Modified Box-Cox transform for modulating the dynamic range of flow cytometry data

We describe an algorithm, Vout = Integer ([2(12)-1/2(12 lambda)-1] V lambda in-1) + 1; lambda greater than 0 based upon Box-Cox transformations as an alternative to nonlinear electronic amplifiers to expand or compress high- or low-amplitude flow cytometer-derived signals. If the indexing parameter lambda less than 1, input channels in the high-amplitude input range are compressed in the output range as occurs when an electronic logarithmic amplifier is used. However, if lambda greater than 1, input channels in the low-amplitude input range are compressed in the output range as occurs when an electronic power amplifier is used. Our modified Box-Cox transform can be implemented either during data collection or off-line for the transformation of previously collected raw data. The transform is the equivalent of an infinite class of nonlinear amplifiers. As the transform is implemented in software, it does not suffer from many of the disadvantages of nonlinear electronic amplifiers.     

Statistical methods for model comparison in parameter estimation problems for distributed systems

In this note we outline some recent results on the development of a statistical testing methodology for inverse problems involving partial differential equation models. Applications to several problems from biology are presented. The statistical tests, which are in the spirit of analysis of variance (ANOVA), are based on asymptotic distributional results for estimators and residuals in a least squares approach.Research supported in part under grants NSF MCS 8504316, NASA NAG-1-517, and AFOSRF-49620-86-C-0111. Part of this research was carried out while the first author was a visiting scientist at the Institute for Computer Applications in Science and Engineering (ICASE), NASA Langley Research Center, Hampton, VA, which is operated under NASA contracts NASI-18107 and NASI-18605     

Herpes simplex virus type 1-specific cytotoxic T lymphocytes recognize immediate-early protein ICP27.

The identity of herpes simplex virus type 1 (HSV-1) antigens that serve as targets for cytotoxic T lymphocytes (CTL) and their ability to induce protective immunity remain uncertain. In this article, we report the identification of the immediate-early protein ICP27 as a CTL antigen in H-2d mice but not in H-2k or H-2b mice. Calculation of the frequencies of H-2d-restricted virus-specific CTL demonstrated that approximately one-fourth of the total HSV-1-specific response was directed against ICP27. To define the location of this CTL epitope, four truncated derivatives of the ICP27 gene which place the epitope in a 217-amino-acid region (amino acids 189 to 406) near the central portion of the protein were constructed. Mice immunized with ICP27 were able both to induce HSV-1-specific CTL and to survive a lethal intraperitoneal challenge with virulent HSV-1. However, neither appreciable antibody nor delayed-type hypersensitivity responses were induced in immunized mice, and they were also unable to clear a local epithelial virus challenge. It appears that ICP27, although capable of inducing several aspects of the immune response, is by itself unable to provide complete immunity.     

Direct ATP photolabeling of Escherichia coli recA proteins: identification of regions required for ATP binding

When the Escherichia coli RecA protein is UV irradiated in the presence of [alpha-32P]ATP, a labeled protein--ATP adduct is formed. All the experimental evidence indicates that, in forming such an adduct, the ATP becomes specifically immobilized in the catalytically relevant ATP binding site. The adduct can also be identified after irradiation of E. coli cell lysates in a similar manner. This direct ATP photolabeling of RecA proteins has been used to identify regions of the polypeptide chain involved in the binding of ATP. The photolabeling of a RecA protein that lacks wild-type carboxy-terminal amino acids is not detectable. A RecA protein in which the amino-terminal sequence NH2-Ala-Ile-Asp-Glu-Asn- is replaced by NH2-Thr-Met-Ile-Thr-Asn-Ser-Ser-Ser- is only about 5% as efficiently photolabeled as the wild-type protein. Both of these RecA protein constructions, however, contain all the elements previously implicated, directly or indirectly, in the binding of ATP. ATP-photolabeled RecA protein has also been chemically cleaved at specific amino acids in order to identify regions of the polypeptide chain to which the nucleotide becomes covalently photolinked. The evidence is consistent with a region comprising amino acids 116-170. Thus, this work and that of others suggest that several disparate regions of the unfolded polypeptide chain may combine to form the ATP binding site upon protein folding or may influence binding through long-range effects.     

Detection of Chlamydia trachomatis in Papanicolaou-stained cervical smears by an indirect immunoperoxidase method

A two-step (indirect) immunoperoxidase method directed against Chlamydia trachomatis was developed. The method was then used to evaluate the specificity of cytologic changes suggestive of C. trachomatis in Papanicolaou smears of cervical specimens from women who were culture-negative for the organism. Positive immunoperoxidase staining was detected in 9 of 21 cases (43%) tested. Technical problems, especially background staining, precluded interpretation in the remainder of the cases. Cervical cytology, as demonstrated by immunoperoxidase staining, may, in some instances, be more sensitive than the culture. However, because the etiology of cytologic changes not specifically identified by immunoperoxidase staining may be due to other organisms or factors, immunoperoxidase procedures, as described, should not replace culture for confirmation of cytologic findings suggestive of C. trachomatis.     

Continuous cultivation of equine lymphocytes: evidence for occasional T cell-like maturation events in horses with hereditary severe combined immunodeficiency

Peripheral blood mononuclear cells (PBMC) from 14 foals with hereditary severe combined immunodeficiency (SCID) were studied to determine the extent of lymphocyte differentiation that occurs in this disorder. PBMC from all 14 horses had the morphologic characteristics of large granular lymphocytes (LGL). Cells from only one of 14 horses were responsive to phytolectin stimulation in a standard blastogenesis assay; however, PBMC from all 14 horses proliferated in continuous culture in the presence of partially purified interleukin 2. Furthermore, there were differences in the growth patterns of these cultured cells that correlated with their ability to respond to phytolectin stimulation. PBMC obtained from the 13 phytolectin-unresponsive foals survived in culture for only 4 to 5 wk, divided very slowly, developed large granules composed primarily of calcium phosphate, and accumulated high concentrations of histamine. In contrast, PBMC from the phytolectin-responsive SCID foal proliferated in continuous culture for over 100 days, divided as rapidly as normal equine PBMC under identical culture conditions, and did not accumulate granules or histamine. These observations indicate that lymphoid cell differentiation occurs in some horses with SCID even though the identity of the LGL is unresolved. Two possibilities are that LGL are products of a pathway separate from that of lymphocytes or that LGL are precursors of mature lymphocytes.     

A comparison of the fecundities of two species of toad (Bufo bufo and B. calamita) from different habitat types in Britain

The fecundities of Natterjack toads, Bufo calamita , on a Cumbrian dune system and a relict heathland site in Hampshire were compared and contrasted with the fecundity of Common toads, B. bufo , on the Cumbrian dunes. For both species, fecundity was positively correlated with length, while in B. calamita length was also correlated with size of eggs produced, and age of the female. Bufo calamita was found to invest more energy exponentially in egg production with increasing length, and therefore age. This species also laid more than twice as many eggs as comparably-sized female B. bufo , and some probably produced two clutches of spawn per year in southern England. The enhanced fecundity of the species was believed to be an adaptation to living in areas with unpredictable spawning sites. Small female B. bufo on the dunes appeared to put more energy into egg production when small than individuals of the same species on other habitat types in Britain, possibly as a result of reduced life expectancy on the dune habitat. There was a link between old age and the production of non-viable spawn in B. calamita , and males of this species which spawned at the end of the prolonged breeding season were found to have reduced fertilization efficiency when spawning on consecutive evenings.     

STENOKOLEOS BIFIDUS SP. N. IN THE UPPER DEVONIAN OF NEW YORK STATE

Stenokoleos is a genus for petrified axes from the Mississippian New Albany Shale to which an Upper Devonian occurrence in New York is added. Two orders of branching were known and the plant was thought to be related to coenopterid ferns. The new petrified axes from New York reveal three orders of branching. A pair of rachides emerges from one side of the stem at each node. Their position alternates at successive nodes (distichous). Each rachis bears alternately arranged pinnae. The shape of the xylem strand and the number of protoxylem areas are variable. Traces to the pairs of rachides arise either as two separate strands or as a single strand that is presumed to divide while still within the cortex of the stem. Traces to pinnae are ellipsoid or clepsydroid. Tracheids are scalariform and uni- or biseriate, circular-bordered pitted. Peripheral loops are present in all orders of branches. Protoxylem strands are numerous and maturation is mesarch. Cortex is parenchymatous where it is preserved but outer cortex is missing. Stenokoleos and Reimanniopsis are placed in a new family, Stenokoleaceae. This is classified as Incertae Sedis among Pterophytina in Tracheophyta. It is suggested that the plant is related more closely to the Mississippian pteridosperms Tristichia and Tetrastichia than to the coenopterid ferns.