Chemical characterization and purification of the beta subunit of the DNA polymerase III holoenzyme from an overproducing strain

We have purified the beta subunit of the DNA polymerase III holoenzyme to homogeneity from an overproducing strain (Blanar, M., Sandler, S., Armengod, M., Ream, L., and Clark, A. (1984) Proc. Natl. Acad. Sci. U.S.A. 81, 4622-4626). From this procedure we can obtain 100 mg quantities of protein. The beta isolated from the overproducer is indistinguishable from that isolated from wild-type cells in terms of its activity and molecular weight. Partial amino acid sequence analysis has confirmed the DNA sequence of the dnaN gene (Ohmori, H., Kimura, M., Nagata, T., and Sakakibara, Y. (1984) Gene (Amst.) 28, 159-170) and established the sites for initiation and termination of translation. No processing that removes amino acid residues from beta occurs since the active protein begins with the initiating methionine and terminates at the position predicted from the DNA sequence. Our knowledge of the precise amino acid composition has been used to determine the extinction coefficient of beta to be 17,900 and 18,700 cm-1 M-1 at 280 and 277 nm, respectively. The extinction coefficient at 280 nm is reduced to 14,700 cm-1 M-1 under denaturing conditions in guanidine HCl. Conditions have been optimized so that 1 N-ethylmaleimide residue can be incorporated per beta monomer with full preservation of activity.     

Antibodies to citrullinated proteins and differences in clinical progression of rheumatoid arthritis

Antibodies to citrullinated proteins (anti-cyclic-citrullinated peptide [anti-CCP] antibodies) are highly specific for rheumatoid arthritis (RA) and precede the onset of disease symptoms, indicating a pathogenetic role for these antibodies in RA. We recently showed that distinct genetic risk factors are associated with either anti-CCP-positive disease or anti-CCP-negative disease. These data are important as they indicate that distinct pathogenic mechanisms are underlying anti-CCP-positive disease or anti-CCP-negative disease. Likewise, these observations raise the question of whether anti-CCP-positive RA and anti-CCP-negative RA are clinically different disease entities. We therefore investigated whether RA patients with anti-CCP antibodies have a different clinical presentation and disease course compared with patients without these autoantibodies. In a cohort of 454 incident patients with RA, 228 patients were anti-CCP-positive and 226 patients were anti-CCP-negative. The early symptoms, tender and swollen joint count, and C-reactive protein level at inclusion, as well as the swollen joint count and radiological destruction during 4 years of follow-up, were compared for the two groups. There were no differences in morning stiffness, type, location and distribution of early symptoms, patients' rated disease activity and C-reactive protein at inclusion between RA patients with and without anti-CCP antibodies. The mean tender and swollen joint count for the different joints at inclusion was similar. At follow-up, patients with anti-CCP antibodies had more swollen joints and more severe radiological destruction. Nevertheless, the distribution of affected joints, for swelling, bone erosions and joint space narrowing, was similar. In conclusion, the phenotype of RA patients with or without anti-CCP antibodies is similar with respect to clinical presentation but differs with respect to disease course.     

Environments and hominin activities across the FLK Peninsula during Zinjanthropus times (1.84 Ma), Olduvai Gorge, Tanzania

We establish through 13 excavations the landscape context and nature of hominin activities across the Zinjanthropus land surface from which the Leakeys recovered the FLK 22 and FLK NN 1 paleoanthropological assemblages. The land surface was created by fluvial incision of the eastern margin of paleo-Lake Olduvai following a major lake withdrawal. Erosion was uneven, leaving a peninsula bounded by a river channel, the FLK Fault, and a freshwater wetland. This FLK Peninsula supported groves of trees that attracted hominins and carnivores, and that preserved the dense concentrations of carcass remains and stone tools they left behind, including those at FLK 22. Some carcasses appear to have been acquired at the ecotone of the Peninsula and Wetland, where another dense artifact and bone assemblage accumulated. A lesser topographic high at the edge of a Typha marsh in the Wetland was the site of FLK NN 1 and a scatter of large stone tools used possibly for rootstock processing.Our landscape reconstruction delimits the vegetation mosaic indicated by previous work and provides a topographical explanation for the existence of FLK 22 and FLK NN 1. Both are unexpected if the FLK area was the flat, featureless lake margin terrain typical of lake basins similar to paleo-Olduvai. The results show that the Leakeys’ sites were not isolated occupation floors but rather parts of a land surface utilized intensively by hominins. Although commonly considered to have been home bases, their likely high predation risk, evidenced by large carnivore feeding traces and the remains of four hominin individuals, suggests visits to them were brief and limited to feeding. Finally, stratigraphic observations confirm that FLK NN 3 accumulated on an older land surface, refuting the hypothesis that the OH 8 foot found there is the same individual as the OH 35 leg from FLK 22.     

Identifying differentially methylated genes using mixed effect and generalized least square models

Background  

DNA methylation plays an important role in the process of tumorigenesis. Identifying differentially methylated genes or CpG islands (CGIs) associated with genes between two tumor subtypes is thus an important biological question. The methylation status of all CGIs in the whole genome can be assayed with differential methylation hybridization (DMH) microarrays. However, patient samples or cell lines are heterogeneous, so their methylation pattern may be very different. In addition, neighboring probes at each CGI are correlated. How these factors affect the analysis of DMH data is unknown.     

Strand Displacement by DNA Polymerase III Occurs through a ��-��-�� Link to Single-stranded DNA-binding Protein Coating the Lagging Strand Template

In addition to the well characterized processive replication reaction catalyzed by the DNA polymerase III holoenzyme on single-stranded DNA templates, the enzyme possesses an intrinsic strand displacement activity on flapped templates. The strand displacement activity is distinguished from the single-stranded DNA-templated reaction by a high dependence upon single-stranded DNA binding protein and an inability of γ-complex to support the reaction in the absence of τ. However, if γ-complex is present to load β₂, a truncated τ protein containing only domains III–V will suffice. This truncated protein is sufficient to bind both the α subunit of DNA polymerase (Pol) III and χψ. This is reminiscent of the minimal requirements for Pol III to replicate short single-stranded DNA-binding protein (SSB)-coated templates where τ is only required to serve as a scaffold to hold Pol III and χ in the same complex (Glover, B., and McHenry, C. (1998) J. Biol. Chem. 273, 23476–23484). We propose a model in which strand displacement by DNA polymerase III holoenzyme depends upon a Pol III-τ-ψ-χ-SSB binding network, where SSB is bound to the displaced strand, stabilizing the Pol III-template interaction. The same interaction network is probably important for stabilizing the leading strand polymerase interactions with authentic replication forks. The specificity constant (k_cat/K_m) for the strand displacement reaction is ∼300-fold less favorable than reactions on single-stranded templates and proceeds with a slower rate (150 nucleotides/s) and only moderate processivity (∼300 nucleotides). PriA, the initiator of replication restart on collapsed or misassembled replication forks, blocks the strand displacement reaction, even if added to an ongoing reaction.     

Cladometric analysis of Pliocene hominids

Quantification of individual crown features allows maximization of information retrieval from isolated hominid molars. The Lukeino specimen demonstrates phenetic affinity to Pan; the Lothagam fossil appears closer to a hypothetical ancestral hominid morphotype than the Laetolil specimens. Consideration of 41 metric features in a cladistic framework establishes Australopithecus afarensis as the sister taxon of Homo and of later australopithecines.