. yoelii, an important model for malaria vaccine development. The technical obstacles associated with limited amounts of RNA material were overcome by PCR-amplifying the transcriptome before cloning. Contamination with mosquito RNA was negligible. Generation of 1,972 expressed sequence tags (EST) resulted in a total of 1,547 unique sequences, allowing insight into sporozoite gene expression. The circumsporozoite protein (CS) and the sporozoite surface protein 2 (SSP2) are well represented in the data set. Ablastxsearch with all tags of the nonredundant protein database gave only 161 unique significant matches (P(N) ≤ 10−4), whereas 1,386 of the unique sequences represented novel sporozoite-expressed genes. We identified ESTs for three proteins that may be involved in host cell invasion and documented their expression in sporozoites. These data should facilitate our understanding of the preerythrocyticPlasmodiumlife cycle stages and the development of preerythrocytic vaccines.
NMR reveals hydrogen bonds between oxygen and distal histidines in oxyhemoglobin
Authors: Lukin Jonathan A. , Simplaceanu Virgil , Zou Ming , Ho Nancy T. , Ho Chien
Published: July 2002

Compared with free heme, the proteins hemoglobin (Hb) and myoglobin (Mb) exhibit greatly enhanced affinity for oxygen relative to carbon monoxide. This physiologically vital property has been attributed to either steric hindrance of CO or stabilization of O
2
binding by a hydrogen bond with the distal histidine. We report here the first direct evidence of such a hydrogen bond in both α- and β-chains of oxyhemoglobin, as revealed by heteronuclear NMR spectra of chain-selectively labeled samples. Using these spectra, we have assigned the imidazole ring
1
H and
15
N chemical shifts of the proximal and distal histidines in both carbonmonoxy- and oxy-Hb. Because of their proximity to the heme, these chemical shifts are extremely sensitive to the heme pocket conformation. Comparison of the measured chemical shifts with values predicted from x-ray structures suggests differences between the solution and crystal structures of oxy-Hb. The chemical shift discrepancies could be accounted for by very small displacements of the proximal and distal histidines. This suggests that NMR could be used to obtain very high-resolution heme pocket structures of Hb, Mb, and other heme proteins.
Hematopoietic colony-forming cells derived from human embryonic stem cells
Authors: Kaufman Dan S. , Hanson Eric T. , Lewis Rachel L. , Auerbach Robert , Thomson James A.
Published: July 2002

Human embryonic stem (ES) cells are undifferentiated, pluripotent cells that can be maintained indefinitely in culture. Here we demonstrate that human ES cells differentiate to hematopoietic precursor cells when cocultured with the murine bone marrow cell line S17 or the yolk sac endothelial cell line C166. This hematopoietic differentiation requires fetal bovine serum, but no other exogenous cytokines. ES cell-derived hematopoietic precursor cells express the cell surface antigen CD34 and the hematopoietic transcription factors TAL-1, LMO-2, and GATA-2. When cultured on semisolid media with hematopoietic growth factors, these hematopoietic precursor cells form characteristic myeloid, erythroid, and megakaryocyte colonies. Selection for CD34+cells derived from human ES cells enriches for hematopoietic colony-forming cells, similar to CD34 selection of primary hematopoietic tissue (bone marrow, umbilical cord blood). More terminally differentiated hematopoietic cells derived from human ES cells under these conditions also express normal surface antigens: glycophorin A on erythroid cells, CD15 on myeloid cells, and CD41 on megakaryocytes. Thein vitrodifferentiation of human ES cells provides an opportunity to better understand human hematopoiesis and could lead to a novel source of cells for transfusion and transplantation therapies.
Serine-345 is required for Rad3-dependent phosphorylation and function of checkpoint kinase Chk1 in fission yeast
Authors: Lopez-Girona Antonia , Tanaka Katsunori , Chen Xiao-Bo , Baber Beth A. , McGowan Clare H. , Russell Paul
Published: July 2002

Genome integrity is monitored by a checkpoint that delays mitosis
in response to DNA damage. This checkpoint is enforced by Chk1, a
protein kinase that inhibits the mitotic inducer Cdc25. In fission
yeast, Chk1 is regulated by a group of proteins that includes Rad3, a
protein kinase related to human ATM and ATR. These kinases
phosphorylate serine or threonine followed by glutamine (SQ/TQ).
Fission yeast and human Chk1 proteins share two conserved SQ motifs at
serine-345 and serine-367. Serine-345 of human Chk1 is phosphorylated
in response to DNA damage. Here we report that Rad3 and ATM
phosphorylate serine-345 of fission yeast Chk1. Mutation of serine-345
(
chk1-S345A
) abrogates Rad3-dependent phosphorylation of
Chk1
in vivo
. The
chk1-S345A
cells are
sensitive to DNA damage and are checkpoint defective. In contrast,
mutations of serine-367 and other SQ/TQ sites do not substantially
impair the checkpoint or cause damage sensitivity. These findings
attest to the importance of serine-345 phosphorylation for Chk1
function and strengthen evidence that transduction of the DNA damage
checkpoint signal requires direct phosphorylation of Chk1 by Rad3.
AGO1, QDE-2, and RDE-1 are related proteins required for post-transcriptional gene silencing in plants, quelling in fungi, and RNA interference in animals
Authors: Fagard Mathilde , Boutet Stéphanie , Morel Jean-Benoit , Bellini Catherine , Vaucheret Hervé
Published: July 2002

Introduction of transgene DNA may lead to specific degradation of
RNAs that are homologous to the transgene transcribed sequence through
phenomena named post-transcriptional gene silencing (PTGS) in plants,
quelling in fungi, and RNA interference (RNAi) in animals. It was shown
previously that PTGS, quelling, and RNAi require a set of related
proteins (SGS2, QDE-1, and EGO-1, respectively). Here we report the
isolation of
Arabidopsis
mutants impaired in PTGS which
are affected at the
Argonaute1
(
AGO1
)
locus. AGO1 is similar to QDE-2 required for quelling and RDE-1
required for RNAi. Sequencing of
ago1
mutants revealed
one amino acid essential for PTGS that is also present in QDE-2 and
RDE-1 in a highly conserved motif. Taken together, these results
confirm the hypothesis that these processes derive from a common
ancestral mechanism that controls expression of invading nucleic acid
molecules at the post-transcriptional level. As opposed to
rde-1
and
qde-2
mutants, which are
viable,
ago1
mutants display several developmental
abnormalities, including sterility. These results raise the possibility
that PTGS, or at least some of its elements, could participate in the
regulation of gene expression during development in plants.
Plasmid-encoded MucB protein is a DNA polymerase (pol RI) specialized for lesion bypass in the presence of MucA′, RecA, and SSB
Authors: Goldsmith Moshe , Sarov-Blat Lea , Livneh Zvi
Published: July 2002

Replication through damaged sites in DNA requires in
Escherichia coli
the SOS stress-inducible DNA polymerase
V (UmuC), which is specialized for lesion bypass. Homologs of the
umuC
gene were found on native conjugative plasmids,
which often carry multiple antibiotic-resistant genes. MucB is a UmuC
homolog present on plasmid R46, and its variant plasmid pKM101 has been
introduced into
Salmonella
strains for use in the Ames
test for mutagens. Using a translesion replication assay based on a
gapped plasmid carrying a site-specific synthetic abasic site in the
single-stranded DNA region, we show that MucB is a DNA polymerase,
termed pol RI, which is specialized for lesion bypass. The activity of
pol RI requires the plasmid-encoded MucA′ protein and the
E.
coli
RecA and single-strand DNA binding proteins. Elimination
of any of the proteins from the reaction abolished lesion bypass and
polymerase activity. The unprocessed MucA could not substitute for
MucA′ in the bypass reaction. The presence of a lesion bypass DNA
polymerase on a native conjugative plasmid, which has a broad host
range specificity and carries multiple antibiotic-resistant genes,
raises the possibility that mutagenesis caused by pol RI plays a
role in the spreading of antibiotic resistance among bacterial
pathogens.
Functional mosaic organization of mouse olfactory receptor neurons
Authors: Ma Minghong , Shepherd Gordon M.
Published: July 2002

In contrast to rapid progress in the molecular biology of
olfaction, there are few physiological data to characterize the odor
response properties of different populations of olfactory receptor
neurons (ORNs) and their spatial distributions across the epithelium,
which is essential for understanding the coding mechanisms underlying
odor discrimination and recognition. We have tested the hypothesis that
the ORNs are arranged in a functional mosaic, using an intact
epithelial preparation from the mouse, in which odor responses of many
ORNs
in situ
can be monitored simultaneously with
calcium imaging techniques. ORNs responding to a given odor were widely
distributed across epithelium and intermingled with ORNs responding to
other odors. Tight clusters of ORNs responding to the same odor were
observed. For a given odor, more ORNs were recruited when the
concentration was increased. ORNs were able to distinguish between
pairs of enantiomers by showing distinct but somewhat overlapping
patterns. The results provide evidence regarding the response spectra
of ORNs
in situ
, supporting the combinatorial coding of
odor quality and intensity by different ORN subsets.
The Ebola virus VP35 protein functions as a type I IFN antagonist
Authors: Basler Christopher F. , Wang Xiuyan , Mühlberger Elke , Volchkov Victor , Paragas Jason , Klenk Hans-Dieter , García-Sastre Adolfo , Palese Peter
Published: July 2002

An assay has been developed that allows the identification of
molecules that function as type I IFN antagonists. Using this assay, we
have identified an Ebola virus-encoded inhibitor of the type I IFN
response, the Ebola virus VP35 protein. The assay relies on the
properties of an influenza virus mutant, influenza delNS1 virus, which
lacks the NS1 ORF and, therefore, does not produce the NS1 protein.
When cells are infected with influenza delNS1 virus, large amounts of
type I IFN are produced. As a consequence, influenza delNS1 virus
replicates poorly. However, high-efficiency transient transfection of a
plasmid encoding a protein that interferes with type I IFN-induced
antiviral functions, such as the influenza A virus NS1 protein or the
herpes simplex virus protein ICP34.5, rescues growth of influenza
delNS1 virus. When plasmids expressing individual Ebola virus proteins
were transfected into Madin Darby canine kidney cells, the Ebola virus
VP35 protein enhanced influenza delNS1 virus growth more than 100-fold.
VP35 subsequently was shown to block double-stranded RNA- and
virus-mediated induction of an IFN-stimulated response element reporter
gene and to block double-stranded RNA- and virus-mediated induction of
the IFN-β promoter. The Ebola virus VP35 therefore is likely to
inhibit induction of type I IFN in Ebola virus-infected cells and may
be an important determinant of Ebola virus virulence
in
vivo
.