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All things Raspberry Pi and Time Lapse

Posts tagged ‘CHDK’

Plan B

The Canon Powershot S2 IS will not fit in the enclosure with the cables connected. So after thinking about the requirements for the camera, I decided that CHDK is not a requirement like I originally thought. I can do everything from gphoto2 using scripts. So I ordered a Canon Powershot A510 from Amazon that is much smaller and as near as I can tell will fit in the enclosure. Now just waiting for it to be delivered!

BOM (Bill of Materials)

Here is a list of the materials (that I have though of so far) needed for the year-long time lapse.

First thing is Location. Its all about location, location, location.

1. A RaspberryPi. This is to control the camera and tell it when to take a picture. It would be possible for the camera to take a picture at certain times, but with the Raspberry Pi there will be more control over when the pictures are taken. This should cost $45 after shipping + handling.

2. A power cable to power the Raspberry Pi. I am planning on using an HTC micro USB cable that is here on Amazon that is $4 after shipping + handling.

I ended up going with a Samsung power supply from Amazon because the HTC power supplies did not have good ratings and people said they were not made by HTC. So I am using that Samsung because it had good rating and it is working good.

3. A SD card to use for the Operating System for the Raspberry Pi and to store images from the camera as well. Amazon once again for about $7 after shipping + handling.

4. A camera that is supported by gphoto2 and also by CHDK for taking the photos. The Canon Powershot SX100 or SX110 are the best camera’s that are supported by both gphoto and CHDK. Here is the SX100 listed on Amazon. I got mine for $100 (used – very good condition – had 1500 shots on it when I got it) after shipping + handling. The Canon Powershot A510 should fit in the enclosure and has full support from gphoto2. I bought one from Amazon for $41 after shipping + handling.

5. The third item is a USB cable that connects the camera to the Raspberry Pi. This is also availble on Amazon and mine cost $12 after shipping + handling.

6. An AC power supply is also necessary to power the camera. Once again Amazon seems to be the best. This cost $15 after shipping + handling.

7. A housing for all of these components is a critical point for the survival of the camera in all kinds of weather. An enclosure made for security cameras seemed to be the best option. I originally looking into building myself one using a waterproof container and a bunch of pieces to make it all work. Then I found this enclosure (also Amazon) and it has a heater and a fan to regulate the temperature. And it is IP66 rated. This costs $47 after shipping + handling.

8. A power supply to power the heater/blower in the enclosure is available at Amazon. It is sold by the same supplier as the enclosure and is confirmed to work with this model of enclosure. This cost $36 after shipping + handling.

9. Silica gel is something that comes in packages and I will put several of  these packets in to reduce moisture.

10. A case to hold all of the power cables that plug into the power strip. This needs to be kept dry and it has to be in a separate case because the enclosure that holds the camera and Raspberry Pi is too small to hold all of this as well. This Sockit Box case from Amazon should do the job nicely! It costs $33 dollars which is a little expensive I thought, but it is a very important part of the project.

11. I bought some plastic screws and nuts to hold the Raspberry Pi in the enclosure and keep it from touching the metal sides. This I bought from my local Lowe’s store and it only cost $5 dollars for all of it.

Still need

A power supply for the enclosure. It does not come with one, but requires one for the heater/fan.

A power cord (120V) to be able to run to the enclosure to power all of the electronics.

At this point all of the materials cost $207 and I hope to keep it under $250 with the rest of the materials that are still needed. And no I am not trying to sell Amazon stuff, but they have been consistently the best price for the quality that I need.

The goal of this project is to have several time lapse videos that show a scene over the course of a year. I am in the planning stage at this point, but have started buying the materials needed. The two main components are a Canon camera and a Raspberry Pi! More details to come…

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Jul. 3rd, 2010

Still working on Melissa's birthday present. Right now, it's doubtful that I'll have it done before her birthday. But I hope to deliver it to her no more than two weeks late.

I really want to go to the movies. I probably won't get to until August -- Mark and I are (hopefully) going to see The Expendables.

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Lead, Risk Management Solutions Architect

Lead, Risk Management Solutions Architect

Great vacations begin with great employees!

Combine your experience and sense of adventure by joining our exciting team of employees in Miami, Florida.  Royal Caribbean Cruises Ltd. is pleased to offer a competitive compensation & benefits package, and excellent career development opportunities, each offering unique ways to explore the world.

Position Summary

This position leads the database design and platform configuration of the Company's incident reporting and claims system (using Force.com platform) to develop and promote optimal design solutions for its users. This role is highly technical in nature and requires demonstrated attention to detail, execution and follow-up on multiple initiatives with the Risk Management department. The ability to analyze, identify, develop and implement process improvements within the organization is a key factor of success in this role.

Career Snapshot

  • Integrate risk management, safety or healthcare industry background with database design and platform configuration knowledge to develop optimal design solutions for the Company's Risk Management System.
  • Implement new features or enhance existing features in the Company's Salesforce.com Risk Management system, including new objects, interfaces, actions and behaviors.
  • Lead discovery sessions with business owners to understand the existing and desired business processes.
  • Serve as a liaison between multiple departments to facilitate project scoping, requirements gathering and solution architecting.
  • Analyze, identify, develop and implement process improvements within the organization, both outside and within the Risk Management system.
  • Promote consistent design and best practice methodologies to solve similar problems across multiple departments.
  • Deliver high-quality documentation of business requirements and design specifications for implementation.
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Join our team as a Lead, Risk Management Solutions Architect.  Once you apply, it will take you 10-15 minutes to complete our application, which will help us better qualify your candidacy. If you are being considered for this position you will hear back from us within the next 30-60 days.  During this time, you can view your application status on our career site.

Join us at Royal Caribbean Cruises Ltd., where great vacations begin with great employees!

RCL is an Equal Employment Opportunity employer.


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BMC Biology

, 6:36 | Cite as

Complex chloroplast RNA metabolism: just debugging the genetic programme?

  • Uwe G Maier
  • Andrew Bozarth
  • Helena T Funk
  • Stefan Zauner
  • Stefan A Rensing
  • Christian Schmitz-Linneweber
  • Thomas Börner
  • Michael Tillich
Open Access
Research article

The gene expression system of chloroplasts is far more complex than that of their cyanobacterial progenitor. This gain in complexity affects in particular RNA metabolism, specifically the transcription and maturation of RNA. Mature chloroplast RNA is generated by a plethora of nuclear-encoded proteins acquired or recruited during plant evolution, comprising additional RNA polymerases and sigma factors, and sequence-specific RNA maturation factors promoting RNA splicing, editing, end formation and translatability. Despite years of intensive research, we still lack a comprehensive explanation for this complexity.

We inspected the available literature and genome databases for information on components of RNA metabolism in land plant chloroplasts. In particular, new inventions of chloroplast-specific mechanisms and the expansion of some gene/protein families detected in land plants lead us to suggest that the primary function of the additional nuclear-encoded components found in chloroplasts is the transgenomic suppression of point mutations, fixation of which occurred due to an enhanced genetic drift exhibited by chloroplast genomes. We further speculate that a fast evolution of transgenomic suppressors occurred after the water-to-land transition of plants.

Our inspections indicate that several chloroplast-specific mechanisms evolved in land plants to remedy point mutations that occurred after the water-to-land transition. Thus, the complexity of chloroplast gene expression evolved to guarantee the functionality of chloroplast genetic information and may not, with some exceptions, be involved in regulatory functions.

Cytoplasmic Male Sterility Land Plant Chloroplast Genome Sigma Factor Editing Site

As the site of oxygenic photosynthesis, chloroplasts are the most in-depth studied plant organelles. The recognition that they carry their own DNA [1] led, in the 1970s, to a race to decipher their genetic content, which eventually resulted in more than 100 [2] sequenced chloroplast genomes to date. These sequences set to rest any remaining doubts that chloroplasts are ancient endosymbionts and are derived from cyanobacterial-like ancestors. Expression analysis of the chloroplast genetic information had been studied right from the dawn of chloroplast molecular biology and several surprising findings emerged. The most puzzling of these was that the chloroplast gene expression system is far more complex than that of its cyanobacterial progenitors (Figure 1). This gain in complexity is due to changes in RNA metabolism, specifically to novelties in the transcription and maturation of RNA. A set of newly acquired or recruited nuclear-encoded proteins comprising RNA polymerases, sigma factors and mono- or merospecific RNA maturation factors promotes transcription [3, 4, 5, 6, 7, 8], RNA splicing [9, 10, 11], RNA editing [12, 13, 14], RNA end formation [15, 16, 17] or translation [18, 19]. Identification and characterization of these factors stimulated research, but a unifying explanation for this Byzantine gene expression system in chloroplasts has not yet been found. Here, we propose a hypothesis on the origin of the complexity of chloroplast gene expression, encompassing recent data on factors involved in chloroplast transcription, RNA editing and RNA processing.
Figure 1

Components of the ancient basal (cyanobacterial-like, grey) and modern extended (grey and black) gene expression system of chloroplasts. We propose that the evolution of RpoTs in plants, the expansion of the gene families coding for chloroplast sigma factors and PPR proteins help to neutralize mutational lesions in the chloroplast genomes (black triangles). RpoTs and additional sigma factors with lower or altered promoter specificity compensate for degenerated promoters. The highly specific members of the versatile PPR family promote or are required for proper translation, coding and splicing of chloroplast mRNAs.

Results and discussion

Amazing complexity: chloroplast RNA transcription, RNA processing and the corresponding machinery

The chloroplast genome contains functional rpo genes encoding subunits of a homolog of the eubacterial RNA polymerase, termed plastid-encoded RNA polymerase (PEP). Surprisingly, in contrast to its eubacterial ancestors, this RNA polymerase does not transcribe the chloroplast genome in higher plants alone [20, 21, 22]. A second, chloroplast-localized, but nuclear-encoded transcription activity, the nuclear-encoded plastid RNA polymerase (NEP), has been identified (Figure 1), which has promoter requirements very different from the canonical -10/-35 PEP promoters. Sequence alignments revealed that most NEP promoters contain a simple core sequence (YRTA), similar to plant mitochondrial promoters. NEP activity consists of one (Liliopsida) or two (eudicotyledonous plant species) phage-type RNA polymerases [23, 24]. These three RNA polymerases produce a dazzling array of transcripts using a multitude of different promoters. As a consequence, almost all chloroplast genes are transcribed from several independent promoters [25].

Similarly to transcription, RNA processing also dramatically increases the variety of transcripts per gene. This is reflected in the complex transcript patterns encountered when performing chloroplast RNA gel blot hybridization experiments. More than 10 transcripts per gene, differing in size and in their coverage of adjacent cistrons, are regularly detected. Additionally, alternative RNA cleavage can produce mature RNAs differing in their translational efficiency [26]. All of this is not known from transcripts in cyanobacteria. Mostly, splicing and cleavage events in chloroplasts cause the breakdown of their long precursor RNAs into monocistronic constituents. For example, there are five precursor RNA species for ndhA and as many as 15 for petD [27, 28]. Both genes carry an intron and are part of a primary precursor encompassing seven and four genes, respectively. Another curiosity adding to the overall complexity of chloroplast RNA processing is RNA editing. In seed plants, about 35 C-to-U editing sites are found per chloroplast genome [summarized in [29, 30]], whereas chloroplast genomes of bryophytes like those of the hornwort Anthoceros can harbour several hundred sites [31]. In cyanobacteria, RNA editing is not observed at all. Furthermore, splicing has a less prominent role in RNA maturation in these prokaryotic relatives of the chloroplast ancestor [32, 33]. Although endonucleolytic cleavage events are important in bacterial RNA degradation, they have not been demonstrated to be a common prerequisite for translation [34]. Thus, complexity in RNA processing arose after endosymbiosis. Given that hundreds of processing events occur, a legitimate question is: who does the job? Certainly, the vast majority of factors involved are nuclear-encoded. One family that came into focus recently as an important player in plant organellar RNA metabolism is the pentatricopeptide repeat (PPR) protein family. Many of its members (about 100 in rice and Arabidopsis) are targeted into chloroplasts [35]. Those that have been analysed genetically are required for specific steps in chloroplast gene expression. PPRs recognize their targets with high specificity [10, 19] and are direct ligands of RNAs [13, 14, 36, 37]. They are currently viewed as the adaptors that are necessary for the myriad sequence-specific processing events occurring in chloroplast transcripts [35, 38]. Besides PPRs, a variety of additional factors of different specificity have been described that execute processing steps left over by PPR proteins [39, 40, 41]. In conclusion, chloroplasts are engaged in a tremendous expenditure of matter and energy to generate multiple RNA species. No clear function is known either for the array of transcripts produced or for the complex transcription and RNA processing itself.

Positive selection for complexity or haphazard accumulation of processing events?

Undoubtedly, many steps in chloroplast RNA metabolism are essential for gene expression; e.g. all splicing events and most editing events. But does 'essential' mean that these processing steps are under positive selection? Or in other words: is there evidence that these processing steps fulfil some sort of regulatory function; i.e. are they rate-limiting for chloroplast gene expression? The currently available data are not adequate to decide in favour of or against this question. This is mostly due to the fact that it is non-trivial to demonstrate unequivocally that a specific transcription initiation, splicing, or editing event is limiting for the amount of the final gene product. While it is an appealing idea that the multitude of transcription and processing steps mediated by nuclear encoded factors represent starting points for the regulation of organelle gene expression and its nuclear control [42], there is only a single study directly supporting this argument, carried out recently in Chlamydomonas reinhardtii. Here, the abundance of the chloroplast PPR protein MCA1 has been demonstrated to limit the amount of the petA mRNA as well as the amount of the encoded protein, cytochrome f [43]. In plants, only marginal evidence for the regulation of gene expression by factors involved in controlling RNA metabolism is available [e. g. [44]]. For example, organellar RNA polymerases have been shown to be expressed in a tissue-specific manner and seem to be modified dependent on light conditions [45, 46]. A variety of studies show that transcription and post-transcriptional events can be modulated by external factors like temperature and light-conditions [47, 48, 49]. None of these studies, however, yielded conclusive evidence as to whether gene expression is truly rate-limiting. Several authors have suggested that there is a dominance of translational and post-translational regulation of gene expression in chloroplasts [50, 51]. In contrast to pre-translational regulation, there is ample evidence for the regulation of translation or subsequent processes, both in C. reinhardtii and seed plants [52, 53, 54, 55]. Taken together, currently there is little evidence that the complexity of organellar RNA metabolism is a result of an increased demand for regulating steps in gene expression, although it cannot be ruled out that we just have not looked hard enough.

An alternative explanation: complexity as a result of transgenomic suppression?

Although positive selection of a complex RNA metabolism of chloroplasts remains a potent possibility for explaining its having come about, we think that there is at least one powerful alternative explanation. In short, this hypothesis puts forth the proposition that complexity in organellar gene expression can be a selectively neutral process, fostered by different mutation rates and a different strength of genetic drift between the organellar and nuclear genomes of plants.

Chloroplasts harbour multiple copies of their genome and are inherited clonally, thus recombination between identical copies has an insignificant role in chloroplast evolution [56]. These are the hallmarks of a degenerative process occurring in genomes of endoparasites, termed Muller's ratchet [57, 58]. Genomes of organisms like the proteobacterium Buchnera, an endosymbiont of aphids, accumulate mildly deleterious mutations [59]. As endosymbionts, chloroplasts should likewise be prone to the same type of genomic degeneration. Of course, countermeasures may evolve in endosymbionts to lighten the mutational burden imposed by Muller's ratchet, like modifications of the DNA repair system [60]. While the welfare of Buchnera depends on such intrinsic relief systems, chloroplasts can draw on a tremendous external resource for treating genomic problems: they can tap the coding potential of the nuclear genome. The plant nuclear genome is much more dynamic and evolves more rapidly than the chloroplast genome, among other reasons because of the benefits of sexual recombination and a higher mutation rate [61, 62, 63]. However, the situation might differ in bryophytes and ferns, in which the dominant generation is haploid. Nevertheless, recent results indicate that as in seed plants, the organellar genomes of ferns and bryophytes exhibit lower mutation rates than their nuclear counterparts [64].

The nuclear genome provides a wealth of genetic information that can be directed into the organelle with relative ease [65, 66]. This way, the more expeditious evolution of nuclear loci could alleviate slow deterioration of chloroplast genetic information, and even mutations with a strong negative impact on organelle development and function might be remedied. We view this compensatory process as being suppressor mutations that do not reverse the original point mutation but find an alternative way to correctly decode the chloroplast genetic information. Thus, chloroplast mutations and nuclear suppressors form co-evolving couples, reciprocally stabilizing each other. This phenomenon is not a mere academic speculation, but has been witnessed in our time by plant breeders. Cytoplasmic male sterility (CMS) is a defect occurring in plant mitochondria that leads to loss of pollen development and thus, male sterility. CMS plant lines have been isolated in many different agronomically important crops. In most cases, illegitimate recombination events in the mitochondrial genome resulted in novel open reading frames (ORFs), the expression of which is detrimental to mitochondrial function. Plant breeders take advantage of CMS lines for their large-scale breeding programmes, because carrier plants do not require emasculation for out-crossing. For many CMS populations, nuclear loci that restore fertility are described. These restorers are specific to their cognate mitochondrial defect. Eight restorer genes have been cloned [summarized in [67]]. All but one of them encode PPR proteins targeted to mitochondria. For rice RF1A it was shown that it leads to endonucleolytic cleavage of the aberrant CMS RNA [68]. In these cases, a nuclear factor alleviates an organellar problem arising due to a genomic mutation.

We propose that transgenomic suppression silences deleterious chloroplast point mutations in all coding sequences as well as in sequence elements required for gene expression. In the following section, we discuss which nuclear factors are models for suppression of chloroplast mutations. We propose that PPR proteins are involved in neutralizing point mutations in coding regions, introns and UTRs, while different RNA polymerases and their co-factors help overcome problems caused by point mutations in promoter regions.

PPRs counteract point mutations in coding regions, introns and UTRs

As outlined above, some PPRs are restorers of fertility that counteract detrimental mutations in mitochondria. In chloroplasts, PPR proteins fulfil a variety of functions in RNA metabolism. PPR proteins are involved in RNA editing [12, 13, 14], RNA splicing [10] and RNA cleavage [36, 69]. Most plant PPR proteins analysed to date are essential proteins. However, no evidence for their being involved in regulating gene expression has been presented thus far, underscored by the fact that most PPR proteins are constitutively expressed [35]. We hypothesise that PPRs are a nuclear remedy of mutations occurring in the chloroplast genome. This is best exemplified by their role in CMS (see above) and plastid RNA editing.

Several lines of evidence suggest that chloroplast RNA editing is one mechanism for compensating damage from point mutations in the chloroplast chromosome. RNA editing has been demonstrated to be essential: the corresponding gene product malfunctions if Cs are not turned into Us on the RNA level. Contrasting its importance for gene function, RNA editing per se is not under positive selection, as indicated by the extraordinary speed with which editing sites evolve [70], and by the fact that experimental removal of a site did not lead to any discernible phenotype [71]. Furthermore, RNA editing sites are most stable in a base context that exhibits low mutation rates. In particular, editing sites seem to be stuck in the T_A context [30]. Cs squeezed between a 5' T and a 3' A have the lowest mutation rates when compared with any other possible immediate C-neighbourhood [72]. It is precisely this context that is most frequently encountered around editing sites. Moreover, editing sites accumulate predominantly in genomic regions of the chloroplast chromosome that are slowly evolving, foremost the inverted repeat [30, 73]. Yet, if RNA editing was under positive selection, a correlation of editing sites with local mutation rates would not be expected. Together, these data suggest that RNA editing sites arose as T-to-C mutations that are not easily removed by mutational reversion. In conclusion, RNA editing is not present in chloroplast genomes for the benefit of regulating gene expression, but rather for getting rid of mutations at the RNA level [30].

Recently, it has been shown that, at least in well-investigated cases, the nuclear encoded factors responsible for recognizing editing sites are PPR proteins [reviewed in [67]]. Thus, RNA editing sites and their cognate editing PPR proteins exactly mirror the situation of CMS mutations and nuclear restorer PPR genes. Again, a nuclear-encoded PPR protein seems to be a remedy for an organellar genomic problem.

As mentioned above, PPR target sites are not restricted to coding regions; neither are point mutations due to organellar DNA degeneration. Organellar introns for instance are highly divergent from their bacterial ancestors [74]. The dominant class of introns in chloroplasts is the so-called group II introns, which fold into a characteristic secondary structure. In bacteria, group II introns are self-splicing in vitro and are by definition ribozymes. Chloroplast group II introns, however, have lost their ability to excise without external help. This might also point to the detrimental effects of Muller's ratchet being active in chloroplasts. For splicing, nuclear encoded factors are required [reviewed in [75]]. Interestingly, several of these factors are PPR proteins [9, 10, 11]. It seems superfluous to invent novel splicing factors for each intron. We deem it more likely that similar to the situation with RNA editing, nuclear factors, foremost PPR proteins, help to counterbalance organellar mutations. For example, secondary structure elements in group II introns disrupted by point mutations could be stabilized by the interaction with PPR proteins.

Besides coding regions and introns, Muller's ratchet should also lead to the weakening or even destruction of expression signals in the 5' and 3' UTR of mRNAs. Sequence elements in the UTR regions are required for RNA stability, but (particularly in the 5' UTR) also for translation initiation. Indeed, the canonical Shine Dalgarno sequence in front of cyanobacterial genes is rarely found in the typical position in front of chloroplast open reading frames, if it is found at all [reviewed in [76, 77]]. Chloroplasts have developed alternative schemes to load ribosomes onto their mRNAs that interact with specific nuclear RNA binding proteins [78]. Not surprisingly, PPR proteins also play a part in this task [18, 19].

Multiple RNA polymerases with relaxed promoter specificities counteract point mutations in promoter regions

Many point mutations can be cured on the RNA level by nuclear factors, i.e. highly specific RNA binding proteins. In contrast, processes depending on DNA as a template will require other means to compensate for deleterious point mutations. These DNA-bound processes are chiefly replication and transcription. Only some features of the replication machinery in chloroplasts are known (e.g. bacterial-type DNA polymerases [79]) but, clearly, bacterial origins of replication are no longer found on chloroplast chromosomes [80], putatively eliminated by Muller's ratchet. Much more is known about transcription initiation and the responsible factors.

In cyanobacteria, promoters of the -10/-35 type are used to drive the transcription of all genes. More than a dozen sigma factors are found per cyanobacterial genome that fall into different functional classes with different consensus sequences in the -10 and -35 boxes [e. g. NC_000911 [81, 82]]. In plants, sigma factors are no longer encoded by the chloroplast genome but their genes have been transferred into the nucleus. The number of sigma factors found in the Arabidopsis thaliana, grapevine (Vitis vinifera), rice (Oryza sativa) and moss Physcomitrella patens genome is six; nine were found in poplar (Populus trichocarpa), but only one is present in the sequenced green algal genomes of C. reinhardtii, Ostreococcus tauri and Ostreococcus lucimarinus (Table 1). This represents a remarkable multiplicity in sigma factors in land plants compared with green algae and a dramatic increase in their number per gene relative to cyanobacteria, considering the small number of chloroplast genes (Table 1). While sigma factors are notorious suspects for gene regulation and indeed have at least in part taken over regulatory functions [reviewed in [44, 83]], the increase in nuclear-encoded sigma factors for chloroplast genes' promoters could originally have been a reaction to promoter degeneration, i.e. diversification. In fact, canonical -10/-35 promoters are rare in chloroplasts. Both a pronounced deviation from the consensus and a spatial shift from the start codon are common. Thus, multiple sigma factors may be needed to recognise deviant promoters in chloroplasts. Remarkably, at least two sigma factors, SIG3 and SIG4, are highly specific and seem to serve only the transcription of a single gene, psbN and ndhF, respectively [44, 84, 85]. This high specificity resembles the situation with PPRs and their specific targets and – in the absence of data indicating regulation for these two sigma factors – might be a sign that at least these two sigma factors are nuclear solutions to cope with a degenerate chloroplast promoter.
Table 1

Compilation of the number of nuclear encoded, chloroplast directed transgenomic suppressor functions (PPR proteins, sigma factors and phage type RNA polymerases) and of plastid genes encoded among plants and unicellular algae.

A. thaliana

P. trichocarpa

V. vinifera

O. sativa

P. patens

C. reinhardtii

O. tauri

O. lucimarinus

T. pseudonana

P. tricornutum

C. merolae

PPR proteins

Sigma 70 factors

Plastid genes

PPR/plastid gene*

Phage-type RNA polymerases

*The PPR protein-plastid gene relations were determined under the assumption that in all taxa 16% of the PPR proteins are plastid proteins (as shown for A. thaliana in [35]).

n.a. = not applicable.

A second transcription system in chloroplasts appears even more suitable to avert problems arising from mutated promoters: the nuclear encoded phage-type RNA polymerases (NEP). Angiosperms possess one or two phage-type RNA polymerases in their chloroplasts, which are needed for transcription in addition to PEP. NEP and PEP recognise different promoters and PEP is discussed as playing a major role in green tissues [44, 83]. A thorough analysis of NEP promoter function (rpoB promoter of tobacco) revealed a CRT-motif (CAT or CGT) at position -8 to -6, which was proven to be critical for transcription [86]. Such a simplistic core promoter of only three nucleotides is expected to be found upstream, proximal to each transcripional unit. Moreover, phage-type NEP enzymes are likely able to recognise promoter sequences without the help of auxiliary factors. The T7 RNA polymerase is known to operate as a single subunit enzyme, i.e. one and the same polypeptide performs promoter recognition and all phases of transcription [87]. At least in vitro, the mitochondrial RNA polymerase of baker's yeast exhibits similar properties, although efficient transcription requires two additional protein factors in organello [88]. Similarly, the A. thaliana phage-type enzymes, including the mitochondrial and a chloroplast-targeted RNA polymerase, were found to act as single-polypeptide transcriptases and to recognise several mitochondrial and chloroplast promoters in vitro [89]. These observations suggest that the targeting of a phage-type RNA polymerase to chloroplasts alone, i.e. without additional transcription factors, might have been sufficient to support transcription from promoters with simple structures. Thus, NEP transcription initiation may avert detrimental effects of point mutations by decreasing specificity. This is a fundamentally different strategy from the one that PPR proteins and sigma factors follow in order to counteract point mutations, as apparently they function with high specificity. In summary, the complexity of the transcription apparatus in chloroplasts could have evolved to compensate for degenerating chloroplast promoters.

Emergence of land plants and transgenomic suppressors coincide

Chloroplast DNA mutation and degeneration should be an ongoing process and the example of restorer genes and CMS highlights that suppression of organellar mutations still occurs in today's plants. However, when examining the different transgenomic suppressors enumerated above under a more phylogenetic perspective, an intriguing bias towards land plants emerges (see Table 1). First, RNA editing is an invention of land plants, absent from algae [90]. Second, although present in all eukaryotic genomes including algae (albeit in low numbers in those: 19 to 26 members, see Table 1), PPR proteins are exceptionally abundant in land plants. More than 450 members have been identified in A. thaliana and rice, more than 600 in poplar and grapevine, and approximately 100 in the moss P. patens (Table 1) [9]. Furthermore, whereas the genomes of the green algae C. reinhardtii, O. tauri and O. lucimarinus encode only one sigma factor, the seed plant and P. patens genomes encode at least six [44]. Finally, seed plants and mosses have evolved plastidal NEPs by duplicating the gene encoding the mitochondrial phage-type enzyme [4, 91], while genomes from green algae and the red alga Cyanidioschyzon merolae only encode one phage-type RNA polymerase [44], which is predicted to be targeted to the mitochondrion. Although some nucleus-encoded factors involved in RNA maturation are known from Chlamydomonas [92], an apparently shared feature of land plants is an increase in proteins that could function in sustaining the functionality of mutationally altered organellar genomes. How can this trend be explained?

Today it is generally accepted that land plants share a common ancestor with the green algal lineage [93, 94, 95]. Because land plants are monophyletic [96, 97], one has to assume that a single green algal-like progenitor successfully went ashore, subsequently adapted to a dramatically different environment, and eventually evolved into the earliest land plant.

Changing from an aquatic to a terrestrial life style must have been a colossal challenge in several regards, yet the colonisation of land by plants was nonetheless very successful. The evolutionary radiation into mosses, liverworts, hornworts, club mosses, ferns and seed plants was accompanied by major developmental and morphological innovations, enabling the adaptation of plants to the new environment [97, 98, 99]. Coevally to the need for the development of new morphotypes, early land plants required adaptations to cope with the exposure to increased solar and stellar radiations, which endangered their genetic information. Conceivably, this increased the need for countermeasures against chloroplast mutations and eventually led to the expansion of the PPR family, the increase in sigma factors per gene, and the redirection of a phage-type RNA polymerase to chloroplasts. If this hypothesis is true, we should see clear differences in the number of PPR proteins, RNA editing and RNA polymerases not only between green algae and land plants, but also between more closely related sister groups of land plants, for example the charophytes. Further genomic information is needed to resolve these questions.

As shown for RNA-editing, species-specific gains and losses of mutations are common as well, which necessitate restoration by nucleus-encoded factors. In the case that losses of mutation sites are predominant, suppressor activity for that mutation can be lost coevally. A very pronounced situation for the loss of a plant-specific mechanism is present in the liverwort Marchantia polymorpha, which secondarily lost organellar RNA editing (as shown recently by the identification of RNA editing within the mitochondrion of an ancestral liverwort [100]). Thus, in the case of a high mutation rate enabling back-mutations or the evolution of additional transgenomic suppressors, other land plant-specific mechanisms such as a second, nucleus-encoded chloroplast RNA polymerase should ultimately become superfluous and be lost.

Here, we put forward a hypothesis to account for the enigmatic complexity of chloroplast gene expression. We propose that nuclear factors evolved to counteract chloroplast mutations that occurred after the water-to-land transition and persist due to the mode of chloroplast genome evolution. These nuclear factors act either on DNA directly or suppress point mutations on the RNA level. Specifically, we suggest that PPR proteins were recruited to counteract point mutations in coding regions, introns and UTRs. In the same way, sigma factors may help to recognise degenerated promoter motifs. Finally, low-specificity phage-type RNA polymerases support transcription despite the loss of canonical PEP-promoters. Intriguingly, all means to suppress chloroplast mutations instanced here seem to have evolved in early land plants. Hypothetically, this could mean that chloroplast genomic decay and parallel counteraction by nuclear-encoded components were accelerated in the common ancestor of all land plants.

The hypothesis put forward here draws on two established concepts: the degeneration of genomes of endosymbiotic organisms and the suppression of organellar defects by nuclear factors (the CMS example). The hypothesis circumvents the need to invoke selective pressures to account for the myriads of processing events in the chloroplast transcriptome (but does not exclude them in individual cases). It is therefore more parsimonious than the assumption that complexity in chloroplast gene expression serves a regulatory function. Finally, our hypothesis may draw a picture of the first land plant, its molecular integration into the new environment and the need to suppress radiation-engendered mutations.

Available genome datasets were screened with the following PFAM ( HMMs with a cutoff of E ≤ 0.0001: Sigma70_r2/3/4 (PF 04542, 04539, 04545); PPR repeat (PF01535). Only those genes containing more than one PPR repeat were taken into account. Numbers of protein-coding plastid genes are derived from [2]. Number of RpoT genes encoding phage-type RNA polymerases in O. tauri, O. lucimarinus, T. pseudonana and P. tricornutum are derived from BLAST hits using the A. thaliana RpoTm, RpoTmp and RpoTp sequences as queries, filtered for > = 30% identity and 300 aa alignment length. RpoT gene numbers in other organisms were taken from the literature [cf. [44]] or communicated by Andreas Weihe and Uwe Richter (Humboldt University, Berlin).

We are supported by the Deutsche Forschungsgemeinschaft within the Collaborative Research Centre TransRegio1 (SFB-TR1) (UGM, HTF), the Graduate School 'Intra- and intercellular transport and communication' (SZ, AB), the Collaborative Research Centre 429 (TB), the Emmy Noether program (MT, CSL), grant RE 837/10-2 (SAR) and BMBF (SAR, grant 0313921, Freiburg Initiative in Systems Biology). We are thankful to Uwe Richter and Andreas Weihe (Institute of Biology, Humboldt University Berlin) for providing data on RpoT gene numbers and to Gerrit Timmerhaus (Freiburg) for assistance.

Supplementary material

12915_2008_189_MOESM1_ESM.pdf (43 kb)
Authors’ original file for figure 1
12915_2008_189_MOESM2_ESM.doc (28 kb)
Authors’ original file for figure 2

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Copyright information

© Maier et al; licensee BioMed Central Ltd. 2008

This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Authors and Affiliations

  • Uwe G Maier
    • 1
  • Andrew Bozarth
    • 1
  • Helena T Funk
    • 1
  • Stefan Zauner
    • 1
  • Stefan A Rensing
    • 2
  • Christian Schmitz-Linneweber
    • 3
  • Thomas Börner
    • 3
  • Michael Tillich
    • 3
  1. 1.Cell BiologyPhilipps University MarburgMarburGermany
  2. 2.Faculty of BiologyUniversity of FreiburgFreiburgGermany
  3. 3.Humboldt University Berlin, Institute of BiologyBerlinGermany

Personalised recommendations


text:
Minimax Theory and Applications

  • Biagio Ricceri
  • Stephen Simons

Part of the Nonconvex Optimization and Its Applications book series (NOIA, volume 26)

Table of contents

  1. Front Matter
    Pages i-xi
  2. Cao-Zong Cheng, Bor-Luh Lin
    Pages 1-20
  3. Cao-Zong Cheng, Bor-Luh Lin, Feng-Shuo Yu
    Pages 21-28
  4. Antonia Chinnì
    Pages 29-33
  5. Gabriele H. Greco, Maria Pia Moschen
    Pages 41-51
  6. Marc Lassonde
    Pages 135-145
  7. Bor-Luh Lin, Feng-Shuo Yu
    Pages 147-156
  8. Michael M. Neumann, Maria Victoria Velasco
    Pages 167-189
  9. Stephen Simons
    Pages 217-240
  10. Peng-Jung Wan, Ding-Zu Du, Panos M. Pardalos
    Pages 261-270
  11. Back Matter
    Pages 271-274

About this book

The present volume contains the proceedings of the workshop on "Minimax Theory and Applications" that was held during the week 30 September - 6 October 1996 at the "G. Stampacchia" International School of Mathematics of the "E. Majorana" Centre for Scientific Cul ture in Erice (Italy) . The main theme of the workshop was minimax theory in its most classical meaning. That is to say, given a real-valued function f on a product space X x Y , one tries to find conditions that ensure the validity of the equality sup inf f(x,y) = inf sup f(x, y). yEY xEX xEX yEY This is not an appropriate place to enter into the technical details of the proofs of minimax theorems, or into the history of the contribu tions to the solution of this basic problem in the last 7 decades. But we do want to stress its intrinsic interest and point out that, in spite of its extremely simple formulation, it conceals a great wealth of ideas. This is clearly shown by the large variety of methods and tools that have been used to study it. The applications of minimax theory are also extremely interesting. In fact, the need for the ability to "switch quantifiers" arises in a seemingly boundless range of different situations. So, the good quality of a minimax theorem can also be judged by its applicability. We hope that this volume will offer a rather complete account of the state of the art of the subject.

Operator theory Sim algorithms calculus functional analysis game theory optimization

Editors and affiliations

  • Biagio Ricceri
    • 1
  • Stephen Simons
    • 2
  1. 1.Department of MathematicsUniversity of CataniaCataniaItaly
  2. 2.Department of MathematicsUniversity of California at Santa BarbaraSanta BarbaraUSA

Bibliographic information

  • DOI
  • Copyright Information Springer Science+Business Media B.V. 1998
  • Publisher Name Springer, Dordrecht
  • eBook Packages Springer Book Archive
  • Print ISBN 978-90-481-5030-4
  • Online ISBN 978-94-015-9113-3
  • Series Print ISSN 1571-568X
  • About this book
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Hunger Games and Protest

220px-Hunger_gamesThis morning’s Weekend Edition/Saturday on NPR included a brief interview with Stephen Carter, a professor and novelist who discusses how Suzanne Collin’s massively popular series of books and movies mirrors much of what’s happening lately, so much so that the District 12 Salute is being used by protesters around the world.

I generally like to wave at everyone on the bandwagon as it passes me by, so the universal fascination with Katniss et al. gave me the reason I needed to leave these books in the bookstore. (NB: I was well into Harry Potter before the world went mad.)

I didn’t like the first book in Collins’ series, yet forced myself to read it a second time and found it a bit more tolerable. Even so, I was not inspired to finish the series. One, there are an awful lot of really good books for adults that I haven’t yet read. Two, the idea of children killing children (pace Lord of the Flies) appalls me. And three, I’m not a huge fan of dystopian novels in the first place!

But after hearing Carter’s analysis of The Hunger Games, six years after publication still relevant to current national and world affairs, I’m starting to rethink my too off-handed dismissal of the series. I’m not yet ready to buy the books, but I know I can find them in my library. Holiday reading! Yay! Or maybe not “Yay”. Maybe just a limp wave of resignation. I’m not expecting a happy read, but with Carter’s analysis in my head, I have hopes for an interesting one.

How far would you go …

9780192733672… to get a copy of a book?

I’ve been wanting to read Julia Lee’s The Mysterious Misadventures of Clemency Wrigglesworth since it was published in 2013 (Oxford University Press), but for some reason it was not available in the US. Why oh why hasn’t OUP done something to resolve that?

Fortunately, I had a trip planned to the UK this summer, and as soon as I arrived I got a copy and sat down to read it. After finishing, I ask, once again, why oh why is this book not in bookstores in the US? It’s the perfect kid-in-jeopardy book, with a dauntless heroine, creepy villains, and madcap sidekicks that will appeal to middle school and younger readers. (A few second-hand copies are available on Amazon, but that’s not quite the same.)

Clemency Wrigglesworth, 11 years old and alone, is sailing back to England from India. Her mother, who died just before embarking, left Clemency with no money or any idea where they were meant to go upon arrival in Southampton. Two letters are the only clues. Luckily, Mrs. Potchard, who makes her living escorting children to and from England, takes Clemency in hand and tries to find those unknown relatives. An ad in the paper brings the attention of a few mysterious characters, and then Miss Clawe appears,

… tall and thin and dressed in deepest black. Her hair was salt-and-pepper grey, scraped back from her face so fiercely that it pulled her eyebrows up into high arches. She wore an old-fashioned bonnet over it, festooned with black satin ribbons. And she carried–not a parasol–but a black umbrella, tightly furled.

Anyone familiar with the genre will recognize a villainess in Miss Clawe, who sets the plot in motion by kidnapping Clemency. Miss Clawe takes the girl to a manor house in Somerset but immediately puts her to work as a scully in the kitchen. It looks bleak for Clemency.

The family she had been staying with, the Marvels (a perfect name for this clever group of people), give chase, partly because they expect payment for their hospitality, but also because they’re truly concerned about Clemency’s welfare. Meanwhile, Clemency, fearing no one will come to her rescue, takes charge of her own fate. She explores the manor, sneaking grapes off the dining table and jam from the store rooms, discovers the reason for her abduction, and makes plans for her escape.

There are layers to this story, and surprises. Just when you think you’ve figured out who Clemency’s friends and enemies are, Lee takes you in a different direction. Just when you think Clemency will get away, someone steps in her path. In the final face-off, a knife-thrower plays a critical role, as do a butler, a gardener, and a spoiled Pekinese lapdog.

This book fits nicely on the shelf between Lemony Snicket’s Series of Unfortunate Events and Philip Pullman’s Count Karlstein, with a hint of Joan Aiken’s Wolves of Willoughby Chase. But leave space for sequels — the afterword suggests there’s more to come.


text:
Wednesday, May 22, 2013

Wagner—on his 200th birthday

When I was singing with the Minnesota Bach Society, we were asked to provide the chorus for a symphonic performance of Wagner's Tannhäuser with the Minnesota Orchestra.  To be perfectly honest, I was not exactly thrilled about this.  I had signed up to sing the delicate polyphonic melodies of Bach—not the heavy and oh-so-serious operas of Wagner.  Not surprisingly, I discovered that singing Wagner was a real hoot and Tannhäuser was not the endurance contest of the Ring Cycle.  I also discovered that there are SERIOUS Wagner fans. I am still mainly a Bach fan, but I have read some of the scholarship, seen the Festspielhaus in Bayreuth, and visited the Herrenchiemsee—one of the more lavish palaces of Ludwig II, Wagner's main patron—in an attempt to understand what all the fuss is about.

Wagner's politics have been discussed in minutest detail over the years—mostly because one of his biggest fans was Hitler.  This is probably a mistake because as I have discovered in life, outside of music it's probably a bad idea to discuss any other subject with a musician.  The reason is simple—music is such a complex subject and requires so much practice in order to do well, anyone who gets good at music hasn't had a lot of time to master much else.  When the musician is Wagner, the music itself is so complicated, discussions of his politics is usually just a distraction for those who cannot or will not deal with the complexities of his music.

Me?  I intend to celebrate the occasion by listening to Tannhäuser one more time and wonder again if the mere act of asserting that the essence of love is lust is such a serious crime, it requires acts of redemption.  Really?

Who was Wagner? On the composer's 200th birthday

The poet, director, conductor, author and, most importantly, composer, born on May 22, 1813 in Leipzig, remains a riddle to many. Two hundred years after his birth, the debate goes on.

DW.DE 22 MAY 13

More has been written about him, it's often said, than about anyone else in history apart from Jesus Christ and Napoleon Bonaparte. Two hundred years after his birth, Richard Wagner is a much-discussed subject. Some see him as the genius who created the "total work of art." Others reject him for his anti-Semitic writings. In any event, his operas are performed today more often than ever before.

He came from a middle-class family. The father, Carl Friedrich Wagner, was a police actuary; his mother, Johanna Rosine Pätz-Wagner, a baker's daughter. The boy, baptized Wilhelm Richard Wagner, was interested in theater from early childhood.

Music of the future

Initially he wanted to be a poet and playwright. But seeing Beethoven's opera "Fidelio" at age 16 resulted in a change of career plans: He decided to be a composer. As early as 1831, as a student of music, he planned his first opera, for which he penned the text himself - an approach he was to take for the rest of his life.

By 20, Wagner was directing the Theater in Magdeburg. There he fell in love with the actress Minna Planer. They married in 1836 and had no children. Riga and Paris were the next stations in the life of the itinerant artist, who was plagued by financial worries and pursued by creditors.

The Wagners lived in Paris under dire circumstances, yet he was able to complete his early operas "Rienzi" and "The Flying Dutchman" there. His interest in the leftist revolutionary currents of the era dates from that time.

In 1842, Wagner moved to Dresden, where he became court composer. In October came a musical breakthrough: the premiere of "Rienzi." Always working on various works simultaneously, he began to develop the vision of a new blend of words, music and action into a "total work of art." The goal: nothing less than "the unconditional, immediate depiction of human nature in a state of completion."

Deus ex Machina

In a recent interview with DW, his great-granddaughter Katharina Wagner put it in these words: "In Wagner's works in particular, it's all about the basic elements of human existence and of basic qualities like jealousy, power, love, and hate. Those are of course things that will always be timely and move us as long as humanity exists."

In May 1849, the composer participated in a grass-roots rebellion in Dresden, after which he became a wanted man and was forced to leave Germany. Then in 1864 - back in Germany and in despair and financial straits - he was close to suicide. At that point a letter from the new King of Bavaria, 18-year-old Ludwig II., arrived. The king offered his full support and continued to do so for the rest of Wagner's life.

In the little Bavarian town of Bayreuth, Wagner eventually found the location for his vision. Far from the bustle of big-city life, in a self-designed festival theater, audiences were able to concentrate totally on the combination of music, stage action and scenery. That happened for the first time in August 1876 at the premiere of Wagner's four-opera cycle, "The Ring of the Nibelung."After many affairs before and after the death of his wife Minna, Wagner lived in Tribschen, near Lucerne, with Cosima von Bülow, daughter of Franz Liszt and wife of the conductor Hans von Bülow, one of his friends and promoters. Three children were born before the couple finally married.

The first Bayreuth Festival was a financial disaster and an artistic fiasco, yet Wagner was able to stage the second edition in 1882. Only a single work was performed then, his final one, "Parsifal." He died on February 13, 1883 in Venice.

What does Wagner stand for?

Was he a socialist? A National Socialist? How are his wide-ranging writings to be interpreted? Nearly every statement made by the composer seems to be contradicted somewhere else. What is the message of the music? Does it, like some of his writings, contain elements of anti-Semitism?Why the fascination with Wagner still today? One of the most influential composers ever, his late-Romantic music has always had an emotionally stimulating quality. Most people react either with rejection or enthusiasm; few are indifferent. Wagner's goal was to revolutionize theater and opera, but he became ensnared in a political revolution and later identified with ultra-nationalistic Germanism.

What did Wagner advocate? In the final analysis: himself. "Networker" and "self-promoter" can be added to the descriptions of the multi-talent, who forced his art onto a world that didn't want it. Today, however, the world is grateful.The debate goes on, but for conductor Christian Thielemann, there is no debate. "You can't politicize music," he told DW. "It's always been a big misunderstanding. And a choice of tempo in 'The Mastersingers of Nuremberg' has nothing to do with politics. You have to perform it for the sake of the work. If you approach it with some sort of intention, it's a shame, or completely wrong." more

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Nov 122008

So this morning I am sitting in front of the TV with my caffeine fix and some news channel on to break up the silence. On comes this item about how a school has shown a dramatic improvement after having introduced a new disciplinary regime. Something like an increase of 25% in pupils getting 5 or more GCSEs (cannot recall the exact numbers and it does not matter anyway).

But wait! The reporter goes on to say this increase does not include English or Maths and when those subjects are included, the increase is not quite as dramatic. So English and Maths are unimportant subjects are they ? Or perhaps the story does not come across as so interesting if the real increase is given.

So this reporter has stretched the truth (i.e. lied) by reporting a meaningless statistic that sounds good rather than a proper set of figures which would still sound good to those who do not have unrealistic expectations.

Why does the media do this ? Well obviously to make things sound better than the really are or more usually worse than they usually are. That is fair enough on an entertainment show, but surely news should present the facts and not try to stretch the truth.

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Tuscan Tilapia Packets

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Nutritional Info
  • Servings Per Recipe: 4
  • Amount Per Serving
  • Calories: 333.1
  • Total Fat: 7.3 g
  • Cholesterol: 0.0 mg
  • Sodium: 376.8 mg
  • Total Carbs: 37.5 g
  • Dietary Fiber: 12.5 g
  • Protein: 34.3 g

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Great recipe for the summer. Great recipe for the summer.
Number of Servings: 4

    2 15oz cans Great Northern Beans
    2 medium tomatoes, chopped
    1 1/2 tsp dried basil
    4 4oz tilapia steaks
    4 tsp olive oil
    4 tsp lemon juice
    2 tsp lemon pepper
    4 lemon slices

Preheat the oven to 450F or prepare a charcoal or gas grill so that the coals are medium-hot or the heat is set to medium-high.

In a mixing bowl, stir together the beans, tomatoes, and 1/2 teaspoon of the basil.

Lay four 12-by-18-inch sheets of heavy duty aluminum foil on the countertop. Spoon a quarter of the bean mixture in the center of each sheet. Top with the tilapia steaks and drizzle with olive oil (1 tsp/steak) and lemon juice (1 tsp/steak). Sprinkle with the remainging basil (1/4 tsp/steak) and the lemon pepper (1 tsp/steak). Top each with a lemon slice.

Bring up the sides of the foil. Double fold the top and ends to seal the packets, leaving room for heat circulation inside. Repeat to make 4 packest. If using the oven, put the packets on a cookie sheet.

Put the cookie sheet in the over or slide the packets onto the grill rack. Bake for 16-20 minutes or grill for 14-18 minutes in a covered grill, or until the fish flakes when tested with a fork.

Number of Servings: 4

Recipe submitted by SparkPeople user CASSIDYR.

TAGS:  Fish | Dinner | Fish Dinner |

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Can I export my Redis data from Redis Enterprise Cloud?

Absolutely! There is no lock-in with Redis Enterprise Cloud. With a click of button, you can export your latest RDB backup file from your cloud storage, FTP or HTTP server to any Redis server of your choice. Free plans do not include this capability.