Biomedical subjects

Jennifer Reed

Publications and source records attributed to Jennifer Reed.

15 recordsLinked to original sources

PubMed2025

Comparative phylogeographic patterns in three pan-Amazonian antwren lineages (Aves: Passeriformes: Thamnophilidae: Myrmotherula and Isleria).

We examined DNA sequences of 328 individuals of three lineages (species or species complexes) of Amazonian antwrens to evaluate their degree of geographical and historical concordance. All lineages (Myrmotherula longipennis, M. menetriesii, and the Isleria guttata-hauxwelli species complex) consist of small insectivorous birds that occupy understory or midstory of terra firme forest and are widely distributed across the Amazon Basin. Individuals of each of the three lineages grouped into genetic clades mainly separated by the Amazon and some major tributaries, although members of different clades of both M. menetriesii and I. hauxwelli were documented in the Madeira-Tapajós interfluvium. Branching patterns differed among taxa, but all taxa were highly differentiated across the lower or upper Amazon. Despite the morphological, ecological, and phylogenetic similarities among lineages, and despite the fact that nearly all taxa are bounded by rivers, the effect of the other major rivers as biogeographic barriers was highly variable. The Marañón, Ucayali, Madeira, Tapajós, Xingu, Napo, Negro, and Branco all separated main clades in one or two lineages but not in the others. Levels of genetic differentiation along the Teles Pires were substantially higher than those across the Tapajós in M. menetriesii and I. hauxwelli, consistent with a proposed historical change of river course for the Tapajós. Genetic units in this study were comparable for the most part to taxonomic units delineated by analyses of vocal and morphological variation, and identical, with one exception, to units defined solely by vocal variation in a companion paper (Isler et al. 2025). These results, in conjunction with those of Isler et al. (2025), provide additional instances of the variability of responses to the historical dynamism of Amazonia, in this case in closely related and ecologically similar species; highlight the consistency of genetic differentiation with vocal differentiation in additional species of Neotropical suboscine birds; support the importance of Amazonian rivers in creating conditions that result in the differentiation of independent evolutionary lineages; and demonstrate that species richness in two of the lineages studied (M. longipennis and M. menetriesii) was previously underestimated.

Passeriformes↗

PubMed2006

The side chain interaction index as a tool for predicting fast-folding elements and the structure and stability of engineered peptides.

The side chain interaction index (SCII) is a method of calculating the propensity for short-range interactions among side chains within a peptide sequence. Here, it is shown that the SCII values of secondary structure elements that have been shown to fold early and independently cluster separately from those of structures that fold later and/or are dependent on long-range interactions. In addition, the SCII values of engineered peptides that spontaneously adopt a particular desired fold in solution are significantly different from those of engineered peptides that fail to exhibit a stable conformation. Thus, the SCII, as a measure of local structural stability, constitutes a useful tool in folding prediction and in protein/peptide engineering. A program that allows rapid calculation of SCII values is presented.

Drug Stability↗

PubMed2005

Significance of Fas receptor protein expression in epithelial ovarian cancer.

Fas receptor (FasR) is a cell surface receptor that, when activated, triggers apoptosis. It has been postulated that this receptor may be involved in the clearance of benign ovarian epithelial inclusion cysts (IC). In this study, we test the hypothesis that the expression of FasR changes among IC, cystadenoma (AD), tumors of low malignant potential (LMP), and invasive cancer (cystadenocarcinoma, CA). Formalin-fixed paraffin-embedded sections from 53 oophorectomy specimens representing 26 IC, 17 AD, 17 LMP, and 24 CA were stained using the immunohistochemical avidin-biotin-peroxidase method. We used a mouse antihuman monoclonal antibody Apo-1/Fas (Dako), at 1:5 dilution, after antigen retrieval. The stain was semiquantitatively scored by 3 observers evaluating the intensity of the stain and percentage of positive tumor cells. Statistical analysis was performed using the Wilcoxon rank sum test. Strong (score 6+/7+) and diffuse (>75%) luminal FasR stain was identified in 22 (85%) of 26 IC and 16 (94%) of 17 AD, but only in 6 (35%) of 17 LMP and 1 (4%) of 24 CA. Conversely, weak (score 2+/3+) and focal (<25%) FasR staining was observed in 7 (29%) of 24 CA, but in none of the IC, AD, or LMP. These differences were statistically significant (P < .05). The decreased expression of FasR in malignant ovarian epithelial neoplasms as compared with benign ovarian epithelial lesions suggests that a decreased sensitivity to Fas-mediated apoptosis may be involved in ovarian epithelial carcinogenesis.

Adult↗

PubMed2004

De novo design of conformationally flexible transmembrane peptides driving membrane fusion.

Fusion of biological membranes is mediated by distinct integral membrane proteins, e.g., soluble N-ethylmaleimide-sensitive factor attachment protein receptors and viral fusion proteins. Previous work has indicated that the transmembrane segments (TMSs) of such integral membrane proteins play an important role in fusion. Furthermore, peptide mimics of the transmembrane part can drive the fusion of liposomes, and evidence had been obtained that fusogenicity depends on their conformational flexibility. To test this hypothesis, we present a series of unnatural TMSs that were designed de novo based on the structural properties of hydrophobic residues. We find that the fusogenicity of these peptides depends on the ratio of alpha-helix-promoting Leu and beta-sheet-promoting Val residues and is enhanced by helix-destabilizing Pro and Gly residues within their hydrophobic cores. The ability of these peptides to refold from an alpha-helical state to a beta-sheet conformation and backwards was determined under different conditions. Membrane fusogenic peptides with mixed Leu/Val sequences tend to switch more readily between different conformations than a nonfusogenic peptide with an oligo-Leu core. We propose that structural flexibility of these TMSs is a prerequisite of fusogenicity.

Amino Acid Sequence↗

PubMed2004

A common pharmacophoric footprint for AIDS vaccine design.

The most promising target antigen for an HIV vaccine designed using the classic antibody strategy has been the viral coat protein gp120. Unfortunately, its high variability has prevented this approach. We examine here a 15-residue peptide derived from the CD4-binding domain of gp120. By use of molecular dynamics computer simulation, it is shown that despite considerable sequence variation, the three-dimensional structure of the peptide is preserved over the full range of clade-specific sequences. Furthermore, sequences threaded onto the structure exhibit common three-dimensional electrostatic and hydrophobic properties. These common physicochemical characteristics constitute a pharmacophoric footprint that promises to be useful in the design of a synthetic antigen for vaccine development.

AIDS Vaccines↗

PubMed2004

Successful design and synthesis of a polarity-triggered beta-->alpha conformational switch using the side chain interaction index (SCII) as a measure of local structural stability.

Certain sequences within proteins have the ability to undergo an abrupt cooperative conformational switch from beta-strand to helix in response to decreasing polarity of the environment. This behavior was first observed at the CD4 binding site of the envelope glycoprotein gp120 of HIV-1, but evidence has accumulated that polarity-driven beta --> alpha switches may be widespread, serving both to facilitate binding on protein/membrane or protein/protein contact and to signal that docking has occurred. The characteristics identified so far that distinguish switch sequences (a reverse turn at the N-terminus that acts as a helix initiation site, a conserved tryptophan residue downstream, and high potential for both the helix and beta-fold) appear to be necessary but not sufficient, as some otherwise promising sequences found in data bank searches proved not to be capable of cooperative refolding. Analysis of existing switches has led to the development of the side chain interaction index (SCII) as a further parameter characterizing the beta --> alpha polarity-driven switch. Data bank searches using this additional parameter have successfully identified a series of new potential switch sequences. All of them have in common the amino acid tetrad LPCR at the N-terminus and a tryptophan 5-20 residues C-terminal to it. Those with a high SCII as well, when synthesized and tested, exhibited strongly cooperative polarity-driven refolding. Control peptides, containing all other parameters but with a low SCII, did not. Using this new information, an artificial sequence was designed that had a high SCII as well as the initiation site, conserved tryptophan, and high Palpha and Pbeta. When synthesized and tested, this sequence did in fact behave as a conformational switch, refolding cooperatively from beta-fold to helix at a threshold value of 30% TFE. The successful design of a polarity-driven conformational switch opens the possibility of using this motif as a tool in protein engineering.

Adenylyl Cyclases↗

PubMed2004

Assistive technology and computer adaptations for individuals with spinal cord injury.

Spinal cord injury (SCI) commonly occurs in individuals during important years for formation of vocational goals, resulting in low post-injury employment rates and higher costs to society. Individuals with SCI who are employed have improved quality of life. Assistive technology, often available at modest cost, can help individuals with SCI to compensate for functional limitations, overcome barriers to employability, enhance technical capacities and computer utilization, and improve ability to compete for gainful employment.

Adult↗

PubMed2003

Alzheimer beta-amyloid homodimers facilitate A beta fibrillization and the generation of conformational antibodies.

We reported previously that stabilized beta-amyloid peptide dimers were derived from mutant amyloid precursor protein with a single cysteine in the ectodomain juxtamembrane position. In vivo studies revealed that two forms of SDS-stable A beta homodimers exist, species ending at A beta 40 and A beta 42. The phenomenon of the transformation of the initially deposited 42-residue beta-amyloid peptide into the amyloid fibrils of Alzheimer's disease plaques remains to be explained in physical terms, i.e. energetically and structurally. We therefore performed spectroscopic analyses revealing that engineered dimeric peptides ending at residue 42 displayed a much more pronounced beta-structural transition than corresponding monomers. Specifically, the single chemically induced dimerization of A beta peptides significantly increased the beta-sheet content by a factor of 2. The C-terminal residues Ile-41 and Ala-42 of dimeric forms further increased the beta-sheet content by roughly one-third. In contrast to A beta 42, the beta-sheet content of the alpha- and gamma-secretase-generated p3 fragments did not necessarily correlate with the tendency to form fibrils, although p3/17-42 had a pronounced thread forming character with fibril lengths of up to 2.5 microM. Electron microscopic images show that forms of p3/17-42 generated smaller granular particles than forms ending at residue 40. We discuss these findings in terms of A beta 1-42 dimers representing paranuclei, which self-aggregate into ribbon-like ordered fibrils by elongation. Based on A beta 42 dimer-specific titers of a polyclonal antiserum we propose that the A beta homodimer represents a nidus for plaque formation and a well defined novel therapeutic target.

Amyloid beta-Peptides↗

PubMed2003

Convergence in peptide folding simulation: multiple trajectories of a potential AIDS pharmacophore.

To examine the conformational properties in aqueous solution of a 15-residue peptide that is a potential pharmacophore for AIDS vaccine development, molecular dynamics simulations were performed in water starting from structures determined experimentally in three different organic solvents. Convergence characteristics of the simulation are examined in Cartesian and conformational spaces. In addition, novel analysis tools are employed including a multidimensional scaling method to represent the distance between trajectory frames. As these methods are based on a variety of physical parameters, they provide a useful cross-check on the structural convergence. Theoretical two-dimensional (2D) 1H-NMR spectra are also generated. These are superficially quite different in appearance, demonstrating that backbone similarities difficult to identify by visual inspection of 2D NMR data can be revealed using the methods described here.

AIDS Vaccines↗

PubMed2003

Sexual interactions of maturing male guinea pigs with their mothers, sisters, and unfamiliar adult females in the home cage.

During observations in the home cage in the light and dark on days 5, 15, 25, 35, and 45, male guinea pigs mounted and exhibited anogenital investigation of the mother, though appropriately directed mounting occurred infrequently and was not shown by all males. Mothers nipped and kicked advancing males. No mounting of a female sibling was observed. When behavioral interactions of approximately 35-day-old males with the mother or an unfamiliar adult female were compared during 1-hr tests in the home cage, males exhibited much higher levels of mounting and anogenital investigation, and received many more nips and kicks, when with the unfamiliar female. The results 1) demonstrate that limited maternally directed sexual behavior occurs in the home cage, 2) support earlier findings indicating that continuous housing with the mother suppresses maternally directed sexual behavior in periadolescent guinea pig males, and 3) suggest that sexual behavior toward female siblings also is suppressed.

Animals↗

PubMed2002

Modelling of the human papillomavirus type 16 E5 protein.

The product of the E5 oncogene in human papillomaviruses (HPVs) participates in cellular transformation. The sequences of E5 from high-risk HPV types are closely related, and the ability to transform is thought to be associated with their structure. Structural determination by standard biophysical methods has proved impossible due to the extreme hydrophobicity of the gene product. We have achieved limited solubility by dividing the sequence into three, structurally distinct domains. Synthetic peptides corresponding to these domains have been examined using circular dichroism (CD) spectroscopy, a method that can detect secondary structure elements in highly dilute protein solutions. Using data on the secondary structure content of these domains under different conditions and in systematic combination to detect constructive domain interactions, a model of HPV E5 structure and position in the membrane is proposed that is consistent with what is known of the larger family of leucine-rich repeat (LRR) proteins to which it belongs.

Amino Acid Sequence↗

PubMed2002

Evidence for a copper-binding superfamily of the amyloid precursor protein.

The amyloid precursor protein (APP) copper-binding domain (CuBD) has been shown to reduce Cu(II) to Cu(I) and to mediate copper-induced oxidation in vitro. However, little is known about copper binding to the homologous domains of APP and APP family paralogs and orthologs (including amyloid precursor-like proteins from Drosophila melanogaster, Xenopus laevis, and Caenorhabditis elegans) and their effects on Cu-induced oxidation and Cu(I) formation. Here, we show that APP homologues with and without conserved histidine residues at positions 147, 149, and 151 all bind Cu(II). Oxidized peptides were the kinetically favored products of the redox reaction of CuBDs promoting the reduction of Cu(II) to Cu(I). These results reveal a molecular phylogeny-based divergence that has taken place between the ancestral Drosophila APPL and C. elegans APL-1 and the recently evolved APP lineage of CuBDs. Whereas higher species CuBDs have a decreased affinity for Cu(II) and high Cu(II) reducing activities, ancestral CuBDs form very tight binding sites for Cu(II) ions and have low Cu(II) reducing activities. Thus, the APP lineage displays a gain in activity toward promoting Cu(II) reduction and Cu(I) release. The findings suggests that the Cu(II)-binding equilibrium at the phylogenetic stage of Drosophila APPL and C. elegans APL-1 is shifted from the exchangeable Cu(II) pool to the tightly bound, nonexchangeable pool and that ancestral CuBDs may exert antioxidation activities in vivo. The more recently evolved homologues of human APP appear to take advantage of unique redox properties for yet unknown biological functions.

Amino Acid Sequence↗

PubMed2002

Solution structure of a putative HIV1 immunogenic peptide: computer simulation of the principal CD4 binding domain of gp120.

A 15-residue segment within the principal CD4 binding domain of gp120 from HIV1 is a natural subject for vaccine development. Knowledge of a three-dimensional structure of this peptide in aqueous solution can in principle be used for pharmacophoric footprint identification. However, the peptide is resistant to structural characterization using nuclear magnetic resonance (NMR) due to aggregation properties. Here we examine the conformational properties of the peptide using molecular dynamics simulation. Three simulations were performed starting from widely different structures of the peptide determined by NMR in organic solvents. The three structures converge during the simulations to a common structure in both Cartesian and in backbone dihedral conformational space. Preliminary examination of the average three-dimensional structure identifies, after sequence threading, characteristics of potential use as a pharmacophoric footprint.

Binding Sites↗

PubMed2002

Hypoxia-induced production of stromal cell-derived factor 1 (CXCL12) and vascular endothelial growth factor by synovial fibroblasts.

OBJECTIVE: Stromal cell-derived factor 1 (SDF-1; or, CXCL12) is a potent chemotactic and angiogenic factor that has been proposed to play a role in the recruitment of lymphocytes into rheumatoid arthritis (RA) synovium. We tested the hypothesis that synovial SDF-1 expression is regulated by cytokine and hypoxic stimulation, the latter being mediated by hypoxia-inducible factor 1alpha (HIF-1alpha). These factors regulate the expression of vascular endothelial growth factor (VEGF), itself an important angiogenic mediator. METHODS: RA and osteoarthritic synovial fibroblasts and whole tissue explants were cultured under normoxic or hypoxic (1% O(2)) conditions for up to 72 hours in the presence or absence of interleukin-1beta (IL-1beta), tumor necrosis factor (TNF), or transforming growth factor beta (TGFbeta). Expression of HIF-1alpha, VEGF, and SDF-1 was detected in synovial tissue and cells by immunohistochemistry and Western blotting. VEGF and SDF-1 expression by cultured synovial fibroblasts was evaluated by reverse transcription-polymerase chain reaction and enzyme-linked immunosorbent assay. RESULTS: Immunohistochemistry revealed the presence of HIF-1alpha, VEGF, and SDF-1 in RA synovium. Patchy expression of HIF-1alpha was detected primarily in the synovial lining and sublining areas; expression in synovial fibroblasts and in the lining cells of whole synovial tissue explants was markedly augmented by hypoxic culture conditions. Hypoxia enhanced the expression of VEGF and SDF-1 messenger RNA in synovial fibroblasts. The production of VEGF and SDF-1 protein by synovial fibroblasts was augmented by 50% and 132%, respectively, after 24 hours of hypoxia. VEGF production was potently induced by TGFbeta, and to a lesser extent by IL-1beta and TNF, and was further augmented by hypoxia. In contrast, none of the tested cytokines induced SDF-1 production. CONCLUSION: As with VEGF, SDF-1 expression is induced by hypoxia; however, cytokines induce VEGF but not SDF-1. Hypoxic conditions in RA synovium, which are likely to be transient and episodic, may contribute to the persistence of synovitis by inducing VEGF and SDF-1.

Antineoplastic Agents↗

PubMed2002

Immunohistochemical staining for c-Kit (CD117) is a rare event in human colorectal carcinoma.

Recent studies have suggested that the presence of a c-Kit/c-Kit ligand autocrine loop may be an important regulator of proliferation and progression of human colorectal cancer, capable of affecting the prognosis of these patients. If present, the c-Kit alteration may provide a suitable target for therapy, similar to what has been observed in gastrointestinal stromal tumors. To determine the incidence of c-Kit expression in human colorectal carcinomas, we studied the immunohistochemical c-Kit expression in a selection of 126 colorectal carcinomas of different stage, using stage-oriented human cancer tissue microarrays. Formalin-fixed, paraffin-embedded tissues of each case were immunostained using the avidin-biotin-peroxidase method and the antihuman c-Kit (CD117) rabbit polyclonal antibody. High cytoplasmic c-Kit staining (Allred score of 7-8) was observed in 1.6% of the colon carcinoma patients evaluated. The c-Kit-positive tumors were poorly differentiated carcinomas arising at the anorectal junction. The remaining tumors revealed no detectable expression of c-Kit. Twenty-seven non-neoplastic tissues, normal colonic mucosa, and adenomas were also CD117 negative. We show the rare expression of c-Kit in normal and neoplastic colorectal tissues, suggesting that routine screening for c-Kit by immunohistochemistry to identify c-Kit-positive carcinomas may be cost ineffective. However, further study of c-Kit expression in poorly differentiated colon cancers may be useful since these generally chemoresistant tumors may respond to therapy with inhibitor compounds directed against c-Kit.

Adenocarcinoma↗