Strong genetic isolation despite wide distribution in a commercially exploited coastal shark

The common smoothhound, Mustelus mustelus, is an epibenthic species targeted by fisheries around the world driven by the increasing demand for shark products. Given the wide-spread occurrence of this species and corresponding lack of molecular data in many areas of said distribution, baseline molecular assessments of this commercially important shark may contribute to finer-scale analyses in areas in which this species is targeted. Therefore, population genetic analyses were conducted along the East Atlantic, from the Mediterranean Sea to the south-east coast of Africa, using microsatellite markers and the mitochondrial control region (mtCR). Overall, M. mustelus displayed low to moderate genetic diversity, with the Mediterranean populations appearing to exhibit the lowest mitochondrial diversity, and the west African populations displaying the lowest nuclear diversity. Microsatellite analysis indicated strong genetic differentiation between the three regions, with finer-scale population structure in each region, without correlation between genetic and geographical distance. For the mtCR sequences, a total of 18 haplotypes were identified, with a high degree of divergence discernable between the regions, largely in accordance with the microsatellite data. The study documents a remarkable level of population isolation across a vast area, suggesting little or no present-day connectivity among extant populations. The findings may serve as an essential baseline for global population management and commercial traceability of this threatened shark.

     

TNFalpha induces NFkappaB/p50 in association with the growth and morphogenesis of normal and transformed rat mammary epithelial cells

In contrast to the cytotoxic or cytostatic effect of TNFalpha on many breast cancer cell lines, TNFalpha stimulates growth and morphogenesis of normal rat mammary epithelial cells (MEC). The present studies were carried out to determine whether there are intrinsic differences between normal and malignant MEC which may explain the differing responsiveness to TNFalpha. Freshly isolated rat MEC organoids from normal mammary gland or 1-methyl-1-nitrosourea-induced mammary tumors were treated with TNFalpha for 21 days. Unexpectedly, TNFalpha stimulated growth and morphogenesis of both normal and transformed MEC in primary culture, although in transformed cells its effects were delayed and the majority of the colonies were histologically abnormal, with multiple cell layers and no lumen. Since NFkappaB is a key mediator of TNFalpha action and has been implicated in carcinogenesis, the expression of the p50, p52, p65, and c-rel NFkappaB proteins in normal and transformed MEC was determined. Expression of p52 was significantly reduced in tumor cells, and p50 was absent, although its putative precursor, p105 was abundant. There were no changes in the levels of p65 or c-rel. TNFalpha induced a pronounced and sustained increase of a p50 homodimeric NFkappaB/DNA complex in both normal and transformed MEC. However, in transformed MEC, NFkappaB binding was initially undetectable but then increased in response to TNFalpha. Thus, NFkappaB expression and DNA binding activity are altered during mammary carcinogenesis. In addition, the significant increase in NFkappaB/p50 DNA-binding was temporally coincident with TNFalpha-induced growth and morphogenesis, suggesting that it may play a significant role in both normal development and carcinogenesis.     

Fine structure of the gill epithelium of the terrestrial mudskipper, Periophthalmodon schlosseri

In this paper, we describe the fine structure of the branchial epithelium of the amphibious, air-breathing mudskipper Periophthalmodon schlosseri, and relate the observed structure to functions in gas exchange, and to the elimination of sodium chloride and ammonia. Also, we describe the fine structure of the opercular epithelimicrom. The gill lamellar epithelium is thickened by the presence of large mitochondria-rich (MR) cells. These MR cells are further characterized by an extensive tubular system that is continuous with the basolateral plasma membrane and by a deep apical crypt often lined with microvilli. There are very few specialized MR accessory cells, which are associated with NaCl excretion in marine teleosts. Instead, MR cells are commonly isolated from each other laterally by flattened cells rich in intermediate filaments. These filament-rich (FR) cells are interconnected by desmosomes and have unusual canaliculi. These branchial FR cells are unique to P. schlosseri and may have a structural role. Electron-dense pavement cells rich in vesicles and large vacuous mitochondria compose the superficial layer of the epithelium. The unusual morphology of P. schlosseri's gill lamellae may be related to the animal's ability to effectively eliminate ammonia during air exposure. The inner opercular lining and parts of the leading edge of the filament have intraepithelial capillaries, which provide a more suitable gas exchange surface than the thickened lamellae with its restricted interlamellar water spaces. The arrangement of respiratory and ion exchange epithelia is opposite to that found in all other fish in which the lamellae typically function in gas exchange and the gill filament in ion regulation.     

Mining Microarrays for Metabolic Meaning: Nutritional Regulation of Hypothalamic Gene Expression

DNA microarray analysis has been used to investigate relative changes in the level of gene expression in the CNS, including changes that are associated with disease, injury, psychiatric disorders, drug exposure or withdrawal, and memory formation. We have used oligonucleotide microarrays to identify hypothalamic genes that respond to nutritional manipulation. In addition to commonly used microarray analysis based on criteria such as fold-regulation, we have also found that simply carrying out multiple t tests then sorting by P value constitutes a highly reliable method to detect true regulation, as assessed by real-time polymerase chain reaction (PCR), even for relatively low abundance genes or relatively low magnitude of regulation. Such analyses directly suggested novel mechanisms that mediate effects of nutritional state on neuroendocrine function and are being used to identify regulated gene products that may elucidate the metabolic pathology of obese ob/ob, lean Vgf-/Vgf-, and other models with profound metabolic impairments.     

Learning the codes of fly immunity

Insect antimicrobial response serves as an excellent model for studying human innate immunity. In this issue of Molecular Cell, Senger and colleagues demonstrate that a large number of immunity genes in Drosophila fat bodies can be regulated by a simple code, REL-GATA.     

Converting weak binders into infinite binders

Monoclonal antibody 2D12.5 binds DOTA chelates of all the rare earths with K(d) approximately 10(-)(8) M, making it useful for the capture of probe molecules with a variety of properties. To make 2D12.5 even more useful for biological applications, we have engineered a single cysteine residue at position 54 of the heavy chain, a site proximal to the protein's binding site, so that weakly electrophilic metal complexes of (S)-2-(4-acrylamidobenzyl)-DOTA (AABD) may bind and form permanent linkages. At 37 degrees C, pH 7.5, all of the rare earth-AABD complexes bind permanently to the 2D12.5 G54C mutant within 5 min, in yields that correlate with their relative binding affinities. Surprisingly, indium-AABD also binds permanently in >50% yield within 5 min, despite the fact that changing the metal to indium reduces the affinity approximately 100x; even copper-AABD, which has approximately 10 000x lower binding affinity than the rare earths, binds permanently in >70% yield within 2 h. However, acrylamido compounds with no measurable affinity do not bind permanently. The important practical implication is that the G54C mutant of 2D12.5 may be used for applications that include not only the rare earths, but also an unexpected range of other elements as well. This infinite binding system can exhibit selective and permanent attachment with a remarkable range of structurally related ligands, albeit at slower rates as affinities decrease.     

Insights into the relation between mRNA and protein expression patterns: I. Theoretical considerations

Translation is a central cellular process in every organism and understanding translation from the systems (genome-wide) perspective is very important for medical and biochemical engineering applications. Moreover, recent advances in cell-wide monitoring tools for both mRNA and protein levels have necessitated the development of such a model to identify parameters and conditions that influence the mapping between mRNA and protein expression. Experimental studies show a lack of correspondence between mRNA and protein expression profiles. In this study, we describe a mechanistic genome-wide model for translation that provides mapping between changes in mRNA levels and changes in protein levels. We use our model to study the system in detail and identify the key parameters that affect this mapping. Our results show that the correlation between mRNA and protein levels is a function of both the kinetic parameters and concentration of ribosomes at the reference state. In particular, changes in concentration of free and total ribosomes in response to a perturbation; changes in initiation and elongation kinetics due to competition for aminoacyl tRNAs; changes in termination kinetics; average changes in mRNA levels in response to the perturbation; and changes in protein stability are all important determinants of the mapping between mRNA and protein expression.     

Escherichia coli--a model system that benefits from and contributes to the evolution of proteomics

The large body of knowledge about Escherichia coli makes it a useful model organism for the expression of heterologous proteins. Proteomic studies have helped to elucidate the complex cellular responses of E. coli and facilitated its use in a variety of biotechnology applications. Knowledge of basic cellular processes provides the means for better control of heterologous protein expression. Beyond such important applications, E. coli is an ideal organism for testing new analytical technologies because of the extensive knowledge base available about the organism. For example, improved technology for characterization of unknown proteins using mass spectrometry has made two-dimensional electrophoresis (2DE) studies more useful and more rewarding, and much of the initial testing of novel protocols is based on well-studied samples derived from E. coli. These techniques have facilitated the construction of more accurate 2DE maps. In this review, we present work that led to the 2DE databases, including a new map based on tandem time-of-flight (TOF) mass spectrometry (MS); describe cellular responses relevant to biotechnology applications; and discuss some emerging proteomic techniques.     

Leukemia inhibitory factor receptor signaling negatively modulates nerve growth factor-induced neurite outgrowth in PC12 cells and sympathetic neurons

Nerve growth factor (NGF) is required for the development of sympathetic neurons and subsets of sensory neurons. Our current knowledge on the molecular mechanisms underlying the biological functions of NGF is in part based on the studies with PC12 rat pheochromocytoma cells, which differentiate into sympathetic neuron-like cells upon NGF treatment. Here we report that the expression of leukemia inhibitory factor receptor (LIFR), one of the signaling molecules shared by several neuropoietic cytokines of the interleukin-6 family, is specifically up-regulated in PC12 cells following treatment with NGF. Attenuation of LIFR signaling through stable transfection of antisense- or dominant negative-LIFR constructs enhances NGF-induced neurite extension in PC12 cells. On the contrary, overexpression of LIFR retards the growth of neurites. More importantly, whereas NGF-induced Rac1 activity is enhanced in antisense-LIFR and dominant negative-LIFR expressing PC12 cells, it is reduced in LIFR expressing PC12 cells. Following combined treatment with NGF and ciliary neurotrophic factor, sympathetic neurons exhibit attenuated neurite growth and branching. On the other hand, in sympathetic neurons lacking LIFR, neurite growth and branching is enhanced when compared with wild type controls. Taken together, our findings demonstrate that LIFR expression can be specifically induced by NGF and, besides its known function in cell survival and phenotype development, activated LIFR signaling can exert negative regulatory effects on neurite extension and branching of sympathetic neurons.