Transcriptional initiation under conditions of anoxia-induced quiescence in mitochondria from Artemia franciscana embryos

In response to anoxia, embryos of the brine shrimp Artemia franciscana are able coordinately to downregulate metabolism to levels low enough to permit survival for several years at room temperature. In addition to dramatic decreases in free ATP levels and heat production, intracellular pH drops from 7.8 to 6.3 overnight. Use of isolated mitochondria to study transcriptional responses to anoxia offers several advantages: (1) the localized nature of transcript initiation, processing and degradation, all of which may be followed in organello; (2) the relatively simple cis- and trans-machinery involved and (3) the ability to provide relevant physiological treatments in vitro. In response to anoxic incubation of embryos in vivo for 4h followed by anoxic mitochondrial isolation and anoxic transcription assay at pH 6.4, a significant decrease in overall UTP incorporation (77%) was seen after 30min relative to normoxic, pH 7.9 controls. A less severe inhibition of transcription under anoxia (52%) was observed compared with controls when pH was raised to 7.9. Similarly, under normoxia, the incubation at low pH (6.4) reduced transcription by 59%. Ribonuclease protection assays showed that the contribution of in vitro initiation during the assay fell from 78% at pH 7.9 to approximately 32% at pH 6.4 under either normoxic or anoxic conditions. DNA footprinting of putative transcriptional promoters revealed proteins at regular intervals upstream of the 12S rRNA in the control region, which previously had been indirectly inferred to contain promoters for H-strand transcription. The area between 12030 and 12065 contains a sequence in the tRNAleu gene believed to bind the transcription termination factor mTERF or TERM, and we provide the first evidence that this sequence is protein-bound in A. franciscana. However, our hypothesis that initiation is reduced at low pH because of a change in DNA binding by mitochondrial transcription factors was not confirmed. We propose that regulation of initiation may be mediated by covalent modification or by protein-protein interactions not detected by footprinting

Mitochondrial mRNA stability and polyadenylation during anoxia-induced quiescence in the brine shrimp Artemia franciscana

Polyadenylation of messenger RNA is known to be an important mechanism for regulating mRNA stability in a variety of systems, including bacteria, chloroplasts and plant mitochondria. By comparison, little is known about the role played by polyadenylation in animal mitochondrial gene expression. We have used embryos of the brine shrimp Artemia franciscana to test hypotheses regarding message stability and polyadenylation under conditions simulating anoxia-induced quiescence. In response to anoxia, these embryos undergo a profound and acute metabolic downregulation, characterized by a steep drop in intracellular pH (pHi) and ATP levels. Using dot blots of total mitochondrial RNA, we show that during in organello incubations both O 2 deprivation and acidic pH (pH 6.4) elicit increases in half-lives of selected mitochondrial transcripts on the order of five- to tenfold or more, relative to normoxic controls at pH 7.8. Polyadenylation of these transcripts was measured under the same incubation conditions using a reverse transcriptase-polymerase chain reaction (RT-PCR)-based assay. The results demonstrate that low pH and anoxia promote significant deadenylation of the stabilized transcripts in several cases, measured either as change over time in the amount of polyadenylation within a given size class of poly(A)+ tail, or as the total amount of polyadenylation at the endpoint of the incubation. This study is the first direct demonstration that for a metazoan mitochondrion, polyadenylation is associated with destabilized mRNA. This pattern has also been demonstrated in bacteria, chloroplasts and plant mitochondria and may indicate a conserved mechanism for regulating message half-life that differs from the paradigm for eukaryotic cytoplasm, where increased mRNA stability is associated with polyadenylation

Contrasting effects of sleep fragmentation and angiotensin-II treatment upon pro-inflammatory responses of mice

Disordered sleep promotes inflammation in brain and peripheral tissues, but the mechanisms that regulate these responses are poorly understood. One hypothesis is that activation of the sympathetic nervous system (SNS) from sleep loss elevates blood pressure to promote vascular sheer stress leading to inflammation. As catecholamines produced from SNS activation can directly regulate inflammation, we pharmacologically altered blood pressure using an alternative approach-manipulation of the renin-angiotensin system (RAS). Male C57BL6/J mice were treated with angiotensin or captopril to elevate and reduce blood pressure, respectively and then exposed to 24-h of sleep fragmentation (SF) or allowed to sleep (control). Pro- and anti-inflammatory cytokine gene expression and as endothelial adhesion gene expression as well as serum glucocorticoids (corticosterone) were measured. RAS manipulation elevated cytokines and endothelial adhesion expression in heart and aorta while SF increased cytokine expression in peripheral tissues, but not brain. However, there were interactive effects of angiotensin-II and SF upon cytokine gene expression in hippocampus and hypothalamus, but not prefrontal cortex. SF, but not RAS manipulation, elevated serum corticosterone concentration. These findings highlight the contrasting effects of RAS manipulation and SF, implying that inflammation from SF is acting on different pathways that are largely independent of RAS manipulation

Sampling Daphnia's expressed genes: preservation, expansion and invention of crustacean genes with reference to insect genomes

<p>Abstract</p> <p>Background</p> <p>Functional and comparative studies of insect genomes have shed light on the complement of genes, which in part, account for shared morphologies, developmental programs and life-histories. Contrasting the gene inventories of insects to those of the nematodes provides insight into the genomic changes responsible for their diversification. However, nematodes have weak relationships to insects, as each belongs to separate animal phyla. A better outgroup to distinguish lineage specific novelties would include other members of Arthropoda. For example, crustaceans are close allies to the insects (together forming Pancrustacea) and their fascinating aquatic lifestyle provides an important comparison for understanding the genetic basis of adaptations to life on land versus life in water.</p> <p>Results</p> <p>This study reports on the first characterization of cDNA libraries and sequences for the model crustacean <it>Daphnia pulex</it>. We analyzed 1,546 ESTs of which 1,414 represent approximately 787 nuclear genes, by measuring their sequence similarities with insect and nematode proteomes. The provisional annotation of genes is supported by expression data from microarray studies described in companion papers. Loci expected to be shared between crustaceans and insects because of their mutual biological features are identified, including genes for reproduction, regulation and cellular processes. We identify genes that are likely derived within Pancrustacea or lost within the nematodes. Moreover, lineage specific gene family expansions are identified, which suggest certain biological demands associated with their ecological setting. In particular, up to seven distinct ferritin loci are found in <it>Daphnia </it>compared to three in most insects. Finally, a substantial fraction of the sampled gene transcripts shares no sequence similarity with those from other arthropods. Genes functioning during development and reproduction are comparatively well conserved between crustaceans and insects. By contrast, genes that were responsive to environmental conditions (metal stress) and not sex-biased included the greatest proportion of genes with no matches to insect proteomes.</p> <p>Conclusion</p> <p>This study along with associated microarray experiments are the initial steps in a coordinated effort by the <it>Daphnia </it>Genomics Consortium to build the necessary genomic platform needed to discover genes that account for the phenotypic diversity within the genus and to gain new insights into crustacean biology. This effort will soon include the first crustacean genome sequence.</p

The K600 Focal Plane Polarimeter

This research was sponsored by the National Science Foundation Grant NSF PHY 87-1440

Eigenstate–Specific Temperatures in Two–Level Paramagnetic Spin Lattices

Increasing interest in the thermodynamics of small and/or isolated systems, in combination with recent observations of negative temperatures of atoms in ultracold optical lattices, has stimulated the need for estimating the conventional, canonical temperature Tconvc of systems in equilibrium with heat baths using eigenstate-specific temperatures (ESTs). Four distinct ESTs—continuous canonical, discrete canonical, continuous microcanonical, and discrete microcanonical—are accordingly derived for two-level paramagnetic spin lattices (PSLs) in external magnetic fields. At large N, the four ESTs are intensive, equal to Tconvc, and obey all four laws of thermodynamics. In contrast, for N \u3c 1000, the ESTs of most PSL eigenstates are non-intensive, differ from Tconvc, and violate each of the thermodynamic laws. Hence, in spite of their similarities to Tconvc at large N, the ESTs are not true thermodynamic temperatures. Even so, each of the ESTs manifests a unique functional dependence on energy which clearly specifies the magnitude and direction of their deviation from Tconvc; the ESTs are thus good temperature estimators for small PSLs. The thermodynamic uncertainty relation is obeyed only by the ESTs of small canonical PSLs; it is violated by large canonical PSLs and by microcanonical PSLs of any size. The ESTs of population-inverted eigenstates are negative (positive) when calculated using Boltzmann (Gibbs) entropies; the thermodynamic implications of these entropically induced differences in sign are discussed in light of adiabatic invariance of the entropies. Potential applications of the four ESTs to nanothermometers and to systems with long-range interactions are discussed

Gene networks in Drosophila melanogaster: integrating experimental data to predict gene function

The first computational interaction network built from Drosophila melanogaster protein-protein and genetic interaction data allows the functional annotation of orphan genes and reveals clusters of functionally-related genes

Search for a Fermiophobic and Standard Model Higgs Boson in Diphoton Final States

We present a search for the standard model Higgs boson and a fermiophobic Higgs boson in the diphoton final states based on 8.2 fb-1 of pp̅ collisions at √s= 1.96 TeV collected with the D0 detector at the Fermilab Tevatron Collider. No excess of data above background predictions is observed and upper limits at the 95% C.L. on the cross section multiplied by the branching fraction are set which are the most restrictive to date. A fermiophobic Higgs boson with a mass below 112.9 GeV is excluded at the 95% C.L