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Monthly Archives: January 2021
What changes to the Vatican may the replacement of the Archpriest of St Peter’s Basilica bring – The Catholic Telegraph
Posted: January 15, 2021 at 2:00 pm
by Andrea Gagliarducci
Vatican City, Jan 14, 2021 / 05:45 pm MT (CNA).- Pope Francis might soon choose a new Archpriest of St. Peters Basilica, to replace Cardinal Angelo Comastri, who turned 77 in September. His replacement, according to Vatican observers, may bring a broader generational change that could involve at least five Vatican dicasteries.
Comastri, who had a private audience with Pope Francis on Jan. 11, is a well-known preacher whose books are good sellers. During the lockdown due to the pandemic, Cardinal Comastri began to pray the rosary at noon in St. Peters Basilica.
St. John Paul II appointed Comastri as his general vicar for the Vatican City State, President of the Fabric of St. Peter, and coadjutor Archpriest of St. Peters Basilica in 2005. In 2006, Benedict XVI appointed Comastri Archpriest of the St. Peters Basilica. He succeeded Cardinal Francesco Marchisano.
One clue of Comastris upcoming retirement is Pope Francis decision to postpone the election of the members of the Chapter of St. Peter, the college of priests that governs the Basilica under the guidance of the archpriest. The elections were supposed to take place at the end of the summer or during the fall, but the Pope asked to hold them after Jan. 11.
The Archpriest of St. Peters Basilica is in charge of the worship and pastoral activity of the basilica. The position is very ancient and has always been assigned to a cardinal. Since 1991, the Archpriest of the St. Peters Basilica is also the Popes vicar for the Vatican City State.
The position is important not only because the Archpriest is one of the Popes closest collaborators, but also because he manages and organizes the worship of the most emblematic temple in the Catholic world.
St. Peters Basilica includes 45 altars and 11 chapels, while the Vatican Grotto has several Marian chapels.
The daily Mass schedule in St. Peters Basilica lists one Mass per hour from 9 to 12 am, in Italian, at the Altar of the Chair. There is another Mass in Italian at 8.30 am at the altar of the Most Holy Sacrament, while every day at 5 pm, there is a Mass in Latin.
On Sundays, there are 5 Masses celebrated in Italian and one in Latin.
Beyond the regular Mass schedule, there is the possibility to celebrate Mass in every chapel of St. Peters Basilica. The chapels are booked by groups of pilgrims or individuals who celebrate Mass in their own language. In fact, every day, St. Peters Basilica is filled with celebrations in several languages at the same time.
The new Archpriest will be called to manage this. Will he keep things as they are?
There is a broad discussion among members of the Chapter of the Basilica regarding whether to keep the possibility to celebrate private masses in the Basilica or instead ruling that the pilgrims who want to take part in a Mass must be at the Masses already scheduled. The debate is also about a possible abolition of the daily Mass in Latin. The Mass is celebrated according to the Paul VI missal, so it is not a Mass in the extraordinary form.
A Vatican source with knowledge of the facts, who asked to remain anonymous, stressed with CNA that these discussions were also behind the power struggle that led to allegations of mismanagement at the Fabric of St. Peter. This institution takes care of the maintenance of St. Peters Basilica.
Following these allegations and investigation initiated by the Vatican prosecutor, Pope Francis made the unprecedented decision to put the Fabric of St. Peter under an extraordinary commissioner, Archbishop Mario Giordana.
According to Vatican sources, there seems to be two candidates to replace Comastri. One is Cardinal Konrad Krajewski, the Papal Almoner. Krajewski is in the Popes inner circle, and the Pope strongly appreciates his work for the poor. Among his initiatives are the installation of showers for the homeless in the St. Peter colonnade, the opening of two dormitories for the homeless in Vatican facilities around St. Peter Basilica, and the doctor and barbershop services on the side of the colonnade.
The other candidate would be Cardinal Mauro Gambetti. Cardinal Gambetti was the exiting Custodian of the Sacred Convent of Assisi. A Franciscan Conventual, Gambetti has no posts assigned yet. After his creation as cardinal, he went back to Assisi, waiting for the Popes call.
If Gambetti indeed becomes Comastris successor, his appointment could be the first step in a generational change in several Vatican top positions. Cardinals Marc Ouellet, Leonardo Sandri, Luis Ladaria, Giuseppe Versaldi, Beniamino Stella, and Giuseppe Bertello are all older than the retiring age. The pope could be already looking for their successors at the helm respectively of the Congregation for Bishops, for the Eastern Churches, for the Doctrine of the Faith, for the Catholic Education, for the Clergy, and at the Vatican City State administration.
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Will an Unholy Alliance of Anti-Vaxxers and Government Incompetence Grab Defeat from the Jaws of Victory? – Byline Times
Posted: at 2:00 pm
Byline Times Chief Medical Officer, Dr John Ashton, considers the continuing challenges ahead in the Coronavirus pandemic despite the development of a vaccine
As we enter the second year of the COVID-19 pandemic, we are faced with a bleak mid-winter.
With the numbers of new Coronavirus cases escalating daily, hospitals and intensive care units are at breaking point. Staff absences are running at more than 20% from COVID-19 through self-isolation from the virus and stress-related conditions. Seriously ill patients are being shipped around the country. But, following the Prime Ministers lax approach on gatherings during Christmas in parts of the country, the worst is sadly still to come.
The death toll stands at more than 1,000 people each day and the grim total is heading towards 100,000 people before the end of January. So much for the Governments Chief Scientific Advisor Sir Patrick Vallances optimistic target of less than 20,000 deaths that he espoused in March, along with his naive embrace of herd immunity.
But it is not all doom and gloom and we must celebrate the remarkable achievement of clinicians and scientists around the world collaborating to produce effective vaccines less than a year after the Coronavirus made its unwelcome appearance.
Coming exactly 100 years after virology came into existence during the period of the influenza pandemic of 1918-19, this is surely the moment when the new discipline has come of age and can be added to the time-tested methods of practical, shoe-leather public health in rooting out and preventing death from natures most devious allies.
Yet, there is many a slip between cup and lip as can be seen from the story of the eradication of smallpox. It took the best part of 200 years from when Edward Jenner first demonstrated the effectiveness of cowpox inoculation against its most dangerous viral relative in 1796, to when the World Health Organisation was able to declare the demise of the virus in 1980. In the interim, efforts at mass vaccination ran into the sands of highly organised opposition.
Although smallpox vaccination was made compulsory for all newborn infants in Britain in 1853, branches of the Anti-Vaccination League soon brought it to a halt. From its centre in Leicester, the league organised a highly successful campaign against vaccination culminating in a large-scale demonstration in 1885, which led to a Royal Commission and the abolition of compulsory vaccination.
The basis of objections to vaccination were to be found in religious superstition and fear of needles, together with arguments about personal liberty and an anti-science movement which seems to have gathered even more momentum today at a time when science has given us greater insights into the natural world than ever before.
It remains to be seen whether the 80% of the population willing to welcome COVID-19 vaccines with open arms will have their public health rights compromised by a fanatical minority.
But it is not only the anti-vaxxers that should arouse our concerns. We must also be aware of the disastrous failures of the Government to take decisive and effective action at each point in the pandemic.
Whether it be testing, tracing and support for isolation, personal protective equipment, or leading from the front and implementing effective interventions in a timely way, the Government has been found wanting.
We are about to see whether the defining characteristic of the handling of the emergency in over-promising and under-delivering is about to be repeated with the roll-out of the vaccination programme.
After a nationalistic rush to be the first out of the blocks with a vaccine in December and implying by sleight of hand that a German-developed vaccine was somehow British the programme has struggled to get into its stride with some 300,000 vaccinations being given out each week.
We are now being asked to believe that, within a week, this will become 300,000 vaccines daily, that all care home residents will have been vaccinated by the end of January, and that the 13.5 million most vulnerable citizens will be protected by mid-February.
These ambitious targets are all too reminiscent of Boris Johnsons wild promises at other points of the pandemic, as well as Health and Social Care Secretary Matt Hancocks confabulation of the difference between capacity and delivery with regards to the Test and Trace operation last year.
Meanwhile, the alibis for failure are already being lined up vaccine manufacturers unable to deliver on the changing production promises, and GPs who say they are being let down by the supply side of the equation.
Setting aside that GPs had previously claimed that they could deliver the vaccination programme without recourse to reinforcements whilst simultaneously being under the cosh for all the extra work thrown up by COVID-19,they were also being promised 10 a shot for delivering vaccinations in contrast to the 11 an hour for the army of vaccinators who were supposed to do the actual work. It has now emerged that the recruitment of the army is also faltering.
Initially, the NHS advertised that non-clinical workers as well as retired doctors and nurses could sign up to be vaccinators to staff an extensive network of vaccination centres around the country. It has subsequently transpired that a Government that could reconvene at the drop of a hat to get Brexit done could not pull off the same trick to authorise the training of non-clinical professionals.
What finally seems to have caught the Prime Ministers fleeting attention has been letters to the broadsheet newspapers from retired clinicians drawing attention to the bureaucratic process that even the most experienced clinician must navigate in order to join the army of jabbers. These include hours of arcane online training, only some of it relevant in a national emergency but including fire safety, guidance on heavy lifting and preventing terrorism, followed up by the need to search out educational verification in the form of 50-year-old O Level certificates.
It is said that history repeats itself, first as tragedy and then as farce. As it stands, it is a toss-up between the Government and the anti-vaxxers when it comes to who will attract the most historical opprobrium.
Dr John Ashton is a former director of public health and the author of Blinded By Corona
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Sailing into the future | The Box, Plymouth – Museums Association
Posted: at 1:59 pm
Plymouths key cultural facility has been literally turned around to face the future. The original grand Victorian entrance into the museum and art gallery from North Hill, which was forbidding and told nothing of its contents, has been replaced by a glass atrium entrance facing a new square on the other side of the building.
The group of ships figureheads visible in the entrance foyer is a clear signal that The Box is in a maritime city. There is also the welcoming sight of visitors in the foyer cafe. In summer, tables will be available on a terrace and, no doubt, the square will be used for events.
The Box is more than just a museum. The building houses facilities that were spread across the city, including the South West Film and Television Archive and the South West Image Bank, as well as those that were already on the site, including the Plymouth and West Devon Record Office and the Plymouth Natural History Collection. One of the most exciting things about this development is the chance for creating symbiotic relationships for the public between these organisations.
Rather than exiting through the gift shop, visitors go through it to reach the galleries. This leads to what was the original entrance to the museum, where one of six contemporary works created as part of the Making It commissions is located. Figurehead II, by Alexandre da Cunha, consists of four huge sections of concrete drainage pipe stacked six metres tall a structure with inviting holes in it that was being explored by children when I was there.
Three gallery spaces lead off this. On entering the first, visitors are greeted by Plymouths life-size model of a mammoth. Interactive displays, and cases holding artefacts, tell stories about the geology of the south-west peninsular, those who lived there from prehistoric times, and its flora and fauna.
Visitors then move into the Port of Plymouth galleries, where a 3D film sequence on a giant screen reveals the port citys role in Britains history. This leads to displays telling the story of Plymouths industries and naval heritage, which is well illustrated with images and oral history.
The 100 Journeys gallery features travellers who departed from Plymouth as well as famous explorers such as the Tudor sea captain and explorer Francis Drake, the 19th-century evolutionary scientist Charles Darwin on the Beagle, the 20th-century explorer Scott of the Antarctic, and Francis Chichester, the pioneering aviator and sailor who solo-circumnavigated the world in 1967 in his boat, Gipsy Moth IV. The intrepid Gertrude Benham, an explorer and mountaineer, is also included. She donated 800 items to the museum in 1934, after having travelled to 60 countries.
All these history-changing events also remind us of the negative journeys that Plymouth has been part of. For instance, it was the port from which the Tolpuddle Martyrs were transported to Australia. And Plymouths part in the slave trade and its abolition is not ignored. Colonial slavery shaped modern Britain and we live with its legacies this is an important sentence in a display case devoted to John Hawkins, one of the originators of the slave trade. The journal of Arthur Frankland, the Plymouth captain of an anti-slavery ship, sits alongside a display of manacles and plans of slave ships a reminder of the appalling conditions that victims of the slave trade endured.
The principal gallery on the second floor contains the Mayflower 400 exhibition, on until September 2021. The importance of this show cannot be overstated, not just because of the significance of the objects, which include the first Bible to be printed in America, Mayflower memorabilia and photos of descendants of the passengers, but also because of the involvement of people from the Wampanoag nation.
The Wampanoag people are an indigenous American population who formerly occupied parts of what are now the states of Rhode Island and Massachusetts. In a message that should be spread widely, Paula Peters of the Mashpee Wampanoag nation writes: I do not hold you responsible for the past, but I do hold you responsible for the future.
There are three distinct elements in the Our Art gallery. One wall shows works on the theme of the artists studio. Highlights are Stanhope Forbes 1884 painting, A Fish Sale on a Cornish Beach, which is shown alongside studies for the work, and items from the studio of the 18th-century portraitist Joshua Reynolds, who was born and bred in Plymouth. Reynolds recently conserved self-portrait is also on show.
The second element is a floor-to-ceiling display containing ceramics, pottery, plates and figurines. The third part is the Plymouth Panorama, which comprises around 30 paintings depicting scenes along the coastline from the River Plym to the River Tamar. These are displayed three-deep on high walls. This allows a large number of paintings to be shown in a small area, the disadvantage being that many are hard to see at a distance.
When I visited, the Media Lab and the Photo Album spaces, which showcase film and photography, were proving popular with visitors. Media Lab shows the development of film and television as well as a sequence of film, featuring everything from the Beatles visit to Plymouth to Barbara Hepworth at work. The relevance to local people was brought home when I heard one visitor say: Oh look! Theres Sues mum!
The exhibition in the Photo Album gallery, Plymouth: the Five Towns, consists of 200 photographs displayed on giant lightboxes. This will facilitate the changing the selections from the vast collection held by The Box.
The Active Archives space provides visitors with a chance to explore some of the holdings of the Plymouth and West Devon Record Office, including reference books. Items on display enable visitors to explore the development of Plymouth following its bombing in the second world war. This space leads into the Cottonian Room, where researchers will be able to order items from the archive.
On the other side of the new square is the restored church of St Lukes, which now provides a space for changing exhibitions of contemporary art. The opening show is of sculptural work by the Portuguese artist Leonor Antunes, who was commissioned to design a new window for the church. The window, made of multicoloured glass, is a glorious enhancement of the space.
There is so much more to explore at The Box, such as the community figurehead project display that can be seen from the cafe, and the powerful Ship of Fools works by the contemporary portraitist Kehinde Wiley in the Arts Institute. Is a day enough to do justice to The Box? No its a place to visit regularly, savouring one element at a time. It is a vital addition to cultural provision in the West Country.
Plymouth City Council; Arts Council England; National Lottery Heritage Fund
Masterplanning, exhibition design and graphic design
Richard Rogers Conservation
Orbis; Mainmast; Hugh Harrison; The Box
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Sailing into the future | The Box, Plymouth - Museums Association
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The government and BJP have consistently undermined Parliament – The Indian Express
Posted: at 1:59 pm
While deprecating the separation of a place from its history, novelist Alan Moore rightly said: A place is much more than the bricks and mortar that go into its construction. I think its more than the accidental topography of the ground it stands on. With the apex court giving its stamp of approval to the Rs 2,000 crore Central Vista project it includes a glittering new Parliament to be built at a cost of Rs 971 crore an analysis of the Narendra Modi governments track record on respecting Parliaments soul and substance is relevant. Has the BJP and the Modi government imbibed the true spirit of our temple of democracy or have they treated it as a necessary evil, to be formally bowed down to while increasingly marginalising it?
During last years budget session, Parliament was allowed to work despite the COVID-19 outbreak because the MP Assembly had to be summoned for the formation of a BJP government against the popular mandate. A full-fledged monsoon session was convened when the virus was at its peak in Delhi because anti-farmer ordinances had to be ratified. Almost all states had their Assembly sessions during the pandemic, exposing the COVID-19 excuse for curtailing Parliament as the fig leaf it was. But when farmers, not allowing the winter to dampen their resolve, sit on roads demanding restoration of MSP for their produce, the winter session of Parliament becomes dispensable. If Parliament is not allowed to become the appropriate forum for the consideration of demands that affect nearly two-thirds of the countrys population, it can hardly qualify as democracys heartbeat, one that was Nehrus priority, the subject of former PM Atal Bihari Vajpayees undying respect and, indeed, PM Modis floor-kissing obeisance, when he first entered its hallowed portal.
Perhaps, BJPs social and political agendas take precedence over such democratic pillars. In 2017, the winter session was delayed because of the Gujarat Assembly elections. Since the government is currently investing all its energy in election management in West Bengal, Tamil Nadu, Assam and Puducherry, it has no time for Parliament. Political priorities seem to have replaced constitutional propriety. The government is fully aware that people across the country are agitated. Therefore, despite the pendency of many important pieces of legislations the Personal Data Protection Bill, 2019, Dam Safety Bill, 2019, Medical Termination of Pregnancy Amendment Bill, 2020, Anti-Maritime Piracy Bill, 2019, Maintenance and Welfare of Parents and Senior Citizens Bill, 2019 the winter session has been guillotined.
The BJPs undermining of Parliament has a long legacy in its relatively short life as a ruling party. Its policies and actions have frequently been antithetical to Parliamentary democracy. In Opposition, its disruption of parliamentary proceedings and blockage of legislations was elevated to a fine art remember the vigorous defence of disruption as a legitimate democratic tool by the late Arun Jaitley. During the 2013 budget session, of the 163 hours available, 146 hours were lost due to disruptions by the BJP.
Since 2014, there have been more subtle stratagems to undermine Parliament. Ordinance, as the preferred legislative route, is being misused as a constitutional tool and Parliament is increasingly ceasing to be a place for debates. Important bills are moved and passed on the same day or rushed through, thus depriving members of their parliamentary rights to contribute effectively. During the 2018-19 budget, 100 per cent of the demands for grants were passed without discussion. The Farm Bills passage was the apogee of all brazen violations and subterfuges.
Parliament has an effective committee system and new bills introduced in the House are generally referred to department-related standing committees for detailed scrutiny. Having been privileged to chair such a committee, one of us (Singhvi) can testify to their sterling non-partisan contributions. Invited domain experts also scrutinise the bills. In the 14thand 15th Lok Sabhas, 60 per cent and 71 per cent bills, respectively, were referred to such committees, whereas in the 16th Lok Sabha, only 25 per cent bills were referred. Not a single bill has been referred to committees in 2020.
Accountability and scrutiny have unfortunately been perceived as irritants by the Modi government. Subversion of the constitutional spirit was evident when the Aadhaar Bill was certified as a Money Bill. Having nothing to do with the imposition, abolition or alteration of taxes nor with financial obligations of the government, it was so certified simply to avoid Rajya Sabha scrutiny. That issue is now pending before a larger apex court bench, but judicial delays are inevitably used to bypass Parliament. During the last monsoon session, the Question Hour was suspended to avoid legislative scrutiny. If every other business could be transacted in both the Houses, there was no plausible reason to suspend the Question Hour except avoiding processes designed to hold the government to account.
The Modi governments decision to freeze the entire MPLAD funds scheme was less about economics or welfare and much more about politics. The impact was disproportionately larger on Opposition MPs who, being out of power, will have no say in any development work in his/her area. Despite marginal aberrations and abuses, the MPLAD scheme, to the co-authors (Singhvi) knowledge as a three term MP, has surpassed all expectations at the grassroots. Meanwhile, there is the unaudited PM Care Fund to take care of the ruling dispensation. Hopefully, the new Central Vista will signify a more meaningful realisation of the true ethos and pulsating spirit of Parliamentary democracy and not merely creation of brick, mortar and concrete structures.
This article first appeared in the print edition on January 14, 2021 under the title Running away from House. Singhvi is a three-term sitting MP, former chairman, Parliamentary Standing Committee and senior national spokesperson, Congress; Shergill is a Supreme Court lawyer and national spokesperson, INC. Views are personal
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PacBio: Year of Expansion, Whole-Genome Clinical Goals – Bio-IT World
Posted: at 1:59 pm
By Allison Proffitt
January 15, 2021 | In his first J.P. Morgan Healthcare Conference presentation on behalf of Pacific Biosciences yesterday, Christian Henry, PacBios August-announced CEO, laid out a route to the clinic for PacBios HiFi sequencing reads, and set a 2021 goal of expansion across the business: improving commercial footprint, driving product development pipelines, and establishing market leadership in whole-genome clinical sequencing.
Perhaps most importantlywere really trying to improve and drive our collaborations with key opinion leaders so we can bring whole genome sequencing into the clinic, Henry said in yesterdays presentation. Its very clear that whole genome sequencing using HiFi chemistry improves diagnostic yield, and were working hard to make sure that we can have those proof statements as we start to scale up.
Invitae Partnership: Clinical Whole Genomes
Key to that effort is the PacBio-Invitae partnership that the two companies announced on Wednesday, the day between the two company presentations. The multi-year collaboration aims to develop a production-scale high-throughput clinical whole-genome sequencing platform leveraging HiFi chemistry. This is perhaps one of the most exciting collaborations weve entered into as a company, Henry said.
We anticipate developing a sequencer with a scale thats unprecedented for long reads and will enable us to deliver a medically-relevant genome at prices substantially lower than $1,000. We believe that will help open adoption in routine medical care, and we also think that will give Invitae the opportunity to dramatically scale their whole genome testing capabilities.
The partnership launches immediately, Henry said, and he expects to develop the sequencer over the next few years with substantial funding from Invitae, and then to transition into a supply agreement. Hopefully, he said, Invitae will move many of their different assays onto the platform so they can offer whole genome sequencing capability at prices that are affordable.
Invitae shares the same vision as PacBio, Henry said: Whole genome sequencing in clinical applications is the path forward. For PacBio, this could be our killer application. Were uniquely positioned; our technology is uniquely capable.
Henry emphasized messaging around the value of the genome, not just price. What were bringing to the table is really a clinical-grade genome that others cant provide. The value of that genome will be different, I believe, than others in the market Im confident that we can deliver a product at high value at a competitive value proposition. Yet when asked if payers are ready to pay widely for whole-genome sequencing, Henry conceded that it still comes down to price.
Expanded Development Pipelines
The planned Invitae platform, however, is not PacBios single focus. This is whats so exciting! Henry said. We need to develop a multi-product portfolio so we can provide the right product to the right customer in multiple parts of the market. This Invitae program will leverage our core technology, of course, and Im sure well get benefits in both directions, but this is a completely separate product than other products we already had in development. Theres no plan at this point to slow any of that down.
He outlined all the areas in which PacBio is working to accelerate development in service of whole genome sequencing workflows. We need to improve our platform so we can create the scale required to create this notion of the Genome as a Platformsolving different disease conditions across different parts of ones life, Henry said, echoing terminology Sean George used in his Tuesday presentation for Invitae. We believe the whole genome will be critical to healthcare much like medical imaging is today.
Thus PacBio is working to increase automation and reduce sample input in the library prep stage so that more sample types can be used. In the core sequencing technology, PacBio is seeking wide-scale improvements in sample loading, platform density, and faster polymerases, all while maintaining the exquisite accuracy that is one of the key aspects of our technology that differentiates us from others. Finally, Henry identified many opportunities to improve data analytics including improvements to raw base calling, simplifying the workflow, refining secondary analysis, reducing costs, and implementing reporting in the cloud.
Youll see us, over the next several years, work in all these different areas to hopefully enable this concept of Genome as a Platform, he said.
Commercial Expansion: Doubled Footprint
But until then, Henry also said the company plans to pursue an aggressive commercial expansion, more than doubling the commercial footprint, adding commercial expertise to the executive team, and increasing the companys digital presence.
Henry predicted the Sequel IIe to be the primary platform the company is shipping in the foreseeable future. The Sequel IIe started shipping in November 2020, offering on-instrument data processing while also being cloud enabled. The company boasts 90% storage reduction and 70-85% reduction in data analysis and a compute savings of $700 per genome. The platform opened doors to new customers, Henry said, who didnt have the compute infrastructure or budgets for prior generations of PacBio sequencers.
The company has shipped several of the Sequel IIe platforms since launch and reported a combined install base of Sequel II and Sequel IIe at 203 platforms.
2020 did bring some nice deployments of the Sequel II system. Henry highlighted that LabCorp is using the Sequel II in its work to characterize SARS-CoV-2 and was recently awarded a CDC contract to provide genomic sequencing of samples of SARS-CoV-2, the virus that causes COVID-19, Henry reported. And the Wellcome Sanger Institute increased its Sequel II investment to support its Darwin Tree of Life project, sequencing all eukaryotes in Britain and Ireland.
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Comprehensive in vivo secondary structure of the SARS-CoV-2 genome reveals novel regulatory motifs and mechanisms – DocWire News
Posted: at 1:59 pm
This article was originally published here
Mol Cell. 2021 Jan 1:S1097-2765(20)30962-X. doi: 10.1016/j.molcel.2020.12.041. Online ahead of print.
ABSTRACT
Severe-acute-respiratory-syndrome-related coronavirus 2 (SARS-CoV-2) is the positive-sense RNA virus that causes coronavirus disease 2019 (COVID-19). The genome of SARS-CoV-2 is unique among viral RNAs in its vast potential to form RNA structures, yet as much as 97% of its 30 kilobases have not been structurally explored. Here, we apply a novel long amplicon strategy to determine the secondary structure of the SARS-CoV-2 RNA genome at single-nucleotide resolution in infected cells. Our in-depth structural analysis reveals networks of well-folded RNA structures throughout Orf1ab and reveals aspects of SARS-CoV-2 genome architecture that distinguish it from other RNA viruses. Evolutionary analysis shows that several features of the SARS-CoV-2 genomic structure are conserved across -coronaviruses, and we pinpoint regions of well-folded RNA structure that merit downstream functional analysis. The native, secondary structure of SARS-CoV-2 presented here is a roadmap that will facilitate focused studies on the viral life cycle, facilitate primer design, and guide the identification of RNA drug targets against COVID-19.
PMID:33444546 | DOI:10.1016/j.molcel.2020.12.041
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Comprehensive in vivo secondary structure of the SARS-CoV-2 genome reveals novel regulatory motifs and mechanisms - DocWire News
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COVID-19 Host Genome SV Consortium Identifies Structural Variants with Possible Roles in Pathogenesis and Outcomes in Severely Ill COVID-19 Patients…
Posted: at 1:58 pm
SAN DIEGO, Jan. 11, 2021 (GLOBE NEWSWIRE) -- Bionano Genomics, Inc. (Nasdaq: BNGO), announced today the first publication from the COVID-19 Host Genome Structural Variant Consortium. The study found that optical genome mapping (OGM) with Bionanos Saphyr System identified structural variants (SVs) that affect genes in pathways that control immune and inflammatory response, viral reproduction and mucosal function. The authors believe these SVs may provide key insights into the pathogenesis of COVID-19 and outcomes in patients who become severely ill.
The consortium was formed by Dr. Ravindra Kolhe from Augusta University with the goal of identifying large SVs that factor into the clinical course and outcomes of patients who contract COVID-19. Unlike other analyses of the host genome which are usually limited to genome-wide association studies or exome/genome sequencing and aim to detect single basepair changes, the consortium focuses on finding larger variants in patients genomes because they are believed to have a greater potential to impact genes. The consortium has selected OGM with the Saphyr System for genome analysis owing to Saphyrs documented performance as the leading platform for detecting these large SVs. The current study received contributions from scientists at Augusta University, the University of California San Diego, Radboud University Medical Center, The Rockefeller University, University of Texas M.D. Anderson Cancer Center, Columbia University Medical Center, Virginia Commonwealth University, New York Genome Center, Harvard Medical School, and Bionano Genomics.
The study reports the analysis of the genomes of 37 patients who were admitted to the ICU at Augusta University with severe COVID-19 disease. 30 patients needed mechanical ventilation with a mean intubation duration of 12 days. Of the 37 patients, 25 recovered and 12 died. The SVs revealed by Saphyr were confirmed with other technologies such as quantitative PCR.
One of the most compelling findings among the SVs identified was the duplication of the STK26 gene,a key element of the Toll-Like Receptor signaling pathway which controls the cells response to viral infection. In the follow-on analysis of the expression of the STK26 gene in patients with the duplication, the study found significant upregulation ofSTK26in all severely ill patients tested but not in asymptomatic COVID-19 patients, implying the duplication to be a potential novel, prognostic biomarker for the severe immune response seen in severely ill patients.
Ravindra Kolhe, MD, PhD, senior author of the study commented: As director of a high-volume testing lab at Augusta University for COVID-19 Ive seen first-hand the pain and devastation this virus can cause in those who get severely ill. The majority of the ICUs across the country are filled with patients fighting for their lives, yet we did not know why some become so severely ill while the same virus causes only mild symptoms in most. Our study shows clearly that many of the severely affected patients carry genetic variants that may cause or at least contribute to the severity of their disease by weakening the effectiveness of the immune response, increasing viral replication, or making it easier for the virus to spread between cells in thebody. Importantly, the large genomic variants detected by optical genome mapping in this study are typically missed by the short-read sequencing or SNP-based methods used in other studies, which explains why previous studies havent made the same impact.
Erik Holmlin, PhD, CEO of Bionano Genomics, commented: The COVID-19 pandemic continues without signs of slowing down. This study demonstrates that the wide variation in symptoms exhibited by patients is likely not random for most of them, but instead, at least partially, the result of SVs affecting critical pathways in patients defenses against infection and immune responses to the disease. The results also demonstrate that even when a disease has already been studied extensively with sequencing, OGM with Saphyr has the potential to reveal significant insights not seen without it. While we are devastated by the loss of lives caused by this global pandemic, we are grateful that our genome analysis platform can contribute to a better understanding of the disease and possibly help save lives.
These results will be presented by the authors at Bionanos Next-Generation Cytogenomics Symposium on January 15, register here: http://bit.ly/3pLPT28
The publication is available at:https://www.medrxiv.org/content/10.1101/2021.01.05.21249190v1
About Bionano GenomicsBionano is a genome analysis company providing tools and services based on its Saphyr system to scientists and clinicians conducting genetic research and patient testing, and providing diagnostic testing for those with autism spectrum disorder (ASD) and other neurodevelopmental disabilities through its Lineagen business. Bionanos Saphyr system is a platform for ultra-sensitive and ultra-specific structural variation detection that enables researchers and clinicians to accelerate the search for new diagnostics and therapeutic targets and to streamline the study of changes in chromosomes, which is known as cytogenetics. The Saphyr system is comprised of an instrument, chip consumables, reagents and a suite of data analysis tools, and genome analysis services to provide access to data generated by the Saphyr system for researchers who prefer not to adopt the Saphyr system in their labs. Lineagen has been providing genetic testing services to families and their healthcare providers for over nine years and has performed over 65,000 tests for those with neurodevelopmental concerns. For more information, visitwww.bionanogenomics.comor http://www.lineagen.com.
Forward-Looking StatementsThis press release contains forward-looking statements within the meaning of the Private Securities Litigation Reform Act of 1995. Words such as may, will, expect, plan, anticipate, estimate, intend and similar expressions (as well as other words or expressions referencing future events, conditions or circumstances) convey uncertainty of future events or outcomes and are intended to identify these forward-looking statements. Forward-looking statements include statements regarding our intentions, beliefs, projections, outlook, analyses or current expectations concerning, among other things: potential key insights into the pathogenesis of COVID-19 provided by SVs identified by Saphyr, including the potential of STK26 gene duplication to be a prognostic biomarker for severe immune response seen in severely ill COVID-19 patients; Saphyrs ability to contribute to a better understanding of COVID-19 and help save lives; and timing of the study results to be presented. Each of these forward-looking statements involves risks and uncertainties. Actual results or developments may differ materially from those projected or implied in these forward-looking statements. Factors that may cause such a difference include the risks and uncertainties associated with: the impact of the COVID-19 pandemic on our business and the global economy; general market conditions; changes in the competitive landscape and the introduction of competitive products; changes in our strategic and commercial plans; our ability to obtain sufficient financing to fund our strategic plans and commercialization efforts; the loss of key members of management and our commercial team; and the risks and uncertainties associated withour business and financial condition in general, including the risks and uncertainties described in our filings with the Securities and Exchange Commission, including, without limitation, our Annual Report on Form 10-K for the year ended December 31, 2019 and in other filings subsequently made by us with the Securities and Exchange Commission. All forward-looking statements contained in this press release speak only as of the date on which they were made and are based on management's assumptions and estimates as of such date. We do not undertake any obligation to publicly update any forward-looking statements, whether as a result of the receipt of new information, the occurrence of future events or otherwise.
CONTACTSCompany Contact:Erik Holmlin, CEOBionano Genomics, Inc.+1 (858) 888-7610eholmlin@bionanogenomics.com
Investor Relations Contact:Ashley R. RobinsonLifeSci Advisors, LLC+1 (617) 430-7577arr@lifesciadvisors.com
Media Contact:Darren Opland, PhDLifeSci Communications+1 (617) 733-7668darren@lifescicomms.com
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Variantyx Surpasses 2500 Genomes Analyzed, Highlights the Value of Its WGS-Based Testing Methodology – Business Wire
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BOSTON--(BUSINESS WIRE)--Clinicians at Variantyx, a leader in high complexity hereditary disease testing, recently completed analysis of their 2,500th patient genome. The milestone highlights the growing need for whole genome sequencing (WGS)-based tests in patient genetic diagnostics.
Variantyxs Genomic Unity tests pair the patients complete DNA sequence with proprietary data analysis algorithms and phenotype-driven filters to uniquely identify and definitively report on all major types of genetic variation within a single assay. Including genome-wide small sequence changes, structural variants, mitochondrial variants and tandem repeat expansions.
Review of the cases identified many examples of positive test results using Variantyx testing after multiple rounds of failed exome and other NGS tests.
Providing diagnoses for patients using the most comprehensive testing available is a milestone like no other and puts Variantyx at the leading edge of genomic technology. Not only are we identifying results for patients at the end of long diagnostic odysseys of years and sometimes decades, but we are also seeing the real impact of genomes being a first line test in diagnosing patients early and during a time where treatments may still be effective, said Christine Stanley, PhD, FACMG, Chief Director of Clinical Genomics at Variantyx. Our team of MDs, PhDs and Genetic Counselors are honored and humbled to lead the way in using genomes to not only identify single nucleotide variants, but, by using our sophisticated software, to also identify challenging variant types like copy number variants, short tandem repeats, Alu insertions, inversions, single exon deletions and mosaic aneuploidy. By overcoming the limitations of all other platforms used today, were providing much needed answers to patients and their families.
About Variantyx
Variantyx is a CLIA/CAP laboratory providing Genomic Unity, a whole genome sequencing (WGS)-based testing program for diagnosis of rare inherited and neurological disorders. Its single method approach to comprehensive genetic testing identifies multiple variant types within a single patient sample to provide a unified clinical report. For more information, please visit http://www.variantyx.com.
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Variantyx Surpasses 2500 Genomes Analyzed, Highlights the Value of Its WGS-Based Testing Methodology - Business Wire
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Ashion Analytics to Present Data on the Value of Comprehensive Genomic Profiling of Gastrointestinal Cancers by Utilizing the GEM ExTra Test -…
Posted: at 1:58 pm
PHOENIX, Jan. 15, 2021 /PRNewswire/ -- Ashion Analytics LLC, a CLIA-certified and CAP-accredited clinical laboratory announced today that they will present data at the 2021 American Society for Clinical Oncology Gastrointestinal (ASCO GI) virtual meeting.
Abstract #109Session Title: Colorectal CancerDate: January 15, 2021; Release Time: 8 am EST
Title: Genomic profiling of gastrointestinal cancers by comprehensive tumor-normal sequencingAuthors: Fadel S. Alyaqoub, Pawan Noel, Szabolcs Szelinger, Thanemozhi G. Natarajan, Susan M. Dombrowski, Audrey A. Ozols, Laurie J. Goodman, Janine LoBello, Thomas Royce, Gargi D. Basu
Background: Gastrointestinal cancers (GIC) account for 26% of global cancer incidence and 35% of cancer-related deaths. We investigated the molecular landscape and therapeutic targets across 22 types of GIC using whole exome (WES) and whole transcriptome sequencing (WTS).Methods: GEM ExTra assay was performed on 844 paired samples (ages 18-90 years, median= 61 years). Targeted sequence coverage was 180X for germline DNA and 400X for tumor DNA. Reportable somatic alterations included single base substitutions, indels, Copy Number Alterations, gene fusions, alternate transcripts, as well as tumor mutational burden (TMB) and microsatellite instability (MSI) status. Germline subtraction identified somatic-specific alterations.Results: Analysis of 844 GIC patient samples, including esophageal, gastric cancer (GC), biliary tract (BT), pancreatic cancer (PC), colorectal cancer (CRC), and other cancers. The median number of alterations was 3 per GIC patient. The 5 most common actionable alterations were in APC, KRAS, CDKN2A, ARID1A and PIK3CA. Activation of Wnt signaling was found in 344/844 (40.8%), with the majority being in CRC cases. Alterations in cell cycle genes including TP53, CDKN2A, CDK4/6 and others were noted in 520/844 (61.6%) cases and in 129/844 (15.3%) excluding TP53 alterations, suggesting benefit from CDK4/6 inhibitors. Alterations in DNA damage repair genes were noted in 66/844 (7.9%) cases. Activation of PI3K/PTEN/Akt/mTOR pathway was noted in 183/844 (17%), with the majority harbored in CRC, suggesting benefit from targeting this pathway. ERBB2 amplification and mutations were noted in 41/844 (4.9%) across different GIC tumor types. Alterations in homologous recombination genes predicting platinum and PARP inhibitor response was noted in 167/844 (19.8%) samples distributed across GIC subtypes. KRAS (G12C) mutation was found in 21/324 (6.5%) of the combined PC and CRC tumors, thus allowing patients to enroll in clinical trials with G12C-specific inhibitors. Most cases with MSI- and TMB-high status were identified in GC and CRC tumors and may be predictive of response to immunotherapy. WTS identified actionable fusions, including FGFR1/2/3 and novel NRG1 fusions in BT cancers.Conclusions: Our study revealed actionable targets used in patient selection for precision therapies, in addition to other mutational profiles of clinical significance. Overall, comprehensive genomic profiling enabled detection of established and novel actionable alterations, including fusions, which may have gone undetected using hotspot panels.
"Our study provides a comprehensive analysis of molecular signatures across 22 different gastrointestinal cancers using whole exome and whole transcriptome analysis. Further, the highly sensitive GEM ExTra assay utilizing tumor and matched normal samples maximizes detection of rare actionable alterations therapy providing treatment options for targeted therapy as well as immunotherapy across gastrointestinal cancers," said Gargi D. Basu, Ph.D., Ashion Analytics Senior Director of Clinical Curation.
About Ashion Analytics LLCAshion Analytics LLC is a CLIA-certified and CAP-accredited clinical laboratory that uses advanced genomic technologies to offer a wide range of testing capabilities, including GEM ExTra to assist physicians in providing options for precision cancer treatments. Ashion was developed and launched by the Translational Genomics Research Institute (TGen), an affiliate of City of Hope. TGen is a pioneer in the use of genomics to identify treatment options for cancer patients.
About TGen, an affiliate of City of HopeTranslational Genomics Research Institute (TGen) is a Phoenix, Arizona-based non-profit organization dedicated to conducting groundbreaking research with life-changing results. TGen is affiliated with City of Hope, a world-renowned independent research and treatment center for cancer, diabetes and other life-threatening diseases: http://www.cityofhope.org. This precision medicine affiliation enables both institutes to complement each other in research and patient care, with City of Hope providing a significant clinical setting to advance scientific discoveries made by TGen. TGen is focused on helping patients with neurological disorders, cancer, diabetes and infectious diseases through cutting-edge translational research (the process of rapidly moving research toward patient benefit). TGen physicians and scientists work to unravel the genetic components of both common and complex rare diseases in adults and children. Working with collaborators in the scientific and medical communities worldwide, TGen makes a substantial contribution to help our patients through efficiency and effectiveness of the translational process. For more information, visit: http://www.tgen.org. Follow TGen on Facebook, LinkedIn and Twitter @TGen.
Ashion Analytics ContactGargi D. Basu, Ph.D.Senior Director, Clinical CurationAshion Analytics LLCgbasu@ashion.com480-734-4081www.Ashion.com
TGen Media Contact:Steve YozwiakTGen Senior Science Writer602-343-8704syozwiak@tgen.org
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Opinion: The ever-changing shape of love – Sumter Item
Posted: at 1:58 pm
MYERS
By Winslow Myers
Ongoing events urge us to redefine and refresh that tired old used-up word - love.
Love is the only force strong enough to be the unifying energy that ties our broken country back together. Hate can't do it. Hate and fear have polarized us. We need to choose: We can't love and hate at the same time.
Love is difficult and takes effort. It is easy to love our children because that is built into us, just as the fear which can lead to hate is built into us. But the consistent, firm love that gives us the patience to set limits on children that will help them grow into good citizens and good parents in their turn - and learn in their turn not to give into hate and fear and exasperated impatience - is not instinctive. It must be learned as we go.
Love is self-reflecting. It admits mistakes and learns from them. It's no fun to realize we have been wrong or done something hurtful - just as it is no fun to be hurt. Love is about interdependence, the Golden Rule, the reality that I am not the center of the universe, that others and their needs are as real as me and my needs, and that we are all more alike than different. The tragedy of Donald Trump is that he still hasn't realized these basic elements of being human.
Love is nonviolent, by definition. Violence can never be loving. Period. Self-defense may be necessary, but it isn't love, it's self-defense. The mob in the Capitol hurting and even killing policemen was not defending itself, nor was it defending liberty or democracy. It rationalized its violence on the basis of misinformation about the results of an election that was proven false in more than 60 court cases.
Love does not preoccupy with enemies. If we are loving, we define ourselves by what we are for, not what we are against. If we are sufficiently against something or someone, it can mistakenly justify violence. Instead love calls us to be constructive and look for common ground with adversaries as creatively as we can. Hate dehumanizes the other; love identifies with the other.
That means inclusivity is part of love. Hate separates into parts; love sees the big picture. To say we are one humanity on one planet is a statement of love - and also a demonstration of how the meaning of love really does evolve over time, because a hundred years ago we had not seen the Earth from space. Back then only religious seers were motivated by this aspect of love; now it is accessible to all. Every day the news carries new proof that we're all in the same boat.
So love inevitably puts us in a mode of learning and discovery. We're in a place we've never been before. Love is self-education. What is the truth in any given situation? Love is honest and authentic in its longing for truth. So love overlaps with science - it searches for what works, what leads to life, to goodness, to truth, to beauty.
Self-education in love means learning to work cooperatively with other people toward whatever larger goal we can agree is important or even necessary for survival. Many in the U.S. House and Senate have demonstrated over the past weeks, and months and years, that they have much to learn about working together.
Love is conservative - it conserves life with responsible care. Love is progressive - it hopes for a better world.
Finally, love takes the larger perspective. It is aware that we are here for only an instant in all time, that others before us sacrificed that we could be here, and that we are the gateway to all the future. Love is acceptance of this condition, a willingness not to resist it. As David Attenborough keeps saying, what we do in the next few years will affect the next 2,000 years of life on Earth. That is a statement of how much we need to discover how to love.
Winslow Myers, syndicated by PeaceVoice, author of "Living Beyond War: A Citizen's Guide," serves on the Advisory Board of the War Preventive Initiative.
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