Discordant patterns of linkage disequilibrium of the peptide-transporter loci within the HLA class II region.

Disequilibrium between genetic markers is expected to decline monotonically with recombinational map distance. We present evidence from the HLA class II region that seems to violate this principle. Pairwise disequilibrium values were calculated from six loci ranging in physical separation from 15 kb to 550 kb. The histocompatibility loci DRB1, DQA1, and DQB1, located on the distal end of the class II region, behave as a single evolutionary unit within which extremely high linkage disequilibrium exists. Lower but still significant levels of disequilibrium are present between these loci and DPB1, located at the proximal edge of the HLA complex. The peptide-transporter loci TAP1 and TAP2, located in the intervening region, reveal no disequilibrium with each other and low or negligible disequilibrium with the flanking loci. The action of two genetic process is required to account for this phenomenon: a recombinational hotspot operating between TAP1 and TAP2, to eliminate disequilibrium between these loci, and at the same time selection operating on particular combinations of alleles across the DR-DP region, to create disequilibrium in the favored haplotypes. The forces producing the patterns of disequilibrium observed here have implications for the mapping of train loci and disease genes: markers of TAP1, for example, would give a false impression as to the influence of DPB1 on a trait known to be associated with DQB1.     

A highly conserved nuclear gene for low-level phylogenetics: elongation factor-1 alpha recovers morphology-based tree for heliothine moths

Molecular systematists need increased access to nuclear genes. Highly conserved, low copy number protein-encoding nuclear genes have attractive features for phylogenetic inference but have heretofore been applied mostly to very ancient divergences. By virtue of their synonymous substitutions, such genes should contain a wealth of information about lower-level taxonomic relationships as well, with the advantage that amino acid conservatism makes both alignment and primer definition straightforward. We tested this postulate for the elongation factor-1 alpha (EF-1 alpha) gene in the noctuid moth subfamily Heliothinae, which has probably diversified since the middle Tertiary. We sequenced 1,240 bp in 18 taxa representing heliothine groupings strongly supported by previous morphological and allozyme studies. The single most parsimonious gene tree and the neighbor-joining tree for all nucleotides show almost complete concordance with the morphological tree. Homoplasy and pairwise divergence levels are low, transition/transversion ratios are high, and phylogenetic information is spread evenly across gene regions. The EF-1 alpha gene and presumably other highly conserved genes hold much promise for phylogenetics of Tertiary age eukaryote groups.      

Mesodern-inducing factors and mesodermal patterning

Identification of the signalling molecules involved in mesoderm formation in amphibian embryos still presents problems. None of the original candidates, such as activin, have been definitively ruled out, and the new factors, such as the nodal-related genes, have come on to the scene. Of the original candidates, activin has been definitively shown to act as a morphogen, whereas bone morphogenetic protein (BMP)-4 has emerged as a ventral inducer and an inhibitor of neural differentiation. The effects of BMP-4 are antagonized by chordin, a molecule related to the product of the Drosophila gene short gastrulation.     

Production of Solvents by Clostridium acetobutylicum Cultures Maintained at Neutral pH

The formation of acetone and n-butanol by Clostridium acetobutylicum NCIB 8052 (ATCC 824) was monitored in batch culture at 35°C in a glucose (2% [wt/vol]) minimal medium maintained throughout at either pH 5.0 or 7.0. At pH 5, good solvent production was obtained in the unsupplemented medium, although addition of acetate plus butyrate (10 mM each) caused solvent production to be initiated at a lower biomass concentration. At pH 7, although a purely acidogenic fermentation was maintained in the unsupplemented medium, low concentrations of acetone and n-butanol were produced when the glucose content of the medium was increased (to 4% [wt/vol]). Substantial solvent concentrations were, however, obtained at pH 7 in the 2% glucose medium supplemented with high concentrations of acetate plus butyrate (100 mM each, supplied as their potassium salts). Thus, C. acetobutylicum NCIB 8052, like C. beijerinckii VPI 13436, is able to produce solvents at neutral pH, although good yields are obtained only when adequately high concentrations of acetate and butyrate are supplied. Supplementation of the glucose minimal medium with propionate (20 mM) at pH 5 led to the production of some n-propanol as well as acetone and n-butanol; the final culture medium was virtually acid free. At pH 7, supplementation with propionate (150 mM) again led to the formation of n-propanol but also provoked production of some acetone and n-butanol, although in considerably smaller amounts than were obtained when the same basal medium had been fortified with acetate and butyrate at pH 7.     

Altered sensitivity of carnitine palmitoyltransferase to inhibition by malonyl-CoA in ketotic diabetic rats.

Carnitine palmitoyltransferase of liver mitochondria prepared from ketotic diabetic rats has a diminished sensitivity to inhibition by malonyl-CoA compared with carnitine palmitoyltransferase of mitochondria prepared from normal fed rats.     

Differential protein synthesis and utilization during cilia formation in sea urchin embryos.

Pulse labeling with [¹⁴C]leucine, hypertonic deciliation, fractionation of axonemes by differential solubilization, and autoradiographic analysis of electrophoretically resolved components reveal that the onset of ciliogenesis is marked by the de novo synthesis of numerous architectural proteins of the “9 + 2” axoneme. The synthesis of most of these components continues, some at reduced rates, after full growth of cilia at hatching. Deciliation results in enhanced synthesis of these minor components, dynein, and tubulin. The A- and B-tubulin dimers, derived from the respective subfibers, have essentially identical specific activities after regeneration in the presence of isotope. Subsequent regeneration in cold leucine demonstrates substantial pools of most of the architectural proteins, but at least two such proteins (nexin and ribbon component-20) are made quantally and in limiting amounts in response to each regeneration. Such second regeneration cilia (whose pools were labeled during the first regeneration) have a decreased specific activity of B-tubulin (10–15%) and an increased specific activity of A-tubulin (30–35%), indicating a limited pool of the former but an apparent retarded synthesis, delayed activation, or initial compartmentalization of the latter. This 45% difference in specific activity of the two tubulin dimer pools offers independent evidence that chemically unique tubulin dimers form the structurally unique subfibers. During natural ciliary augmentation or after stimulation by repeated deciliation, the bulk of the initial incorporation occurs in the quantal, minor components, while newly synthesized dynein and tubulin are not maximally utilized until the succeeding generation. The limited, quantal synthesis of microtubule-associated proteins may be a control mechanism for ciliary assembly or elongation, while a delayed utilization of the major proteins of the axoneme may reflect a replenishment of pools and a requisite activation or post-translational modification of stored components.     

METABOLIC SEGREGATION OF INTRACELLULAR FREE AMINO ACIDS IN PLATYMONAS (CHLOROPHYTA)1

¹⁴C-amino acids were supplied to Platymonas subcordiformis (Wille) Hazen and the incorporation of radioactivity into protein and other compounds was followed. Alanine was rapidly metabolized by both N-limited and N-sufficient cells. Arginine and lysine were metabolized rapidly by N-limited cells, but were sequestered from metabolism in N-sufficient cells. This suggests the existence of two functionally distinct pools; a “metabolic” pool that is rapidly metabolized and preferentially used for incorporation into protein, and a “storage” pool rich in basic amino acids that is sequestered from metabolism.