Scientists can now sequence an entire genome overnight

"The sequencing of a virus, much like the sequencing of human DNA from a cheek swab or a drop of blood, is painstaking. Samples are moved along what is essentially an assembly line: “weighed” on exquisitely sensitive “scales” to check the mass of the specimen; bathed with chemical solutions known as reagents; tagged with a “bar code” of genetic material so each sample can be individually tracked. Most of the preparations are about checking the quality of the virus sample and then amplifying its genetic material — in effect, transforming a tiny and invisible amount of the coronavirus extracted from a swab into vast quantities of DNA, all in preparation for being read and analyzed by a device built to do exactly that.

The Illumina NovaSeq 6000 — or “Nova-seeks,” as they’re called are similar to the machines used in China to sequence the coronavirus for the first time. The NovaSeqs are about the size of an office photocopier and have few distinguishing features, apart from a large touch-screen interface and a vent pipe that rises from the back of the device to the ceiling. Each machine costs roughly $1 million; there are about 1,000 of them in the world right now.

The NovaSeqs represent the culmination of about two decades of technological development that in large part began with the Human Genome Project, which was completed in 2003 and funded mainly by the USA National Institutes of Health. The project showed that the human genome — “nature’s complete genetic blueprint for building a human being,” as the N.I.H. describes it — is composed of a sequence of about three billion “base pairs.” These are bonded chemicals coded as A, C, G and T, where A stands for adenine, C for cytosine, G for guanine and T for thymine. The chemical pairs are frequently grouped together on our chromosomes, in about 30,000 information-dense strings, or clumps. The clumps are our genes.

By 2015, the pace of improvement was breathtaking. “When I was a postdoctoral fellow, I actually worked in Fred Sanger’s lab,” Tom Maniatis, the head of the New York Genome Center, told me. “I had to sequence a piece of DNA that was about 35 base pairs, and it took me a year to do that. And now, you can do a genome, with three billion base pairs, overnight.” Also astounding was the decrease in cost. Illumina achieved the $1,000 genome in 2014. Last summer, the company announced that its NovaSeq 6000 could sequence a whole human genome for $600; at the time, deSouza, Illumina’s chief executive, told me that his company’s path to a $100 genome would not entail a breakthrough, just incremental technical improvements. “At this point, there’s no miracle that’s required,” he said. Several of Illumina’s competitors — including BGI, a Chinese genomics company — have indicated that they will also soon achieve a $100 genome. Those in the industry whom I spoke with predicted that it may be only a year or two away. 

These numbers don’t fully explain what faster speeds and affordability might portend. But in health care, the prospect of a cheap whole-genome test, perhaps from birth, suggests a significant step closer to the realization of personalized medicines and lifestyle plans, tailored to our genetic strengths and vulnerabilities. “When that happens, that’s probably going to be the most powerful and valuable clinical test you could have, because it’s a lifetime record,” Maniatis told me.

Yet the biggest difference may be its portability. In 2015, Oxford Nanopore began selling a sampling and sequencing gadget called the Minion (pronounced MIN-eye-on) for $1,000. It is smaller than a small iPhone. The chief executive of Oxford Nanopore, Gordon Sanghera, told me he sees his company’s tool as enabling a future in which sequencing insights can be derived during every minute of every day. Inspection officers working in meatpacking plants would get results about pathogenic infection in minutes; surveyors doing environmental monitoring or wastewater analysis can already do the same. Your dentist might one day do a check of your oral microbiome during a regular visit, or your oncologist might sequence your blood once a month to see if you’re still in remission. A transplantation specialist might even check, on the spot, about the genomic compatibility of an organ donation. “The company’s ethos,” Sanghera says, “is the analysis of anything, by anyone, anywhere.” Indeed, there happens to be a Minion on the International Space Station right now.

The technology, compared with Illumina’s, is considered by most scientists I spoke with to be less accurate, but it has advantages beyond those that Sanghera mentioned. It was the Minion that enabled scientists to test for diseases like Zika without any infrastructure beyond a laptop; more recently, it’s what allowed Esteé Torok and other researchers in Britain to track viral mutations in real time in a hospital. “That ability to do sequencing in the field, even in rural Africa, has opened up possibilities that were never previously even envisioned,” Eric Green, who runs the National Human Genome Research Institute, part of the N.I.H., told me recently."

 If it can be done in an African village, then maybe it can be done in Vilnius? What do you think, ladies and gentlemen recently coming from the Lithuanian countryside?

Lietuvoje prasideda eksponentinė užsikrėtimų koronaviruso variantais fazė

Grafiką galima rasti čia. Dabar pamatysime tikrą krizę. Šimonytė ir Landsbergio anūkas pasikars ant lempų virš jų darbo stalų. Mergelės iš liberaliųjų partijų rūkys marichuaną nesustodamos, kaip garvežiai. 

Ar kas nors moka Lietuvoje dar gražiai gyventi? O taip... Svetka iš Baltarusijos. Ji atidėjo revoliuciją Baltarusijoje iki rugsėjo. Vasaros atostogos. Kaitinsis saulėje prie Žaliųjų ežerų. Neima į galvą pralaimėjimo. Jėga.

Antikūnų vaistai mažina riziką, sako tyrimas

 „Regeneron Pharmaceuticals Inc.“ teigė, kad jo antikūnų vaistas, atlikdamas didžiulį klinikinį tyrimą, maždaug 70% sumažino Covid-19 hospitalizavimo ar mirties riziką, o tai yra pats aiškiausias įrodymas, kad šis vaistas gali padėti pasveikti ankstyvoje ligos stadijoje. 

Tarp asmenų, vartojusių mažesnę antikūnų dozę, 1% buvo hospitalizuoti arba mirė, palyginti su 3,2% pacientų, vartojusių placebą, antradienį pranešė „Regeneron“. 

Tyrimo subjektams, gaunantiems didesnę dozę, buvo panašiai sumažinta rizika, pranešė bendrovė. „Regeneron“ teigė, kad sieks mažesnės dozės FDA leidimo po to, kai ji pasirodys panaši į didesnę šiuo metu turimą dozę. Pokyčiai iš tikrųjų padvigubintų vaisto gamybos pajėgumus. Duomenys dar nebuvo paskelbti išsamiai ar recenzuojamame žurnale. 

 „Regeneron“ vaistas yra vienas iš kelių gydymo būdų, leistų naudoti „Covid-19“ pacientams, siekiant užkirsti kelią sunkioms ligoms ir hospitalizavimui. 

Vaistai skirti pacientams ligos pradžioje, kai manoma, kad virusas yra jautriausias gydymui. 

Tačiau terapija buvo naudojama mažai, nes, pasak gydytojų, yra sudėtingas jų administravimo procesas ir trūksta patikimų klinikinių tyrimų duomenų, įrodančių jų veiksmingumą. „Regeneron“ antradienį paskelbti nauji tyrimo duomenys gali padėti sustiprinti entuziazmą dėl vaistų tarp gydytojų ir ligoninių. Šie duomenys taip pat gali paskatinti įtakingas ekspertų grupes, kurias sukvietė Nacionaliniai sveikatos institutai ir Amerikos infekcinių ligų draugija, išleisti gydymo gaires, kuriose rekomenduojama vartoti vaistą. Lapkritį JAV maisto ir vaistų administracija leido naudoti „Regeneron“ vaistą ir dar vieną antikūnų gydymą, kurį „Eli Lilly & Co“ atliko žmonėms, sergantiems lengvais ar vidutinio sunkumo Covid-19 simptomais, ir kuriems yra didelė rizika susirgti sunkiais atvejais “[1].

1. Antibody Drug Cuts Risks, Study Says
Walker, Joseph. Wall Street Journal, Eastern edition; New York, N.Y. [New York, N.Y]24 Mar 2021: A.6.

Antibody Drug Cuts Risks, Study Says

"Regeneron Pharmaceuticals Inc. said its antibody drug reduced the risk of Covid-19 hospitalization or death by about 70% in a large clinical trial, the most definitive evidence yet that the medicine can aid recovery early in the course of disease.

Among subjects in a late-stage trial receiving a lower dose of the antibody drug, 1% were hospitalized or died, compared with 3.2% of patients receiving placebos, Regeneron said Tuesday. Study subjects getting a higher dose had a similar risk reduction, the company said.

Regeneron said it would seek FDA authorization for the lower dose after it proved similarly effective to the higher dose currently available. The change would effectively double manufacturing capacity of the medicine going forward. The data haven't yet been published in detail or in a peer-reviewed journal.

Regeneron's drug is among a handful of therapies authorized for Covid-19 patients to prevent severe disease and hospitalization. The drugs are targeted at patients early in the disease, when the virus is thought to be most susceptible to treatment.

The therapies have been scantily used, however, because of what doctors say is a cumbersome process for administering them and a lack of robust clinical trial data proving their effectiveness.

The new study data released by Regeneron on Tuesday could help boost enthusiasm for the medication among doctors and hospitals. The data could also eventually prompt influential expert panels convened by the National Institutes of Health and the Infectious Diseases Society of America to issue treatment guidelines recommending the drug's use.

In November, the U.S. Food and Drug Administration cleared Regeneron's drug and another antibody treatment made by Eli Lilly & Co. for treating people with mild or moderate symptoms of Covid-19 who are at high risk of developing severe cases." [1]

1. Antibody Drug Cuts Risks, Study Says
Walker, Joseph. Wall Street Journal, Eastern edition; New York, N.Y. [New York, N.Y]24 Mar 2021: A.6.

Sueco kanalas užblokuotas, užstrigus jame milžiniškam konteinerių laivui

„Laivas, kurio ilgis yra daugiau nei 1300 pėdų, užplaukė ant seklumos ir užblokavo vieną gyvybiškai svarbiausių pasaulio laivybos kelių, kiekviename kanalo gale užstrigus daugiau nei 100 laivų. Maži prieš jų taikinį, vilkikų būriai bandė ištraukti „Ever Given free“, o priekinis krautuvas įtempė jį iškasti iš rytinio kanalo pylimo, kur jo priekis įstrigo. Pasak GAC, nesiliaujantys stiprūs vėjai ir didžiulis laivo dydis apsunkino užduotį. Laivo dydis padidino kiekvieną iššūkį. 

Nors vėjo gūsis gali pasirodyti neįtikėtinas Dovydas prieš laivo Galijotą, bent devynis aukštus ant denio sukrauti konteineriai pasielgė, kaip milžiniška burė, sakė kpt. Konradas, suteikdamas antradienio stipriam vėjui daugiau paviršiaus, į kurį būtų galima atsispirti. 

Konteinerių laivams augant, tai baigėsi naujos kartos itin dideliais laivais, į kuriuos įeina 1312 pėdų ilgio „Ever Given“, Sueco kanalas ir pasauliniai uostai stengėsi išlaikyti tempą. Prieš kelerius metus kanalo dalys buvo išplėstos, nors to nebuvo pakankamai, kad pašalintų įtampą pilotams, įpareigotiems juo plaukioti. Įgulos dydis nepadidėjo, kad atitiktų laivus, sakė kapitonas Konradas, o pilotavimo siaurais kanalais technologijos nepagerėjo.

Tada yra gelbėjimo reikalas. Jei dėl laivo masės neįmanoma nutempti vilkiku, gelbėtojų įgulai gali tekti jį palengvinti pašalinant konteinerius, išpumpuojant vandens balionus, kurie yra jo balastas, ir gilinantis aplink laivo priekį ir laivagalį, sakė jis. Kai 2016 m. netoli Hamburgo uosto, Vokietijoje, užstrigo panašaus dydžio laivas - CSCL "Indijos vandenynas", jį išlaisvinti prireikė 12 vilkikų ir beveik savaitės“. 

Brangzz, tik ne butai Vilniuje, o viskas, kas vežama laivais, įskaitant mūsų pamėgtą dyzeliną.

Suez Canal Blocked After Giant Container Ship Gets Stuck

"The ship, stretching more than 1,300 feet, ran aground and blocked one of the world’s most vital shipping lanes, leaving more than 100 ships stuck at each end of the canal. 

Tiny against their quarry’s bulk, swarms of tugboats raced to try to wrench the Ever Given free, and a front-end loader strained to dig it out from the canal’s eastern embankment, where its bow sat wedged. Continued high winds, along with the sheer size of the ship, complicated the task, according to GAC.
The ship’s size has magnified every challenge. Though a gust of wind may seem an improbable David to the ship’s Goliath, the containers stacked at least nine-high atop the deck would have acted like a giant sail, Capt. Konrad said, giving Tuesday’s high winds more surface area to push against. 

As container ships have grown in scale, culminating in a new generation of ultra-large ships that includes the 1,312-foot-long Ever Given, the Suez Canal and global ports have struggled to keep pace. Parts of the canal were widened several years ago, though not enough to eliminate the tension for pilots charged with navigating it. Crew sizes have not increased to match the vessels, said Capt. Konrad, and technology for piloting through narrow channels has not improved. 

Then there is the matter of rescue. If the ship’s bulk makes it impossible to drag out by tugboat, a salvage crew may need to lighten it by removing containers, pumping out the water tanks that serve as its ballast and dredging around the bow and stern, he said. 

When a similarly sized ship, the CSCL Indian Ocean, became stuck in 2016 near the port of Hamburg, Germany, it took 12 tugboats and nearly a week to free it."

It will be more expensive, just not the apartments in Vilnius, but everything that is transported by ships, including our favorite diesel. 

Vakcinuotieji privalo turėti kaukes, kaip ir visi kiti

 "Vienas tyrimas parodė, kad tik keturi iš 8121 visiškai paskiepytų nuo Covid-19 darbuotojų Teksaso universiteto Pietvakarių medicinos centre Dalase užsikrėtė koronavirusu. Kitas nustatė, kad tik septynių iš 14 990 darbuotojų UC San Diego sveikatos ir Davido Geffeno medicinos mokykloje Kalifornijos universiteto Los Andžele rezultatas buvo teigiamas praėjus dviem ar daugiau savaičių, kai buvo gauta antra vakcinų „Pfizer-BioNTech“ arba „Moderna“ dozė. 

Abi antradienį „New England Journal of Medicine“ paskelbtos ataskaitos rodo, kaip gerai vakcinos veikia realiai intensyvaus viruso perdavimo laikotarpiu. Tačiau šie proveržio atvejai, nors ir gana reti, aiškiai primena, kad skiepyti žmonės nėra nenugalimi, ypač kai virusas ir toliau plačiai cirkuliuoja. Pasak tyrimų, tik kai kuriems Kalifornijos tyrime koronaviruso paveiktiems sveikatos priežiūros darbuotojams pasireiškė simptomai, jie paprastai buvo lengvi, o tai rodo, kad vakcinos buvo apsauginės. Tai pakartoja vakcinos tyrimų duomenis, rodančius, kad proveržio infekcijos buvo lengvos ir nereikėjo hospitalizuoti. Kai kuriems žmonėms visiškai nebuvo jokių simptomų ir jie buvo atrasti, tik atliekant tyrimus arba medicininės priežiūros eigoje“.