ageing population
A few days ago, I attended the 2009 meeting of the British Society for Research on Ageing (BSRA) in Manchester. It helps to reminded again of the current statistics:
—Of the current total world population of over 6.8 billion, there are over 750 million people aged 60 and over (11% of the total population).
—By 2050, the over-60 population is predicted to be just over 2 billion.
— By the end of the decade, there will be about 106 million people aged 80 or over. By 2050, this figure is projected to nearly quadruple to 395 million.
—By 2050, there are expected to be eight times as many people aged 100 and over as there will be in 2010.
—By 2050, there will be more people aged 60 and over than aged 14 or less.
—In China by 2050, there will be 438 million people aged 60 and over. Of those, 103 million will be 80 or older.
(source: UN World Population Prospects 2009)
Next time, I will write a lengthier account of the highlights from that meeting.
moments of not knowing
We are still struggling up to this moment in purifying the molecule that we are interested in – DmWRNexo. It appears to behave in some “mysterious” ways. The peaks that come out after chromatography seems to vary. Last Friday, we got three peaks (three fractions). Under the electron microscope, I saw this morning how the individual particles from the first fraction look like. Quite nice, they remind me of tiny doughnuts (with a hole in the middle). But there weren’t enough of them in a single field of view, so we did not take a photo. Tomorrow, we shall see. We have a new sample today (completed at 1700), but the chromatography profile was so different, it had only one peak! In the end, Ivan and I exclaimed, “What is going on? We don’t know!”
rDNA theory of aging
The ribosomes are the most abundant protein complexes in the cell. They are synthesised from ribosomal DNA (rDNA) genes within nucleoli. In most eukaryotic cells, rDNA exists in tandem arrays, which are repeating units of similar sequences. Oftentimes the rDNA provide sites for recombination, and the copy number seems to fluctuate. In this regard, the rDNA is hypothesised to be involved in genome stability and cellular senescence.
There was a paper written by Takehiko Kobayashi last year, 2008, in the journal BioEssays, wherein he proposed the rDNA theory of aging, stating that the rDNA may be the region most sensitive to DNA damage. He highlighted two key molecular entities that would link rDNA to aging: FOB1 and SIR2. These two are well known aging genes.
“… in yeast Saccharomyces cerevisiae … lifespan expansion in a fob1 mutant is associated with increased rDNA stability (no copy number variation), while the lifespan reduction in a sir2 mutant is associated with decreased rDNA stability (high copy number variation) …”
“rDNA is more unstable and induces checkpoint control faster than any other part of genome, and that the nucleolus may be more sensitive to protein damage because it is protein-dense …”
He stated further that rDNA may serve as ‘‘sensor’’ for DNA damage, and also as ‘‘shock absorber’’ that protects the genome from damage. I think these are broad statements as of this time.
He and his colleagues have observed that fob1 mutants show better growth than wild type, indicating checkpoint induction is reduced and lifespan is extended. More specifically, he mentioned that rDNA copy number gradually decreases in a fob1 mutant by a FOB1-independent form of homologous recombination. This implies termination of growth, presumbaly because of a shortage of rRNA and ribosomes. In this manner, lifespan extends due growth delay or termination. And yet, the number of abnormal cells is likely to increase.
In contrast, he described that sir2 mutants show increased rDNA instability. He stated that this leads to greater checkpoint control and shorter lifespan. I shall look further into this as it seems unclear to me.
Below is one of the images he presented in the paper:
A new role of the rDNA and nucleolus in the nucleus – rDNA instability maintains genome integrity
Takehiko Kobayashi
National Institute of Genetics and The Graduate University for Advanced Studies, SOKENDAI, 1111 Yata, Mishima 411-8540 Japan
email: Takehiko Kobayashi (takobaya@lab.nig.ac.jp)
BioEssays (2008)
Volume 30 Issue 3, Pages 267 – 272
picking molecules
So I have been busy “picking molecules” for quite some time now. To make sense of what I have been doing, keeping the principle in mind seemed a nice thing to do. Below is a diagram showing how the EM images are prepared. It also shows the what kind of structures represent those “particles” to be “picked.” I’m eager as a beaver to see how DmWRNexo looks like.
Saibil (2000) Acta Cryst. D56, 1215-1222
after two weeks
After two weeks of transition, I am now back to my routine. I have transferred from Milton Keynes to Oxford, and I brought some of my flies with me. Now I can sit down, clear my thoughts from the whirlwind of moving from one lab to the other, and think of what needs to be achieved within the next 351 days. I have started preliminary analysis of the EM images of DmWRNexo and hWRNexo. Previously, Ivan B prepared the sample while Catherine V-B took the photos on the EM. A certain Mademoiselle Dorthe did the first set of “picking molecules” from the images. I continued from what she had done. Three consecutive days of staring at EM images and “picking molecules” was alright. It was not really very tiring, but it was time-consuming. The goal is to “pick” a minimum of 2000 particles in order to generate a reliable molecular structure. Catherine V-B says 8000 is even better. I’m excited how DmWRNexo would look like. More on this in the coming days.
re-write the textbooks: transcription is bidirectional
Genes that contain instructions for making proteins make up less than 2% of the human genome. Yet, for unknown reasons, most of our genome is transcribed into RNA. The same is true for many other organisms that are easier to study than humans. Researchers in the groups of Lars Steinmetz at the European Molecular Biology Laboratory [EMBL] in Heidelberg and Wolfgang Huber at the European Bioinformatics Institute [EMBL-EBI] in Hinxton have now unravelled how yeast generates its transcripts and have come a step closer to understanding their function. The study redefines the concept of promoters [the start sites of transcription] contradicting the established notion that they support transcription in one direction only. The results are also representative of transcription in humans.
Investigating all transcripts produced in a yeast cell, the scientists found that most regions of the yeast genome produce several transcripts starting at the same promoter. These transcripts are interleaved and overlapping on the DNA. In contrast to what was previously thought, the vast majority of promoters seem to initiate transcription in both directions.
Not all of the produced transcripts are stable, many are degraded rapidly making it difficult to observe what they do. While some of the RNA molecules might be ‘transcriptional noise’ without function, other transcripts control the expression of genes and production of proteins. The act of transcription itself is also likely to play an important role in regulation of gene expression. Transcribing one stretch of DNA might either help or in other cases interfere with the transcription of a gene close by. Moreover, transcripts without a current purpose can serve as ‘raw material for evolution’ and acquire new functions over time.
The results shed light on the complex organisation of the yeast genome and the insights gained extend to transcription in humans. A better understanding of transcription mechanisms could find application in new technologies to tune gene regulation in the future.
—EMBL
oxidatively damaged DNA in the germ line
Alberto Velando and colleagues wrote a paper entitled “Avoiding bad genes: oxidatively damaged DNA in germ line and mate choice.”
Below is the abstract:
August Weismann proposed that genetic changes in somatic cells cannot pass to germ cells and hence to next generations. Nevertheless, evidence is accumulating that some environmental effects can promote heritable changes in the DNA of germ cells, which implies that some somatic influence on germ line is possible. This influence is mostly detrimental and related to the presence of oxidative stress, which induces mutations and epigenetic changes. This effect should be stronger in males due to the particular characteristics of sperm. Here, we propose the hypothesis that females are able to avoid males with oxidatively damaged DNA in the germ line by using oxidative-dependent (pre- and post-mating) signals. This new hypothesis may shed light on unsolved questions in evolutionary biology, such as the benefits of polyandry, the lek paradox, or the role of sexual selection on the evolution of aging.
somatic mtDNA mutations
A paper by Alexandra Kukat and Aleksandra Trifunovic demonstrates that somatic mtDNA mutations have the capacity to cause a variety of aging phenotypes in mammals. However, the relative importance of somatic mtDNA mutations in mammalian aging remains unclear, as the overall mutation load in normal mammalian aging tissues is much lower than needed to cause mitochondrial dysfunction. However, results from single cells argue that despite a relatively low overall level of mtDNA mutations, the mutational load in single cells could be substantial. Therefore, this may result in a functional impairment of the tissue by the loss of critical cells by cellular senescence or cell death.
BLAP75/Rmi1
Liudmila Chelysheva and colleagues studied BLAP75/Rmi1 in relation to BLM/Sgs1 and TopoIIIα/Top3. Their paper appeared on the December 2008 issue of PLoS Genetics journal. Below is the summary:
“Recombination is a process by which cells can repair DNA damage. Such repair can either be crossovers (CO), in which DNA molecules are submitted to major exchanges, or non-crossover (NCO) events. Eukaryotic cells have developed several mechanisms to maintain genome stability during vegetative development by limiting the occurrence of CO events in favour of NCO. BLAP75/Rmi1, BLM/Sgs1, and TopoIIIα/Top3 act together in a complex (BTB/RTR) known to be a crucial component of regulation mechanisms against CO formation. However, CO/NCO regulation is thought to be very different during meiosis since homologous chromosomes (paternal and maternal) overcome at least one CO/pair. In this study, we investigate the role of the BTB/RTR complex during meiotic recombination through the analysis of a function of one of its members: the A. thaliana homologue of BLAP75/Rmi1. We show for the first time that BLAP75/Rmi1 is also a key protein of the meiotic homologous recombination machinery. In Arabidopsis, we found that this protein is dispensable for homologous chromosome recognition and synapsis, but necessary for the repair of meiotic double-strand breaks. Furthermore, in the absence of BLAP75, bivalent formation can happen even in the absence of CO.”
Note: A. thaliana blap75 mutants are sterile. They examined the reproductive development of these mutants and found that blap75 sterility is due to abortion of male and female gametophytes. In particular, blap75 mutants show defects in male sporogenesis.
