Three chromosome-level duck genome assemblies provide insights into genomic variation during domestication

Domestic ducks are raised for meat, eggs and feather down, and almost all varieties are descended from the Mallard (Anas platyrhynchos). Here, we report chromosome-level high-quality genome assemblies for meat and laying duck breeds, and the Mallard. Our new genomic databases contain annotations for thousands of new protein-coding genes and recover a major percentage of the presumed "missing genes" in birds. We obtain the entire genomic sequences for the C-type lectin (CTL) family members that regulate eggshell biomineralization. Our population and comparative genomics analyses provide more than 36 million sequence variants between duck populations. Furthermore, a mutant cell line allows confirmation of the predicted anti-adipogenic function of NR2F2 in the duck, and uncovered mutations specific to Pekin duck that potentially affect adipose deposition. Our study provides insights into avian evolution and the genetics of oviparity, and will be a rich resource for the future genetic improvement of commercial traits in the duck.

Modeling of sensitivity and resolution to an included object in homogeneous scattering media and in MRI-derived breast maps

We have examined the measured sensitivity and edge resolution to an included tumor in MR-derived maps of the breast exposed to NIR illumination. A large parameter space was explored, enabling a systematic examination of the influence that measurement parameters (e.g., view angle, source position, wavelength) and target medium parameters (e.g., breast and tumor size, background tissue properties, and tumor contrast) have on the computed responses. The significance of these finding on data collection schemes for imaging studies is discussed.

Brain membrane protein band 3 performs the same functions as erythrocyte band 3

We report the presence of band 3 protein(s) in mammalian brain that performs the same functions as those of erythroid band 3. These functions are anion transport, ankyrin binding, and generation of senescent cell antigen, an aging antigen that terminates the life of cells. Structural similarity of brain and erythroid band 3 is suggested by the reaction of antibodies to synthetic peptides of erythroid band 3 with brain band 3, the inhibition of anion transport by the same inhibitors, and an equal degree of inhibition of brain and erythrocyte anion transport by synthetic peptides of erythroid band 3 (pep-ANION 2, residues 588-602; pep-COOH, residues 812-827; pep-COOH-N6, residues 813-818). One of these segments, pep-COOH, contains antigenic determinants of senescent cell antigen. These findings suggest that the transport domains of erythroid and neural band 3 are similar functionally and structurally and support the hypothesis that the immunological mechanism of maintaining homeostasis is a general physiologic process for removing senescent and damaged cells in mammals and other vertebrates.

Molecular mapping of the active site of an aging antigen: senescent cell antigen requires lysine(s) for antigenicity and is located on an anion-binding segment of band 3 membrane transport protein

An aging antigen, senescent cell antigen, resides on the 911 amino acid membrane protein band 3. It marks cells for removal by initiating specific IgG binding. The active antigenic sites of the aging antigen have been localized to residues 538-554 and 778-827. Two peptides within these regions interact synergistically to generate a synthetic aging antigen that is an effective inhibitor of senescent cell IgG binding to old cells. We synthesized peptides corresponding to these residues (pep-ANION 1: SKLIKIFQDHPLQKTYN, and pep-COOH: LFKPPKYHPDVPYVKR). These are extracellular regions of band 3 containing lysines which are implicated in anion transport. The contribution of lysine to the antigenicity of the aging antigen and to anion transport was examined by chemically modifying the lysines on both synthetic peptides and whole cells, and by synthesizing peptides in which glycines or arginines were substituted for lysines. Anion transport sites were localized using 16- to 18-mer peptides followed by 6- to 8-mer peptides. Functional studies with the peptide pep-COOH indicate that it contains sulfate-binding sites and inhibits sulfate transport in addition to carrying aging antigenic determinants. Substitution of arginines or glycines for lysines in pep-COOH reduces the sulfate-binding properties of the peptide although significant inhibition still occurs. Residues 812-827 (pep-COOH) and 813-818 (N6, the six amino acids on the amino side of pep-COOH) and 822-839 are inhibitors of anion transport when used in equimolar amounts with sulfate suggesting that these regions may be transport regions in situ. Results of this study indicate that: (a) lysines are required for the integrity of the aging antigenic site; (b) pep-COOH (residues 812-827) is part of senescent cell antigen and an anion-binding site; (c) pep-ANION 1 (538-554), which has been reported to be a transport segment of band 3, does not bind sulfate; (d) residues 588-602 are part of an anion binding/transport segment; (e) band 3 residues 822-839 are part of an anion binding/transport site, and (f) lysines contribute to anion binding but are not the only amino acid(s) required for anion binding and, thus, anion transport.