The next version of Noteit Posts (v1.3-0) will support multiple languages. But I can only speak English fluently, so I will need help. If you can help translate Noteit Posts into another language, please read on.

Translating Noteit Posts

All text in Noteit Posts is stored in the file lang.js. This file can be provided in multiple languages, allowing for easy translation of the Noteit Posts interface.

Download the original lang.js file.

Open the downloaded lang.js file in a text editor, such as notepad, you should see something like this:

The top section, between the stars/asterisks provides information about the translation and the mod in general.

Language: Defines the language of the translation. Please include the language code here, you can include a full text description in brackets afterwards. Specifying regional variations (eg. fr-CA) is not necessary but can be included.

Translator: Your name. This is purely for administrative purposes and is optional.

Contact: An E-mail address. This provides contact details in the language file itself. It is optional. While the information will not be displayed by the extension it WILL be accessible to anyone who looks at the extensions files.

Short Desc: The extension short description, used in the extension catalogue. To avoid confusion, please translate the English text, rather than writing a different description.

Long Desc: The extension long description, used in the extension catalogue and the manage extensions page. To avoid confusion, please translate the English text, rather than writing a different description.

The next section defines the text which will be used in the extension itself. It includes error messages, preferences screen text, and text displayed by the extension itself. The var string = { //Declare the String variable line is important and should not be modified.

lang: “en-gb” Defines the language of the translation. Replace en-gb with the language code here as in the header. Do not include other text.

credit: “…” Displayed on the preferences screen when your translation is being used. Replace the text between the quotes (“) to give yourself credit. If you do not wish to be credited, leave this blank.

The remaining lines each follow the same: format: number: "text",. In each case, simply translate the text between the two quotation marks. Leave the number alone and do not remove the quotes or the comma. Some lines contain // followed by a comment. These comments provide more information to help your translation, they do not need to be translated.

Completed Translations

English
en-gb Me
en-us Me

My blog is currently causing peaks of CPU usage, which are causing problems for my web-host. However, traffic levels are at their usual low. In an attempt to diagnose the problem, I am in the process of disabling plugins. As a result, some features of the site may not be working as intended.

I apologise for any inconvenience.

About the Extension

Noteit posts can easily be created, edited, resized and recoloured.

Noteit Posts is an extension for the Opera web browser, that allows for the addition of persistent notes to any webpage. A simple interface allows for notes to be edited freely, recoloured, and moved about and resized through a simple drag and drop interface. Notes can be tied to a single page, or and entire domain, and can easily be managed, edited and deleted from a centralised interface.

The configuration screens provide a quick and easy overview of all your notes, as well as means for altering the default note appearence.

Features

• Easily create notes from the extension’s button.
• Notes are persistent and will remain on the page on future visits.
• Notes are stored in the extensions webSQL database, so will not be lost if you clear your cookies.
• Notes can easily be moved, resized and recoloured using the simple interface.
• Attach a note to a page or a domain as you decide!
• A central configuration page allows complete control over all your created notes.
• Easily choose default note appearance.
• Create notes via a customizable keyboard shortcut (Ctrl+# by default)
• Import and export notes via XML

Got other ideas? Use the suggestions tab on the left hand side of this page to make or vote on suggestions. Alternatively visit the suggestions page directly.

Usage

This extension requires that you be using the Opera browser, at version 11.0 or above. It was developed and tested with Opera 11.0.1 under windows, but should work in the Mac and Linux versions. This extension will not work with Opera mini, Opera mobile, or other embedded versions, such as the Wii browser.

Download the extension using the link further down this page. Extensions can be installed by opening them, or by dragging and dropping them onto Opera. When prompted, confirm that you wish to install the extension. I eventually hope to get the extension listed on the extension’s catalogue.

To create a new note, simply click the orange pencil symbol in the opera extensions tool-bar. This will usually be located to the right of the address bar. This will create a note on the webpage you are currently viewing. If the icon is greyed out, ensure you have an active tab selected, and that the page has finished loading. It is not possible to add notes to the Opera speed dial page, or other elements of the Opera interface.

The newly created note should look like this:

An Example Note

To add content to the note, click within the dotted box and begin typing. Once done, just click elsewhere on the page, and the note will save. To move the note, click on the dark bar at the top, while holding down your mouse button, drag the note around, just as you would move a window using its title bar. To resize a note, place your pointer over the dark triangle in the bottom right hand corner, the pointer should turn into diagonal arrows. Simply click and drag to resize the note, just as you would a window.

Notes can be closed by clicking the X symbol in the top right hand corner. Be aware, this will also delete the note from your database. Once closed, a notes contents is lost and can’t be recovered. Adjacent to the close button is the minimize button , this will shrink the note down to the size of the dark bar, and is useful if you wish to temporarily see the underlying website. Minimized notes can be restored by clicking the restore button , that will replace the minimize icon.

The configuration panel can be accessed via the configure icon in the top left hand corner. The configuration panel allows you to set the colour of a note, or alter whether it is attached to the page, or the domain. For example, if you created a note while viewing this post, ‘page’ would ensure that it only appeared when you were reading this post. However, if you choose ‘domain’ then the note will appear on any page at blog.jaspsplace.co.uk.

The Preferences Page

If you right click on the noteit orange pencil and select preferences, you will enter the Noteit posts preferences page. Here you can tweak the default settings, and manage your notes database.

The about section contains information about the extension, including the version you have installed.

The options section allows you to change the default settings for newly created notes. Width and height control the size of the note in pixels. Left and top control where the note will appear on the page, a value of 0 for both for instance will have the note appearing in the top left hand corner. Colour can be used to set the default note colour, whereas ‘page or domain’ determines if a note is associated with the page or the domain by default.

The stored notes section provides a table showing all notes you have created. ‘Refresh table’ will reload the table, displaying any changes that may have been made since the preferences page was opened. This is especially useful if you have had the page open in the background, and have modified notes in other tabs. ‘Delete Selected’ will remove any selected notes from your database, preventing them from displaying in future. Notes can be selected by ensuring that there is a check mark in the box in their row of the table. Finally, ‘Reset Database’ will clear all notes, and rebuild the table. This action will cause you to lose all notes and is not recommended.

By clicking the ‘configure’ button next to each note, it is possible to manually tweak a notes size, position, colour, content, and even associated page. This feature allows you to modify notes, without requiring that you visit their containing page. It is also the only way to move a note from one domain to another.

Changelog

v0.0.1 - Limited First release (Released as 1.0)
v0.0.2 - Change UID to blog post
- Converted urls to lowercase before comparison as well as storage
v0.0.3 - Switched the default setting to page specific, rather than domain
- Switching the note from domain mode to page mode now ties it to the current page
- Increased security to validate field names
- Ensure that pages making changes to, or deleting notes are those which own the note.
v0.0.4 – Fixed a but introduced just prior to release that prevented minimization.
v0.0.5 - Removed implication that the stored notes feature is incomplete.
v1.0.0 - Added link to website
- Added timed onInput event to save notes in case focus is not lost before the page is left.
- Added ability to position notes relative to viewport
v1.0.1 - Corrected bug, opera doesn’t recognise ‘input’ for content editable divs
- Corrected code that had previously not been running as a result
V1.1.0 - Minimization state of notes is now saved as intended
- Minimizing and restoring notes no longer results in errors
v1.1.1 – Changes to default note height now saved correctly.
v1.1.3 - Unofficial release: Carriage returns correctly saved. (Should also solve some issues with other ‘special’ characters.)
v1.2.0 - Added the ability to customize note fonts.
- Added link to suggestions page.
- Menubar now displays a preview of each note to allow easy identification when minimized.
- More tightly defined the style of notes to increase consistency across pages.
v1.3.0 - Added lang.js file to allow for easy localisation
- Reorganization and optimisation of code to allow for easier maintenance
- New lines in note body no longer cause HTML to appear in note title on refresh
- Dragging/resizing notes no longer selects underlying text
- The note edit area will have a scrollbar if the contents become too long, the edit area will still adjust as the note resizes
- Font inheritance now occurs as expected: Font no longer lost if press return.
- New paragraphs in notes no longer result in a large top-margin
- Minor spelling and grammatical errors corrected.
- Added ability to create notes via keyboard short-cut (Ctrl-# by default, user customizable).
- Extension bar icon now optional.
- Further improvement of stylesheets to maintain note appearance.
- Added ability to export and import notes to allow for backing up

Download Extension

 
 
Noteit Posts is now available from the Opera extensions catalogue, it is recommended that you install the extension from there as this will allow for easy auto-updating. It is strongly recommended that users of the version hosted on this website export all their notes and import them into the version hosted on the extensions catalogue.
 
 
Visit the extension page (Recommended)
 
 
 
Download Version v1.3.0 (58.7 KB) (Extension Catalogue Version Recommended)
 
 
 
Bugs, suggestions? Use the suggestions tab on the left hand side of this page to make or vote on suggestions. Alternatively visit the suggestions page directly.
Noteit posts is a free extension, however, if you would like to show your thanks:

Web standards can be split into three major elements: HTML, CSS and javascript. HTML controls content, and gives it meaning and semantic structure. CSS controls style and form, it gives web documents their colour and shape. The third element, javascript, can be used to control the activity of the other two; it instils interactivity and makes the content dynamic and responsive.

I’ve been familiar with both HTML and CSS for a few years now, and, while caught in the dull cycle of job searching, I decided it was a good time to add javascript to my belt as well. I had already dabbled with a few other programming languages, many of which used similar mark-up to javascript, so was already familiar with the overall concepts, which meant I felt happy starting with a reasonably ambitious goal. I would make an Opera extension.

Opera extensions are built on the technology of the web, as this makes them ideal for interacting with web content. As a result, by choosing to make an Opera extension, I would also learn valuable lessons that could apply to more traditional web content, as well as familiarising myself with the Opera extension API. I also already had an idea, and one which would take me through several different lessons.

When looking for jobs, I would sometimes find myself looking at an advert I had already read, trying to work out why I had rejected it. Often these reasons were buried deep in the job advert, and I’d waste time trying to re-find them. Unfortunately, while job sites make it easy to mark jobs you are interested in, they rarely make it easy to indicate those you aren’t. If only I could stick a post-it note on the page, which would stay there if I returned. I quickly formulated a plan for the extension I wanted to make.

The Requirements

In order of importance.

1. Clicking a button in the menubar would add a ‘post-it’ note to the page.
2. The contents of this note could be edited from the keyboard.
3. The note would be saved, and would reappear on the page if I were to return to it.
4. The note could be moved about the page, and resized at will. Ideally through a similar mechanism to moving and resizing windows. The size and position of the note would be remembered.
5. The note could be recoloured.
6. Notes could be attached to a specific page, or a whole domain.
7. Notes would remain until specifically deleted. They would not disappear over time, or on simple cookie deletion.
8. Notes could be administered from a central interface.
9. The central interface could be used to change the default note settings.

This list of requirements hinted at a neat work flow, and ensured I covered a range of topics, from simple manipulation of the DOM, communication between the browser and the web page and setting up a suitable storage system.

Introducing Noteit Posts

Today I finished the first version of the extension, which meets all the criteria listed above. While it is complete, it hasn’t been extensively tested, and could probably do with some optimisation. Additionally, there are a couple of minor issues that I’d like to get solved:

1. Saved notes are loaded onto the website with the DOMContentLoaded event. Loosely speaking this means when the base of the website has finished loading. With larger websites or slow servers this can introduce unsatisfactory delay. Ideally I want the notes to appear as soon as I can add children to the document body.
2. Searching the database for saved notes is unsuccessful with more complicated URL’s. I’m assuming that this is an issue with how some characters are processed before being added to the database. I’ve found the cause of this bug. I converted everything into lower-case before storing in the database, and then forgot to do the same before checking it. Ironically I did the first step to avoid case sensitive situations just like this one. I’ll correct it in the next version.
3. In a couple of cases, by WebSQL transactions are composed dynamically. While security is unnecessary in this extension, and all content directly editable by the user is scrubbed, I realise that this is not best practice and would love to avoid it is possible. If anyone has any advice on how best to accomplish something like the following, it would be greatly appreciated: transaction.executeSql('UPDATE Notes SET '+field1+'=? WHERE id=?',[value1,id], null, function (transaction,error) {errorhandle('updatenote',transaction,error);})

I’m making this early version available for anyone who wishes to play around with it, for the purposes of beta testing. If you have any issues, please let me know. Also, if you are familiar with javascript, and opera extension development, then please feel free to look at my code. Any feedback, especially with respect to ‘bad practice’ would be greatly appreciated.

Edit: Uploaded a new version to correct the case-sensitivity bug. Additionally modified the version number to be more suitable for pre-official release version, and altered the ID to refer to this blog post, as Opera seem to like URLs as IDs.

Edit: Version 0.0.3 uploaded to provide increased security, and to ensure that posts are correctly assigned to the current page when switching from domain mode to page mode.

Download Noteit Posts 0.0.3

I picked up Divinity II: Dragon Knight Saga with some slight trepidation; while I had been first attracted to the game prior to its initial release in the form of Divinity II: Ego Draconis, poor reviews for the first release dissuaded me from taking the plunge. With the release of the expansion pack, Flames of Vengeance, Larian Studios remastered the first game, incorporating an improved graphics engine and a number of other improvements. The Dragon Knight Saga release includes this remastered version of the first game, and the Flames of Vengeance expansion, which extends and concludes the story. With reports that these improvements had addressed some of the main issues that had marred the original release, I picked up Dragon Knight Saga in the Steam sale, and was pleasantly surprised. In many ways it is a B-list game, lacking spit and polish of your AAA games, while at the same time avoiding the true levels of innovation which would help it truly step above the competition. However, if your looking for an enjoyable RPG romp, with a few neat ideas, then it manages to deliver solidly.

The most obvious of these neat ideas is the central conceit, the ability to turn into a dragon, something which ensured that the game jumped on to my radar. However, while the idea isn’t exactly squandered, it certainly isn’t used to its full potential, barely making an appearance until halfway through the game, and remaining almost entirely unused in the “Flames of Vengence” expansion. For the most part, dragon sections feel like a separate mini-game, albeit one which is remarkably useful for making a rapid escape from danger. They are competent enough, but for the most part lack the depth and variety of the human portions of the game. Instead, the draconic nature of the main character plays a far more interesting role in the development of the plot, although again, this scenario is not explored to its full potential. In practice, neither of these decisions should be seen as a major failing on the part of the game; instead the reflect on clear design decision, in terms of gameplay and exposition respectively. However, if your primary reasons for looking at the game were to take part in epic in air combat, or to experience a detailed consideration of the nature of the self and the nature of humanity (or draconity) then you’d best look elsewhere.

While the central conceit may fail to deliver anything more than a distraction, the rest of the game provides more than enough satisfaction. The mind-reading skill provides a neat mechanic, providing a few rewards or alternative quest solutions along the way. In many ways it acts in a similar manner to speech checks in other RPGs, but the experience cost for mind reading means that its use becomes considered, rather than the ‘speech check option’ magic button seen in games like Mass Effect.

The game is classless, allowing you to easily develop your character as you wish. I was easily able to create a battle mage, giving myself a nice selection of DPS spells, summons, healing and crowd control, while still ensuring I was durable in melee combat and could deal out considerable damage with my dual wield weapons. The ability to upgrade skills ensures that spells do not become underpowered as the game progresses, and it is easy to respec your skill tree later should you have a change of heart.

Other nice mechanics are the weapon and armour enchantment, which can make significant differences to the performance of your kit. However, one criticism is that the weapon damaged modifications are ridiculously overpowered at the higher levels, making them no-brainer choices when compared to the other possibilities. The problem is further compounded for dual wield characters, as damage modifiers on your main hand, also effect your off hand, and vice versa. By the end of the game I was dealing more damage due to my enchantments than due to the base damage of the weapons themselves.

Necromancy provides a ‘creature,’ which acts as a summon for all character builds. The choice of different limb sets allows the creature to be customised to perform different roles, loosely falling into mage, ranger and tank. While in the early game your creature can be a valuable ally, by the end game a maxed out creature will be only a minor distraction for your enemies. It would have been nice to see a bit more tactical depth introduced at this point, allowing the player to issue basic commands to the creature, although it is possible that the developers wished to avoid the feeling that you need to micromanage your summons.

While combat provides enough depth to allow the player to customise their approach, and to ensure they aren’t reduced to continually spamming the same skill, it is slightly lacking in variety. While enemies show slight differences in damage sensitivities, it isn’t sufficient to discourage a one size fits all approach, especially in the later stages. Additionally, power games are likely to find themselves becoming overpowered towards the end of the expansion, although I can be partly blamed here as I entirely forgot I could turn up the difficulty.

The game isn’t going to win any awards for writing, and the plot, while entertaining, is lacking in depth, or any striking originality. However, it is entirely serviceable, and has enough twists and variations to prevent it from becoming overly predictable. ‘Dark’ fantasy this is not, and the game never takes itself too seriously; it is perfectly willing to mock itself when it needs to, voice acting is often served with a large side order of ham, and most conversations have a few witty retorts.

Quest design is pleasantly varied, and often enough allows for a couple of different solutions; although in many cases the repercussions of these decisions are decidedly limited. A few quests even involve jumping puzzles, unusual for an RPG; for the most part the third person perspective, and decent platform placement, ensures that these are pleasant change of pace, rather than a source of hair pulling frustration. Especially nice are the unmarked quests, such as small puzzles in dungeons that may lead to a chest of loot. These latter puzzles couple well with the games rewarding of exploration. With the tutorial out the way, it is theoretically possible to run through the world that will host most of the original campaign. In practice you’ll soon be killed by enemies outside your level; the game features no level scaling, and until the expansion pack, pretty much no respawning.

One of the nicest features of the game is the great art design, and there are some fantastic areas and enemies. While it would have been nice had the designers gone completely overboard with some of these designs, there are still obvious efforts to ensure that some of the more cookie cutter sections, such as the flying fortresses, are still given their own flavour.

I realise that this review might sound a bit 70%, however the game holds together remarkably well; it is better than this. It is, for the large part enjoyably competent, but with a few touches of something much better. Like a cheap summer blockbuster, that somehow manages to get all the elements in the right place, and shines through because the people who made it were genuinely enjoying what they were doing. Divinity II knows that it is not AAA material, and it gloriously recognises this fact and revels in it. It reminds me of games from the 90s, before they were ‘serious business,’ and never worries about being a bit silly if that means things will be more fun. Finally, although you shouldn’t buy it solely because of this fact, you can play a bloody dragon.

In the UK, Divinity II: Dragon Knight Saga is currently available on PC by digital distrubution only.

• Steam
• Direct from the developers
• Gamers Gate

You know how it is, a family discussion leads to debate over who was best known for a particular song, followed by a brief poll over twitter and facebook, which only serves to split the debate further.

The subject of this particular debate “The Power of Love.”

Now, I can’t remember what actually triggered this discussion, but as a Child of the 80′s I immediately plumped for Huey Lewis and the News, which formed the sound track to the 1985 film, Back to the Future. Meanwhile, after a quick and misleading Spotify search my Mum went for the great Jimmy Hendrix, whereas Dad was running for Celien Dion. My slightly illphrased questioning on twitter and facebook turned up Jesus, more Huey Lewis, someone’s auntie and Frankie Goes to Hollywood.

But clearly one of these had to be the original, didn’t they. Well, no. It appears that we were all looking at different songs:

Power of Love 1

Well, going with my choice first we have the Huey Lewis and the News version. The most popular option in my informal poll, this formed the soundtrack of 1985 time travel comedy Back to the Future. It also sits at the top of the ambiguity page on wikipedia, and is the first suggestion in Spotify and Youtube.

Spotify Link

But, naturally, this has been covered, including a slightly disapointing 8-bit inspired mix which infused the back to the future theme by I Fight Dragons (Spotify).

Power of Love 2

I was actualy familiar with this song, even though the Huey Lewis and the News version would come to mind first. Originally done by Frankie Goes To Hollywood, Spotify would suggest that this is one of the most covered songs with this name. Dated from 1984, this predates the Huey Lewis and the News song.

Then a few of the covers.
Free4 (DALA), Dune, Omph! (Quite different), Anneke Van Giersbergen, LOndon Symphony Orchestra

The Power of Love 3

Clearly the mid 1980s were all about the Power of Love, as 1984 also saw the release of the Jennifer Rush song of the Same name. Subsequently covered by Celine Dion, who picked up my Dads vote.

Jennifer Rush (Spotify)
Celine Dion
Gregorian Chants

The Power of Love 3+x

Of course, this being the second decade of the 21st century, we are no longer limited by who manages to find a record label. These enterprising folk clearly decided that they’d release a song under a title that people were doubtlessly fed up of even during 1985. Still, if they had called it something else I wouldn’t be linking it here, so a win on one level I suppose.
DJ Stephanie, Lunatica

Pre-dating all of these we have the Everly Brothers with [You Got] The Power of Love, 1966. Makes you wonder why they they bothered with the brackets. If you want to be strict though, first example of a Power of Love without the brackets appears to be Joe Simon, 1972, shortly followed by Gary Wright, from 1975.

So…

More songs called ‘Power of Love’ than you can shake a stick at. Seems that my mum was completely off with her suggestion of Hendrix, but I blame the erroneous prompting of Spotify on my Android for that. Seems she was actually thinking of Power to Love.

Very A-typical blog post, and I guess plenty of folk will have known all this already, but bah, I can bore you all with science, politics or gaming again at some other point.

Last night I was directed towards an article claiming that scientists had inadvertently found evidence to support astrology:

Principle of astrology proven to be scientific: planetary position imprints biological clocks of mammals

(NaturalNews) Mention the word “astrology” and skeptics go into an epileptic fit. The idea that someone’s personality could be imprinted at birth according to the position of the sun, moon and planets has long been derided as “quackery” by the so-called “scientific” community which resists any notion based on holistic connections between individuals and the cosmos.
…
Skeptics must be further bewildered by the new research published in Nature Neuroscience and conducted at Vanderbilt University which unintentionally provides scientific support for the fundamental principle of astrology — namely, that the position of the planets at your time of birth influences your personality.

As a member of the “so-called “scientific” community” I admit that I immediately suspected quackery, or woeful misinterpretation on the part of the astrologers writing the article. However, were I to write off their claims entirely based on this suspicion, then I would be guilty of the close mindedness that they accuse me of. So, in order to dissect their claims, I had to go back to the primary source, the paper they were referencing¹ .

What do the astrologers claim?

Before we take a look at the original paper, lets have a look at what the astrologers claim. I’ll only concern myself with the claims directly relevant to the paper they are discussing; their claims regarding scientific arrogance, their straw-man scientists, and cold fusion can be left for someone else to tackle.

The first claim is that “according to the conventional view, your genes and your parenting determine your personality, and the position of planet Earth at the time of your birth has nothing to do with it.” This attempt to set out the conventional scientific viewpoint ignores the large number of other environmental effects that scientists accept can influence development. These environmental effects can be influenced indirectly by the position of the earth, as it is the movement of the earth that is responsible for influencing the seasons.

The astrologers then make the following claims regarding the findings of Ciarleglio et al.:

1. That the position of the planets at the time of your birth influences your personality.
2. That mice born in the winter show a “consistent slowing of their daytime activity”
3. That mice born in the winter are more susceptible to Seasonal Affective Disorder (SAD).

They then summarise by claiming that “one of the core principles of astrology [is] that the position of the planets at the time of your birth (which might be called the “season” of your birth) can actually result in changes in your brain physiology which impact lifelong behavior.”

So, does the paper actually support the claims they make of it?

The Paper

Unfortunately the writers of the article don’t actually provide a link to the original paper, something which is sadly all too common . However, they do provide enough information to let us find the paper:

Perinatal photoperiod imprints the circadian clock

Christopher M Ciarleglio, John C Axley, Benjamin R Strauss, Karen L Gamble & Douglas G McMahon
Nature Neuroscience (2010) doi:10.1038/nn.2699
Received 24 August 2010 Accepted 21 October 2010 Published online 05 December 2010

Using real-time gene expression imaging and behavioral analysis, we found that the perinatal photoperiod has lasting effects on the circadian rhythms expressed by clock neurons as well as on mouse behavior, and sets the responsiveness of the biological clock to subsequent changes in photoperiod. These developmental gene × environment interactions tune circadian clock responses to subsequent seasonal photoperiods and may contribute to the influence of season on neurobehavioral disorders in humans.

As far as I can tell, the paper is open access, which means that anyone should be able to read it. I’m afraid the same can’t be said for all the papers I’ve referenced here.

What do they do?

Mice were exposed to either short-day or long-day light cycles (8 or 16 hours of ‘daylight’ respectively) from before birth until weaning (The perinatal phase). Following weaning, mice were either maintained under the same light cycle, or were stitched to the opposite cycle for a further 28 days (The continuation phase, Figure 1). Experiments were repeated in both winter and summer, to take into account variations that may be induced by the actual season.

Figure 1: Mice were expose to either long or short day light cycles prior to weaning. Subsequently mice were either maintained under the same conditions, or were switched to the opposite cycle.

What do they find?

The authors found that the ‘day length’ at birth continues to have an impact on the circadian rhythms of the mice, even after they have been shifted to a different cycle. In particular, long-day born mice, showed a narrower peak of activity in the SCN, and in addition showed a shorter internal clock cycle, this resulted in more consistency between subsequent exposure to either long or short day cycles. In contrast, short-day born mice generally showed wider peaks of activity, and longer internal clock cycles. They were also subject to more variation in circadian rhythm behaviour between subsequent ‘summer’ or ‘winter’ cycles.

What does this mean?

This indicates that the day length at birth may have long term effect on subsequent circadian rhythms, even when the day length changes. In particular, mice born during a ‘winter’ cycle seem to show more variation in subsequent seasonal changes. The authors indicate that this may have implications with respect to previous findings, which show that mice born during winter-like cycles show increased levels of depression like symptoms, and that winter born humans show increased levels of SAD, bipolar disorder and schizophrenia. However at this stage it is not possible to draw a firm link between the findings.

What are the limitations of the study?

One of the primary limitations of the study is that it only addresses a short time span, and the authors acknowledge that they have no indication as to how long the effects may last. This may be especially relevant when attempting to translate the results to humans: not only a different species, but one with a significantly longer lifespan.

Additionally, I am also concerned that the study only considered two phases, the perinatal phase, and then either a continuation of the initial levels, or a switch to the opposite seasonal cycle. The possibility remains that exposure to a long-day cycle outside the perinatal period is sufficient to, at least partially, imprint the same pattern as seen in the long-day born mice. In support of this possibility is the considerably lower variation between short-day and long-day born mice under long-day conditions. However it should be pointed out that there are still significant differences between shot-day and long-day born mice.

Does the paper support the claims of the original article?

In short no.

Firstly, the only planet whose position has effect on day length is planet earth, where the orientation of its axis relative to the sun determines the season, and hence the day length. The other planets have different orbital periods, which means that Mars won’t be at the same point in the sky on December 17th 2010, as it was on December 17th 2000. Furthermore, while the northern hemisphere is in the grip of winter, the southern hemisphere is in the middle of summer, meaning that any seasonal effects are going to depend on the hemisphere, as much as the location of the earth.

But importantly, the researchers have been careful to isolate day length as the variable, separating other seasonal effects, such as temperature, or indeed the earth’s location. Furthermore, by conducting the experiment in summer AND winter, the effectively prevent any actual seasonal variations from having an effect.

In short, the findings have nothing to do with astrology. Ironically, the ‘tabloid horoscopes’ derided in the article have more to gain; your star sign is correlated with day length when you were born, at least assuming we confine ourselves to a narrow latitude.

Oddly the article also ascribes the findings regarding depression like symptoms in winter-born mice to this study, when in fact they were conducted separately. But again, these findings were purely associated with day length, not planetary position.

So in summary we have either a gross misrepresentation of scientific findings, or a major misunderstanding. We also have a paper which is potentially interesting, although I’d like to see how stable the effects are through multiple changes in day-length. If the effect is isolated to a short period of possible imprinting, then it will be interesting to narrow this period down in different organisms.

1. Ciarleglio, C. M., Axley, J. C., Strauss, B. R., Gamble, K. L., & McMahon, D. G. (2010). Perinatal photoperiod imprints the circadian clock. Nature neuroscience. doi:10.1038/nn.2699.
2. Wheel usage

When I turned my 2010 facebook status updates into a word cloud, I was unsurprised to see the word thesis looming large at the centre. It has certainly been one of the defining elements of the year for me, and facebook was a good outlet. By contrast, my twitter feed was probably more dominated by the election, and the associated politics; I can’t know for sure, as ’2010 in statuses’ didn’t seem to look back beyond the past few days.

On seeing my facebook status cloud, a friend, who has had a similarly thesis dominated year, suggested turning my thesis into a word cloud. So I did.

A word cloud of my thesis

When proteins become damaged or are no longer required by the cell, they can be broken down into their component peptides, allowing these resources to be reclaimed. Much of this recycling occurs at proteasomes, hollow barrel like structures located in the cytoplasm and nucleus of the cell. Breakdown of proteins occurs in a catalytic chamber at the centre of the structure, and entry of potential substrates is tightly regulated by caps at either end of the chamber.

In most cases, a protein’s fate at the centre of the proteasome is determined by the attachment of a chain of ubiquitin: a small protein, which can be covalently attached to lysine residues on other proteins. This chain is recognised by components of the proteasome, as well as by shuttle factors, which help recruit substrates to the proteasome.

Proteins within the cytoplasm or nucleus have easy access to the proteasome, however those within membrane bound organelles must first be translocated into the cytosol. The first evidence for such processes occurring was found in association with the endoplasmic reticulum.

Endoplasmic reticulum associated degradation, or ERAD, describes the process by which unwanted proteins within the endoplasmic reticulum are retro-translocated to the cytosol. Here they are tagged with ubiquitin, and delivered to the proteasome. ERAD relies on the co-operation of a large number of factors. A series of chaperones identify proteins which are undergoing difficulty folding and in turn they deliver them to complexes in the ER membrane. From here, proteins are transferred to the cytosolic face of the organelle, and chains of ubiquitin are attached, marking them for proteasome mediated degradation. The hydrolysis of ATP by the hexameric Cdc48/p97 provides the energy to extract ubiquitinated proteins from the membrane, and co-factor proteins ensure efficient delivery to the proteasome or its shuttle factors.

For a long time it was assumed that no such system existed in mitochondria, the respiratory centres of the cell, as they have their own complement of proteases. However, increasing evidence is suggesting that the proteasome may play an important role in the degradation of some mitochondrial proteins, leading to the proposition of mitochondria associated degradation, or MAD.

Traditionally, the degradation of mitochondrial proteins has been seen to be the domain of the mitochondrially localised ATP dependent proteases. The inner mitochondrial membrane contains multi-subunit proteases with their catalytic activity orientated to face either the inter-membrane space, or the mitochondrial matrix. Additional proteases, such as Lon/PIM and ClpXP, are found within the mitochondrial matrix. This collection of proteases is sufficient to provide protein degradation in the mitochondrial matrix, inner mitochondrial membrane and the inter-membrane space, however analysis of the products of proteolysis indicate that inter-membrane space proteins are under-represented.

Some of the earliest evidence of proteasome dependent degradation of mitochondrial proteins came in 1985, when Rapoport et al.¹discovered that some mitochondrial proteins were ubiquitinated, and degraded in an ATP dependent manner. Subsequent to this, other ubiquitinated proteins have been found to localise to the mitochondria, and appear to undergo proteasome mediated degradation.

More direct evidence arose when Margineantu et al.² found that the heat-shock protein Hsp90 appeared to promote ubiquitination of OSCP, a matrix localised subunit of the mitochondiral F1F0-ATPase. Further investigation revealed that disruption of Hsp90 resulted in reduced turnover of OSCP and other mitochondrial proteins, resulting in accumulation on the outer mitochondrial membrane; similar changes were observed on proteasome inhibition. This accumulated protein appeared to be a result of retro-translocation of mature mitochondrial proteins, indicating that mitochondria possessed a pathway of retro-translocation and proteasome mediated degradation, analogous to the ERAD pathway.

Dissection of the mitochondria associated degradation pathway is still in its early stages, and as yet many of the required components remain speculative. Comparison with the better characterised ERAD pathway is inevitable, and it remains to be seen if any elements will be shared between the two pathways. Recent work by Heo et al.³ discovered that Cdc48/p97 was recruited to mitochondria in a stress responsive manner by a protein they called Vms1 (VCP/Cdc48-associated mitochondrial stress-responsive). Disruption of this process resulted in a reduction in ubiquitin-dependent degradation of mitochondrial proteins, leading the authors to propose that Cdc48/p97 may perform a key role in MAD, as well as in ERAD.

The highly oxidative environment of the mitochondria means that its proteins are particularly prone to damage. Mitochondrial proteases have long been known to provide one line of protein quality control, and it is increasingly apparent that the proteasome dependent degradation of the MAD pathway may provide another. Dissection of the MAD pathway will be essential for forming a complete picture of the mitochondrial protection against damaged proteins, and may provide insights into diseases such as amyotrophic lateral sclerosis, which are associated with an accumulation of misfolded proteins in the mitochondria.

1. Rapoport, S., Dubiel, W., & Müller, M. (1985). Proteolysis of mitochondria in reticulocytes during maturation is ubiquitin-dependent and is accompanied by a high rate of ATP hydrolysis. FEBS letters, 180(2), 249-52. Pubmed.
2. Margineantu, D. H., Emerson, C. B., Diaz, D., & Hockenbery, D. M. (2007). Hsp90 inhibition decreases mitochondrial protein turnover. PloS one, 2(10), e1066. doi: 10.1371/journal.pone.0001066.
3. Heo, J.-M., Livnat-Levanon, N., Taylor, E. B., Jones, K. T., Dephoure, N., Ring, J., et al. (2010). A stress-responsive system for mitochondrial protein degradation. Molecular cell, 40(3), 465-80. doi: 10.1016/j.molcel.2010.10.021.

About a week and a half ago I finally submitted my thesis, 40 months lab-work condensed into a document that was worryingly thinner than most. However, you work with what you have; padding the document with unnecessary figures and paragraphs will only serve to increase the length, to the detriment of the quality. As a secondary benefit, a short thesis also means that there is less to be familiar with for the viva, although I’m sure it will not work out that way in practice.

With the thesis submitted, there were few reasons to remain in Edinburgh; the viva itself isn’t until September. So last Saturday I headed south on the train, met my parents and a brother in Birmingham, and then headed off with my parents back to their house. For the first time in five years, I was back in my childhood room, not living out of a suitcase. It also meant, that for the first time in a year, I could get my desktop set up with a decent broadband connection again.

One of the problems with being back home, is the isolation. While I can’t pretend that my village is some rural backwater, without sewers, running water or electricity, it does lack basic facilities, such as a place to buy Jaffa cakes when you get a sudden craving at 8.30 pm.  This dire lack of Jaffa cake suppliers is made even more apparent when you consider the colour of my driving license: it’s green. The inability to drive may seem surprising for someone who grew up in a rural area, but despite the obvious usefulness of the skill, cars bore me, and early attempts at learning soon made it apparent that I wasn’t exactly a natural. Then it wasn’t long before I was off to university, and for the past eight years I have not only not needed a car, but have been living in situations where its often easier not using one. I’m sure I will learn eventually, but I’m wary of doing so, and then not driving for a few years.

Yet now I’m back in rural Wiltshire, and while I don’t intend to be here long, it is certainly far longer than I could cope with being housebound. On top of this, a somewhat lacking public transport system means that I’d be constantly relying on parents or other people for lifts, which is neither polite, fair, or convenient. This is especially true over the next two weeks, as my parents will be in Spain, and the drive back would require I give them a couple of days notice, hardly convenient; oh, and it might break the polite and fair requirements as well.

Without the ability to drive four wheels, I have instead settled on two, and have purchased my first bike for several years¹; it has also been ten or more years since I last cycled. While they say that you never forget how to ride a bike, I was still a bit cautious as I set out on it for the first time. Last night I began with a simple ride up and down the road to make sure everything was flowing smoothly, and today I took it for a short 6 mile round trip to a local walking spot. Fortunately it appears that I do still remember how to ride a bike, and failed to have any embarrassing crashes. The trip also revealed that I need to raise my handlebars slightly, and to tilt the saddle back, something that will depend on my finding a suitable Alan key. The bike however does give me mobility, and in concert with the rail network it should mean I can get almost anywhere. And who knows, perhaps even if I do fail to drive a car for a few years after learning, I’ll slip back behind the wheel with similar ease to slipping back behind the handlebars.

I hope to get back to writing some of the more structured blog entries shortly, once I’ve had a bit more consideration about how I intend to use this website in future.

1. A Trek 7.0 FX, if you are interested, or even for that matter, if you are not.