A program for drawing evolutionary trees

From the measures of evolutionary distance between pairs ofsequences in a set, it is possible to infer the genetic treeor trees which best fit these known data. DENDRON is a new program,written in FORTRAN 66, which computes an initial tree from thebottom-up, then searches among increasingly divergent treesfor a better fit. As a check on the consistency of the measures,the program tests all triplets for the triangle inequality.DENDRON also calculates a single ‘top-down’ tree,progressing from the trunk to the twigs, for comparison withthe ‘bottom-up’ trees. Received on August 17, 1987; accepted on June 1, 1988     

Understorey vegetation change in a Picea mariana chronosequence

Eighteen black spruce (Picea mariana) stands, representing postfire ages of 26 to 120 yr, were surveyed for understorey vegetation and site/microsite characteristics at two spatial scales. This enabled comparison of within- versus among-stand compositional variation.Detrended correspondence analysis (DCA) ordination among the 18 stands revealed a complex age/moisture gradient. DCA ordination among 1 800 quadrats within the stands indicated a similar gradient with much compositional overlap. Quadrats were grouped, using two-way indicator species analysis (TWINSPAN), into 9 classes each representing a phase in understorey vegetation composition. These phases shifted in abundance from young to old stands with a high degree of concordance among replicates in the same age class. Understorey succession is strongly linked to the stages in tree growth, mortality and thinning coupled with the accumulation of site moisture.Abbreviations DCA Detrended Corrospondence Analysis     

Tree replacement patterns in subalpine Abies-Betula forests,Wolong Natural Reserve,China

Vegetation in canopy gaps of two old-growth Abies-Betula forest stands, one with bamboo the other without, was measured. The structure of gap vegetation at each site was used to derive tree replacement probabilities. Transition probabilities indicate different tree replacement trends in forests with bamboo compared to those without. Projected compositions show Betula to be the most abundant species in bamboo stands while Abies remains most abundant where bamboo was absent. A dense bamboo sward seems to reduce the probability of Abies filling gaps by inhibiting establishment and growth of seedlings. Bamboo preempts space after canopy gap formation by increasing shoot production which reduces opportunities for establishment and growth of other woody species. Differences in dispersal ability and longevity of Abies and Betula appear to be important factors contributing to their coexistence forests with a small canopy gap disturbance regime.     

Electro and acoustic myography for noninvasive assessment of lumbar paraspinal muscle function

In 31 normal subjects (17 male), aged 19-48 years, and 8 patients with chronic low back pain (4 male), aged 37-55 years, the repeatability of surface recordings of acoustic myography (AMG) and electromyography (EMG) were examined in the lumbar paraspinal muscles. Five isometric test positions were examined. In 21 of the normal subjects, four positions tested were: quiet standing, half extension from prone lying, full extension from prone with and without resistance. In 10 of the normal subjects and the 8 back pain patients, a standardised, unsupported horizontal position with the upper body over the end of a couch was tested. The AMG and EMG signals were full-wave rectified and integrated (iAMG and iEMG). The variability of recordings during repeated 5-s isometric contractions was assessed by analysis of variance (ANOVA) and the coefficient of variation (CV) was calculated from the ANOVA. Both recording techniques produced the most repeatable results during the unsupported, horizontal hold position. In the normal subjects, CV were, iAMG 5.6%, iEMG 4.9%; and in the patients, iAMG 4.4%, iEMG 2.6%. The CV for the other four isometric test positions ranged from 15.3% to 29.4% for iAMG, and 8% to 15.7% for iEMG. These results demonstrated that a controlled test manoeuvre for examining AMG and EMG of the paraspinal muscles was vital for repeatable recordings. The CV for the standardised, horizontal position were lower than for previously published results.(ABSTRACT TRUNCATED AT 250 WORDS)     

PCNA-induced DNA synthesis past cis-syn and trans-syn-I thymine dimers by calf thymus DNA polymerase delta in vitro.

Calf thymus proliferating cell nuclear antigen (PCNA) promoted DNA synthesis past cis-syn and trans-syn-I cyclobutane thymine dimers by calf thymus DNA polymerase delta (Pol delta) in vitro. Templates containing site-specific cis-syn and trans-syn-I thymine dimers were prepared via a combination of solid phase synthesis with photoproduct building blocks and DNA ligation. Extension of a 15-mer primer on the UV dimer-containing templates by Pol delta produced termination and bypass products in a dNTP and PCNA dependent manner. In the absence of PCNA and at dNTP concentrations varying between 1 and 100 microM, Pol delta could not bypass the cis-syn dimer and terminated elongation one nucleotide prior to the 3'-T of the dimer. DNA synthesis past the trans-syn-I dimer was even less efficient. In the presence of PCNA, termination occurred primarily one nucleotide prior to the 3'-T of both dimers at 1 microM dNTPs but opposite the 5'-T of the dimers at 100 microM dNTPs. In addition, under the latter conditions, bypass of the dimers was observed, to the extent of about 30% of the products for the cis-syn dimer and about 15% for the trans-syn-I dimer.     

A transgenic mouse that expresses a diversity of human sequence heavy and light chain immunoglobulins.

We have generated transgenic mice that express a diverse repertoire of human sequence immunoglobulins. The expression of this repertoire is directed by light and heavy chain minilocus transgenes comprised of human protein coding sequences in an unrearranged, germ-line configuration. In this paper we describe the construction of these miniloci and the composition of the CDR3 repertoire generated by the transgenic mice. The largest transgene discussed is a heavy chain minilocus that includes human mu and gamma 1 coding sequences together with their respective switch regions. It consists of a single 61 kb DNA fragment propagated in a bacterial plasmid vector. Both human heavy chain classes are expressed in animals that carry the transgene. In light chain transgenic animals the unrearranged minilocus sequences recombine to form VJ joints that use all five human J kappa segments, resulting in a diversity of human-like CDR3 regions. Similarly, in heavy chain transgenics the inserted sequences undergo VDJ joining complete with N region addition to generate a human-like VH CDR3 repertoire. All six human JH segments and at least eight of the ten transgene encoded human D segments are expressed. The transgenic animals described in this paper represent a potential source of human sequence antibodies for in vivo therapeutic applications.     

Purification and biochemical characterisation of the EcoR124 type I modification methylase.

Large scale purification of the type I modification methylase EcoR124 has been achieved from an over-expressing strain by a two step procedure using ion-exchange and heparin chromatography. Pure methylase is obtained at a yield of 30 mg per gm of cell paste. Measurements of the molecular weight and subunit stoichiometry show that the enzyme is a trimeric complex of 162 kDa consisting of two subunits of HsdM (58 kDa) and one subunit of HsdS (46 kDa). The purified enzyme can methylate a DNA fragment bearing its cognate recognition sequence. Binding of the methylase to synthetic DNA fragments containing either the EcoR124 recognition sequence GAAN6RTCG, or the recognition sequence GAAN7RTCG of the related enzyme EcoR124/3, was followed by fluorescence competition assays and by gel retardation analysis. The results show that the methylase binds to its correct sequence with an affinity of the order 10(8) M-1 forming a 1:1 complex with the DNA. The affinity for the incorrect sequence, differing by an additional base pair in the non-specific spacer, is almost two orders of magnitude lower.     

Seroreactivity to HPV-16 proteins in women with early cervical neoplasia

Summary Although serological reactivity to human papillomavirus type 16 (HPV-16) proteins has been demonstrated in patients with invasive cervical carcinoma, the degree of seroreactivity to these proteins in women with preinvasive disease and its relationship to the HPV type associated with the disease are unclear. We obtained sera from 27 women undergoing cone biopsy for cervical precursor lesions and 22 controls and analyzed seroreactivity by Western blot to fusion proteins containing portions of the HPV-16 E4, L1 and L2 open-reading frames (ORFs). Positives were analyzed by scanning densitometry and intensity values for each case plotted relative to controls. Cervical biopsy specimens from patients were analyzed for HPV-16 nucleic acids by DNA · DNA in situ hybridization. Mean intensity values for seroreactivity to the pATH-E4 protein approached significance (P = 0.058) and a significantly higher proportion of cases vs controls registered values over 4.0 for pATH-E4 (26% vs 4.5%;P = 0.04) and pATH-L2 (48% vs 18%;P = 0.03) proteins. A significantly higher mean intensity value for E4 was observed for cases containing HPV-16 DNA vs HPV-16 negative cases or controls. Thus, seroreactivity to HPV-16-derived proteins may be more common in women with preinvasive cervical disease, and for some protein targets (E4) may indicate a relatively type-specific response.Supported in part by grants from the National Cancer Institute [CA 47676 (C.P.C.)], American Cancer Society [MV-395 (C.P.C.)] and an institutional support grant (J.K.R.). Dr. Crum is a recipient of a Physician Scientist Award from the National Institute of Allergy and Infectious Disease (AI00628)     

Phylogenetic evidence for the herbaceous origin of angiosperms

The ancestral angiosperm is commonly interpreted as an arborescent to shrubby magnolialean with large, multiparted, complex flowers. We examined this hypothesis using a phylogenetic analysis of new and reevaluated characters polarizabled with outgroup comparison. Our cladistic analysis of basal angiosperms placed the nonmagnolialeanChloranthaceae andPiperaceae at the bottom of the tree. We further inferred the probable ancestral states of characters not polarizable with outgroup comparison by examining their distribution among taxa at the base of our cladogram. The sum of ancestral character states suggests that the protoangiosperm was a diminutive, rhizomatous to scrambling perennial herb, with small, simple flowers.     

Somatic embryogenesis and plant regeneration from immature embryos of western larch

Somatic embryogenesis was initiated from immature embryos of western larch (Larix occidentalis Nutt.) on media containing 2,4-dichlorophenoxyacetic acid and N6- benzyladenine. The effects of explant type and ammonium nitrate and glutamine concentrations on initiation were tested. Although 21–93% of explants rendered cultures in various experiments, only 3% yielded sustainable embryogenic lines. Excised embryos at the early cotyledonary stage were optimal for initiation. Maturation of somatic embryos was promoted by abscisic acid. Response to abscisic acid concentrations and duration of exposure to abscisic acid varied with genotype. Maximal results were obtained with 0.025 M abscisic acid for 1 to 2 weeks followed by individual culture on medium without growth regulators. Mature somatic embryos developed into shoots with roots. Plantlets have been established in peat.Abbreviations 2,4-D 2,4-dichlorophenoxyacetic acid - BA N⁶-benzyladenine - IBA indole-3-butyric acid - ABA abscisic acid