Structure creates Function

Fusarium ओक्स्य्स्पोरुम genome

2009-10-14T04:12:00.001-07:00

Genome information:
Name GenBank
Master WGS AAXH00000000
Chromosome 1 CM000589
Chromosome 2 CM000590
Chromosome 3 CM000591
Chromosome 4 CM000592
Chromosome 5 CM000593
Chromosome 6 CM000594
Chromosome 7 CM000595
Chromosome 8 CM000596
Chromosome 9 CM000597
Chromosome 10 CM000598
Chromosome 11 CM000599
Chromosome 12 CM000600
Chromosome 13 CM000601
Chromosome 14 CM000602
Chromosome 15 CM000603

Whole genome sequence fungi list

2009-10-14T04:04:00.000-07:00

Aspergillus clavatus
Aspergillus fumigatus
Aspergillus niger
Candida glabrata
Cryptococcus neoformans
Debaryomyces hansenii
Encephalitozoon cuniculi
Eremothecium gossypii
Gibberella zeae
Kluyveromyces lactis
Magnaporthe grisea
Neurospora crassa
Pichia stipitis
Saccharomyces cerevisiae
Schizosaccharomyces pombe
Ustilago maydis
Yarrowia lipolytica

A MicroRNA Imparts Robustness against Environmental Fluctuation during Development

2009-10-06T16:45:00.001-07:00

Article
A MicroRNA Imparts Robustness against Environmental Fluctuation during Development

Xin Li1, 2, 3, Justin J. Cassidy1, 2, Catherine A. Reinke1, Stephen Fischboeck1 and Richard W. Carthew1, ,

1Department of Biochemistry, Molecular Biology and Cell Biology, 2205 Tech Drive, Northwestern University, Evanston, Illinois 60208, USA

Received 16 May 2008; revised 25 November 2008; accepted 29 January 2009. Published: April 16, 2009. Available online 16 April 2009.

Summary
The microRNA miR-7 is perfectly conserved from annelids to humans, and yet some of the genes that it regulates in Drosophila are not regulated in mammals. We have explored the role of lineage restricted targets, using Drosophila, in order to better understand the evolutionary significance of microRNA-target relationships. From studies of two well characterized developmental regulatory networks, we find that miR-7 functions in several interlocking feedback and feedforward loops, and propose that its role in these networks is to buffer them against perturbation. To directly demonstrate this function for miR-7, we subjected the networks to temperature fluctuation and found that miR-7 is essential for the maintenance of regulatory stability under conditions of environmental flux. We suggest that some conserved microRNAs like miR-7 may enter into novel genetic relationships to buffer developmental programs against variation and impart robustness to diverse regulatory networks.

Fusarium oxysporum

2009-10-06T06:45:00.000-07:00

Eukaryota;
Fungi;
Dikarya;
Ascomycota;
Pezizomycotina;
Sordariomycetes;
Hypocreomycetidae;
Hypocreales;
mitosporic Hypocreales;
Fusarium;
Fusarium oxysporum species complex;
Fusarium oxysporum

Structure creates Function: Network analysis of genes determining vascular wilt disease

2009-10-05T22:12:00.000-07:00

Structure creates Function: Network analysis of genes determining vascular wilt disease: "Lead Supervisor: Dr Louise Thatcher
Associates: Dr Kemal Kazan, Dr Donald Gardiner

Vascular wilt disease caused by the root infecting fungus Fusarium oxysporum affects over 100 plant species, including many economically important crops. This pathogen survives in soil for long periods and can be extremely difficult to eradicate once soils become infested.

High-throughput screening for altered Fusarium resistance on the model host Arabidopsis thaliana has identified many host mutants with increased susceptibility or resistance. This project aims to confirm the Fusarium disease phenotypes of a selected subset of mutants and develop hypotheses on the involvement of mutated genes in resistance or susceptibility mechanisms to Fusarium. This will involve screening second independent mutant lines in the genes of interest, confirming the mutations through PCR analysis, and the use of other pathogen assays, gene expression analysis and/or bioinformatic approaches to develop a network map of genes determining vascular wilt disease outcomes"

http://www.csiro.au/science/Summer-Studentships-Projects--ci_pageNo-2.html#6

Network analysis of genes determining vascular wilt disease

2009-10-05T22:06:00.000-07:00

Network analysis of genes determining vascular wilt disease.

Lead Supervisor: Dr Louise Thatcher
Associates: Dr Kemal Kazan, Dr Donald Gardiner

Vascular wilt disease caused by the root infecting fungus Fusarium oxysporum affects over 100 plant species, including many economically important crops. This pathogen survives in soil for long periods and can be extremely difficult to eradicate once soils become infested.

High-throughput screening for altered Fusarium resistance on the model host Arabidopsis thaliana has identified many host mutants with increased susceptibility or resistance. This project aims to confirm the Fusarium disease phenotypes of a selected subset of mutants and develop hypotheses on the involvement of mutated genes in resistance or susceptibility mechanisms to Fusarium. This will involve screening second independent mutant lines in the genes of interest, confirming the mutations through PCR analysis, and the use of other pathogen assays, gene expression analysis and/or bioinformatic approaches to develop a network map of genes determining vascular wilt disease outcomes

DNA repair proteins

2009-09-10T13:51:00.000-07:00

Redox signaling between DNA repair proteins for efficient lesion detection

Published online before print August 31, 2009, doi: 10.1073/pnas.0908059106
PNAS September 8, 2009 vol. 106 no. 36

1. Amie K. Boala,
2. Joseph C. Genereuxa,
3. Pamela A. Sontza,
4. Jeffrey A. Gralnickb,
5. Dianne K. Newmanc,1 and
6. Jacqueline K. Bartona,1

+ Author Affiliations

1.
aDivision of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125;
2.
bDepartment of Microbiology, BioTechnology Institute, University of Minnesota, St. Paul, MN 55108; and
3.
cDepartments of Biology and Earth, Atomospheric and Planetary Science, and Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02139

1.

Contributed by Jacqueline K. Barton, July 21, 2009 (received for review June 25, 2009)

Abstract

Base excision repair (BER) enzymes maintain the integrity of the genome, and in humans, BER mutations are associated with cancer. Given the remarkable sensitivity of DNA-mediated charge transport (CT) to mismatched and damaged base pairs, we have proposed that DNA repair glycosylases (EndoIII and MutY) containing a redox-active [4Fe4S] cluster could use DNA CT in signaling one another to search cooperatively for damage in the genome. Here, we examine this model, where we estimate that electron transfers over a few hundred base pairs are sufficient for rapid interrogation of the full genome. Using atomic force microscopy, we found a redistribution of repair proteins onto DNA strands containing a single base mismatch, consistent with our model for CT scanning. We also demonstrated in Escherichia coli a cooperativity between EndoIII and MutY that is predicted by the CT scanning model. This relationship does not require the enzymatic activity of the glycosylase. Y82A EndoIII, a mutation that renders the protein deficient in DNA-mediated CT, however, inhibits cooperativity between MutY and EndoIII. These results illustrate how repair proteins might efficiently locate DNA lesions and point to a biological role for DNA-mediated CT within the cell.

sexual activity on cycle ergometer stress test parameters

2009-09-08T21:28:00.000-07:00

Effect of sexual activity on cycle ergometer stress test parameters, on plasmatic testosterone levels and on concentration capacity - A study in high-level male athletes performed in the laboratory

Author(s): Sztajzel J, Periat M, Marti V, Krall P, Rutishauser W
Source: JOURNAL OF SPORTS MEDICINE AND PHYSICAL FITNESS
Volume: 40
Issue: 3
Pages: 233-239
Published: SEP 2000

Abstract: Background. The purpose of this study was to investigate the effect of sexual activity on cycle ergometer stress test parameters, on plasmatic testosterone levels and on concentration capacity in high-level mate athletes.

Methods. Experimental design. Analysis of two days of testing accomplished in a laboratory setting, comparing a day with to a day without sexual activity (control day). Participants. Fifteen high-level male athletes, consisting of 8 team players, 5 endurance athletes and 2 weight-lifters, participated in the study. Measures. Each subject completed the following on each test day: two maximal graded stress tests on a cycle ergometer and a one-hour exercise stress test coupled to an arithmetic mental concentration test. Blood samples of testosterone were obtained and cardiac activity of each athlete was monitored with a 24-hour ECG tape recording over the two test days.

Results, Significantly higher differences were achieved for posteffort heart rate (HR) values at 5 minutes (p<0.01) and at 10 minutes (p<0.01) during the recovery phase of the morning stress test 2 hours after sexual activity. These differences disappeared during the recovery phase of the afternoon stress test performed approximately 10 hours after sexual intercourse took place.

Conclusions, Our findings show that sexual activity had no detrimental influence on the maximal workload achieved and on the athletes' mental concentration. However, the higher posteffort HR values after the maximal stress test on the morning of sexual intercourse suggest that the recovery capacity of an athlete could be affected if he had sexual intercourse approximately 2 hours before a competition event.

Does Sex the Night Before Competition Decrease Performance?

2009-09-08T21:24:00.001-07:00

Does Sex the Night Before Competition Decrease Performance?

McGlone, Samantha; Shrier, Ian MD, PhD*†
Author Information
*Department of Physiology, McGill University, and †Centre for Clinical Epidemiology and Community Studies, Montreal, Quebec, Canada
Received June 7, 1999; accepted August 9, 2000.
Address correspondence and reprint requests to Ian Shrier, MD, Centre for Clinical Epidemiology and Community Studies, 3755 Cote Sainte Catherine Road, Montreal, Quebec H3T 1E2, Canada.

For many years, football coaches, Olympic athletes, and even Muhammad Ali have advocated sexual abstinence the night before an athletic event. 1 Marty Liquori, one the world's number one-ranked 5,000-meter runner believes that “Sex makes you happy, and happy people don't run a 3:47 mile.”2 Marv Levy, head coach of the Buffalo Bills, insisted that the team be separated from their wives before their appearance in four Super Bowls; a policy that apparently was not successful (four losses out of four Super Bowls). On the other hand, there are also plenty of anecdotal stories of athletes who claim to have benefited from sex the night before an event. Both U.S. track star David Wottle and Canadian downhill skier Karin Lee Gardner attribute their Olympic gold medals in part to their “pre-race preparation.”2 As legendary New York Yankees manager Casey Stengel put it, “It's not the sex that wrecks these guys, it's staying up all night looking for it.” Considering the controversy surrounding the topic, the objective of this editorial is to summarize the literature on whether sex the night before competition affects performance, and to suggest possible future areas for research.

The long-standing myth that athletes should practice abstinence before important competitions may stem from the theory that sexual frustration leads to increased aggression, and that the act of ejaculation draws testosterone from the body. 1 In actual fact, sex could alter performance through either physiological or psychological factors. To answer this question, we searched SportDiscus (1975–1988/1989, key words: Coitus and Sexual Intercourse) and MEDLINE for relevant articles. Of the 31 articles we retrieved, only 3 were scientific studies (all physiological). All of these studies suggested that sex the night before competition does not alter physiological testing results. For instance, 14 married male former athletes were given a maximum-effort grip strength test the morning after coitus, and the same test following at least 6 days of abstinence. 3 The results suggested that strength and endurance of the palmar flexing muscles are not adversely affected by sex the previous night. An unpublished follow-up to this study was conducted by researchers at Colorado State University on 10 fit, married men, ages 18–45 years (cited in ref. 4). In their tests for grip strength, balance, lateral movement, reaction time, aerobic power (stair-climbing exercise), and VO2max (treadmill test), the results did not change with sexual activity. Finally, the results from a 1995 randomized cross-over study suggested that sexual intercourse 12 hours prior to the test had no significant effects on maximal aerobic power, oxygen pulse, or double product. 5

Based on the results of these studies, one might conclude that sexual activity the night before competition would not affect performance. However, each of the above-mentioned studies focused on the physiological effects of precompetition sex, which would only be expected to decrease performance if the activity led to exhaustion. Considering that normal sexual intercourse between married partners expends only 25–50 calories (the energy equivalent of walking up two flights of stairs), 6 it is doubtful that sex the previous night would affect laboratory physiological performance tests.

Remembering that the original hypothesis suggested that performance would only be affected through a change in aggression, researchers really should have measured variables that are affected by aggression (e.g., motivation, alertness, and attitude toward competition). According to the current “inverted U” sport psychology hypothesis, 4 there is an optimal level of alertness/anxiety before a competition, and a poor performance will result from either being too anxious or not alert enough. If athletes are too anxious and restless the night before an event, then sex may be a relaxing distraction. If they are already relaxed or, like some athletes, have little interest in sex the night before a big competition, then a good night's sleep is all they need. This theory predicts that the results will be dependent on individual preferences and routines. The night before an important race is not a good time for drastic changes in routine. Consistency is the key.

Clearly there is a need for more research on the topic of sexual activity and athletic performance. However, any research will have difficulty controlling factors related to such sexual behavior such as the time of day, frequency and duration of sexual activity, behavior of subjects between data collection, diet, fatigue, stress, and individual response to sexual activity. Anshel also poses a question worth considering: “How valid are test results when a natural activity such as coitus becomes a required act occurring within a specific time period?”7 In addition, results may be dependent on the sexual partner. For instance, heart rate and blood pressure responses are different if sex is with a spouse of 10 years, compared to a new partner or in strange surroundings. 8 Therefore, any future research will have to control for interindividual variation of the above-mentioned variables with a randomized design, or at least control for differences at the analysis stage.

Finally, the inverted U hypothesis for alertness/anxiety suggests that the performance of some people will improve with sex the night before competition (i.e., responders) and the performance of others will be hindered (i.e., nonresponders). If true, a randomized controlled trial may not be able to detect any differences. For instance, if the “truth” is that 50% of the population improves with sex the night before a competition and 50% is hindered by sex the night before competition, a randomized controlled trial will show that on average there is no effect. Therefore, the best way to test the hypothesis is with a repeated-measures, cross-over design in which the same athletes are tested several times following abstinence, and several times following sex the night before competition. This would allow one to determine not only if sex the night before competition affects performance in certain individuals, but also if there are indeed “responders” and “nonresponders.”

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REFERENCES

1. Krieger L. Scoring before a big event. Winning 1997; 1:88–89. [Context Link]

2. Bloom M. The sex factor. Runner's World 1994; 11:71–74. [Context Link]

3. Johnson W. Muscular performance following coitus. J Sex Res 1968; 4:247–248. Library Holdings [Context Link]

4. Thornton J. Sexual activity and athletic performance: is there a relationship? Phys Sport Med 1990; 18:148–153. [Context Link]

5. Boone T, Gilmore S. Effects of sexual intercourse on maximal aerobic power, oxygen pulse, and double product in male sedentary subjects. J Sports Med Phys Fitness 1995; 35:214–217. Library Holdings [Context Link]

6. Mirkin G. Sex before competition. Report #6750. Mar. 10, 1996. http://drmirkin.com/archive/6750.html [Context Link]

7. Anshel M. Effects of sexual activity on athletic performance. Phys Sports Med 1981; 9:65–68. Library Holdings [Context Link]

8. Bohlen J, Held J, Sanderson M, et al. Heart rate, rate pressure point, and oxygen uptake during four sexual activities. Arch Intern Med 1984; 144:1745–1748. Bibliographic Links Library Holdings [Context Link]

The effect of losing virginity on academic performance

2009-09-08T21:13:00.000-07:00

Reading, writing, and sex: The effect of losing virginity on academic performance

View full text from the publisher Blackwell Science
Author(s): Sabia JJ (Sabia, Joseph J.)
Source: ECONOMIC INQUIRY
Volume: 45
Issue: 4
Pages: 647-670
Published: OCT 2007

Abstract: Controlling for a wide set of individual- and family-level observables available in the National Longitudinal Study of Adolescent Health, ordinary least squares (OLS) estimates show that sexually active adolescents have grade point averages that are approximately 0.2 points lower than virgins. However, when information on the timing of intercourse decisions is exploited and individual fixed effects are included, the negative effect of sexual intercourse disappears for females, but persists for males. Taken together, the results of this study suggest that while there may be adverse academic spillovers from engaging in intercourse for some adolescents, previous studies' estimates are overstated due to unmeasured heterogeneity.

DNA methylation analysis by प्य्रोसेक़ुएन्किन्ग

2009-09-02T03:40:00.000-07:00

Figure 1 - Enzymatic cascade of the pyrosequencing reaction in the example of a bisulfite-treated template sequence, including a CpG position that is methylated on approximately 50% of all molecules.
From the following article

DNA methylation analysis by pyrosequencing

Jörg Tost & Ivo G Gut

Nature Protocols 2, 2265 - 2275 (2007) Published online: 6 September 2007

doi:10.1038/nprot.2007.314

Importing Mitochondrial Proteins: Machineries and Mechanisms

2009-08-30T03:36:00.000-07:00

Review
Importing Mitochondrial Proteins: Machineries and Mechanisms

Agnieszka Chacinska1,2, Carla M. Koehler3, Dusanka Milenkovic1, 2, Trevor Lithgow4 and Nikolaus Pfanner1, 2,

1Institut für Biochemie und Molekularbiologie, ZBMZ, Universität Freiburg, 79104 Freiburg, Germany

2Centre for Biological Signalling Studies, Universität Freiburg, 79104 Freiburg, Germany

3Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA 90095, USA

4Department of Biochemistry and Molecular Biology, Monash University, Victoria 3800, Australia

Most mitochondrial proteins are synthesized on cytosolic ribosomes and must be imported across one or both mitochondrial membranes. There is an amazingly versatile set of machineries and mechanisms, and at least four different pathways, for the importing and sorting of mitochondrial precursor proteins. The translocases that catalyze these processes are highly dynamic machines driven by the membrane potential, ATP, or redox reactions, and they cooperate with molecular chaperones and assembly complexes to direct mitochondrial proteins to their correct destinations. Here, we discuss recent insights into the importing and sorting of mitochondrial proteins and their contributions to mitochondrial biogenesis.

sliding β clamp subunit

2009-08-30T03:00:00.000-07:00

Preview
Clamping Down on Transposon Targeting

Mick Chandler

1Laboratoire de Microbiologie et Génétique Moléculaire UMR 5100, CNRS, 31062 Toulouse CEDEX, France

Cell, Volume 138, Issue 4, 21 August 2009, Pages 685-695,
Adam R. Parks, Zaoping Li, Qiaojuan Shi, Roisin M. Owens, Moonsoo M. Jin, Joseph E. Peters

The sliding β clamp subunit of the DNA replication machinery in the bacterium Escherichia coli coordinates multiple functions in the cell beyond genome duplication. In this issue, Parks et al. (2009) find that the β clamp interacts with the transposition protein TnsE to target the Tn7 transposon to discontinuously replicating DNA at the replication fork.

सेल Volume 138, Issue 2, 23 July 2009, Pages 271-285

2009-08-10T04:15:00.000-07:00

Article
CD47 Is Upregulated on Circulating Hematopoietic Stem Cells and Leukemia Cells to Avoid Phagocytosis

Cell, Volume 138, Issue 2, 23 July 2009, Pages 271-285

References and further reading may be available for this article. To view references and further reading you must purchase this article.

Siddhartha Jaiswal1, Corresponding Author Contact Information, E-mail The Corresponding Author, Catriona H.M. Jamieson2, Wendy W. Pang1, Christopher Y. Park1, Mark P. Chao1, Ravindra Majeti1, David Traver3, Nico van Rooijen4 and Irving L. Weissman1

Summary

Macrophages clear pathogens and damaged or aged cells from the blood stream via phagocytosis. Cell-surface CD47 interacts with its receptor on macrophages, SIRPα, to inhibit phagocytosis of normal, healthy cells. We find that mobilizing cytokines and inflammatory stimuli cause CD47 to be transiently upregulated on mouse hematopoietic stem cells (HSCs) and progenitors just prior to and during their migratory phase, and that the level of CD47 on these cells determines the probability that they are engulfed in vivo. CD47 is also constitutively upregulated on mouse and human myeloid leukemias, and overexpression of CD47 on a myeloid leukemia line increases its pathogenicity by allowing it to evade phagocytosis. We conclude that CD47 upregulation is an important mechanism that provides protection to normal HSCs during inflammation-mediated mobilization, and that leukemic progenitors co-opt this ability in order to evade macrophage killing.

Ergot alkaloid biosynthesis in Aspergillus fumigatus

2009-06-03T21:41:00.000-07:00

Ergot alkaloid biosynthesis in Aspergillus fumigatus - Overproduction and biochemical characterization of a 4-dimethylallyltryptophan N-methyltransferase

Author(s): Rigbers O (Rigbers, Ole), Li SM (Li, Shu-Ming)1
Source: JOURNAL OF BIOLOGICAL CHEMISTRY
Volume: 283 Issue: 40 Pages: 26859-26868 Published: OCT 3 2008

Abstract: The putative gene fgaMT was identified in the biosynthetic gene cluster of fumigaclavines in Aspergillus fumigatus. The coding region of fgaMT was amplified by PCR from a cDNA library, cloned into pQE60, and overexpressed in Escherichia coli. FgaMT comprises 339 amino acids with a molecular mass of about 38.1 kDa. The soluble dimeric His(6)-FgaMT was purified to near homogeneity and characterized biochemically. FgaMT was found to catalyze the N-methylation of 4-dimethylallyltryptophan in the presence of S-adenosylmethionine, resulting in the formation of 4-dimethylallyl-L-abrine, which was identified by NMR and mass spectrometry analysis. Therefore, FgaMT represents the second pathway-specific enzyme in the biosynthesis of ergot alkaloids. The enzyme did not require metal ions for its enzymatic reaction and showed a relatively high specificity toward the prenyl moiety at position C-4 of the indole ring. 4-Dimethylallyltryptophan derivatives with modification at the indole ring were also accepted by FgaMT as substrates. Km values for 4-dimethylallyltryptophan and S-adenosylmethionine were determined at 0.12 and 2.4 mM, respectively. The turnover number was 2.0 s(-1).

Determination of Ergot Alkaloids

2009-06-03T21:40:00.000-07:00

Determination of Ergot Alkaloids: Purity and Stability Assessment of Standards and Optimization of Extraction Conditions for Cereal Samples

Author(s): Krska R (Krska, Rudolf)1,2, Berthiller F (Berthiller, Franz)1, Schuhmacher R (Schuhmacher, Rainer)1, Nielsen KF (Nielsen, Kristian F.)3, Crews C (Crews, Colin)2

Source: JOURNAL OF AOAC INTERNATIONAL Volume: 91 Issue: 6 Pages: 1363-1371 Published: NOV-DEC 2008

Abstract: Results obtained from a purity study on standards of the 6 major ergot alkaloids ergometrine, ergotamine, ergosine, ergocristine, ergocryptine, and ergocornine and their corresponding epimers are discussed. The 6 ergot alkaloids studied have been defined by the European Food Safety Authority as those that are the most common and physiologically active. The purity of the standards was investigated by means of liquid chromatography with diode array detection, electrospray ionization, and time-of-flight mass spectrometry (LC-DAD-ESI-TOF-MS). All of the standards assessed showed purity levels considerably above 98% apart from ergocristinine (94%), ergosine (96%), and ergosinine (95%). Also discussed is the optimization of extraction conditions presented in a recently published method for the quantitation of ergot alkaloids in food samples using solid-phase extraction with primary secondary amine (PSA) before LC/MS/MS. Based on the results obtained from these optimization studies, a mixture of acetonitrile with ammonium carbonate buffer was used as extraction solvent, as recoveries for all analyzed ergot alkaloids were significantly higher than those with the other solvents. Different sample-solvent ratios and extraction times showed just minor influences in extraction efficacy. Finally, the stability of the ergot alkaloids in both raw cereals and cereal-based processed food extracts was studied. According to these studies, extracts should be prepared and analyzed the same day or stored below ambient temperatures. Barley and rye extracts, which were stored at 4 and 15 degrees C after PSA cleanup, proved to be stable overnight. However, storage over a period of 14 days at 4 degrees C resulted in significant epimerization, which was most pronounced in rye and particularly for ergocornine, ergocryptine, and ergocristine.

The Venus of Hohle Fels.

2009-05-20T18:17:00.000-07:00

The Venus of Hohle Fels. (Credit: Photo by H. Jensen; Copyright: Universität Tübingen)

Good News for Night Owls

2009-05-06T06:21:00.001-07:00

Good News for Night Owls
By Elsa Youngsteadt
ScienceNOW Daily News
23 April 2009

Night owls seem to have a cognitive edge over early risers--at least when they're on their natural sleep schedule. That's one upshot of a new brain-imaging study that also gives surprising new insights into how the brain manages the urge to sleep and wake. The results, sleep researchers say, may improve predictions of when people are most at risk for drowsy accidents.
Two factors control our bedtime. The first is hardwired: A master clock in the brain regulates a so-called circadian rhythm, which synchronizes activity patterns to the 24-hour day. Some people's clocks tell them to go to bed at 9 p.m., others' at 3 a.m., (ScienceNOW, 24 June 2003). The second factor--called sleep pressure--depends not on time of day but simply on how long someone has been awake already.

Because sleep pressure accumulates during waking hours, logic suggests that we should be most alert--and hence sharpest--shortly after we get up versus right before we go to bed, regardless of whether we're night owls or larks.

But that's not what Christina Schmidt found. The doctoral student at the University of Liège in Belgium and her collaborators, led by sleep researcher Philippe Peigneux, recruited 16 morning people and 15 night people to take alertness tests in a brain scanner. Subjects had to pay attention to numbers on a computer screen and hit a button whenever the numbers began to change. To control for the effect of the circadian clock, the subjects were allowed to sleep on their own natural schedules and take the test 1.5 hours and 10.5 hours after waking, regardless of the actual time of day.

Both groups performed equally well on the test when they took it 1.5 hours after waking. But after 10.5 hours without sleep, the night owls pulled ahead. Their reaction times improved by about 6% relative to the morning people and to their own earlier performance, the researchers report in tomorrow's issue of Science. This suggests that once they wake up, sleep pressure builds up faster in early birds, says Peigneux, and that this hurts their cognition over time.

It's a result with "real-world consequences," says sleep researcher David Dinges of the University of Pennsylvania School of Medicine in Philadelphia. Current risk analyses use the time of day and hours worked to predict when people are in greatest danger of accidents--such as aviation errors. But now, Dinges says, they may need to take into account that morning people tend to lose their concentration faster. At the very least, according to sleep researcher Amita Sehgal, also at the University of Pennsylvania School of Medicine, this is a new and "intriguing" explanation for larks' and owls' different habits.

But the really provocative result, adds Dinges, came from the brain imaging. The night owls showed greater activity in the master-clock region of their brains--a cluster of cells known as the suprachiasmatic nucleus--than the larks when taking the later test. That suggests that sleep pressure and the circadian clock can influence each other directly--bringing together two systems that, for decades, had been thought to operate separately.

Homeostatic Sleep Pressure and Responses to Sustained Attention in the Suprachiasmatic Area

2009-05-06T06:13:00.001-07:00

Science 24 April 2009:
Vol. 324. no. 5926, pp. 516 - 519
DOI: 10.1126/science.1167337
Prev | Table of Contents | Next
Reports
Homeostatic Sleep Pressure and Responses to Sustained Attention in the Suprachiasmatic Area
Christina Schmidt,1,2,* Fabienne Collette,1,2 Yves Leclercq,1 Virginie Sterpenich,1 Gilles Vandewalle,1 Pierre Berthomier,3 Christian Berthomier,3 Christophe Phillips,1 Gilberte Tinguely,1 Annabelle Darsaud,1 Steffen Gais,1 Manuel Schabus,1 Martin Desseilles,1 Thien Thanh Dang-Vu,1 Eric Salmon,1 Evelyne Balteau,1 Christian Degueldre,1 André Luxen,1 Pierre Maquet,1 Christian Cajochen,4 Philippe Peigneux1,5,*

Throughout the day, cognitive performance is under the combined influence of circadian processes and homeostatic sleep pressure. Some people perform best in the morning, whereas others are more alert in the evening. These chronotypes provide a unique way to study the effects of sleep-wake regulation on the cerebral mechanisms supporting cognition. Using functional magnetic resonance imaging in extreme chronotypes, we found that maintaining attention in the evening was associated with higher activity in evening than morning chronotypes in a region of the locus coeruleus and in a suprachiasmatic area (SCA) including the circadian master clock. Activity in the SCA decreased with increasing homeostatic sleep pressure. This result shows the direct influence of the homeostatic and circadian interaction on the neural activity underpinning human behavior.

2 micron plasmid hitchhikes on mitotic mechanism of Saccharomyces cerevisiae to maintain equal distribution in host

2009-05-05T16:23:00.000-07:00

Published online April 13, 2009
doi:10.1083/jcb.200810130
The Journal of Cell Biology, Vol. 185, No. 2, 251-264
The Rockefeller University Press, 0021-9525 $30.00
© 2009 Cui et al.

The selfish yeast plasmid uses the nuclear motor Kip1p but not Cin8p for its localization and equal segregation

Hong Cui, Santanu K. Ghosh, and Makkuni Jayaram
Section of Molecular Genetics and Microbiology, University of Texas at Austin, Austin, TX 78712

Correspondence to Makkuni Jayaram: jayaram@icmb.utexas.edu

The 2 micron plasmid of Saccharomyces cerevisiae uses the Kip1 motor, but not the functionally redundant Cin8 motor, for its precise nuclear localization and equal segregation. The timing and lifetime of Kip1p association with the plasmid partitioning locus STB are consistent with Kip1p being an authentic component of the plasmid partitioning complex. Kip1–STB association is not blocked by disassembling the mitotic spindle. Lack of Kip1p disrupts recruitment of the cohesin complex at STB and cohesion of replicated plasmid molecules. Colocalization of a 2 micron reporter plasmid with Kip1p in close proximity to the spindle pole body is reminiscent of that of a CEN reporter plasmid. Absence of Kip1p displaces the plasmid from this nuclear address, where it has the potential to tether to a chromosome or poach chromosome segregation factors. Exploiting Kip1p, which is subsidiary to Cin8p for chromosome segregation, to direct itself to a "partitioning center" represents yet another facet of the benign parasitism of the yeast plasmid.

Biogeochemistry: Less nickel for more oxygen

2009-04-28T15:57:00.001-07:00

News and Views
Nature 458, 714-715 (9 April 2009) | doi:10.1038/458714a; Published online 8 April 2009

Biogeochemistry: Less nickel for more oxygen
Mak A. Saito1

Top of pageAbstractThe availability (or lack) of oceanic trace elements is providing fresh lines of explanation for turning points in Earth's history — the Great Oxidation Event being one such momentous occasion.

About 2.4 billion years ago, the oxygen content of Earth's atmosphere increased in what is called the Great Oxidation Event (GOE). This marked the beginning of the most significant series of chemical changes Earth has ever experienced, setting the stage for oxidative weathering of the continents, successive changes in ocean chemistry, and the eventual rise of multicellular life.

Yet the sequence of events leading up to the GOE is not well understood. Most researchers agree that the evolution of oxygenic photosynthesis within a group called the cyanobacteria was the source of the molecular oxygen that caused the GOE1. But the timing of the rise of these bacteria is uncertain2, 3, and there may have been a period of inertia — due, for example, to chemical reactions with methane that consumed oxygen4 — that prevented a swift increase in atmospheric oxygen. It remains a matter of debate how these two phenomena might have induced the GOE: an early rise of cyanobacteria and slow crumbling of chemical resistance3, 4; or a late rise of cyanobacteria leading to rapid initiation of the GOE5.

On page 750 of this issue6, Konhauser et al. report evidence for an alternative driving mechanism of the GOE, one that would have decreased microbial methane production in the oceans and paved the way for increased oxygen abundances. The authors find significant decreases in the nickel-to-iron ratios in ancient rocks, known as banded iron formations, that provide records of element concentrations in the oceans (Fig. 1). They estimate that a major decrease in the oceanic inventory of nickel must have occurred around 2.7 billion years ago. This, they conclude, led to a cascade of events in which methanogens, with their gluttonous appetite for nickel to feed three nickel-containing metalloenzymes, would have become starved of the element and so have produced much less methane. With the decrease in chemical inertia associated with methane4, the stage was set for cyanobacterial oxygen to accumulate, leading to the GOE. Moreover, although Konhauser et al. don't go into detail, the decline in atmospheric methane, a powerful greenhouse gas, is believed to help account for the initiation of a planetary-scale glaciation known as Snowball Earth that is thought to have begun between 2.3 billion and 2.2 billion years ago4, 5.

Figure 1: Record site.
This is a view of Dales Gorge, northwest Australia, one of the banded iron formations sampled by Konhauser et al.6.

High resolution image and legend (151K)

The idea that significant changes in seawater trace-metal abundance have occurred during Earth's history is becoming popular7, 8. For example, it is thought that iron and cobalt were abundant in ancient oceans, whereas zinc and copper were probably extremely scarce owing to precipitation with sulphides8. When the oceans became oxygenated, it is likely that this scheme was reversed, with iron and cobalt becoming scarce through oxidation and precipitation as oxyhydroxides, and zinc and copper becoming much more abundant upon the oxidation of sulphide to sulphate in sea water. These predictions of broad changes in ocean chemistry are mirrored by the physiological and genomic traits of archaea and bacteria, relative to those of the later-evolving eukaryotes8, 9.

Nickel has largely been left out of this intriguing story. On the evidence of chemical modelling8, it seems that nickel was not as strongly affected by the variations in sulphide and oxygen during Earth's history. But such a conclusion does not take into account the possible involvement of external factors. Konhauser et al. show how such a factor might have come into play, with the cooling of Earth's mantle resulting in decreased eruption of nickel-rich rocks and causing an estimated 50% fall in the oceanic nickel inventory.

Konhauser and colleagues' thinking6 may come as a surprise to those familiar with the chemistry of the modern oceans. Trace metals — as their name suggests — are extraordinarily scarce in sea water. In vast regions of the modern oceans, photosynthesis is limited by low iron availability, with iron concentrations often being less than 0.05 nanomoles per litre10. Yet, of the trace metals required by life, nickel is one of the more abundant in sea water, with surface water concentrations of 1–2 nanomoles per litre11. In this modern context, the idea of a nickel famine seems odd. But the nickel requirements of methanogens are reported6 to be in the hundreds of nanomoles per litre, suggesting that methanogens cannot live in the modern oceans and are perhaps relegated to sedimentary, coastal and freshwater environments, where nickel is more abundant.

By connecting changes in mantle temperature to nickel fluxes and methanogens, Konhauser and colleagues' study is particularly satisfying. Instead of relying on the uncertain timing of the rise of cyanobacteria to explain the GOE, that event can instead be tied to a specific mechanism recorded in the banded iron formations. In addition, this 'nickel famine' mechanism is consistent with evidence12 of 'whiffs of oxygen' that occurred more than 50 million years before the GOE. But I cannot help but wonder whether there is a reason — such as the slow chemical kinetics of nickel ions — why methanogens could not evolve a high-affinity nickel-uptake mechanism similar to those that exist for the uptake of iron, zinc and cobalt13, 14, 15.

Finally, there is another context in which the research of Konhauser et al. is set — the exciting endeavour of trying to understand how the elemental cycles (of nickel, carbon, iron, nitrogen and so on) have 'co-evolved' with microbial life. Many of the changes in element cycling were probably caused by the rise and fall of specific microbial metabolisms, while also strongly affecting the trajectory and composition of life on Earth. Life and the cycling of elements have both been changing throughout Earth's history, often influencing each other profoundly along the way. One of the sobering realizations of studies such as this is that, although natural selection provides a clear, single positive-feedback mechanism for the continuation of life, elemental cycles are instead influenced by an aggregate of mechanisms, including biological evolution, chemical reactions, changes in ocean circulation and geological events. If, as Konhauser et al. suggest, a single geological change can starve a major oceanic microbial community, and thereby change the trajectory of life on Earth, it suggests that there is a fragility to Earth's elemental cycles that we are only beginning to uncover.

Kinetochore geometry defined by cohesion within the centromere

2009-04-28T15:50:00.001-07:00

Article
Nature 458, 852-858 (16 April 2009) | doi:10.1038/nature07876; Received 9 September 2008; Accepted 12 February 2009

Kinetochore geometry defined by cohesion within the centromere
Takeshi Sakuno1,2, Kenji Tada1,3 & Yoshinori Watanabe1,3

Laboratory of Chromosome Dynamics, Institute of Molecular and Cellular Biosciences,
Promotion of Independence for Young Investigators,
Graduate Program in Biophysics and Biochemistry, Graduate School of Science, University of Tokyo, Yayoi, Tokyo 113-0032, Japan
Correspondence to: Yoshinori Watanabe1,3 Correspondence and requests for materials should be addressed to Y.W. (Email: ywatanab@iam.u-tokyo.ac.jp).

Top of pageAbstractDuring cell division microtubules capture chromosomes by binding to the kinetochore assembled in the centromeric region of chromosomes. In mitosis sister chromatids are captured by microtubules emanating from both spindle poles, a process called bipolar attachment, whereas in meiosis I sisters are attached to microtubules originating from one spindle pole, called monopolar attachment. For determining chromosome orientation, kinetochore geometry or structure might be an important target of regulation. However, the molecular basis of this regulation has remained elusive. Here we show the link between kinetochore orientation and cohesion within the centromere in fission yeast Schizosaccharomyces pombe by strategies developed to visualize the concealed cohesion within the centromere, and to introduce artificial tethers that can influence kinetochore geometry. Our data imply that cohesion at the core centromere induces the mono-orientation of kinetochores whereas cohesion at the peri-centromeric region promotes bi-orientation. Our study may reveal a general mechanism for the geometric regulation of kinetochores, which collaborates with previously defined tension-dependent reorientation machinery.

The dark side of light at night: physiological, epidemiological, and ecological consequences

2009-04-16T20:37:00.001-07:00

The dark side of light at night: physiological, epidemiological, and ecological consequences

Author(s): Navara KJ (Navara, Kristen J.), Nelson RJ (Nelson, Randy J.)
Source: JOURNAL OF PINEAL RESEARCH Volume: 43 Issue: 3 Pages: 215-224 Published: OCT 2007

Abstract: Organisms must adapt to the temporal characteristics of their surroundings to successfully survive and reproduce. Variation in the daily light cycle, for example, acts through endocrine and neurobiological mechanisms to control several downstream physiological and behavioral processes. Interruptions in normal circadian light cycles and the resulting disruption of normal melatonin rhythms cause widespread disruptive effects involving multiple body systems, the results of which can have serious medical consequences for individuals, as well as large-scale ecological implications for populations. With the invention of electrical lights about a century ago, the temporal organization of the environment has been drastically altered for many species, including humans. In addition to the incidental exposure to light at night through light pollution, humans also engage in increasing amounts of shift-work, resulting in repeated and often long-term circadian disruption. The increasing prevalence of exposure to light at night has significant social, ecological, behavioral, and health consequences that are only now becoming apparent. This review addresses the complicated web of potential behavioral and physiological consequences resulting from exposure to light at night, as well as the large-scale medical and ecological implications that may result.

Light pollution, reproductive function and cancer risk

2009-04-16T20:34:00.002-07:00

Light pollution, reproductive function and cancer risk

Author(s): Anisimov VN
Source: NEUROENDOCRINOLOGY LETTERS Volume: 27 Issue: 1-2 Pages: 35-52 Published: FEB-APR 2006

Abstract: At present, light pollution (exposure to light-at-night) both in the form of occupational exposure during night work and as a personal choice and life style, is experienced by numerous night-active members of our society. Disruption of the circadian rhythms induced by light pollution has been associated with cancer in humans. There are epidemiological evidences of increased breast and colon cancer risk in shift workers. An inhibition of the pineal gland function with exposure to the constant light (LL) regimen promoted carcinogenesis whereas the light deprivation inhibits the carcinogenesis. Treatment with pineal indole hormone melatonin inhibits carcinogenesis in pinealectomized rats or animals kept at the standard light/dark regimen (LD) or at the LL regimen. These observations might lead to use melatonin for cancer prevention in groups of humans at risk of light pollution.

Exposure to light-at-night increases the growth of DMBA-induced mammary adenocarcinomas in rats

2009-04-16T20:34:00.001-07:00

Exposure to light-at-night increases the growth of DMBA-induced mammary adenocarcinomas in rats

Author(s): Cos S, Mediavilla D, Martinez-Campa C, Gonzalez A, Alonso-Gonzalez C, Sanchez-Barcelo EJ
Source: CANCER LETTERS Volume: 235 Issue: 2 Pages: 266-271 Published: APR 28 2006

Abstract: In order to assess whether light exposure at night influences the growth of mammary tumors, as well as the role of melatonin in this process, female rats bearing DMBA-induced mammary adenocarcinomas were exposed to different lighting environments. Animals exposed to light-at-night, especially those under a constant dim light during the darkness phase, showed: (a) significantly higher rates of tumor growth as well as lower survival than controls, (b) higher concentration of serum estradiol, and (c) lower nocturnal excretion of 6-sulfatoxymelatonin, without there being differences between nocturnal and diurnal levels. These results suggest that circadian and endocrine disruption induced by light pollution, could induce the growth of mammary tumors. (c) 2005 Elsevier Ireland Ltd. All rights reserved.