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21.
Circadian rhythms can be reset by both photic and non-photic stimuli. Recent studies have used long light exposure to produce photic phase shifts or to enhance non-photic phase shifts. The presence or absence of light can also influence the expression of locomotor rhythms through masking; light during the night attenuates locomotor activity, while darkness during the day induces locomotor activity in nocturnal animals. Given this dual role of light, the current study was designed to examine the relative contributions of photic and non-photic components present in a long light pulse paradigm. Mice entrained to a light/dark cycle were exposed to light pulses of various durations (0, 3, 6, 9, or 12 h) starting at the time of lights-off. After the light exposure, animals were placed in DD and were either left undisturbed in their home cages or had their wheels locked for the remainder of the subjective night and subsequent subjective day. Light treatments of 6, 9, and 12 h produced large phase delays. These treatments were associated with decreased activity during the nocturnal light and increased activity during the initial hours of darkness following light exposure. When the wheels were locked to prevent high-amplitude activity, the resulting phase delays to the light were significantly attenuated, suggesting that the activity following the light exposure may have contributed to the overall phase shift. In a second experiment, telemetry probes were used to assess what effect permanently locking the wheels had on the phase shift to the long light pulses. These animals had phase shifts fully as large as animals without any form of wheel lock, suggesting that while non-photic events can modulate photic phase shifts, they do not play a role in the full phase-shift response observed in animals exposed to long light pulses. This paradigm will facilitate investigations into non-photic responses of the mouse circadian system. 相似文献
22.
Bartlett BJ Isakson P Lewerenz J Sanchez H Kotzebue RW Cumming RC Harris GL Nezis IP Schubert DR Simonsen A Finley KD 《Autophagy》2011,7(6):572-583
Suppression of macroautophagy, due to mutations or through processes linked to aging, results in the accumulation of cytoplasmic substrates that are normally eliminated by the pathway. This is a significant problem in long-lived cells like neurons, where pathway defects can result in the accumulation of aggregates containing ubiquitinated proteins. The p62/Ref(2)P family of proteins is involved in the autophagic clearance of cytoplasmic protein bodies or sequestosomes. These unique structures are closely associated with protein inclusions containing ubiquitin as well as key components of the autophagy pathway. In this study we show that detergent fractionation followed by western blot analysis of insoluble ubiquitinated proteins (IUP), mammalian p62 and its Drosophila homologue, Ref(2)P can be used to quantitatively assess the activity level of aggregate clearance (aggrephagy) in complex tissues. Using this technique we show that genetic or age-dependent changes that modify the long-term enhancement or suppression of aggrephagy can be identified. Moreover, using the Drosophila model system this method can be used to establish autophagy-dependent protein clearance profiles that are occurring under a wide range of physiological conditions including developmental, fasting and altered metabolic pathways. This technique can also be used to examine proteopathies that are associated with human disorders such as frontotemporal dementia, Huntington and Alzheimer disease. Our findings indicate that measuring IUP profiles together with an assessment of p62/Ref(2)P proteins can be used as a screening or diagnostic tool to characterize genetic and age-dependent factors that alter the long-term function of autophagy and the clearance of protein aggregates occurring within complex tissues and cells. 相似文献
23.
Anderson I Risso C Holmes D Lucas S Copeland A Lapidus A Cheng JF Bruce D Goodwin L Pitluck S Saunders E Brettin T Detter JC Han C Tapia R Larimer F Land M Hauser L Woyke T Lovley D Kyrpides N Ivanova N 《Standards in genomic sciences》2011,5(1):50-60
Ferroglobus placidus belongs to the order Archaeoglobales within the archaeal phylum Euryarchaeota. Strain AEDII12DO is the type strain of the species and was isolated from a shallow marine hydrothermal system at Vulcano, Italy. It is a hyperthermophilic, anaerobic chemolithoautotroph, but it can also use a variety of aromatic compounds as electron donors. Here we describe the features of this organism together with the complete genome sequence and annotation. The 2,196,266 bp genome with its 2,567 protein-coding and 55 RNA genes was sequenced as part of a DOE Joint Genome Institute Laboratory Sequencing Program (LSP) project. 相似文献
24.
Copeland A O'Connor K Lucas S Lapidus A Berry KW Detter JC Del Rio TG Hammon N Dalin E Tice H Pitluck S Bruce D Goodwin L Han C Tapia R Saunders E Schmutz J Brettin T Larimer F Land M Hauser L Vargas C Nieto JJ Kyrpides NC Ivanova N Göker M Klenk HP Csonka LN Woyke T 《Standards in genomic sciences》2011,5(3):379-388
Chromohalobacter salexigens is one of nine currently known species of the genus Chromohalobacter in the family Halomonadaceae. It is the most halotolerant of the so-called 'moderately halophilic bacteria' currently known and, due to its strong euryhaline phenotype, it is an established model organism for prokaryotic osmoadaptation. C. salexigens strain 1H11(T) and Halomonas elongata are the first and the second members of the family Halomonadaceae with a completely sequenced genome. The 3,696,649 bp long chromosome with a total of 3,319 protein-coding and 93 RNA genes was sequenced as part of the DOE Joint Genome Institute Program DOEM 2004. 相似文献
25.
Zeytun A Sikorski J Nolan M Lapidus A Lucas S Han J Tice H Cheng JF Tapia R Goodwin L Pitluck S Liolios K Ivanova N Mavromatis K Mikhailova N Ovchinnikova G Pati A Chen A Palaniappan K Ngatchou-Djao OD Land M Hauser L Jeffries CD Han C Detter JC Ubler S Rohde M Tindall BJ Göker M Wirth R Woyke T Bristow J Eisen JA Markowitz V Hugenholtz P Klenk HP Kyrpides NC 《Standards in genomic sciences》2011,4(2):131-143
Hydrogenobacter thermophilus Kawasumi et al. 1984 is the type species of the genus Hydrogenobacter. H. thermophilus was the first obligate autotrophic organism reported among aerobic hydrogen-oxidizing bacteria. Strain TK-6(T) is of interest because of the unusually efficient hydrogen-oxidizing ability of this strain, which results in a faster generation time compared to other autotrophs. It is also able to grow anaerobically using nitrate as an electron acceptor when molecular hydrogen is used as the energy source, and able to aerobically fix CO(2)via the reductive tricarboxylic acid cycle. This is the fifth completed genome sequence in the family Aquificaceae, and the second genome sequence determined from a strain derived from the original isolate. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 1,742,932 bp long genome with its 1,899 protein-coding and 49 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project. 相似文献
26.
Sikorski J Teshima H Nolan M Lucas S Hammon N Deshpande S Cheng JF Pitluck S Liolios K Pagani I Ivanova N Huntemann M Mavromatis K Ovchinikova G Pati A Tapia R Han C Goodwin L Chen A Palaniappan K Land M Hauser L Ngatchou-Djao OD Rohde M Pukall R Spring S Abt B Göker M Detter JC Woyke T Bristow J Markowitz V Hugenholtz P Eisen JA Kyrpides NC Klenk HP Lapidus A 《Standards in genomic sciences》2011,4(3):331-341
Mahella australiensis Bonilla Salinas et al. 2004 is the type species of the genus Mahella, which belongs to the family Thermoanaerobacteraceae. The species is of interest because it differs from other known anaerobic spore-forming bacteria in its G+C content, and in certain phenotypic traits, such as carbon source utilization and relationship to temperature. Moreover, it has been discussed that this species might be an indigenous member of petroleum and oil reservoirs. This is the first completed genome sequence of a member of the genus Mahella and the ninth completed type strain genome sequence from the family Thermoanaerobacteraceae. The 3,135,972 bp long genome with its 2,974 protein-coding and 59 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project. 相似文献
27.
Pati A Gronow S Lu M Lapidus A Nolan M Lucas S Hammon N Deshpande S Cheng JF Tapia R Han C Goodwin L Pitluck S Liolios K Pagani I Mavromatis K Mikhailova N Huntemann M Chen A Palaniappan K Land M Hauser L Detter JC Brambilla EM Rohde M Göker M Woyke T Bristow J Eisen JA Markowitz V Hugenholtz P Kyrpides NC Klenk HP Ivanova N 《Standards in genomic sciences》2011,5(1):41-49
Prevotella multisaccharivorax Sakamoto et al. 2005 is a species of the large genus Prevotella, which belongs to the family Prevotellaceae. The species is of medical interest because its members are able to cause diseases in the human oral cavity such as periodontitis, root caries and others. Although 77 Prevotella genomes have already been sequenced or are targeted for sequencing, this is only the second completed genome sequence of a type strain of a species within the genus Prevotella to be published. The 3,388,644 bp long genome is assembled in three non-contiguous contigs, harbors 2,876 protein-coding and 75 RNA genes and is a part of the Genomic Encyclopedia of Bacteria and Archaea project. 相似文献
28.
Munk AC Copeland A Lucas S Lapidus A Del Rio TG Barry K Detter JC Hammon N Israni S Pitluck S Brettin T Bruce D Han C Tapia R Gilna P Schmutz J Larimer F Land M Kyrpides NC Mavromatis K Richardson P Rohde M Göker M Klenk HP Zhang Y Roberts GP Reslewic S Schwartz DC 《Standards in genomic sciences》2011,4(3):293-302
Rhodospirillum rubrum (Esmarch 1887) Molisch 1907 is the type species of the genus Rhodospirillum, which is the type genus of the family Rhodospirillaceae in the class Alphaproteobacteria. The species is of special interest because it is an anoxygenic phototroph that produces extracellular elemental sulfur (instead of oxygen) while harvesting light. It contains one of the most simple photosynthetic systems currently known, lacking light harvesting complex 2. Strain S1(T) can grow on carbon monoxide as sole energy source. With currently over 1,750 PubMed entries, R. rubrum is one of the most intensively studied microbial species, in particular for physiological and genetic studies. Next to R. centenum strain SW, the genome sequence of strain S1(T) is only the second genome of a member of the genus Rhodospirillum to be published, but the first type strain genome from the genus. The 4,352,825 bp long chromosome and 53,732 bp plasmid with a total of 3,850 protein-coding and 83 RNA genes were sequenced as part of the DOE Joint Genome Institute Program DOEM 2002. 相似文献
29.
Huntemann M Lu M Nolan M Lapidus A Lucas S Hammon N Deshpande S Cheng JF Tapia R Han C Goodwin L Pitluck S Liolios K Pagani I Ivanova N Ovchinikova G Pati A Chen A Palaniappan K Land M Hauser L Jeffries CD Detter JC Brambilla EM Rohde M Spring S Göker M Woyke T Bristow J Eisen JA Markowitz V Hugenholtz P Kyrpides NC Klenk HP Mavromatis K 《Standards in genomic sciences》2011,4(3):303-311
Hippea maritima (Miroshnichenko et al. 1999) is the type species of the genus Hippea, which belongs to the family Desulfurellaceae within the class Deltaproteobacteria. The anaerobic, moderately thermophilic marine sulfur-reducer was first isolated from shallow-water hot vents in Matipur Harbor, Papua New Guinea. H. maritima was of interest for genome sequencing because of its isolated phylogenetic location, as a distant next neighbor of the genus Desulfurella. Strain MH(2) (T) is the first type strain from the order Desulfurellales with a completely sequenced genome. The 1,694,430 bp long linear genome with its 1,723 protein-coding and 57 RNA genes consists of one circular chromosome and is a part of the Genomic Encyclopedia of Bacteria and Archaea project. 相似文献
30.
Speed N Saunders C Davis AR Owens WA Matthies HJ Saadat S Kennedy JP Vaughan RA Neve RL Lindsley CW Russo SJ Daws LC Niswender KD Galli A 《PloS one》2011,6(9):e25169