Orbital-forcing glacio-eustasy: A sequence-stratigraphic time scale

ABSTRACT This essay provides further explanation of the mathematical details of orbital forcing and glacio-eustatic modeling (Parametric Forward Modeling, PFM) aspects and applications. A slight tune-up of the Earth’s eccentricity calculations (LA04 of Lasker et al., 2004) produces a near-perfect repeat of 14.58 million-year period and allows PFM to predict the glacio-eustatic component of sea-level fluctuation throughout the Phanerozoic. Generalities of an exploratory grid search of the parameter space of the model are reviewed and repetitive peak sea levels and low sea levels are noted in context of the Arabian Orbital Stratigraphy (AROS) terminology and time scale. Emphasis on the straton (405,000 year “tuning fork” of stratigraphic time) will lead to improvements in sequence-stratigraphic methods and results.

The 3′ untranslated regions of Kamiti River virus and Cell fusing agent virus originated by self-duplication

Previously, it was shown that the 3′ untranslated region (3′UTR) of Kamiti River virus (KRV) is nearly twice as long as the 3′UTR of other flaviviruses (1208 nucleotides compared with 730 nucleotides for the longest 3′UTR of any virus in the Tick-borne encephalitis virus species). Additionally, KRV and the closely related Cell fusing agent virus (CFAV) were shown to contain two short, almost perfect repeat sequences of 67 nucleotides. However, the construction of a robust comparative nucleotide alignment has now revealed that the double-length 3′UTR and the direct repeats resulted from the virtually complete duplication of a primordial KRV 3′UTR. We also propose that the CFAV 3′UTR was derived from a KRV-like precursor sequence with a large deletion that nevertheless preserved the two direct repeat sequences. These data provide new insights into the evolution of the flavivirus 3′UTR.

Features of a 103-kb gene-rich region in soybean include an inverted perfect repeat cluster of CHS genes comprising the I locus

The I locus in soybean (Glycine max) corresponds to a region of chalcone synthase (CHS) gene duplications affecting seed pigmentation. We sequenced and annotated BAC clone 104J7, which harbors a dominant ii allele from Glycine max 'Williams 82', to gain insight into the genetic structure of this multigenic region in addition to examining its flanking regions. The 103-kb BAC encompasses a gene-rich region with 11 putatively expressed genes. In addition to six copies of CHS, these genes include: a geranylgeranyltransferase type II β subunit (E.C.2.5.1.60), a β-galactosidase, a putative spermine and (or) spermidine synthase (E.C.2.5.1.16), and an unknown expressed gene. Strikingly, sequencing data revealed that the 10.91-kb CHS1, CHS3, CHS4 cluster is present as a perfect inverted repeat separated by 5.87 kb. Contiguous arrangement of CHS paralogs could lead to folding into multiple secondary structures, hypothesized to induce deletions that have previously been shown to effect CHS expression. BAC104J7 also contains several gene fragments representing a cation/hydrogen exchanger, a 40S ribosomal protein, a CBL-interacting protein kinase, and the amino terminus of a subtilisin. Chimeric ESTs were identified that may represent read-through transcription from a flanking truncated gene into a CHS cluster, generating aberrant CHS RNA molecules that could play a role in CHS gene silencing.Key words: chalcone synthase, gene duplication, gene silencing, gene-rich region, soybean, BAC.

Dynamics of Microsatellite Divergence Under Stepwise Mutation and Proportional Slippage/Point Mutation Models

Recently Kruglyak, Durrett, Schug, and Aquadro showed that microsatellite equilibrium distributions can result from a balance between polymerase slippage and point mutations. Here, we introduce an elaboration of their model that keeps track of all parts of a perfect repeat and a simplification that ignores point mutations. We develop a detailed mathematical theory for these models that exhibits properties of microsatellite distributions, such as positive skewness of allele lengths, that are consistent with data but are inconsistent with the predictions of the stepwise mutation model. We use our theoretical results to analyze the successes and failures of the genetic distances (δμ)2 and DSW when used to date four divergences: African vs. non-African human populations, humans vs. chimpanzees, Drosophila melanogaster vs. D. simulans, and sheep vs. cattle. The influence of point mutations explains some of the problems with the last two examples, as does the fact that these genetic distances have large stochastic variance. However, we find that these two features are not enough to explain the problems of dating the human-chimpanzee split. One possible explanation of this phenomenon is that long microsatellites have a mutational bias that favors contractions over expansions.

Ultrastructural Observations on Induced Retraction of the Reticulopodial Network of Allogromia SP. (Foraminifera)

Allogromia sp. (strain N.F. Lee) provides a convenient model system for studying intracellular transport. We have been examining ultrastructural changes which occur in the reticulopodial network (RN) and cell body (CB) of Allogromia at various stages in the retraction response stimulated by 0.4M MgCl2 solution. As retraction proceeds, microtubules (MT) disassemble and form areas of regularly packed cytoplasm (TP-tigroid patterning) resembling vinca alkaloid induced paracrystals of tubulin. TP is first seen in the RN, and later in the CB. TP consists of dark filamentous material 12.5 nm in width separated by a light spacing of 8 nm when plane of section gives a perfect repeat pattern (arrow-fig. 6). TP may fill the entire profile of a reticulopod and in early stages of retraction is seen in close juxtaposition to MT. In the CB, TP occurs in patches 0.3-2.0 μm in diameter. TP is seen with great frequency in retracting Allogromia, but also, it can be seen occasionally in animals with fully extended RN.