Interpreting interest in interferon-α

The aim of the present study was to investigate the expression of Fas in periarticular tenocytes of patients with osteoarthritis (OA) and to study their susceptibility to Fas ligand-mediated apoptosis. Tendon samples were obtained from the quadriceps femoris muscle of patients with knee OA and used for histological evaluation, for immunohistochemical detection of Fas, and to establish tenocyte cultures. The expression of Fas mRNA was determined by quantitative PCR. Levels of soluble Fas and soluble tumour necrosis factor (TNF) receptor I were measured using ELISA. Apoptosis was induced with recombinant human Fas ligand and measured by a histone fragmentation assay and flow cytometry. The effects of TNF-α were studied by stimulation with TNF-α alone or 24 hours before the induction of apoptosis. Tendon samples from non-OA patients were used as controls. Histological evaluation revealed degenerative changes in the tendons of all OA patients but not in the controls. Fas was detected by immunohistochemistry in all specimens, but quantitative PCR revealed significantly higher levels of Fas mRNA in OA tenocytes. In contrast, lower levels of soluble Fas were found in OA tenocytes by ELISA. OA tenocytes were significantly more susceptible to Fas ligand induced apoptosis than were control cells. TNF-α reduced the Fas ligand induced apoptosis in OA tenocytes but had no effects on control tenocytes. These data suggest that knee OA is associated with higher susceptibility of periarticular tenocytes to Fas ligand induced apoptosis because of higher expression of Fas but lower levels of apoptosis-inhibiting soluble Fas. These changes may contribute to decreased cellularity in degenerative tendons and promote their rupturing. The antiapoptotic effects of TNF-α in OA tenocytes most likely reflect regenerative attempts and must be taken into account when anti-TNF strategies are considered for OA.     

Interpreting phenotypic variation in plants

Plant ecologists and evolutionary biologists frequently examine patterns of phenotypic variation across variable environments or genetic identities. Too often, we ignore the fact that most phenotypic traits change throughout growth and development of individual plants, and that rates of growth and development are highly variable. Plants growing in different environments are likely to grow at different rates, and will be of different sizes and stages of development at a particular age. When we compare plants as a function of plant size or developmental stage, as well as a function of age, we broaden our understanding of phenotypic variation between plants.     

Interpreting recruitment limitation in forests

Studies of tree recruitment are many, but they provide few general insights into the role of recruitment limitation for population dynamics. That role depends on the vital rates (transitions) from seed production to sapling stages and on overall population growth. To determine the state of our understanding of recruitment limitation we examined how well we can estimate parameters corresponding to these vital rates. Our two-part analysis consists of (1) a survey of published literature to determine the spatial and temporal scale of sampling that is basis for parameter estimates, and (2) an analysis of extensive data sets to evaluate sampling intensity found in the literature. We find that published studies focus on fine spatial scales, emphasizing large numbers of small samples within a single stand, and tend not to sample multiple stands or variability across landscapes. Where multiple stands are sampled, sampling is often inconsistent. Sampling of seed rain, seed banks, and seedlings typically span <1 yr and rarely last 5 yr. Most studies of seeding establishment and growth consider effects of a single variable and a single life history stage. By examining how parameter estimates are affected by the spatial and temporal extent of sampling we find that few published studies are sufficiently extensive to capture the variability in recruitment stages. Early recruitment stages are especially variable and require samples across multiple years and multiple stands. Ironically, the longest duration data sets are used to estimate mortality rates, which are less variable (in time) than are early life history stages. Because variables that affect recruitment rates interact, studies of these interactions are needed to assess their full impacts. We conclude that greater attention to spatially extensive and longer duration sampling for early life history stages is needed to assess the role of recruitment limitation in forests.     

Polymorphism in the interferon-alpha gene family.

A pronounced genetic polymorphism of the interferon type I gene family has been assumed on the basis of RFLP analysis of the genomic region as well as the large number of sequences published compared to the number of loci. However, IFNA2 is the only locus that has been carefully analyzed concerning gene frequency, and only naturally occurring rare alleles have been found. We have extended the studies on a variation of expressed sequences by studying the IFNA1, IFNA2, IFNA10, IFNA13, IFNA14, and IFNA17 genes. Genomic white-blood-cell DNA from a population sample of blood donors and from a family material were screened by single-nucleotide primer extension (allele-specific primer extension) of PCR fragments. Because of sequence similarities, in some cases "nested" PCR was used, and, when applicable, restriction analysis or control sequencing was performed. All individuals carried the interferon-alpha 1 and interferon-alpha 13 variants but not the LeIF D variant. At the IFNA2 and IFNA14 loci only one sequence variant was found, while in the IFNA10 and IFNA17 groups two alleles were detected in each group. The IFNA10 and IFNA17 alleles segregated in families and showed a close fit to the Hardy-Weinberg equilibrium. There was a significant linkage disequilibrium between IFNA10 and IFNA17 alleles. The fact that the extent of genetic polymorphism was lower than expected suggests that a majority of the previously described gene sequences represent nonpolymorphic rare mutants that may have arisen in tumor cell lines.     

Radiolabeling of the interferon-alpha receptor

The action of alpha interferon (IFN-alpha) is initiated by its binding to a specific cell-surface glycoprotein, the IFN-alpha receptor, which is not well characterized. IFN-alpha A was reacted with an 125I-labeled, cleavable, heterobifunctional reagent. The derivatized IFN-alpha A was bound to human Daudi cells and photoactivated, forming a covalent IFN/receptor complex of apparent molecular weight 130,000-140,000 by SDS-polyacrylamide gel electrophoresis. Cleavage of the complex produced a new 125I-labeled 110 kDa band, representing the 125I-labeled IFN-alpha receptor free of IFN-alpha. This result provides a better estimate of the apparent molecular weight of the IFN-alpha receptor, and also provides a tool for tracking the migration of the free receptor in SDS-polyacrylamide gel electrophoresis.     

Interpreting DNA evidence

By Ian W. Evett and Bruce S. Weir. Sunderland, MA: Sinauer Associates. 1998. 278 pp. ISBN 0‐87893‐155‐4. $34.95 (paper).     

Site-specific lipophilic modification of interferon-alpha

Interferon- (IFN),⁴ a cytokine with modulatory activities on many cell types, is useful for treating many types of cancer and infectious diseases. This study investigates whether modification of a protein, using IFN as an example, with a lipophilic group can alter its distribution and kinetic properties in the body. Ser163 of IFN2a was mutated to Cys to generate a free sulfhydryl group for site-specific chemical modification. IFN2a(S163C) was conjugated by iodoacetamide derivatives of varying lengths, and the modified IFN2a was purified by gel filtration chromatography. The biological activities of IFN2a(S163C) and lipophilized IFN2a(S163C) were similar to that of IFN2a, as evidenced by their inhibitory effects on the growth of Daudi cells and on the replication of vesicular stomatitis virus in Madin-Darby bovine kidney cells. Lipophilized IFN2a(S163C) bound to human serum albumin and cell membranes more readily than did IFN2a. Future experiments will investigate whether lipophilized IFN2a(S163C) has improved pharmacokinetic properties.     

Interpreting Dynamically-Averaged Scalar Couplings in Proteins

The experimental determination of scalar three-bond coupling constants represents a powerful method to probe both the structure and dynamics of proteins. The detailed structural interpretation of such coupling constants is usually based on Karplus relationships, which allow the measured couplings to be related to the torsion angles of the molecules. As the measured couplings are sensitive to thermal fluctuations, the parameters in the Karplus relationships are better derived from ensembles representing the distributions of dihedral angles present in solution, rather than from single conformations. We present a method to derive such parameters that uses ensembles of conformations determined through dynamic-ensemble refinement – a method that provides structural ensembles that simultaneously represent both the structure and the associated dynamics of a protein.     

Stimulation of in vitro immunoglobulin production by interferon-alpha

The effect of various natural and recombinant DNA-derived human interferon-alpha (IFN-alpha) on immunoglobulin (Ig) production by human B cells was investigated. The cell populations examined included peripheral blood mononuclear cells (PBMC) and highly purified B cell and helper T cell populations obtained by negative selection by using monoclonal antibodies and a fluorescence-activated cell sorter. In the presence of all forms of IFN-alpha tested, IgG and IgM production by PBMC increased twofold to fourfold. This increase was noted in the absence of pokeweed mitogen (PWM), was not affected by depletion of monocytes, required that IFN-alpha was present early in the culture period, and reached maximal levels around 500 U/ml IFN-alpha. Both IgG and IgM production were affected, but the magnitude of the IgM response was greater. The augmentation of Ig production was noted with the recombinant DNA-derived subtype, IFN-alpha F, two analogs, IFN-alpha Con1 and IFN-alpha Con2, as well as with buffy-coat-derived (leukocyte) IFN-alpha. The recombinant DNA-derived forms of IFN-alpha appeared to differ in their ability to augment Ig production. In the presence of PWM, IFN-alpha Con1 failed to increase Ig production by PBMC. In contrast to these results with PBMC, IFN-alpha Con1 increased the Ig production of purified B cells 10- to 20-fold in the presence of PWM. This increase reached maximal levels around 500 U/ml IFN-alpha Con1. Although purified B cells responded to IFN-alpha and PWM, maximal responses occurred in the presence of low numbers of helper T cells. Cell dilution experiments suggested that the effect observed with purified B cells was the result of the interaction of B cells with residual cells, e.g., helper T cells, remaining in the preparations.     

Interpreting Geographic Variation in Life-History Traits

The geographic variation in the length of the larval periodand the size at metamorphosis of the wood frog,Rana sylvatica,is examined for populations in the tundra of Canada, the mountainsof Virginia, and the lowlands of Maryland. We argue that theobserved differences in developmental plasticity, heriisbilitiesand genetic covariances of traits among localities result fromdifferential selection pressures in each environment, and arerelated to the physiological constraints inherent in developmentand to the degree of compromise between the timing and sizeat metamorphosis allowed in each environment. In Maryland populationsfitness has been maximized by evolutionary changes in size alone;body size in this population is canalized, has low heritabilityand is highly correlated with juvenile survival relative todevelopmental time. In Canada, minimum developmental time yieldsmaximum fitness; the length of the larval period in this populationis canalized and genetically monomorphic relative to body size.In contrast, fitness in the Virginia populations has been determinedby correlated and pleiotropic effects of genes on both developmentaltime and larval body size, and both traits are equally canalized,affect juvenile survivorship equally and display moderate heritabilities.These results stress the importance of interpreting variationin life-history traits relative to constraints inherent in developmentand those imposed by the environment. Heritability and survivorshipdata support the general notion that fitness traits should havelow levels of additive genetic variation, but also suggest thatantagonistic pleiotropy may act to preserve genetic variationin fitness traits under simultaneous selection, and cautionagainst inferring evolutionary importance of individual traitswithout considering the possible presence of pleiotropy.