Neural correlates of singing behavior in male zebra finches (Taeniopygia guttata)

This study examined the relationship between the volumes of four song control nuclei: the high vocal center (HVC), the lateral part of the magnocellular nucleus of the anterior neostriatum (lMAN), Area X, and the robust nucleus of the archistriatum (RA), as well as syrinx mass, with several measures of song output and song complexity in male zebra finches (Taeniopygia guttata). Male zebra finches' songs were recorded in standardized recording sessions. The syrinx and brain were subsequently collected from each bird. Volumes of the song control nuclei were reconstructed by measuring the cross-sectional area of serial sections. Syrinx mass was positively correlated with RA volume. The volume of lMAN was negatively related to element repertoire size and the number of elements per phrase. We found no other correlations between brain and behavioral measures. This study, combined with others, indicates that the evidence for a general relationship among songbirds between HVC volume and song complexity is equivocal. There are clear species differences in this brain-behavior correlation. © 1998 John Wiley & Sons, Inc. J Neurobiol 36: 421–430, 1998     

Distinct Functions of Human Cohesin-SA1 and Cohesin-SA2 in Double-Strand Break Repair

Cohesin is an essential multiprotein complex that mediates sister chromatid cohesion critical for proper segregation of chromosomes during cell division. Cohesin is also involved in DNA double-strand break (DSB) repair. In mammalian cells, cohesin is involved in both DSB repair and the damage checkpoint response, although the relationship between these two functions is unclear. Two cohesins differing by one subunit (SA1 or SA2) are present in somatic cells, but their functional specificities with regard to DNA repair remain enigmatic. We found that cohesin-SA2 is the main complex corecruited with the cohesin-loading factor NIPBL to DNA damage sites in an S/G₂-phase-specific manner. Replacing the diverged C-terminal region of SA1 with the corresponding region of SA2 confers this activity on SA1. Depletion of SA2 but not SA1 decreased sister chromatid homologous recombination repair and affected repair pathway choice, indicating that DNA repair activity is specifically associated with cohesin recruited to damage sites. In contrast, both cohesin complexes function in the intra-S checkpoint, indicating that cell cycle-specific damage site accumulation is not a prerequisite for cohesin''s intra-S checkpoint function. Our findings reveal the unique ways in which cohesin-SA1 and cohesin-SA2 participate in the DNA damage response, coordinately protecting genome integrity in human cells.     

Exceptional preservation of a novel gill grade in large Cretaceous inoceramids: systematic and palaeobiological implications

Organised mineralised structures observed in large inoceramids (valves on a metre scale) from the Late Albian, Toolebuc Formation, Australia (Inoceramus sutherlandi McCoy, 1865), and the Santonian, Niobrara Formation, USA (Platyceramus sp.), were investigated using variable pressure scanning electron microscope (SEM) with energy‐dispersive X‐ray spectroscopy (EDX), X‐ray microcomputed tomography (micro‐CT) and X‐ray diffraction (XRD) analyses. These indicate that the structures comprised a phosphate framework of aligned tubes and shallow troughs overlain perpendicularly by evenly spaced structures. In the Toolebuc Inoceramus, these are U‐shaped cross‐structures, whilst in the Niobrara Platyceramus, they comprise bundled fibre elements. Comparison with modern bivalves indicates that the observed phosphatised structures represent soft‐tissue preservation of the gills, as suggested in earlier publications. The tubes and troughs are remnants of a filamental support framework comprising ordinary and primary filaments, whilst the U‐shaped cross‐structures (I. sutherlandi) and fibrous bands (Platyceramus) represent preserved longitudinal gill musculature. Internal perforate and strand‐like fabric observed on the internal surface of some Platyceramus tubular structures suggests that the framework comprised collagen. The presence of primary and ordinary filaments in numerous unusually large plicae, in at least two lamellae, indicates that the gill structures were heterorhabdic. Each plica has at least 40 ordinary filaments, an exceptional number when compared with the maximum of 20 present in modern heterorhabdic gills. The absence of incontrovertible interfilament junctions makes it difficult to say whether inoceramids were filibranch, pseudolamellibranch or eulamellibranch. However, structures that are best attributed to intraplical junctions between filaments suggest the Inoceramidae had gills akin to those of pseudolamellibranch bivalves, although their unusually large number of filaments per plica is more reminiscent of homorhabdic eulamellibranch gills. The general form of the gill is similar to that described in some other pteriomorphs, most specifically Pteria. However, it has more complex junctions and interconnections, although these are not as intricate or pervasive as those observed in the pseudolamellibranch Ostreidae. The connections and well‐developed filament framework allowed the gill to reach its unusually large size, supporting the large size of these inoceramid species. The unusually large size of the gill and its components indicate that the organism fed on the larger suspended organic particles in the water column. It would also have been capable of processing large volumes of water quickly, leading to greater potential for food accumulation and with likely implications for respiratory efficiency. This may help explain the common association of inoceramids with oxygen‐deficient palaeoenvironments, particularly as the general structure of the inoceramid gill is very different to that observed in the commonest extant chemosymbiotic bivalves.     

Steric hindrance controls pyridine nucleotide specificity of a flavin‐dependent NADH:quinone oxidoreductase

The crystal structure of the NADH:quinone oxidoreductase PA1024 has been solved in complex with NAD⁺ to 2.2 Å resolution. The nicotinamide C4 is 3.6 Å from the FMN N5 atom, with a suitable orientation for facile hydride transfer. NAD⁺ binds in a folded conformation at the interface of the TIM‐barrel domain and the extended domain of the enzyme. Comparison of the enzyme‐NAD⁺ structure with that of the ligand‐free enzyme revealed a different conformation of a short loop (75–86) that is part of the NAD⁺‐binding pocket. P78, P82, and P84 provide internal rigidity to the loop, whereas Q80 serves as an active site latch that secures the NAD⁺ within the binding pocket. An interrupted helix consisting of two α‐helices connected by a small three‐residue loop binds the pyrophosphate moiety of NAD⁺. The adenine moiety of NAD⁺ appears to π–π stack with Y261. Steric constraints between the adenosine ribose of NAD⁺, P78, and Q80, control the strict specificity of the enzyme for NADH. Charged residues do not play a role in the specificity of PA1024 for the NADH substrate.     

Serum concentrations of amino acids,fatty acids,lipoproteins, vitamins A and E,and minerals in apparently healthy,free‐ranging southern giraffe (Giraffa camelopardalis giraffe)

This pilot project began establishing a nutritional profile for free‐ranging giraffe. The results will be used as a tool to begin assessing the nutritional status of captive giraffe. In October 2004 serum samples were collected opportunistically from seven adult and 17 sub‐adult giraffe being anesthetized for different studies. Seventeen animals were from Double Drift Game Reserve and seven animals were from Kariega Private Game Reserve. The serum samples were analyzed for circulating concentrations of amino acids, fatty acids, lipoproteins, vitamins, and minerals. Information from 15 serum samples collected from anesthetized giraffe in Kruger National Park during April and August 2003 was included in the calcium and phosphorus concentration data. No significant differences were identified between genders. Significant differences between locations were identified for concentrations of certain amino acids, fatty acids, and lipoproteins. Differences between locations are likely due to different nutrient concentrations of foods and possibly the result of different animal densities forcing different food choices among locations. This pilot project may expand to include changes in circulating nutrient concentrations for free‐ranging giraffe as is influenced by other locations, seasonal food availability, and different giraffe subspecies. Zoo Biol 0:1–13, 2007. © 2006 Wiley‐Liss, Inc.     

Definition of a conserved immunodominant domain on hepatitis C virus E2 glycoprotein by neutralizing human monoclonal antibodies

Development of a successful hepatitis C virus (HCV) vaccine requires the definition of neutralization epitopes that are conserved among different HCV genotypes. Five human monoclonal antibodies (HMAbs) are described that cross-compete with other antibodies to a cluster of overlapping epitopes, previously designated domain B. Each HMAb broadly neutralizes retroviral pseudotype particles expressing HCV E1 and E2 glycoproteins, as well as the infectious chimeric genotype 1a and genotype 2a viruses. Alanine substitutions of residues within a region of E2 involved in binding to CD81 showed that critical E2 contact residues involved in the binding of representative antibodies are identical to those involved in the binding of E2 to CD81.     

Large-scale genetic differentiation of Pagrus pagrus in the Atlantic

Red porgy Pagrus pagrus from the north-eastern, north-western and south-western Atlantic were found to be genetically distinct as determined by mitochondrial DNA analysis. There were no shared composite restriction fragment haplotypes, and nucleotide sequence differences averaged 2% among these locations.     

Protein secretion in Pseudomonas aeruginosa: characterization of seven xcp genes and processing of secretory apparatus components by prepilin peptidase

The xcp genes are required for the secretion of most extracellular proteins by Pseudomonas aeruginosa. The products of these genes are essential for the transport of exoproteins across the outer membrane after they have reached the periplasm via a signal sequence-dependent pathway. To date, analysis of three xcp genes has suggested the conservation of this secretion pathway in many Gram-negative bacteria. Furthermore, the xcpA gene was shown to be identical to pilD, which encodes a peptidase involved in the processing of fimbrial (pili) subunits, suggesting a connection between pili biogenesis and protein secretion. Here the nucleotide sequences of seven other xcp genes, designated xcpR to -X, are presented. The N-termini of four of the encoded Xcp proteins display similarity to the N-termini of type IV pili, suggesting that XcpA is involved in the processing of these Xcp proteins. This could indeed be demonstrated in vivo. Furthermore, two other proteins, XcpR and XcpS, show similarity to the PilB and PilC proteins required for fimbriae assembly. Since XcpR and PilB display a canonical nucleotide-binding site, ATP hydrolysis may provide energy for both systems.