bluuebunny/crossref_metadata_2025 huggingface dataset:
Ewing′s Sarcoma of the Head and Neck: A Retrospective Analysis of 24 Cases
Authors: Allam Ayman , El-Husseiny Gamal , Khafaga Yasser , Kandil Alaa , Gray Alan , Ezzat Adnan , Schultz Henrik
Published: July 2002

Introduction and purpose. Primary Ewing′s sarcoma arising from the
bones of the head and neck region is extremely rare representing only 1– 4% of all Ewing′s
sarcoma cases. Previous reports suggest a better prognosis for that particular anatomic site.
The purpose of this study was to analyze the clinico‐epidemiologic characteristics of that rare clinical presentation, as
well as its patterns of failure and prognosis following treatment.

Materials and methods. This study included a retrospective review of the medical records
of patients with the diagnosis of Ewing′s sarcoma of the head and neck region treated at King
Faisal Specialist Hospital and Research Center between 1975 and 1996.

Results. Out of a total number of 24 cases analyzed, there were 17 males and
7 females with a ratio of 2.4:1. The median age at diagnosis was 16.5 years. A painful swelling was
the most common clinical presentation.The maxilla was the most common site of presentation
(9/24 cases). There were 3/24 cases who presented with metastatic disease at diagnosis.The
majority of patients (16/24 cases) had a tumor size >10 cm. Most patients were treated with systemic
chemotherapy plus localized irradiation following an initial biopsy.With a mean follow
up of 3.4 years, the 5‐year actual overall survival (OS) for the whole group was 53%, while
the 5‐year actuarial disease‐free survival (DFS) was 30%. These figures were higher than those
repor ted from our institution for young patients (≤ 14 years treated for Ewing′ s sarcoma in other
anatomic locations (30% v 15%). The response to chemotherapy was the only prognostic factor
that affected both the OS and DFS.

Conclusion. The prognosis of Ewing′s sarcoma of the head and neck
region is slightly better than that of other anatomic sites.The response to systemic chemotherapy
is one of the most important prognostic factors affecting both DFS and OS of Ewing′s sarcoma of
the head and neck. Multimodality therapy consisting of an initial biopsy, aggressive combination
chemotherapy and localized radiotherapy is the treatment of choice for Ewing′s sarcoma of
the head and neck region and may result in long‐term survival.
MR Imaging of Bone Marrow in Patients with Musculoskeletal Tumors
Authors: Panicek David M. , Schwartz Lawrence H.
Published: July 2002

Knowledge of the appearances of normal bone marrow, metastases involving marrow,
and therapy‐related marrow changes shown by MR imaging is necessary in order to avoid
misdiagnosis. This article reviews MR imaging techniques and the findings that allow
distinction of normal yellow (fatty) marrow and red marrow from tumor in marrow,
as well as the identification of marrow changes resulting from radiation therapy or
treatment with marrow‐stimulating drugs in patients with musculoskeletal tumors.
Interleukin 1β-converting Enzyme Related Proteases/Caspases Are Involved in TRAIL-induced Apoptosis of Myeloma and Leukemia Cells
Authors: Mariani Sara M. , Matiba Bernd , Armandola Elena A. , Krammer Peter H.
Published: July 2002

The Fas/APO-1/CD95 ligand (CD95L) and the recently cloned TRAIL ligand belong to the TNFfamily and share the ability to induce apoptosis in sensitive target cells. Little information is available on the degree of functional redundancy between these two ligands in terms of target selectivity and intracellular signalling pathway(s). To address these issues, we have expressed and characterized recombinant mouse TRAIL. Specific detection with newly developed rabbit anti-TRAIL antibodies showed that the functional TRAIL molecule released into the supernatant of recombinant baculovirus-infected Sf9 cells is very similar to that associated with the membrane fraction of Sf9 cells. CD95L resistant myeloma cells were found to be sensitive to TRAIL, displaying apoptotic features similar to those of the CD95L- and TRAIL-sensitive T leukemia cells Jurkat. To assess if IL-1β-converting enzyme (ICE) and/or ICE-related proteases (IRPs) (caspases) are involved in TRAIL-induced apoptosis of both cell types, peptide inhibition experiments were performed. The irreversible IRP/caspase-inhibitor AcYVAD-cmk and the reversible IRP/caspase-inhibitor Ac-DEVD-CHO blocked the morphological changes, disorganization of plasma membrane phospholipids, DNA fragmentation, and loss of cell viability associated with TRAIL-induced apoptosis. In addition, cells undergoing TRAIL-mediated apoptosis displayed cleavage of poly(ADP)-ribose polymerase (PARP) that was completely blocked by Ac-DEVD-CHO.

These results indicate that TRAIL seems to complement the activity of the CD95 system as it allows cells, otherwise resistant, to undergo apoptosis triggered by specific extracellular ligands. Conversely, however, induction of apoptosis in sensitive cells by TRAIL involves IRPs/caspases in a fashion similar to CD95L. Thus, differential sensitivity to CD95L and TRAIL seems to map to the proximal signaling events associated with receptor triggering.
Direct and Regulated Interaction of Integrin αEβ7 with E-Cadherin
Authors: Higgins Jonathan M.G. , Mandlebrot Didier A. , Shaw Sunil K. , Russell Gary J. , Murphy Elizabeth A. , Chen Yih-Tai , Nelson W. James , Parker Christina M. , Brenner Michael B.
Published: July 2002

The cadherins are a family of homophilic adhesion molecules that play a vital role in the formation of cellular junctions and in tissue morphogenesis. Members of the integrin family are also involved in cell to cell adhesion, but bind heterophilically to immunoglobulin superfamily molecules such as intracellular adhesion molecule (ICAM)–1, vascular cell adhesion molecule (VCAM)–1, or mucosal addressin cell adhesion molecule (MadCAM)–1. Recently, an interaction between epithelial (E-) cadherin and the mucosal lymphocyte integrin, αEβ7, has been proposed. Here, we demonstrate that a human E-cadherin–Fc fusion protein binds directly to soluble recombinant αEβ7, and to αEβ7 solubilized from intraepithelial T lymphocytes. Furthermore, intraepithelial lymphocytes or transfected JY′ cells expressing the αEβ7 integrin adhere strongly to purified E-cadherin–Fc coated on plastic, and the adhesion can be inhibited by antibodies to αEβ7 or E-cadherin.

The binding of αEβ7 integrin to cadherins is selective since cell adhesion to P-cadherin–Fc through αEβ7 requires >100-fold more fusion protein than to E-cadherin–Fc. Although the structure of the αE-chain is unique among integrins, the avidity of αEβ7 for E-cadherin can be regulated by divalent cations or phorbol myristate acetate. Cross-linking of the T cell receptor complex on intraepithelial lymphocytes increases the avidity of αEβ7 for E-cadherin, and may provide a mechanism for the adherence and activation of lymphocytes within the epithelium in the presence of specific foreign antigen. Thus, despite its dissimilarity to known integrin ligands, the specific molecular interaction demonstrated here indicates that E-cadherin is a direct counter receptor for the αEβ7 integrin.
Interphase Cell Cycle Dynamics of a Late-Replicating, Heterochromatic Homogeneously Staining Region: Precise Choreography of Condensation/Decondensation and Nuclear Positioning
Authors: Li Gang , Sudlow Gail , Belmont Andrew S.
Published: July 2002

Recently we described a new method for in situ localization of specific DNA sequences, based on lac operator/repressor recognition (Robinett, C.C., A. Straight, G. Li, C. Willhelm, G. Sudlow, A. Murray, and A.S. Belmont. 1996. J. Cell Biol. 135:1685–1700). We have applied this methodology to visualize the cell cycle dynamics of an ∼90 Mbp, late-replicating, heterochromatic homogeneously staining region (HSR) in CHO cells, combining immunostaining with direct in vivo observations. Between anaphase and early G1, the HSR extends approximately twofold to a linear, ∼0.3-μm-diam chromatid, and then recondenses to a compact mass adjacent to the nuclear envelope. No further changes in HSR conformation or position are seen through mid-S phase. However, HSR DNA replication is preceded by a decondensation and movement of the HSR into the nuclear interior 4–6 h into S phase. During DNA replication the HSR resolves into linear chromatids and then recondenses into a compact mass; this is followed by a third extension of the HSR during G2/ prophase. Surprisingly, compaction of the HSR is extremely high at all stages of interphase. Preliminary ultrastructural analysis of the HSR suggests at least three levels of large-scale chromatin organization above the 30-nm fiber.
The Tyrosine Kinase p56lck Mediates Activation of Swelling-induced Chloride Channels in Lymphocytes
Authors: Lepple-Wienhues Albrecht , Szabò Ildikò , Laun Tilmann , Kaba Nubia Kristen , Gulbins Erich , Lang Florian
Published: July 2002

Osmotic cell swelling activates Cl− channels to achieve anion efflux. In this study, we find that both the tyrosine kinase inhibitor herbimycin A and genetic knockout of p56lck, a src-like tyrosine kinase, block regulatory volume decrease (RVD) in a human T cell line. Activation of a swelling-activated chloride current (ICl−swell) by osmotic swelling in whole-cell patch-clamp experiments is blocked by herbimycin A and lavendustin. Osmotic activation of ICl−swell is defective in p56lck-deficient cells. Retransfection of p56lck restores osmotic current activation. Furthermore, tyrosine kinase activity is sufficient for activation of ICl−swell. Addition of purified p56lck to excised patches activates an outwardly rectifying chloride channel with 31 pS unitary conductance. Purified p56lck washed into the cytoplasm activates ICl−swell in native and p56lck-deficient cells even when hypotonic intracellular solutions lead to cell shrinkage. When whole-cell currents are activated either by swelling or by p56lck, slow single-channel gating events can be observed revealing a unitary conductance of 25–28 pS. In accordance with our patch-clamp data, osmotic swelling increases activity of immunoprecipitated p56lck. We conclude that osmotic swelling activates ICl−swell in lymphocytes via the tyrosine kinase p56lck.
PSD-95 and SAP97 Exhibit Distinct Mechanisms for Regulating K+ Channel Surface Expression and Clustering
Authors: Tiffany Amanda M. , Manganas Louis N. , Kim Eunjoon , Hsueh Yi-Ping , Sheng Morgan , Trimmer James S.
Published: July 2002

Mechanisms of ion channel clustering by cytoplasmic membrane-associated guanylate kinases such as postsynaptic density 95 (PSD-95) and synapse-associated protein 97 (SAP97) are poorly understood. Here, we investigated the interaction of PSD-95 and SAP97 with voltage-gated or Kv K+ channels. Using Kv channels with different surface expression properties, we found that clustering by PSD-95 depended on channel cell surface expression. Moreover, PSD-95–induced clusters of Kv1 K+ channels were present on the cell surface. This was most dramatically demonstrated for Kv1.2 K+ channels, where surface expression and clustering by PSD-95 were coincidentally promoted by coexpression with cytoplasmic Kvβ subunits. Consistent with a mechanism of plasma membrane channel–PSD-95 binding, coexpression with PSD-95 did not affect the intrinsic surface expression characteristics of the different Kv channels. In contrast, the interaction of Kv1 channels with SAP97 was independent of Kv1 surface expression, occurred intracellularly, and prevented further biosynthetic trafficking of Kv1 channels. As such, SAP97 binding caused an intracellular accumulation of each Kv1 channel tested, through the accretion of SAP97 channel clusters in large (3–5 μm) ER-derived intracellular membrane vesicles. Together, these data show that ion channel clustering by PSD-95 and SAP97 occurs by distinct mechanisms, and suggests that these channel-clustering proteins may play diverse roles in regulating the abundance and distribution of channels at synapses and other neuronal membrane specializations.
Enhanced Expression of the α7β1 Integrin Reduces Muscular Dystrophy and Restores Viability in Dystrophic Mice
Authors: Burkin Dean J. , Wallace Gregory Q. , Nicol Kimberly J. , Kaufman David J. , Kaufman Stephen J.
Published: July 2002

Muscle fibers attach to laminin in the basal lamina using two distinct mechanisms: the dystrophin glycoprotein complex and the α7β1 integrin. Defects in these linkage systems result in Duchenne muscular dystrophy (DMD), α2 laminin congenital muscular dystrophy, sarcoglycan-related muscular dystrophy, and α7 integrin congenital muscular dystrophy. Therefore, the molecular continuity between the extracellular matrix and cell cytoskeleton is essential for the structural and functional integrity of skeletal muscle. To test whether the α7β1 integrin can compensate for the absence of dystrophin, we expressed the rat α7 chain in mdx/utr−/− mice that lack both dystrophin and utrophin. These mice develop a severe muscular dystrophy highly akin to that in DMD, and they also die prematurely. Using the muscle creatine kinase promoter, expression of the α7BX2 integrin chain was increased 2.0–2.3-fold in mdx/utr−/− mice. Concomitant with the increase in the α7 chain, its heterodimeric partner, β1D, was also increased in the transgenic animals. Transgenic expression of the α7BX2 chain in the mdx/utr−/− mice extended their longevity by threefold, reduced kyphosis and the development of muscle disease, and maintained mobility and the structure of the neuromuscular junction. Thus, bolstering α7β1 integrin–mediated association of muscle cells with the extracellular matrix alleviates many of the symptoms of disease observed in mdx/utr−/− mice and compensates for the absence of the dystrophin- and utrophin-mediated linkage systems. This suggests that enhanced expression of the α7β1 integrin may provide a novel approach to treat DMD and other muscle diseases that arise due to defects in the dystrophin glycoprotein complex. A video that contrasts kyphosis, gait, joint contractures, and mobility in mdx/utr−/− and α7BX2-mdx/utr−/−mice can be accessed at http://www.jcb.org/cgi/content/full/152/6/1207.
Discovery of a novel murine keratin 6 (K6) isoform explains the absence of hair and nail defects in mice deficient for K6a and K6b
Authors: Wojcik Sonja M. , Longley Mary A. , Roop Dennis R.
Published: July 2002

The murine genome is known to have two keratin 6 (K6) genes, mouse K6 (MK6)a and MK6b. These genes display a complex expression pattern with constitutive expression in the epithelia of oral mucosa, hair follicles, and nail beds. We generated mice deficient for both genes through embryonic stem cell technology. The majority of MK6a/b−/− mice die of starvation within the first two weeks of life. This is due to a localized disintegration of the dorsal tongue epithelium, which results in the build up of a plaque of cell debris that severely impairs feeding. However, ∼25% of MK6a/b−/− mice survive to adulthood. Remarkably, the surviving MK6a/b−/− mice have normal hair and nails. To our surprise, we discovered MK6 staining both in the hair follicle and the nail bed of MK6a/b−/− mice, indicating the presence of a third MK6 gene. We cloned this previously unknown murine keratin gene and found it to be highly homologous to human K6hf, which is expressed in hair follicles. We therefore termed this gene MK6 hair follicle (MK6hf). The presence of MK6hf in the MK6a/b−/− follicles and nails offers an explanation for the absence of hair and nail defects in MK6a/b−/− animals.
Myelination
Authors: Scherer Steven S.
Published: July 2002

Feltri et al. (2001)(this issue) succeed in disrupting β1 integrin specifically in Schwann cells, and in so doing, demonstrate that it is required for normal myelination. Their results reveal that signaling by an extracellular matrix receptor plays a key role in the differentiation of myelinating Schwann cells.
T Cell Receptor–initiated Calcium Release Is Uncoupled from Capacitative Calcium Entry in Itk-deficient T Cells
Authors: Liu Karen-Qianye , Bunnell Stephen C. , Gurniak Christine B. , Berg Leslie J.
Published: July 2002

Itk, a Tec family tyrosine kinase, plays an important but as yet undefined role in T cell receptor (TCR) signaling. Here we show that T cells from Itk-deficient mice have a TCR-proximal signaling defect, resulting in defective interleukin 2 secretion. Upon TCR stimulation, Itk−/− T cells release normal amounts of calcium from intracellular stores, but fail to open plasma membrane calcium channels. Since thapsigargin-induced store depletion triggers normal calcium entry in Itk−/− T cells, an impaired biochemical link between store depletion and channel opening is unlikely to be responsible for this defect. Biochemical studies indicate that TCR-induced inositol 1,4,5 tris-phosphate (IP3) generation and phospholipase C γ1 tyrosine phosphorylation are substantially reduced in Itk−/− T cells. In contrast, TCR-ζ and ZAP-70 are phosphorylated normally, suggesting that Itk functions downstream of, or in parallel to, ZAP-70 to facilitate TCR-induced IP3 production. These findings support a model in which quantitative differences in cytosolic IP3 trigger distinct responses, and in which only high concentrations of IP3 trigger the influx of extracellular calcium.
Endothelial Cell “Memory” of Inflammatory Stimulation: Human Venular Endothelial Cells Store Interleukin 8 in Weibel-Palade Bodies
Authors: Wolff Barbara , Burns Alan R. , Middleton James , Rot Antal
Published: July 2002

The expression and secretion of interleukin (IL)-8, the prototype member of the C-X-C subfamily of chemokines, can be induced by diverse inflammatory stimuli in many cells, including endothelial cells (EC). Upon de novo synthesis, IL-8 localizes intracellularly in the Golgi apparatus, from where it is secreted. In addition to this constitutive secretory pathway, we describe a depot storage and separate regulated secretory pathway of IL-8 in EC.

The prolonged stimulation of primary human EC with inflammatory mediators resulted in the accumulation of IL-8 in Weibel-Palade bodies, where it colocalized with von Willebrand factor. IL-8 was retained in these storage organelles for several days after the removal of the stimulus and could be released by EC secretagogues such as phorbol myristate acetate, the calcium ionophore A23187, and histamine. These findings suggest that storage of IL-8 in Weibel-Palade bodies may serve as the EC “memory” of a preceding inflammatory insult, which then enables the cells to secrete IL-8 immediately without de novo protein synthesis.
The Role of β7 Integrins in CD8 T Cell Trafficking During an Antiviral Immune Response
Authors: Lefrançois Leo , Parker Christina M. , Olson Sara , Muller Werner , Wagner Norbert , Puddington Lynn
Published: July 2002

The requirement of β7 integrins for lymphocyte migration was examined during an ongoing immune response in vivo. Transgenic mice (OT-I) expressing an ovalbumin-specific major histocompatibility complex class I–restricted T cell receptor for antigen were rendered deficient in expression of all β7 integrins or only the αEβ7 integrin. To quantitate the relative use of β7 integrins in migration in vivo, equal numbers of OT-I and OT-I-β7−/− or OT-I-αE−/− lymph node (LN) cells were adoptively transferred to normal mice. Although OT-I-β7−/− LN cells migrated to mesenteric LN and peripheral LN as well as wild-type cells, β7 integrins were required for naive CD8 T cell and B cell migration to Peyer's patch. After infection with a recombinant virus (vesicular stomatitis virus) encoding ovalbumin, β7 integrins became critical for migration of activated CD8 T cells to the mesenteric LN and Peyer's patch. Naive CD8 T cells did not enter the lamina propria or the intestinal epithelium, and the majority of migration of activated CD8 T cells to the small and large intestinal mucosa, including the epithelium, was β7 integrin–mediated. The αEβ7 integrin appeared to play no role in migration during a primary CD8 T cell immune response in vivo. Furthermore, despite dramatic upregulation of αEβ7 by CD8 T cells after entry into the epithelium, long-term retention of intestinal intraepithelial lymphocytes was also αEβ7 independent.
Endothelial-Monocyte Activating Polypeptide Ii, a Novel Antitumor Cytokine That Suppresses Primary and Metastatic Tumor Growth and Induces Apoptosis in Growing Endothelial Cells
Authors: Schwarz Margaret A. , Kandel Jessica , Brett Jerald , Li Jun , Hayward Joanne , Schwarz Roderich E. , Chappey Olivier , Wautier Jean-Luc , Chabot John , Gerfo Paul Lo , Stern David
Published: July 2002

Neovascularization is essential for growth and spread of primary and metastatic tumors. We have identified a novel cytokine, endothelial-monocyte activating polypeptide (EMAP) II, that potently inhibits tumor growth, and appears to have antiangiogenic activity. Mice implanted with Matrigel showed an intense local angiogenic response, which EMAP II blocked by 76% (P < 0.001). Neovascularization of the mouse cornea was similarly prevented by EMAP II (P < 0.003). Intraperitoneally administered EMAP II suppressed the growth of primary Lewis lung carcinomas, with a reduction in tumor volume of 65% versus controls (P < 0.003). Tumors from human breast carcinoma–derived MDA-MB 468 cells were suppressed by >80% in EMAP II–treated animals (P < 0.005). In a lung metastasis model, EMAP II blocked outgrowth of Lewis lung carcinoma macrometastases; total surface metastases were diminished by 65%, and of the 35% metastases present, ≈80% were inhibited with maximum diameter <2 mm (P < 0.002 vs. controls). In growing capillary endothelial cultures, EMAP II induced apoptosis in a time- and dose-dependent manner, whereas other cell types were unaffected. These data suggest that EMAP II is a tumor-suppressive mediator with antiangiogenic properties allowing it to target growing endothelium and limit establishment of neovasculature.
In Vivo Expression of Natural Killer Cell Inhibitory Receptors by Human Melanoma–Specific Cytolytic T Lymphocytes
Authors: Speiser Daniel E. , Pittet Mikaël J. , Valmori Danila , Dunbar Rod , Rimoldi Donata , Liénard Danielle , MacDonald H. Robson , Cerottini Jean-Charles , Cerundolo Vincenzo , Romero Pedro
Published: July 2002

Natural killer (NK) receptor signaling can lead to reduced cytotoxicity by NK cells and cytolytic T lymphocytes (CTLs) in vitro. Whether T cells are inhibited in vivo remains unknown, since peptide antigen–specific CD8+ T cells have so far not been found to express NK receptors in vivo. Here we demonstrate that melanoma patients may bear tumor-specific CTLs expressing NK receptors. The lysis of melanoma cells by patient-derived CTLs was inhibited by the NK receptor CD94/NKG2A. Thus, tumor-specific CTL activity may be decreased through NK receptor triggering in vivo.
Deregulated E2f Transcriptional Activity in Autonomously Growing Melanoma Cells
Authors: Halaban Ruth , Cheng Elaine , Smicun Yoel , Germino Joseph
Published: July 2002

Inactivation of the retinoblastoma tumor suppressor protein (pRb) has been implicated in melanoma cells, but the molecular basis for this phenotype has not yet been elucidated, and the status of additional family members (p107 and p130, together termed pocket proteins) or the consequences on downstream targets such as E2F transcription factors are not known. Because cell cycle progression is dependent on the transcriptional activity of E2F family members (E2F1–E2F6), most of them regulated by suppressive association with pocket proteins, we characterized E2F–pocket protein DNA binding activity in normal versus malignant human melanocytes. By gel shift analysis, we show that in mitogen-dependent normal melanocytes, external growth factors tightly controlled the levels of growth-promoting free E2F DNA binding activity, composed largely of E2F2 and E2F4, and the growth-suppressive E2F4–p130 complexes. In contrast, in melanoma cells, free E2F DNA binding activity (E2F2 and E2F4, to a lesser extent E2F1, E2F3, and occasionally E2F5), was constitutively maintained at high levels independently of external melanocyte mitogens. E2F1 was the only family member more abundant in the melanoma cells compared with normal melanocytes, and the approximately fivefold increase in DNA binding activity could be accounted for mostly by a similar increase in the levels of the dimerization partner DP1. The continuous high expression of cyclin D1, A2, and E, the persistent cyclin-dependent kinase 4 (CDK4) and CDK2 activities, and the presence of hyperphosphorylated forms of pRb, p107, and p130, suggest that melanoma cells acquired the capacity for autonomous growth through inactivation of all three pocket proteins and release of E2F activity, otherwise tightly regulated in normal melanocytes by external growth factors.
Mutations in the S4 Region Isolate the Final Voltage-dependent Cooperative Step in Potassium Channel Activation
Authors: Ledwell Jennifer L. , Aldrich Richard W.
Published: July 2002

Charged residues in the S4 transmembrane segment play a key role in determining the sensitivity of voltage-gated ion channels to changes in voltage across the cell membrane. However, cooperative interactions between subunits also affect the voltage dependence of channel opening, and these interactions can be altered by making substitutions at uncharged residues in the S4 region. We have studied the activation of two mutant Shaker channels that have different S4 amino acid sequences, ILT (V369I, I372L, and S376T) and Shaw S4 (the S4 of Drosophila Shaw substituted into Shaker), and yet have very similar ionic current properties. Both mutations affect cooperativity, making a cooperative transition in the activation pathway rate limiting and shifting it to very positive voltages, but analysis of gating and ionic current recordings reveals that the ILT and Shaw S4 mutant channels have different activation pathways. Analysis of gating currents suggests that the dominant effect of the ILT mutation is to make the final cooperative transition to the open state of the channel rate limiting in an activation pathway that otherwise resembles that of Shaker. The charge movement associated with the final gating transition in ILT activation can be measured as an isolated component of charge movement in the voltage range of channel opening and accounts for 13% (∼1.8 e0) of the total charge moved in the ILT activation pathway. The remainder of the ILT gating charge (87%) moves at negative voltages, where channels do not open, and confirms the presence of Shaker-like conformational changes between closed states in the activation pathway. In contrast to ILT, the activation pathway of Shaw S4 seems to involve a single cooperative charge-moving step between a closed and an open state. We cannot detect any voltage-dependent transitions between closed states for Shaw S4. Restoring basic residues that are missing in Shaw S4 (R1, R2, and K7) rescues charge movement between closed states in the activation pathway, but does not alter the voltage dependence of the rate-limiting transition in activation.
Packing measure of the sample paths of fractional Brownian motion
Authors: Xiao Yimin
Published: July 2002

Let

X
(
t
)
(
t
∈

R

)

X(t) (t \in \mathbf {R})

be a fractional Brownian motion of index

α
\alpha

in

R

d

.

\mathbf {R}^d.

If

1
>
α
d

1 > \alpha d

, then there exists a positive finite constant

K
K

such that with probability 1,
\[

ϕ
−
p
(
X
(
[
0
,
t
]
)
)
=
K
t

for any 

t
>
0

,

\phi -p(X([0,t])) = Kt\quad \text {for any $t > 0$},

\]
where
<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" alttext="phi left-parenthesis s right-parenthesis equals s Superscript StartFraction 1 Over alpha EndFraction Baseline slash left-parenthesis log log StartFraction 1 Over s EndFraction right-parenthesis Superscript StartFraction 1 Over 2 alpha EndFraction">

ϕ
(
s
)
=

s

1
α

/

(
log
⁡
log
⁡

1
s

)

1

2
α

\phi (s) = s^{\frac 1 { \alpha }}/ (\log \log \frac 1 s)^{\frac 1 {2 \alpha }}

and

ϕ
\phi

-

p
(
X
(
[
0
,
t
]
)
)

p (X([0,t]))

is the

ϕ
\phi

-packing measure of

X
(
[
0
,
t
]
)

X([0,t])

.
An approximate inertial manifolds approach to postprocessing the Galerkin method for the Navier-Stokes equations
Authors: García-Archilla Bosco , Novo Julia , Titi Edriss
Published: July 2002

In a recent paper we have introduced a postprocessing procedure for the Galerkin method for dissipative evolution partial differential equations with periodic boundary conditions. The postprocessing technique uses approximate inertial manifolds to approximate the high modes (the small scale components) in the exact solutions in terms of the Galerkin approximations, which in this case play the role of the lower modes (large scale components). This procedure can be seen as a defect-correction technique. But contrary to standard procedures, the correction is computed only when the time evolution is completed. Here we extend these results to more realistic boundary conditions. Specifically, we study in detail the two-dimensional Navier-Stokes equations subject to homogeneous (nonslip) Dirichlet boundary conditions. We also discuss other equations, such as reaction-diffusion systems and the Cahn-Hilliard equations.
Aspects of global Riemannian geometry
Authors: Petersen Peter
Published: July 2002

In this article we survey some of the developments in Riemannian geometry. We place special emphasis on explaining the relationship between curvature and topology for Riemannian manifolds with lower curvature bounds.
10-11 bp periodicities in complete genomes reflect protein structure and DNA folding.
Authors: Herzel H , Weiss O , Trifonov E N
Published: July 2002

MOTIVATION: Completely sequenced genomes allow for detection and analysis of the relatively weak periodicities of 10-11 basepairs (bp). Two sources contribute to such signals: correlations in the corresponding protein sequences due to the amphipatic character of alpha-helices and the folding of DNA (nucleosomal patterns, DNA supercoiling). Since the topological state of genomic DNA is of importance for its replication, recombination and transcription, there is an immediate interest to obtain information about the supercoiled state from sequence periodicities. RESULTS: We show that correlations within proteins affect mainly the oscillations at distances below 35 bp. The long-ranging correlations up to 100 bp reflect primarily DNA folding. For the yeast genome these oscillations are consistent in detail with the chromatin structure. For eubacteria and archaea the periods deviate significantly from the 10.55 bp value for free DNA. These deviations suggest that while a period of 11 bp in bacteria reflects negative supercoiling, the significantly different period of thermophilic archaea close to 10 bp corresponds to positive supercoiling of thermophilic archaeal genomes. AVAILABILITY: Protein sets and C programs for the calculation of correlation functions are available on request from the authors (see http://itb.biologie.hu-berlin.de).
Protein analyst--a distributed object environment for protein sequence and structure analysis.
Authors: Saqi M A , Wild D L , Hartshorn M J
Published: July 2002

SUMMARY: Protein Analyst is a flexible tool for the analysis of protein sequences with emphasis on the integration of sequence and structural information. AVAILABILITY: The software will be available from the Oxford Molecular Biolib web site (http://www. oxmol.co.uk/biolib) and will be free to the academic research community.
Immunocytochemical Localization of the Menkes Copper Transport Protein (ATP7A) to the Trans-Golgi Network
Authors: Dierick Herman A. , Adam Ayla N. , Escara-Wilke June F. , Glover Thomas W.
Published: July 2002

We have generated polyclonal antibodies against the amino-terminal third of the Menkes protein (ATP7A; MNK) by immunizing rabbits with a histidine-tagged MNK fusion construct containing metal-binding domains 1–4. The purified antibodies were used in Western analysis of cell lysates and in indirect immunofluorescence experiments on cultured cells. On Western blots, the antibodies recognized the ∼165 kDa MNK protein in CHO cells and human fibroblasts. No MNK signal could be detected in fibroblasts from a patient with Menkes disease or in Hep3B hepatocellular carcinoma cells, confirming the specificity of the antibodies. Immunocytochemical analysis of CHO cells and human fibroblasts showed a distinct perinuclear signal corresponding to the pattern of the Golgi complex. This staining pattern was similar to that of α-mannosidase II which is a known resident enzyme of the Golgi complex. Using brefeldin A, a fungal inhibitor of protein secretion, we further demonstrated that the MNK protein is localized to the trans-Golgi network. This data provides direct evidence for a subcellular localization of the MNK protein which is similar to the proposed vacuolar localization of Ccc2p, the yeast homolog of MNK and WND (ATP7B), the Wilson disease gene product. In light of the proposed role of MNK both in subcellular copper trafficking and in copper efflux, these data suggest a model for how these two processes are linked and represent an important step in the functional analysis of the MNK protein.
Ecosystem feedbacks on climate at the landscape scale
Authors: Hayden Bruce P.
Published: July 2002

Vegetation controls aspects of climate at all scales. These controls operate through fluxes of mass (water vapour, particulates, trace gases, condensation nuclei, and ice nuclei) and energy (latent and sensible heat, radiative exchanges, and momentum dissipation) between the biosphere and the atmosphere. The role these fluxes play in controlling minimum and maximum temperature, temperature range, rainfall, and precipitation processes are detailed. On the hemispheric scale, the importance of evapotranspiration, vegetation surface roughness, and vegetation albedo in the current generation of atmospheric general circulation models is reviewed. Finally, I assess at the planetary scale the global climate effects of biogenic emissions that are well mixed throughout the troposphere. I show that daily maximum and minimum temperatures are, in part, controlled by the emission of non–methane hydrocarbons and transpired water vapour. In many regions, a substantial fraction of the rainfall arises from upstream evapotranspiration rather than from oceanic evaporation. Biosphere evapotranspiration, surface roughness, and albedo are key controls in the general circulation of the atmosphere: climate models that lack adequate specifications for these biosphere attributes fail. The biosphere modulates climate at all scales.
Plant hormone perception and action: a role for G–protein signal transduction?
Authors: Hooley Richard
Published: July 2002

Plants perceive and respond to a profusion of environmental and endogenous signals that influence their growth and development. The G–protein signalling pathway is a mechanism for transducing extracellular signals that is highly conserved in a range of eukaryotes and prokaryotes. Evidence for the existence of G–protein signalling pathways in higher plants is reviewed, and their potential involvement in plant hormone signal transduction evaluated. A range of biochemical and molecular studies have identified potential components of G–protein signalling in plants, most notably a homologue of the G–protein coupled receptor superfamily (
GCR1
) and the G
α
and G
β
subunits of heterotrimeric G–proteins. G–protein agonists and antagonists are known to influence a variety of signalling events in plants and have been used to implicate heterotrimeric G–proteins in gibberellin and possibly auxin signalling. Antisense suppression of
GCR1
in
Arabidopsis
leads to a phenotype which supports a role for this receptor in cytokinin signalling. These observations suggest that higher plants have at least some of the components of G–protein signalling pathways and that these might be involved in the action of certain plant hormones.
Vertical jumping in Galago senegalensis: the quest for an obligate mechanical power amplifier
Authors: Aerts P.
Published: July 2002

Bushbabies (Galago senegalensis) are renowned for their phenomenal jumping capacity. It was postulated that mechanical power amplification must be involved. Dynamic analysis of the vertical jumps performed by two bushbabies confirms the need for a power amplifier. Inverse dynamics coupled to a geometric musculo–skeletal model were used to elucidate the precise nature of the mechanism powering maximal vertical jumps. Most of the power required for jumping is delivered by the vastus muscle–tendon systems (knee extensor). Comparison with the external joint–powers revealed, however, an important power transport from this extensor (about 65%) to the ankle and the midfoot via the bi–articular calf muscles. Peak power output likely implies elastic recoil of the complex aponeurotic system of the vastus muscle. Patterns of changes in length and tension of the muscle–tendon complex during different phases of the jump were found which provide strong evidence for substantial power amplification (times 15). It is argued here that the multiple internal connective tissue sheets and attachment structures of the well–developed bundles of the vastus muscle become increasingly stretched during preparatory crouching and throughout the extension phase, except for the last 13 ms of the push–off (i.e. when power requirements peak). Then, tension in the knee extensors abruptly falls from its maximum, allowing the necessary fast recoil of the tensed tendon structures to occur.
How microbial ancient DNA, found in association with human remains, can be interpreted
Authors: Rollo Franco , Marota Isolina
Published: July 2002

The analysis of the DNA of ancient micro–organisms in archaeological and palaeontological human remains can contribute to the understanding of issues as different as the spreading of a new disease, a mummification process or the effect of diets on historical human populations. The quest for this type of DNA, however, can represent a particularly demanding task. This is mainly due to the abundance and diffusion of bacteria, fungi, yeasts, algae and protozoans in the most diverse environments of the present–day biosphere and the resulting difficulty in distinguishing between ancient and modern DNA. Nevertheless, at least under some special circumstances, by using rigorous protocols, which include an archaeometric survey of the specimens and evaluation of the palaeoecological consistency of the results of DNA sequence analysis, glimpses of the composition of the original microbial flora (e.g. colonic flora) can be caught in ancient human remains. Potentials and pitfalls of this research field are illustrated by the results of research works performed on prehistoric, pre–Columbian and Renaissance human mummies.
Model–based development of neuroprostheses for paraplegic patients
Authors: Robert Riener
Published: July 2002

In paraplegic patients with upper motor neuron lesions the signal path from the central nervous system to the muscles is interrupted. Functional electrical stimulation applied to the lower motor neurons can replace the lacking signals. A so–called neuroprosthesis may be used to restore motor function in paraplegic patients on the basis of functional electrical stimulation. However, the control of multiple joints is difficult due to the complexity, nonlinearity, and time–variance of the system involved. Furthermore, effects such as muscle fatigue, spasticity, and limited force in the stimulated muscle further complicate the control task. Mathematical models of the human musculoskeletal system can support the development of neuroprostheses. In this article a detailed overview of the existing work in the literature is given and two examples developed by the author are presented that give an insight into model–based development of neuroprostheses for paraplegic patients. It is shown that modelling the musculoskeletal system can provide better understanding of muscular force production and movement coordination principles. Models can also be used to design and test stimulation patterns and feedback control strategies. Additionally, model components can be implemented in a controller to improve control performance. Eventually, the use of musculoskeletal models for neuroprosthesis design may help to avoid internal disturbances such as fatigue and optimize muscular force output. Furthermore, better controller quality can be obtained than in previous empirical approaches. In addition, the number of experimental tests to be performed with human subjects can be reduced. It is concluded that mathematical models play an increasing role in the development of reliable closed–loop controlled, lower extremity neuroprostheses.
Introduction
Authors: Charlesworth Brian , Harvey Paul
Published: July 2002

John Maynard Smith is one of the most influential evolutionary biologists of our time. This year he celebrates his 80th birthday, and it seemed appropriate to mark this occasion with a collection of papers by his former associates, and distinguished evolutionists whose work has been influenced by his example. John is noted for his breadth of interests and his ability to spot important but soluble problems, which he continues to attack by deceptively simple methods. He has published 13 books and collections of papers on an astonishing diversity of subjects. He has also published many semi–popular articles on biology, which are remarkable for their clarity and diversity. He is a widely sought–after lecturer, who is famous for his humorous and lucid presentations.
A comparison of position‐specific score matrices based on sequence and structure alignments
Authors: Panchenko Anna R. , Bryant Stephen H.
Published: July 2002

Sequence comparison methods based on position‐specific score matrices (PSSMs) have proven a useful tool for recognition of the divergent members of a protein family and for annotation of functional sites. Here we investigate one of the factors that affects overall performance of PSSMs in a PSI‐BLAST search, the algorithm used to construct the seed alignment upon which the PSSM is based. We compare PSSMs based on alignments constructed by global sequence similarity (ClustalW and ClustalW‐pairwise), local sequence similarity (BLAST), and local structure similarity (VAST). To assess performance with respect to identification of conserved functional or structural sites, we examine the accuracy of the three‐dimensional molecular models predicted by PSSM‐sequence alignments. Using the known structures of those sequences as the standard of truth, we find that model accuracy varies with the algorithm used for seed alignment construction in the pattern local‐structure (VAST) > local‐sequence (BLAST) > global‐sequence (ClustalW). Using structural similarity of query and database proteins as the standard of truth, we find that PSSM recognition sensitivity depends primarily on the diversity of the sequences included in the alignment, with an optimum around 30–50% average pairwise identity. We discuss these observations, and suggest a strategy for constructing seed alignments that optimize PSSM‐sequence alignment accuracy and recognition sensitivity.
Independent tyrosyl contributions to the CD of Ff gene 5 protein and the distinctive effects of Y41H and Y41F mutants on protein–protein cooperative interactions
Authors: Mou Tung‐Chung , Sreerama Narasimha , Terwilliger Thomas C. , Woody Robert W. , Gray Donald M.
Published: July 2002

The gene 5 protein (g5p) of the Ff virus contains five Tyr, individual mutants of which have now all been characterized by CD spectroscopy. The protein has a dominant tyrosyl 229‐nm La CD band that is shown to be approximately the sum of the five individual Tyr contributions. Tyr41 is particularly important in contributing to the high cooperativity with which the g5p binds to ssDNA, and Y41F and Y41H mutants are known to differ in dimer–dimer packing interactions in crystal structures. We compared the solution structures and binding properties of the Y41F and Y41H mutants using CD spectroscopy. Secondary structures of the mutants were similar by CD analyses and close to those derived from the crystal structures. However, there were significant differences in the binding properties of the two mutant proteins. The Y41H protein had an especially low binding affinity and perturbed the spectrum of poly[d(A)] in 2 mM Na+ much less than did Y41F and the wild‐type gene 5 proteins. Moreover, a change in the Tyr 229 nm band, assigned to the perturbation of Tyr34 at the dimer–dimer interface, was absent in titrations with the Y41H mutant under low salt conditions. In contrast, titrations with the Y41H mutant in 50 mM Na+ exhibited typical CD changes of both the nucleic acid and the Tyr 229‐nm band. Thus, protein–protein and g5p–ssDNA interactions appeared to be mutually influenced by ionic strength, indicative of correlated changes in the ssDNA binding and cooperativity loops of the protein or of indirect structural constraints.
Deadtime correction for two multihead Anger cameras in dual‐energy‐window‐acquisition mode
Authors: Koral Kenneth F. , Zasadny Kenneth R. , Ackermann Robert J. , Ficaro Edward P.
Published: July 2002

Two side‐by‐side energy windows, one at the photopeak and one at lower energy, are sometimes employed in quantitative SPECT studies. We measured the count‐rate losses at moderately high activities offor two multihead Anger cameras in such a dual‐window‐acquisition mode by imaging a decaying source composed of two hot spheres within a warm cylinder successively over a total of 23 days. The window locations were kept fixed and the paralyzable model was assumed. In addition, for the Picker Prism 3000 XP camera, the source was viewed from three different angles separated by 120° and the final results are from an average over these three angles. For the Picker camera, the fits to the data from the individual windows are good (the mean of the squared correlation coefficient equals 0.98) while for the Siemens Multispect camera fits to the data from head 1 and from the lower‐energy, monitor window are relatively poor. Therefore, with the Siemens camera the data from the two windows are combined for deadtime computation. Repeated autopeaking might improve the fits. At the maximum count rate, corresponding to a total activity of 740 MBq (20 mCi) in the phantom, the multiplicative deadtime correction factor is considerably larger for the Picker than for the Siemens camera. For the Picker camera, it is 1.11, 1.12, and 1.12 for heads 1–3 with the photopeak window and 1.10 for all heads with the lower‐energy monitor window. For the Siemens camera, the combined‐window deadtime correction factor is 1.02 for head 1 and 1.03 for head 2. Differences between the deadtime correction factor for focal activity and for the total activity do not support the hypothesis of count misplacement between foci of activity at these count rates. Therefore, the total‐image dead time correction is recommended for any and all parts of the image.
Multiresolution elastic image registration
Authors: Kostelec Peter J. , Weaver John B. , Healy Dennis M.
Published: July 2002

We have developed a multiscale algorithm for elastic (or molded) alignment of images. There is a wide array of medical applications of elastic (as opposed to strictly rigid) alignment: Subtraction of previous images from current ones to identify changes is perhaps the most obvious. We present preliminary results of this molding technique on a variety of images, and conclude with some closing remarks about this and future directions and goals of this work.