The spatial distribution of fixed mutations within genes coding for proteins

We have examined the extensive amino acid sequence data now available for five protein families - the alpha crystallin A chain, myoglobin, alpha and beta hemoglobin, and the cytochromes c - with the goal of estimating the true spatial distribution of base substitutions within genes that code for proteins. In every case the commonly used Poisson density failed to even approximate the experimental pattern of base substitution. For the 87 species of beta hemoglobin examined, for example, the probability that the observed results were from a Poisson process was the minuscule 10(-44). Analogous results were obtained for the other functional families. All the data were reasonably, but not perfectly, described by the negative binomial density. In particular, most of the data were described by one of the very simple limiting forms of this density, the geometric density. The implications of this for evolutionary inference are discussed. It is evident that most estimates of total base substitutions between genes are badly in need of revision.     

Ontogeny,auditory structures,and primate evolution

The anatomy of the auditory region, particularly the carotid circulatory patterns and ectotympanic-petrosal relationships, has played a prominent role in primate systematics and phylogenetic reconstructions. Ontogenetic stages of petrosal-ectotympanic relationship are presented for certain strepsirhines. It is suggested that the “ectotympanic tube” or “ossified annulus membrane” found in early Tertiary primates is not necessarily an homologous structure to the true ectotympanic tube seen in haplorhines, and thus cannot be considered a shared, derived feature linking known Paleogene primates from Europe or North America to tarsioid and/or anthropoid ancestry. No fossil primate yet discovered makes a convincing ancestor for the earliest known anthropoids from the Oligocene of Africa. This is probably due to the fact that it still lies undiscovered in the Paleogene of Africa.     

An enzyme-linked immunosorbent assay for zein and other proteins using unconventional solvents for antigen adsorption

An enzyme-linked immunosorbent assay (ELISA) performed in polystyrene microtiter plates that can detect and quantitate the maize prolamin zein is described. The assay yields positive reactions with as little as 1 ng of antigen and uses solvents not ordinarily employed in ELISA methods. A systematic investigation of zein adsorption to polystyrene in various solvents supports the hypothesis that antigen binding occurs through nonpolar interactions. The method was also used to determine structural relationships among three zein polypeptides differing in size and charge. Additional experiments indicate that a number of soluble proteins are absorbed to polystyrene in the denaturing agent urea and retain immunological reactivity. The retention of antigen reactivity after solubilization in 6-8 M urea suggests that ELISA methods may be applicable to other proteins which are insoluble, or rendered insoluble, in aqueous buffers.     

Inositol lipids and phosphates in the regulation of the growth and differentiation of haemopoietic and other cells

Stimulation of phosphatidylinositol 4,5-bisphosphate hydrolysis is an important signalling reaction involved in the responses of cells to some, but not all, stimuli that promote cell proliferation. Active agents in this regard include antigens activating T and B lymphocytes, angiotensin (employing a receptor encoded by the mas oncogene), bombesin and platelet-derived growth factor PDGF). However, accumulating evidence suggests that inositol lipids and phosphates also have other roles in the regulation of cell growth and differentiation. Growth factor receptors that encode tyrosine kinases (such as that for PDGF) activate a kinase that synthesises phosphatidylinositol 3-phosphate, a novel lipid, and loss of this kinase-activating function abolishes growth-promoting activity. Human interleukin-4, a lymphokine that activates B lymphocytes, appears to employ phosphatidylinositol 4,5-bisphosphate hydrolysis as a brief initial signal that is followed by a sustained rise in cyclic adenosine monophosphate (cAMP): both signals are needed for the successful induction of the surface antigen CD23. Moreover, the same inositol lipid signalling pathway as is employed by antigen-stimulated mature T lymphocytes to provoke proliferation may be redeployed in immature T cells to trigger their elimination when they encounter self-antigens. Finally, studies of HL60 promyelocytic cells have shown that these cells contain high concentrations of inositol 3,4,5,6-tetrakisphosphate, 1,3,4,5,6-pentakisphosphate and hexakisphosphate, three inositol polyphosphates that are probably formed independently of inositol lipid metabolism. When these cells are induced to differentiate either towards neutrophils (in the presence of dimethylsulphoxide) or macrophages (in phorbol myristate acetate), cessation of growth and acquisition of differentiated characteristics are accompanied by large and different changes in the concentrations of these inositol phosphates that may be characteristic of these two pathways of differentiation.     

Antisera against an acetylcholine receptor alpha 3 fusion protein bind to ganglionic but not to brain nicotinic acetylcholine receptors

Neuronal nicotinic acetylcholine receptor (AChR) subtypes have been defined pharmacologically, immunologically, and by DNA cloning, but the correlations between these approaches are incomplete. Vertebrate neuronal AChRs that have been isolated are composed of structural subunits and ACh-binding subunits. A single kind of subunit can be used in more than one AChR subtype. Monoclonal antibody (mAb) 35 binds to structural subunits of subtypes of AChRs from both chicken brain and ganglia. By using antisera to a unique sequence of alpha 3 ACh-binding subunits expressed in bacteria, we show that ganglionic AChRs contain alpha 3 ACh-binding subunits, whereas the brain AChR subtype that binds mAb 35 does not. Subunit-specific antisera raised against recombinant proteins should be a valuable approach for identifying the subunit composition of receptors in multigene, multisubunit families.     

Three-dimensional surface reconstruction software system for IBM personal computers

Surface and volumetric three-dimensional imaging methods have found application in fields as diverse as diagnostic medical imaging and paleontological research. The acquisition, modeling, classification, and computer graphics rendering of discrete image volumes will be introduced. Applications in diagnosis (craniofacial, orthopedic, cardiovascular, and others) as well as reconstruction methods for generic serial sections will be described. C language software for three-dimensional reconstruction which operates on an IBM PC/AT clone is described.     

Sequence and structure of yeast phosphoglycerate kinase.

The structure of yeast phosphoglycerate kinase has been determined with data obtained from amino acid sequence, nucleotide sequence, and X-ray crystallographic studies. The substrate binding sites, as deduced from electron density maps, are compatible with known substrate specificity and the stereochemical requirements for the enzymic reaction. A carboxyl-imidazole interaction appears to be involved in controlling the transition between the open and closed forms of the enzyme.     

Impaired clearance and enhanced pulmonary inflammatory/fibrotic response to carbon nanotubes in myeloperoxidase-deficient mice

Advancement of biomedical applications of carbonaceous nanomaterials is hampered by their biopersistence and pro-inflammatory action in vivo. Here, we used myeloperoxidase knockout B6.129X1-MPO (MPO k/o) mice and showed that oxidation and clearance of single walled carbon nanotubes (SWCNT) from the lungs of these animals after pharyngeal aspiration was markedly less effective whereas the inflammatory response was more robust than in wild-type C57Bl/6 mice. Our results provide direct evidence for the participation of MPO - one of the key-orchestrators of inflammatory response - in the in vivo pulmonary oxidative biodegradation of SWCNT and suggest new ways to control the biopersistence of nanomaterials through genetic or pharmacological manipulations.     

MAC: identifying and correcting annotation for multi-nucleotide variations

Background

Next-Generation Sequencing (NGS) technologies have rapidly advanced our understanding of human variation in cancer. To accurately translate the raw sequencing data into practical knowledge, annotation tools, algorithms and pipelines must be developed that keep pace with the rapidly evolving technology. Currently, a challenge exists in accurately annotating multi-nucleotide variants (MNVs). These tandem substitutions, when affecting multiple nucleotides within a single protein codon of a gene, result in a translated amino acid involving all nucleotides in that codon. Most existing variant callers report a MNV as individual single-nucleotide variants (SNVs), often resulting in multiple triplet codon sequences and incorrect amino acid predictions. To correct potentially misannotated MNVs among reported SNVs, a primary challenge resides in haplotype phasing which is to determine whether the neighboring SNVs are co-located on the same chromosome.

Results

Here we describe MAC (Multi-Nucleotide Variant Annotation Corrector), an integrative pipeline developed to correct potentially mis-annotated MNVs. MAC was designed as an application that only requires a SNV file and the matching BAM file as data inputs. Using an example data set containing 3024 SNVs and the corresponding whole-genome sequencing BAM files, we show that MAC identified eight potentially mis-annotated SNVs, and accurately updated the amino acid predictions for seven of the variant calls.

Conclusions

MAC can identify and correct amino acid predictions that result from MNVs affecting multiple nucleotides within a single protein codon, which cannot be handled by most existing SNV-based variant pipelines. The MAC software is freely available and represents a useful tool for the accurate translation of genomic sequence to protein function.     

The emissary foramina: Their value in platyrrhine systematics

A discriminant analysis was performed on 226 ceboid skulls using data on emissary foramina size and shape. The purposes of the study are to 1) measure the success with which these discriminating variables can distinguish among platyrrhine genera and 2) derive a set of classification functions which will permit the classification of new cases with unknown group membership (i.e., fossil skulls). This technique is able to correctly classify 80% of the 226 ceboid skulls. Support is given to the allocation of Chiropotes, Cacajao, and Pithecia into one morphologically unified subfamily, Pitheciinae. Alouatta, Ateles, and Lagothrix also share many similarities in emissary foramina size and shape and their inclusion into one subfamily, Atelinae, is probably warranted. The distinctiveness of Cebus in these same morphological features is apparent. Possibilities for extending this procedure to study fossil lineages in platyrrhines are discussed.