Simian immunodeficiency virus from African green monkeys.

Simian immunodeficiency virus (SIV) was isolated from the total peripheral blood mononuclear cell population and the monocyte-macrophage adherent cell population of three seropositive green monkeys originating from Kenya. SIV from these African green monkeys (SIVagm) was isolated and continuously produced with the MOLT-4 clone 8 (M4C18) cell line but not with a variety of other cells including HUT-78, H9, CEM, MT-4, U937, and uncloned MOLT-4 cells. Once isolated, these SIVagm isolates were found to replicate efficiently in M4C18, SupT1, MT-4, U937, and Jurkat-T cells but much less efficiently if at all in HUT-78, H9, CEM, and MOLT-4 cells. The range of CD4+ cells fully permissive for replication of these SIVagm isolates thus differs markedly from that of previous SIV isolates from macaques (SIVmac). These SIVagm isolates had a morphogenesis and morphology like that of human immunodeficiency virus (HIV) and other SIV isolates. Antigens of SIVagm and SIVmac cross-reacted by comparative enzyme-linked immunosorbent assay only with reduced efficiency, and optimal results were obtained when homologous antibody and antigen were used. Western blotting (immunoblotting) of purified preparations of SIVagm isolate 385 (SIVagm385) revealed major viral proteins of 120, 27, and 16 kilodaltons (kDa). The presumed major core protein of 27 kDa cross-reacted antigenically with the corresponding proteins of SIVmac (28 kDa) and HIV-1 (24 kDa) by Western blotting. Hirt supernatant replicative-intermediate DNA prepared from cells freshly infected with SIVagm hybridized to SIVmac and HIV-2 DNA probes. Detection of cross-hybridizing DNA sequences, however, required very low stringency, and the restriction endonuclease fragmentation patterns of SIVagm were not similar to those of SIVmac and HIV-2. The nucleotide sequence of a portion of the pol gene of SIVagm385 revealed amino acid identities of 65% with SIVmac142, 64% with HIV-2ROD, and 56% with HIV-1BRU; SIVagm385 is thus related to but distinct from previously described primate lentiviruses SIVmac, HIV-1, and HIV-2. Precise information on the genetic makeup of these and other SIV isolates will possibly lead to better understanding of the history and evolution of these viruses and may provide insight into the origin of viruses that cause acquired immunodeficiency syndrome in humans.     

Y chromosome polymorphisms in Native American and Siberian populations: identification of Native American Y chromosome haplotypes

We have initiated a study of ancient male migrations from Siberia to the Americas using Y chromosome polymorphisms. The first polymorphism examined, a C→T transition at nucleotide position 181 of the DYS199 locus, was previously reported only in Native American populations. To investigate the origin of this DYS199 polymorphism, we screened Y chromosomes from a number of Siberian, Asian, and Native American populations for this and other markers. This survey detected the T allele in all five Native American populations studied at an average frequency of 61%, and in two of nine native Siberian populations, the Siberian Eskimo (21%) and the Chukchi (17%). This finding suggested that the DYS199 T allele may have originated in Beringia and was then spread throughout the New World by the founding populations of the major subgroups of modern Native Americans. We further characterized Native American Y chromosome variation by analyzing two additional Y chromosome polymorphisms, the DYS287 Y Alu polymorphic (YAP) element insertion and a YAP-associated A→G transition at DYS271, both commonly found in Africans. We found neither African allele associated with the DYS199 T allele in any of the Native American or native Siberian populations. However, we did find DYS287 YAP+ individuals who harbored the DYS199 C allele in one Native American population, the Mixe, and in one Asian group, the Tibetans. A correlation of these Y chromosome alleles in Native Americans with those of the DYS1 locus, as detected by the p49a/p49f (p49a,f) probes on TaqI-digested genomic DNA, revealed a complete association of DYS1 alleles (p49a,f haplotypes) 13, 18, 66, 67 and 69 with the DYS199 T allele, while DYS1 alleles 8 and 63 were associated with both the DYS199 C and T allele. Received: 18 November 1996 / Accepted: 19 May 1997     

Corneal dystrophy in Fischer 344 rats

A spontaneous degenerative lesion of the cornea resembling calcific band keratopathy in man has been observed in 10-15% of the F-344 rats (aged 35-300 days) purchased from a private vendor's closed breeding colony. The lesion appears clinically as punctuate to linear superficial corneal opacities located in the interpalpebral fissure of one or both eyes. Occasional roughening, bleb formation, or pitting of the corneal surface resembling superficial ulcers may be observed. The lesion occurs in both sexes. It is rarely associated with inflammation or irritation. Histologically, it consists of mineral deposits along the epithelial basement membrane and Bowman's space, some of which are large enough to disrupt or destroy portions of the basilar epithelium. Energy dispersive X-ray analysis of the deposits proved them to be composed of calcium and phosphorus. Electron microscopic examination revealed a variety of extracellular laminated and crystalline arrays similar to those seen in humans with band keratopathy. The etiology of the lesion is as yet undetermined. A genetic-associated susceptibility due to hypercalcemia may be involved.     

Temperature and cholesterol composition-dependent behavior of 1-myristoyl-2-[12-[(5-dimethylamino-1-naphthalenesulfonyl)amino]dodecanoyl]-sn-glycero-3-phosphocholine in 1,2-dimyristoyl-sn-glycero-3-phosphocholine membranes

We present a steady-state and time-resolved fluorescence emission spectra analysis of the membrane probe 1-myristoyl-2-[12-[(5-dimethylamino-1-naphthalenesulfonyl)amino]dodecanoyl]-sn-glycero-3-phosphocholine (DANSYL) in 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) and cholesterol multi-lamellar vesicles (MLV) prepared by modified rapid solvent exchange. We report that the dose-dependent cholesterol-induced blue shifts in the steady-state fluorescence emission spectra observed in DMPC MLV are due to complex solvent effects that include time-dependent dipolar relaxation and the formation of internal charge transfer (ICT) states. A key finding of this investigation is identification of two distinguishable DANSYL populations existing at both shallow and deep locations in the membrane; these two DANSYL populations are evidence of laterally phase-separated domains at cholesterol compositions between X(chol) = 0.30 and 0.60 at 30 degrees C in DMPC MLV.     

Strengths and Limitations of Period Estimation Methods for Circadian Data

A key step in the analysis of circadian data is to make an accurate estimate of the underlying period. There are many different techniques and algorithms for determining period, all with different assumptions and with differing levels of complexity. Choosing which algorithm, which implementation and which measures of accuracy to use can offer many pitfalls, especially for the non-expert. We have developed the BioDare system, an online service allowing data-sharing (including public dissemination), data-processing and analysis. Circadian experiments are the main focus of BioDare hence performing period analysis is a major feature of the system. Six methods have been incorporated into BioDare: Enright and Lomb-Scargle periodograms, FFT-NLLS, mFourfit, MESA and Spectrum Resampling. Here we review those six techniques, explain the principles behind each algorithm and evaluate their performance. In order to quantify the methods'' accuracy, we examine the algorithms against artificial mathematical test signals and model-generated mRNA data. Our re-implementation of each method in Java allows meaningful comparisons of the computational complexity and computing time associated with each algorithm. Finally, we provide guidelines on which algorithms are most appropriate for which data types, and recommendations on experimental design to extract optimal data for analysis.     

Use of simian immunodeficiency virus for vaccine research

Rhesus monkeys were immunized with purified, disrupted, noninfectious simian immunodeficiency virus (SIV) in adjuvant induced SIV neutralizing antibodies. Two of six previously vaccinated macaques were protected against infection when challenged with 200-1,000 animal infectious doses of uncloned, pathogenic SIV and both have remained free of signs of virus infection for 19 and 30 months. Prior vaccination appeared to be of benefit in decreasing the virus load and in delaying the onset of AIDS in animals that became infected. Nonetheless, two of four previously vaccinated monkeys that became infected following challenge eventually developed AIDS and died 505 and 538 days after infection. Thus, for a vaccine to be truly effective against AIDS, it may have to protect absolutely against initial infection.     

The Genome Sequence DataBase (GSDB): meeting the challenge of genomic sequencing.

The genome sequence database (GSDB) is a complete, publicly available relational database of DNA sequences and annotation maintained by the National Center for Genome Resources (NCGR) under a Cooperative Agreement with the US Department of Energy (DOE). GSDB provides direct, client- server access to the database for data contributions, community annotation and SQL queries. The GSDB Annotator, a multi-platform graphic user interface, is freely available. Automatically updated relational replicates of GSDB are also freely available.     

Effect of high-intensity exercise training on functional capacity of limb skeletal muscle

The purpose of this study was to determine whether a program of regular sprint exercise training alters the functional properties or protects against the development of fatigue in fast- and slow-twitch rat skeletal muscle. The training program consisted of 6 sprints of 4.5-min duration at 40 m/min and 15% slope with 2.5-min rest intervals, performed 5 days/wk for 6 wk. The exercise program significantly increased (P less than 0.05) citrate synthase activity (mumol X g-1 X min-1) in the predominantly type I soleus (SOL) from 28 +/- 2 to 44 +/- 2; the type IIb superficial region of the vastus lateralis (SVL) from 10 +/- 1 to 16 +/- 1; and the type IIa deep region of the vastus lateralis (DVL) from 34 +/- 2 to 53 +/- 2. Phosphofructokinase activity (mumol X g-1 X min-1) also increased with training in the SOL (17 +/- 1 vs. 23 +/- 1) and the DVL (64 +/- 5 vs. 79 +/- 5). Sprint training reduced (P less than 0.05) the contraction time (CT) (111 +/- 7 vs. 92 +/- 3 ms) and the one-half relaxation time (118 +/- 3 vs. 104 +/- 2 ms) in the slow-twitch soleus. The exercise program also induced a decreased CT in the fast-twitch extensor digitorum longus (EDL), but significance was limited to the P less than 0.1 level. Muscle fatigue was produced by electrical stimulation at 45 trains/min and either 15 trains/min in SOL or 10 trains/min in the EDL and SVL for 1, 5, or 10 min.(ABSTRACT TRUNCATED AT 250 WORDS)