̽��ֱ�� of Cambridge - database

New database for vital model organism launched

gm349 — Mon, 28 Nov 2011 16:16:10 +0000

A new database promises to be an invaluable resource to scientists who use a unique single-celled fungus to study human diseases.

̽��ֱ��new database for the fission yeast Schizosaccharomyces pombe, called PomBase, was launched today by a consortium of researchers at the ̽��ֱ�� of Cambridge, the European Bioinformatics Institute (EBI), and ̽��ֱ�� College London (UCL).

Fission yeast is a single-celled fungus (yeast). Because their cells function much like our own, and it is an important model for studying cellular processes frequently associated with heritable diseases and cancers.

Scientists have already discovered that fission yeast has equivalents of many human genes which are known causes of rare genetic diseases and syndromes (including Batten', Bloom's, Birt-Hogg-Dube, Liddle, Lowe, Niemann-Pick). Additionally, fission yeast have counterparts of human genes implicated in diseases with multiple causes, to include many cancers, deafness, neurological diseases, heart disease, Parkinson's, and anaemia.

Biologists today are very dependent on computer databases that catalogue the functions of the genes of the organisms they study and give access to other supporting information. ̽��ֱ��PomBase website will therefore prove to be an important tool for researchers studying fission yeast.

Its launch is the first stage of a 5-year project funded by the Wellcome Trust to provide a model organism database that allows researchers around the world to participate directly in the curation process in addition to using automated procedures based on the genetic blueprint of the fission yeast. ̽��ֱ��project uses Ensembl software for genome browsing, which is already used to present data for many other important experimental species. Novel tools and resources generated by this project will also be available to researchers working on other species, including human pathogens, to create similar databases.

Steve Oliver, Professor of Systems Biology & Biochemistry, who is spearheading the initiative, commented: "Organism specific database projects frequently have limited resources, and large backlogs of uncurated literature. An important novel component of this project is the construction of intuitive tools to allow the research community to involve itself in database curation, and ensure that the scientific information published in their papers is visible to the entire biological research community. These tools can also be shared with other groups and implemented for their organism of interest.”

Valerie Wood, PomBase Manager and co-investigator, said: "PomBase is not only establishing a database for this important model, it is also adapting the EBI's Ensembl Genomes platform and constructing tools to allow the research community to curate their own publications. ̽��ֱ��PomBase protocols will enable other research communities to establish and sustain similar databases for other experimental organisms. We have already identified counterparts for over 300 human disease genes in PomBase and many of these are being studied to elucidate the cellular basis of a diverse range of diseases.”

Jurg Bahler, fission yeast researcher and PomBase co-investigator from UCL, added: “Many basic cellular processes are conserved between yeast and humans, and PomBase will used extensively by biological and biomedical researchers world-wide to study mechanisms involved in cell growth and division.”

Paul Kersey, PomBase co-investigator from EBI, said: “PomBase has adapted the EBI's Ensembl platform to provide a multi-faceted resource dedicated to the needs of fission yeast researchers. These developments will enable other research communities to establish and sustain similar databases for their favourite experimental organisms.”

̽��ֱ��community curation initiative for PomBase will be launched in Spring 2012. ̽��ֱ��database can be found at: www.pombase.org

̽��ֱ��database, PomBase, important new tool for scientists researching fission yeast.

An important novel component of this project is the construction of intuitive tools to allow the research community to involve itself in database curation, and ensure that the scientific information published in their papers is visible to the entire biological research community.

Steve Oliver, Professor of Systems Biology & Biochemistry, who is spearheading the initiative

Image UCL

Pombe

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Yes

Translating science for conservation: bees benefit first

bjb42 — Wed, 08 Sep 2010 00:00:00 +0000

For the first time, scientific knowledge and experience about how to conserve wild bees around the world has been brought together by conservation scientists led by Professor William J. Sutherland and Dr Lynn Dicks at the ̽��ֱ�� of Cambridge.

̽��ֱ��synopsis of evidence on bee conservation is meant to inform people taking action or spending money to help wild bees - anyone from farmers to international NGOs - about what works and what doesn't. It is part of a project called Conservation Evidence, which aims to make conservation practice more science-based.

Bees are the most important pollinators globally, and their decline has received much publicity. "There are more than 25,000 species of bee worldwide," says Dr Simon G. Potts, an expert on pollinator conservation from the ̽��ֱ�� of Reading who advised on the development of the bee synopsis. "In areas where good quality data are available, severe declines in many species have been documented." In response, governments and international organisations are now investing in pollinator conservation.

̽��ֱ��bee synopsis, developed in partnership with an international group of bee experts, lists 59 different actions you could take to benefit wild bees. They range from providing nest boxes or planting flowers to training beekeepers to keep native species. For each intervention, evidence is summarised in plain English.

In some cases, the evidence tells a clear story. Leaving strips at the edge of crop fields untreated with herbicides and pesticides does not help bumblebees, for example - two replicated trials in the UK have found no more bees on these strips than in ordinary crop fields. But there is evidence from many parts of the world that providing nest boxes on agricultural land can benefit solitary bees. Twenty-nine studies show that solitary bees, including endangered species, will use nest boxes and three studies show numbers of nesting bees can double over three years with repeated nest box provision.

Bees can be problematic in places where they are not native, and there is some evidence about how to reduce the impacts of invasive bee species. A concerted effort to eradicate European buff-tailed bumblebees from small patches of Japanese countryside, for example, increased numbers of native bumblebees, but did not remove the invaders altogether.

"This synopsis is a great step forward in providing a clear evidence base for anyone setting out to conserve wild bees, from conservation agencies to individuals," says Professor Andrew Bourke, a bumblebee expert from the ̽��ֱ�� of East Anglia, UK, and member of the Advisory Board for the bee synopsis. He was surprised by the often low success rate of artificial nest boxes for bumblebees. "This work highlights how much more there is to learn about bees," he says.

As well as helping to inform decisions about bee conservation, the synopsis shows where there are gaps in our knowledge. There is no direct evidence to show whether increasing the amount of natural habitat in farmed areas can help bees, for example, and very little evidence for the effects of restricting pesticide use on bees, although conservationists often advocate these actions. "Habitat preservation and the proper application and use of insecticides are the most important issues in bee conservation now," says Peter Kwapong, of the International Stingless Bee Centre in Ghana, a member of the Advisory Board. Clearly, these are areas where research should focus.

̽��ֱ��Conservation Evidence project also has an open access journal where conservationists can document their experience and an online database of evidence published elsewhere, relating to conservation interventions. ̽��ֱ��series of synopses, of which Bee Conservation is the first, will cover other major species groups, habitat types and issues. Synopses are already being prepared for birds, butterflies, grassland and farmland.

" ̽��ֱ��bee synopsis brings together, for the first time, a systematic overview of conservation practices that can really help protect bees," says Potts. " ̽��ֱ��challenge now is for policymakers to take up these actions."

A project to make conservation science accessible and relevant to conservationists and policymakers launches its first major synopsis of evidence, on bee conservation.

In areas where good quality data are available, severe declines in many species have been documented

Dr Simon G. Potts

rumpleteaser from Flickr

Bee in flight

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Yes

Domesday database launched online

bjb42 — Mon, 09 Aug 2010 00:00:00 +0000

"PASE Domesday", which is released today, links information from the Domesday survey (1086) to maps showing the location of estates throughout England.

It has been created by a team of researchers from the ̽��ֱ�� of Cambridge and King's College, London, and can be visited for free at:https://domesday.pase.ac.uk:443/

̽��ֱ��site enables users to list, map and quantify the estates of all the landholders named in William the Conqueror's great Domesday survey of 1086 at the click of a button.

Visitors can find out who owned their town or village, create maps and tables of the estates held by the same lords elsewhere in England, and examine the scale of the dispossession of the English by the Normans following the conquest of 1066.

̽��ֱ��launch coincides with, and will be featured in, a one-hour documentary on Domesday Book which will be broadcast on Tuesday, 10 August. It also forms part of a wider project, " ̽��ֱ��Prosopography of Anglo-Saxon England" (PASE), which aims to capture information relating to all the recorded inhabitants of England, from the late sixth to the late 11th century, in a single online database, and will be launched later this year.

̽��ֱ��project was funded from 2000 to 2004 by the Arts and Humanities Research Board, and from 2005 to 2008 by the Arts and Humanities Research Council (AHRC).

PASE Domesday is designed to help answer one of the great unsolved questions of English medieval history: What was the structure of English landed society in 1066?

Although Domesday Book, the most complete survey of any medieval landed society, has been intensively studied, the sheer logistical difficulty involved in assembling information from its own contents and other sources has prevented scholars from forming a complete picture of the aristocracy that was defeated by the Normans at Hastings.

By removing the logistical barriers, PASE Domesday opens up the prospect of a breakthrough in the way historians understand a critical phase of English history, enabling them to build up a profile of the Anglo-Saxon elite that was overrun after William the Conqueror's victory.

To create it, researchers painstakingly processed the vast quantity of data found in the various products of the Domesday survey of 1086. ̽��ֱ��work was carried out by scholars in the ̽��ֱ�� of Cambridge's Department of Anglo-Saxon, Norse and Celtic, and at King's College, London.

"Constructing this database has been quite an exercise, but it is a phenomenally useful research tool," Dr. Stephen Baxter, who led the Domesday part of the project, said. "Essentially, it's now possible for anyone to do in a few seconds what it has taken scholars weeks to achieve in the past."

" ̽��ֱ��breakthrough has been made possible by the wonders of modern technology, in selecting and arranging the data, in generating the maps, and in presenting the possibilities," added Professor Simon Keynes, of the Department of Anglo-Saxon, Norse and Celtic, and a co-director of the PASE project. "One can then begin to detect the patterns and to make the informed judgements which will help to produce a significant result."

Further details about the PASE project as a whole can be found at https://pase.ac.uk:443/

PASE Domesday will feature in the "Domesday" special as part of the BBC's Norman Season on Tuesday, 10 August, at 8pm.

An online database which promises to change our understanding of English society on the eve and in the aftermath of the Norman Conquest has been launched online.

Essentially, it's now possible for anyone to do in a few seconds what it has taken scholars weeks to achieve in the past.

Dr. Stephen Baxter

electropod from Flickr

Domesday

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Yes

A scriptorium of commonplace books

bjb42 — Sat, 01 May 2010 00:00:00 +0000

‘Scriptorium’ is the culmination of a three-year project in the Faculty of English to digitise and preserve a type of manuscript book well known in 15th- to 18th-century Europe: the commonplace book or manuscript miscellany. And at the heart of the project, which was funded by the Arts and Humanities Research Council (AHRC), lies an innovative tool that will help you to read them.

A literary phenomenon

Commonplace books were the personal organisers of their day. Learned men (and, more rarely, women) would compile books containing recipes, accounts, sonnets, quotes, prayers, songs, legal treatises and medical instructions. Sometimes passed from one owner to another and continued over decades, if not centuries, commonplace books would be filled with snippets of contemporary information and culture. ̽��ֱ��keeping of such books was regular practice in the period, enabling their owners to record and remember what they had read, been told or overheard. Each is a unique collection of knowledge: an intellectual scrapbook, the filofax of its time.

A total of 20 commonplace books and miscellanies forms the backbone of the Scriptorium project. These books have been sourced from Cambridge college libraries and the ̽��ֱ�� Library, as well as from archives in country houses like Holkham Hall in Norfolk. Some have a known provenance, such as a 17th-century book of estate management written by William Heveningham, part of which was written during his 18-year incarceration in Windsor Castle for his role in Charles I’s execution. ̽��ֱ��Glastonbury miscellany (c. 1450), a 114-page collection of literary texts in Latin and English, started life as a Glastonbury monk’s accounts book and, after successive interventions by five more scribes, was still being added to a century later.

Daleks aid digitisation

Over the course of three years, the project team, led by Drs Richard Beadle, Raphael Lyne, Andrew Zurcher and Colin Burrow, adapted and developed painstaking techniques to minimise the risk of damage to texts during photography. ‘Daleks’, made from an aluminium bolt and two sewing needles, provided one means of safely applying adjustable levels of pressure on manuscript leaves, to lay them flat for photography. Project researchers, including Drs Christopher Burlinson, Angus Vine and Sebastiaan Verweij, also pioneered new descriptive methods and representational strategies for publishing rare manuscript materials online, including full and searchable analyses of each manuscript, and transcriptions of key selections.

Working in collaboration with the Centre for Applied Research in Educational Technologies (CARET), and IT developer Mariko Brittain, the team also developed an expansible, automated manuscript image database that will continue to function and grow beyond the life of the funded project. And with conservation in mind, high-resolution manuscript images have been securely dark-archived in DSpace@Cambridge, Cambridge ̽��ֱ�� Library’s digital repository.

Help with handwriting

̽��ֱ��art of deciphering old handwriting, known as palaeography, is a difficult decoding process that can be complicated by factors such as the scribe’s style, evolving letter-forms and unusual punctuation. Help in cracking this code is now available from the Scriptorium project’s fully interactive online English Handwriting course. ̽��ֱ��course makes full use of the wide range of hands, styles and idiosyncratic habits represented by the Scriptorium project manuscripts, which were chosen with an eye to their palaeographical range and complexity. This and other resources within the Scriptorium project are dovetailing with teaching and research in the Faculty of English, opening up the literature, history, theology and philosophy of earlier periods to a new generation of students and scholars in Cambridge and across the world.

For more information, please contact Dr Richard Beadle (rb243@cam.ac.uk), Dr Raphael Lyne (rtrl100@cam.ac.uk) and Dr Andrew Zurcher (aez20@hermes.cam.ac.uk) at the Faculty of English or visit Scriptorium (http://scriptorium.english.cam.ac.uk/).

A digital archive of 500-year-old 'filofaxes' offers extraordinary insight into early thought and writing practices.

̽��ֱ��keeping of such books was regular practice in the period, enabling their owners to record and remember what they had read, been told or overheard. 

By permission of the Syndics of Cambridge ̽��ֱ�� Library

15th-century manuscript

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Yes

Rebellion, repression, retribution

tdk25 — Fri, 01 Feb 2008 00:00:00 +0000

̽��ֱ��true course of events of the Irish rebellion of 1641 has never been fully known. Initiated by disaffected Irish Catholics rebelling against Protestant settlers, the rebellion quickly escalated in violence, resulting in widespread killing. But was the rebellion intended to be a bloodless coup that spiralled out of control, or were the thousands of Protestants deliberately driven out and massacred? What’s clear is that the years that followed were a time of savage revenge for the events of 1641 – Oliver Cromwell arrived with 30,000 English troops to conquer Ireland in the name of the English Republic and to exact ‘a just judgement of God upon those barbarous wretches, who have imbrued their hands in so much innocent blood’ – and the groundwork was laid for Ireland’s Catholic–Protestant divide.

A curious aspect of the rebellion is that although it is the least understood of all the great massacres of European history, it is amongst the best recorded. Historical narratives in the form of eyewitness accounts of those who lived through the rebellion are still in existence in the library of Trinity College Dublin, where they have remained largely unstudied. This is chiefly because there is too much of a record of what happened and it has taken until now, with improvements in technology and the political climate, to conspire finally to make it possible for the secrets of the ‘1641 depositions’ to be unlocked. A team of scholars in Cambridge, Dublin and Aberdeen are poised to do just this. Professor John Morrill from Cambridge’s Faculty of History is chairing the three-year project, working alongside Professor Jane Ohlmeyer and Dr Micheál Ó Siochrú (Trinity College Dublin), and Professor Tom Bartlett ( ̽��ֱ�� of Aberdeen).

Roots of an uprising

̽��ֱ��1641 rebellion had roots stretching back to the mid-16th century, when the Irish provinces were heavily colonised by English settlers. Throughout the reign of Queen Elizabeth I, the English government, fearful that continental Catholic kings would use Ireland as a springboard for invading England to exploit the dynastic weaknesses (Elizabeth was, in Catholic eyes, a heretic bastard tyrant, unmarried and the last of her line), sought to impose strong Protestant control of Ireland. This led to a dreadful cycle: Catholic rebellion, repression of the uprising, replacement of Irish landowners by English as part of a ‘Plantation’ policy, then more rebellion, more repression and further Plantation.

In and after 1610, the largest of the Plantation policies, in which not only the Irish landowners but also the tenant farmers and urban elites were displaced, affected large parts of Ulster in the far north of Ireland. Previous Catholic owners and occupiers were driven into exile, where thousands either became mercenary soldiers (‘Wild Geese’) in the armies of the Habsburg kings or fell into destitution.

For 30 years, the strong authoritarian government, softened by a blind-eye to private Catholic worship, kept the dispossessed of Ulster and elsewhere in check. But in 1641, England was paralysed by the disputes that were to lead, a year later, to civil war.

King Charles I’s puritan opponents had plans to introduce much more effective religious persecution of the Catholic Irish and to make Ireland increasingly part of an enlarged English state. This provoked, from late October 1641, a series of pre-emptive strikes by members of the Catholic nobility and, in the ensuing chaos, a series of what (unless this research project tells otherwise) appear to be spontaneous revenge attacks on Protestant settlers that quickly got out of control.

An imperfect account

Although we have no idea how many people were killed during the events of 1641, the most prudent estimates are that 4000 died through acts of violence and that 6000 more died of the consequences of being driven out naked into the winter cold, while many more fled from their homes and made their way eventually back to England. So much is clear. But the precise chronology and geography of the rebellion have remained hazy at best.

̽��ֱ��English government had to do something to protect the English Protestant settlers, but their own country was in chaos. They could not raise taxes to fund the army. So they borrowed money from 2000 venture capitalists (the ‘Adventurers’) against the promise that they would receive two million acres of Irish land once Ireland was conquered. To establish which land was to be confiscated, all (mainly Protestant) witnesses to the rebellion were questioned by government-appointed commissioners and their accounts recorded as ‘depositions’ that could be used in court.

Today, 3400 depositions are in existence, providing the fullest and most dramatic evidence we have for any event of this kind before the 20th century. They add to up 19,000 pages of testimony in crabbed 17th-century hands. Trinity College Library acquired the documents in 1741 and for centuries there they have remained, far too extensive for any one scholar to explore them all and in too poor a condition for widespread access. Even with a team of researchers, it will take a total of more than eight person years to transcribe the accounts.

A new kind of history

̽��ֱ��spirit of co-operation between the UK and Irish governments following the Good Friday agreement has made it possible to fund a project of this size – the most ambitious British-Irish collaboration in the humanities ever undertaken. Separate but linked funding streams in the UK and Ireland have raised more than 1 million euros from the Arts and Humanities Research Council (AHRC) in the UK, the Irish Research Council for the Humanities and Social Sciences (IRCHSS) and Trinity College Dublin.

Once the depositions are captured and online, they will constitute a database that can be arranged and re-arranged in any way a scholar would like: by date, by map reference, even by act of violence. Many of the depositions give detailed inventories of goods taken and destroyed, affording unique insights into the material culture of a colonial society. Members of the general public might even use depositions to trace family trees. There are endless possibilities for further study, both looking backwards to the pattern of exploitation that provoked the explosion of Catholic violence, and forwards to the way in which these massacres resulted in the confiscation of 40% of the land of Ireland and its transfer from Catholics born in Ireland to Protestants born in England. These are events that transformed Irish history and therefore British and world history. This collaborative project represents a new kind of history: one where the medium and the message can change how we understand ourselves in time.

For more information, please contact the author Professor John Morrill (jsm1000@cam.ac.uk) at the Faculty of History.

John Morrill explores one of the most extraordinary and least understood aspects of Anglo-Irish history - the rebellion of 1641.

But was the rebellion intended to be a bloodless coup that spiralled out of control, or were the thousands of Protestants deliberately driven out and massacred?

Credit- the Board of Trinity College, Dublin

Deposition taken from a witness to the 1641 Irish rebellion

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Yes

Can a voice identify a criminal?

tdk25 — Sat, 01 Sep 2007 00:00:00 +0000

Recognising a voice is a familiar experience for most people – identifying a friend’s voice over the telephone, recognising the voice of a well-known personality on the radio, hearing the voice of a colleague call out from behind. But why do voices sound distinctive? Given our ability to recognise individuals, it seems reasonable to assume that voices are unique, but it has not been scientifically demonstrated that all voices are measurably distinctive. In spite of the impression given by televised crime shows, as yet there is no technique available to identify a speaker with 100% reliability.

This is a serious problem for forensic speaker identification, a branch of forensic phonetics in which a phonetician is asked to identify an unknown speaker whose voice has been recorded during the committing of a crime, for example a bomb threat, ransom demand, hoax emergency call or drug deal. ̽��ֱ��phonetician compares the incriminating recording with samples of speech from a suspect with a view to identifying the perpetrator or eliminating the suspect. These cases are often controversial, and since the extent to which an individual’s voice is idiosyncratic has not yet been established, research in this area is crucial.

A key problem in attempting to characterise a speaker is that each individual’s voice can vary greatly. We change our voices depending on who we are talking to, how formal the situation is, the emotion we wish to express and whether there is background noise. Speakers’ voices also change if they are tired, drunk or have a cold or sore throat, and of course speakers can disguise their voices. So a voice is much more complicated to capture than a fingerprint, which is a fixed, unchanging feature of an individual.

DyViS: investigating speech

A team of researchers in the Department of Linguistics – Dr Kirsty McDougall, Dr Gea de Jong, Toby Hudson and Professor Francis Nolan – is carrying out innovative research in speaker identification in the DyViS project (Dynamic Variability in Speech: A Forensic Phonetic Study of British English), funded by the Economic and Social Research Council (ESRC).

To investigate the problem of variation within a speaker’s voice, the DyViS team have compiled a large-scale database of recordings of southern British English spoken across a range of speaking styles. Speakers participated in several tasks: a mock police interview where they were required to ‘lie’ about a particular scenario, a telephone call with a friend involving a more casual and relaxed style of speech, and a number of reading tasks. All of the speaking tasks included a particular selection of words that the participants had to utter in different contexts. These data enable the researchers to investigate how phonetic features of these words change for a given individual across the different speaking styles, and to what extent these features can be used to distinguish individuals.

Identifying the speaker

One particular feature being examined is a phenomenon known as ‘formant frequency dynamics’. Formant frequencies are the resonances of the vocal tract during speech – the frequencies at which vibrations of air are at maximum amplitude in the vocal tract in speech sounds such as vowels. Formant frequencies appear as roughly horizontal dark bands on a spectrogram, a computer-generated representation of the acoustic speech signal. These frequencies are powerful cues to speaker identity since they are determined by both the physical dimensions of a speaker’s vocal tract and the way the speaker configures the vocal organs to produce each sound.

Previous research on speaker differences has typically measured the formant frequencies only at the centre of the sound. ̽��ֱ��DyViS research goes beyond these ‘static’ measures to investigate the dynamics of formant frequencies, which reflect the movement of a person’s speech organs and are likely to reveal more fine-grained differences among speakers. Just as people exhibit personal styles for walking, running and other skilled motor activities, they move their vocal organs in individual ways when producing speech.

Dr McDougall’s experiments have investigated the speaker-distinguishing potential of the formant frequency dynamics of the vowel sound in spoken words like bike and hike, of the vowel sound in who’d, and of sequences containing an ‘r’ sound preceded and followed by vowel sounds such as a route and a rack. ̽��ֱ��work shows that formant frequency dynamics carry considerable speaker-specific information. By taking measurements along the formant contours surrounding the centre of a speech sound, a significant improvement in speaker discrimination is achieved.

Forensic phonetics

Together with research into other features of speech being investigated by the DyViS team, this work offers crucial new directions for solutions to the problem of extracting a speaker’s ‘signature’ from the speech signal. Findings from the DyViS project suggest that dynamic features of speech could provide a clue in speaker identification, which has clear applications in forensic evidence – in comparing voices and speech for purposes of identification, and in analysing speech recordings.

̽��ֱ��research also has important implications for phonetic theory. Current models of speech production and perception do not provide a good explanation of the role of individual variation in speech communication. ̽��ֱ��analysis of dynamic features of speech being undertaken by the DyViS team will lead to important theoretical developments in these areas, contributing to our understanding of how individual speakers can communicate with the same language yet sound so different from each other.

Innovative research in the Department of Linguistics suggests that dynamic features of speech could provide a clue to forensic speaker identification.

Travis Isaacs from Flickr

Ear

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Yes