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Okazaki A, Horpaopan S, Zhang QR, Randesi M, Ott J
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Genotype Pattern Mining for Pairs of Interacting Variants Underlying Digenic Traits
GENES 2021 AUG; 12(8):? Article 1160
Some genetic diseases ("digenic traits") are due to the interaction between two DNA variants, which presumably reflects biochemical interactions. For example, certain forms of Retinitis Pigmentosa, a type of blindness, occur in the presence of two mutant variants, one each in the ROM1 and RDS genes, while the occurrence of only one such variant results in a normal phenotype. Detecting variant pairs underlying digenic traits by standard genetic methods is difficult and is downright impossible when individual variants alone have minimal effects. Frequent pattern mining (FPM) methods are known to detect patterns of items. We make use of FPM approaches to find pairs of genotypes (from different variants) that can discriminate between cases and controls. Our method is based on genotype patterns of length two, and permutation testing allows assigning p-values to genotype patterns, where the null hypothesis refers to equal pattern frequencies in cases and controls. We compare different interaction search approaches and their properties on the basis of published datasets. Our implementation of FPM to case-control studies is freely available.
Bosch B, De Jesus MA, Poulton NC, Zhang WZ, Engelhart CA, Zaveri A, Lavalette S, Ruecker N, Trujillo C, Wallach JB, Li SQ, Ehrt S, Chait BT, Schnappinger D, Rock JM
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Genome-wide gene expression tuning reveals diverse vulnerabilities of M. tuberculosis
CELL 2021 AUG 19; 184(17):4579-4592.e24 Article e24
Antibacterial agents target the products of essential genes but rarely achieve complete target inhibition. Thus, the all-or-none definition of essentiality afforded by traditional genetic approaches fails to discern the most attractive bacterial targets: those whose incomplete inhibition results in major fitness costs. In contrast, gene "vulnerability'' is a continuous, quantifiable trait that relates the magnitude of gene inhibition to the effect on bacterial fitness. We developed a CRISPR interference-based functional genomicsmethod to systematically titrate gene expression in Mycobacterium tuberculosis (Mtb) and monitor fitness outcomes. We identified highly vulnerable genes in various processes, including novel targets unexplored for drug discovery. Equally important, we identified invulnerable essential genes, potentially explaining failed drug discovery efforts. Comparison of vulnerability between the reference and a hypervirulent Mtb isolate revealed incomplete conservation of vulnerability and that differential vulnerability can predict differential antibacterial susceptibility. Our results quantitatively redefine essential bacterial processes and identify high-value targets for drug development.
Eberhardt KA, Sarfo FS, Klupp EM, Dompreh A, Di Cristanziano V, Kuffour EO, Boateng R, Norman B, Phillips RO, Aepfelbacher M, Feldt T
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Intestinal Colonization with Tropheryma whipplei-Clinical and Immunological Implications for HIV Positive Adults in Ghana
MICROORGANISMS 2021 AUG; 9(8):? Article 1781
Background: Recent studies demonstrated higher prevalence rates of Tropheryma whipplei (T. whipplei) in HIV positive than in HIV negative subjects. However, associations with the immune status in HIV positive participants were conflicting. Methods: For this cross-sectional study, stool samples of 906 HIV positive and 98 HIV negative individuals in Ghana were tested for T. whipplei. Additionally, sociodemographic parameters, clinical symptoms, medical drug intake, and laboratory parameters were assessed. Results: The prevalence of T. whipplei was 5.85% in HIV positive and 2.04% in HIV negative participants. Within the group of HIV positive participants, the prevalence reached 7.18% in patients without co-trimoxazole prophylaxis, 10.26% in subjects with ART intake, and 12.31% in obese participants. Frequencies of clinical symptoms were not found to be higher in HIV positive T. whipplei carriers compared to T. whipplei negative participants. Markers of immune activation were lower in patients colonized with T. whipplei. Multivariate regression models demonstrated an independent relationship of a high CD4+ T cell count, a low HIV-1 viral load, and an obese body weight with the presence of T. whipplei. Conclusions: Among HIV positive individuals, T. whipplei colonization was associated with a better immune status but not with clinical consequences. Our data suggest that the withdrawal of co-trimoxazole chemoprophylaxis among people living with HIV on stable cART regimen may inadvertently increase the propensity towards colonization with T. whipplei.
Nirody JA, Duran LA, Johnston D, Cohen DJ
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Tardigrades exhibit robust interlimb coordination across walking speeds and terrains
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 2021 AUG 31; 118(35):? Article e2107289118
Tardigrades must negotiate heterogeneous, fluctuating environments and accordingly utilize locomotive strategies capable of dealing with variable terrain. We analyze the kinematics and interleg coordination of freely walking tardigrades (species: Hypsibius exemplaris). We find that tardigrade walking replicates several key features of walking in insects despite disparities in size, skeleton, and habitat. To test the effect of environmental changes on tardigrade locomotor control circuits we measure kinematics and interleg coordination during walking on two substrates of different stiffnesses. We find that the phase offset between contralateral leg pairs is flexible, while ipsilateral coordination is preserved across environmental conditions. This mirrors similar results in insects and crustaceans. We propose that these functional similarities in walking coordination between tardigrades and arthropods is either due to a generalized locomotor control circuit common to panarthropods or to independent convergence onto an optimal strategy for robust multilegged control in small animals with simple circuitry. Our results highlight the value of tardigrades as a comparative system toward understanding the mechanisms-neural and/or mechanical-underlying coordination in panarthropod locomotion.
Aldridge BB, Barros-Aguirre D, Barry CE, Bates RH, Berthel SJ, Boshoff HI, Chibale K, Chu XJ, Cooper CB, Dartois V, Duncan K, Fotouhi N, Gusovsky F, Hipskind PA, Kempf DJ, Lelievre J, Lenaerts AJ, McNamara CW, Mizrahi V, Nathan C, Olsen DB, Parish T, Petrassi HM, Pym A, Rhee KY, Robertson GT, Rock JM, Rubin EJ, Russell B, Russell DG, Sacchettini JC, Schnappinger D, Schrimpf M, Upton AM, Warner P, Wyatt PG, Yuan Y
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The Tuberculosis Drug Accelerator at year 10: what have we learned?
NATURE MEDICINE 2021 AUG; 27(8):1333-1337
The Tuberculosis Drug Accelerator, an experiment designed to facilitate collaboration in tuberculosis drug discovery by breaking down barriers among competing labs and institutions, has reached a 10-year landmark. We review the consortium's achievements, advantages and limitations and advocate for the application of similar models to other diseases.
Gleicher N, Patrizio P, Brivanlou A
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Preimplantation Genetic Testing for Aneuploidy - a Castle Built on Sand
TRENDS IN MOLECULAR MEDICINE 2021 AUG; 27(8):731-742
Preimplantation genetic testing for aneuploidy (PGT-A) has become a routine add-on for in vitro fertilization (IVF) to determine whether human embryos are to be clinically utilized or disposed of. Studies claiming IVF outcome improvements following PGT-A, however, used highly selected patient populations or inappropriate statistical methodologies. PGT-A was never clinically validated in its ability to define a human embryo as chromosomal normal, mosaic, or aneuploid, nor certified by a regulatory body, or an authoritative professional organization. Because of a high false-positive rate, PGT-A, actually reduces live IVF birth chances for many patients. Furthermore, in recent studies the PGT-A hypothesis was demonstrated to be mistaken for biological, mathematical and technical reasons. PGT-A, therefore, should clinically only be offered within experimental study frameworks.
Brandt JN, Kim Y
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Targeting Polo-like kinase in space and time during C. elegans meiosis
CELL CYCLE 2021 AUG 18; 20(16):1519-1526
A central player in meiotic chromosome dynamics is the conserved Polo-like kinase (PLK) family. PLKs are dynamically localized to distinct structures during meiotic prophase and phosphorylate a diverse group of substrates to control homolog pairing, synapsis, and meiotic recombination. In a recent study, we uncovered the mechanisms that control the targeting of a meiosis-specific PLK-2 in C. elegans. In early meiotic prophase, PLK-2 localizes to special chromosome regions known as pairing centers and drives homolog pairing and synapsis. PLK-2 then relocates to the synaptonemal complex (SC) after crossover designation and mediates chromosome remodeling required for homolog separation. What controls this intricate targeting of PLK-2 in space and time? We discuss recent findings and remaining questions for the future.
Yang ZT, Freiwald WA
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Joint encoding of facial identity, orientation, gaze, and expression in the middle dorsal face area
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 2021 AUG 17; 118(33):? Article e2108283118
The last two decades have established that a network of face-selective areas in the temporal lobe of macaque monkeys supports the visual processing of faces. Each area within the network contains a large fraction of face-selective cells. And each area encodes facial identity and head orientation differently. A recent brain-imaging study discovered an area outside of this network selective for naturalistic facial motion, the middle dorsal (MD) face area. This finding offers the opportunity to determine whether coding principles revealed inside the core network would generalize to face areas outside the core network. We investigated the encoding of static faces and objects, facial identity, and head orientation, dimensions which had been studied in multiple areas of the core face-processing network before, as well as facial expressions and gaze. We found that MD populations form a faceselective cluster with a degree of selectivity comparable to that of areas in the core face-processing network. MD encodes facial identity robustly across changes in head orientation and expression, it encodes head orientation robustly against changes in identity and expression, and it encodes expression robustly across changes in identity and head orientation. These three dimensions are encoded in a separable manner. Furthermore, MD also encodes the direction of gaze in addition to head orientation. Thus, MD encodes both structural properties (identity) and changeable ones (expression and gaze) and thus provides information about another animal's direction of attention (head orientation and gaze). MD contains a heterogeneous population of cells that establish a multidimensional code for faces.
Sirunyan AM, Tumasyan A, Adam W, Ambrogi F, Bergauer T, Dragicevic M, Ero J, Del Valle AE, Fruhwirth R, Jeitler M, Krammer N, Lechner L, Liko D, Madlener T, Mikulec I, Pitters FM, Rad N, Schieck J, Schofbeck R, Spanring M, Templ S, Waltenberger W, Wulz CE, Zarucki M, Chekhovsky V, Litomin A, Makarenko V, Gonzalez JS, Darwish MR, De Wolf EA, Di Croce D, Janssen X, Kello T, Lelek A, Pieters M, Sfar HR, Van Haevermaet H, Van Mechelen P, Van Putte S, Van Remortel N, Blekman F, Bols ES, Chhibra SS, D'Hondt J, De Clercq J, Lontkovskyi D, Lowette S, Marchesini I, Moortgat S, Morton A, Python Q, Tavernier S, Van Doninck W, Van Mulders P, Beghin D, Bilin B, Clerbaux B, De Lentdecker G, Delannoy H, Dorney B, Favart L, Grebenyuk A, Kalsi AK, Makarenko I, Moureaux L, Petre L, Popov A, Postiau N, Starling E, Thomas L, Vander Velde C, Vanlaer P, Vannerom D, Wezenbeek L, Cornelis T, Dobur D, Gruchala M, Khvastunov I, Niedziela M, Roskas C, Skovpen K, Tytgat M, Verbeke W, Vermassen B, Vit M, Bruno G, Bury F, Caputo C, David P, Delaere C, Delcourt M, Donertas IS, Giammanco A, Lemaitre V, Mondal K, Prisciandaro J, Taliercio A, Teklishyn M, Vischia P, Wuyckens S, Zobec J, Alves GA, Silva GC, Hensel C, Moraes A, Junior WLA, Das Chagas EBB, Malbouisson HB, Carvalho W, Chinellato J, Coelho E, Da Costa EM, Da Silveira GG, Damiao DD, De Souza SF, Martins J, Figueiredo DM, Jaime MM, De Almeida MM, Herrera CM, Mundim L, Nogima H, Teles PR, Rosas LJS, Santoro A, Do Amaral SMS, Sznajder A, Thiel M, Manganote EJT, De Araujo FTD, Pereira AV, Bernardes CA, Calligaris L, Tomei TRFP, Gregores EM, Lemos DS, Mercadante PG, Novaes SF, Padula SS, Aleksandrov A, Hadjiiska R, Iaydjiev P, Misheva M, Rodozov M, Shopova M, Sultanov G, Bonchev M, Dimitrov A, Ivanov T, Litov L, Pavlov B, Petkov P, Petrov A, Fang W, Guo Q, Wang H, Yuan L, Ahmad M, Hu Z, Wang Y, Chapon E, Chen GM, Chen HS, Chen M, Leggat D, Liao H, Liu Z, Sharma R, Spiezia A, Tao J, Thomas-wilsker J, Wang J, Zhang H, Zhang S, Zhao J, Agapitos A, Ban Y, Chen C, Levin A, Li J, Li Q, Lu M, Lyu X, Mao Y, Qian SJ, Wang D, Wang Q, Xiao J, You Z, Gao X, Xiao M, Avila C, Cabrera A, Florez C, Fraga J, Sarkar A, Delgado MAS, Jaramillo J, Guisao JM, Ramirez F, Alvarez JDR, Gonzalez CAS, Arbelaez NV, Giljanovic D, Godinovic N, Lelas D, Puljak I, Sculac T, Antunovic Z, Kovac M, Brigljevic V, Ferencek D, Majumder D, Mesic B, Roguljic M, Starodumov A, Susa T, Ather MW, Attikis A, Erodotou E, Ioannou A, Kole G, Kolosova M, Konstantinou S, Mavromanolakis G, Mousa J, Nicolaou C, Ptochos F, Razis PA, Rykaczewski H, Saka H, Tsiakkouri D, Finger M, Finger M, Kveton A, Tomsa J, Ayala E, Jarrin EC, Abdelalim AA, Abu Zeid S, Khalil S, Mahmoud MA, Mohammed Y, Bhowmik S, De Oliveira ACA, Dewanjee RK, Ehataht K, Kadastik M, Raidal M, Veelken C, Eerola P, Kirschenmann H, Voutilainen M, Brucken E, Havukainen J, Karimaki V, Kim MS, Kinnunen R, Lampen T, Lassila-Perini K, Laurila S, Lehti S, Linden T, Siikonen H, Tuominen E, Tuominiemi J, Luukka P, Tuuva T, Besancon M, Couderc F, Dejardin M, Denegri D, Faure JL, Ferri F, Ganjour S, Givernaud A, Gras P, de Monchenault GH, Jarry P, Lenzi B, Locci E, Malcles J, Rander J, Rosowsky A, Sahin MO, Savoy-Navarro A, Titov M, Yu GB, Ahuja S, Amendola C, Beaudette F, Bonanomi M, Busson P, Charlot C, Davignon O, Diab B, Falmagne G, de Cassagnac RG, Hakimi A, Kucher I, Lobanov A, Perez CM, Nguyen M, Ochando C, Paganini P, Rembser J, Salerno R, Sauvan JB, Sirois Y, Zabi A, Zghiche A, Agram JL, Andrea J, Bloch D, Bourgatte G, Brom JM, Chabert EC, Collard C, Fontaine JC, Gele D, Goerlach U, Grimault C, Le Bihan AC, Van Hove P, Asilar E, Beauceron S, Bernet C, Boudoul G, Camen C, Carle A, Chanon N, Contardo D, Depasse P, El Mamouni H, Fay J, Gascon S, Gouzevitch M, Ille B, Jain S, Laktineh IB, Lattaud H, Lesauvage A, Lethuillier M, Mirabito L, Torterotot L, Touquet G, Vander Donckt M, Viret S, Toriashvili T, Tsamalaidze Z, Feld L, Klein K, Lipinski M, Meuser D, Pauls A, Preuten M, Rauch MP, Schulz J, Teroerde M, Eliseev D, Erdmann M, Fackeldey P, Fischer B, Ghosh S, Hebbeker T, Hoepfner K, Keller H, Mastrolorenzo L, Merschmeyer M, Meyer A, Millet P, Mocellin G, Mondal S, Mukherjee S, Noll D, Novak A, Pook T, Pozdnyakov A, Quast T, Radziej M, Rath Y, Reithler H, Roemer J, Schmidt A, Schuler SC, Sharma A, Wiedenbeck S, Zaleski S, Dziwok C, Flugge G, Ahmad WH, Hlushchenko O, Kress T, Nowack A, Pistone C, Pooth O, Roy D, Sert H, Stahl A, Ziemons T, Petersen HA, Martin MA, Asmuss P, Babounikau I, Baxter S, Behnke O, Martinez AB, Bin Anuar AA, Borras K, Botta V, Brunner D, Campbell A, Cardini A, Connor P, Rodriguez SC, Danilov V, De Wit A, Defranchis MM, Didukh L, Damiani DD, Eckerlin G, Eckstein D, Eichhorn T, Elwood A, Banos LIE, Gallo E, Geiser A, Giraldi A, Grohsjean A, Guthoff M, Harb A, Jafari A, Jomhari NZ, Jung H, Kasem A, Kasemann M, Kaveh H, Kleinwort C, Knolle J, Krucker D, Lange W, Lenz T, Lidrych J, Lipka K, Lohmann W, Mankel R, Melzer-Pellmann IA, Metwally J, Meyer AB, Meyer M, Missiroli M, Mnich J, Mussgiller A, Myronenko V, Otarid Y, Adan DP, Pflitsch SK, Pitzl D, Raspereza A, Saggio A, Saibel A, Savitskyi M, Scheurer V, Schutze P, Schwanenberger C, Shevchenko R, Singh A, Ricardo RES, Tholen H, Tonon N, Turkot O, Vagnerini A, Van de Klundert M, Walsh R, Walter D, Wen Y, Wichmann K, Wissing C, Wuchterl S, Zenaiev O, Zlebcik R, Aggleton R, Bein S, Benato L, Benecke A, De Leo K, Dreyer T, Ebrahimi A, Feindt F, Frohlich A, Garbers C, Garutti E, Gunnellini P, Haller J, Hinzmann A, Karavdina A, Kasieczka G, Klanner R, Kogler R, Kutzner V, Lange J, Lange T, Malara A, Multhaup J, Niemeyer CEN, Nigamova A, Rodriguez KJP, Rieger O, Schleper P, Schumann S, Schwandt J, Schwarz D, Sonneveld J, Stadie H, Steinbruck G, Vormwald B, Zoi I, Baselga M, Baur S, Bechtel J, Berger T, Butz E, Caspart R, Chwalek T, De Boer W, Dierlamm A, Droll A, El Morabit K, Faltermann N, Floh K, Giffels M, Gottmann A, Hartmann F, Heidecker C, Husemann U, Iqbal MA, Katkov I, Keicher P, Koppenhofer R, Maier S, Metzler M, Mitra S, Mozer MU, Muller D, Muller T, Musich M, Quast G, Rabbertz K, Rauser J, Savoiu D, Schafer D, Schnepf M, Schroder M, Seith D, Shvetsov I, Simonis HJ, Ulrich R, Wassmer M, Weber M, Wohrmann C, Wolf R, Wozniewski S, Anagnostou G, Asenov P, Daskalakis G, Geralis T, Kyriakis A, Loukas D, Paspalaki G, Stakia A, Diamantopoulou M, Karasavvas D, Karathanasis G, Kontaxakis P, Koraka CK, Manousakis-katsikakis A, Panagiotou A, Papavergou I, Saoulidou N, Theofilatos K, Vellidis K, Vourliotis E, Bakas G, Kousouris K, Papakrivopoulos I, Tsipolitis G, Zacharopoulou A, Evangelou I, Foudas C, Gianneios P, Katsoulis P, Kokkas P, Mallios S, Manitara K, Manthos N, Papadopoulos I, Strologas J, Bartok M, Chudasama R, Gadallah MMA, Lokos S, Major P, Mandal K, Mehta A, Pasztor G, Suranyi O, Veres GI, Bencze G, Hajdu C, Horvath D, Sikler F, Veszpremi V, Vesztergombi G, Czellar S, Karancsi J, Molnar J, Szillasi Z, Teyssier D, Raics P, Trocsanyi ZL, Ujvari B, Choudhury S, Komaragiri JR, Kumar D, Panwar L, Tiwari PC, Bahinipati S, Dash D, Kar C, Mal P, Mishra T, Bindhu VKMN, Nayak A, Sahoo DK, Sur N, Swain SK, Bansal S, Beri SB, Bhatnagar V, Chauhan S, Dhingra N, Gupta R, Kaur A, Kaur S, Kumari P, Lohan M, Meena M, Sandeep K, Sharma S, Singh JB, Virdi AK, Ahmed A, Bhardwaj A, Choudhary BC, Garg RB, Gola M, Keshri S, Kumar A, Naimuddin M, Priyanka P, Ranjan K, Shah A, Bharti M, Bhattacharya R, Bhattacharya S, Bhowmik D, Dutta S, Ghosh S, Gomber B, Maity M, Nandan S, Palit P, Purohit A, Rout PK, Saha G, Sarkar S, Sharan M, Singh B, Thakur S, Behera PK, Behera SC, Kalbhor P, Muhammad A, Pradhan R, Pujahari PR, Sharma A, Sikdar AK, Dutta D, Jha V, Kumar V, Mishra DK, Naskar K, Netrakanti PK, Pant LM, Shukla P, Aziz T, Bhat MA, Dugad S, Verma RK, Sarkar U, Banerjee S, Bhattacharya S, Chatterjee S, Das P, Guchait M, Karmakar S, Kumar S, Majumder G, Mazumdar K, Mukherjee S, Roy D, Sahoo N, Dube S, Kansal B, Kapoor A, Kothekar K, Pandey S, Rane A, Rastogi A, Sharma S, Bakhshiansohi H, Chenarani S, Etesami SM, Khakzad M, Najafabadi MM, Felcini M, Grunewald M, Abbrescia M, Aly R, Aruta C, Colaleo A, Creanza D, De Filippis N, De Palma M, Di Florio A, Di Pilato A, Elmetenawee W, Fiore L, Gelmi A, Gul M, Iaselli G, Ince M, Lezki S, Maggi G, Maggi M, Margjeka I, Merlin JA, My S, Nuzzo S, Pompili A, Pugliese G, Ranieri A, Selvaggi G, Silvestris L, Simone FM, Venditti R, Verwilligen P, Abbiendi G, Battilana C, Bonacorsi D, Borgonovi L, Braibant-Giacomelli S, Campanini R, Capiluppi P, Castro A, Cavallo FR, Ciocca C, Cuffiani M, Dallavalle GM, Diotalevi T, Fabbri F, Fanfani A, Fontanesi E, Giacomelli P, Giommi L, Grandi C, Guiducci L, Iemmi F, Lo Meo S, Marcellini S, Masetti G, Navarria FL, Perrotta A, Primavera F, Rovelli T, Siroli GP, Tosi N, Albergo S, Costa S, Di Mattia A, Potenza R, Tricomi A, Tuve C, Barbagli G, Cassese A, Ceccarelli R, Ciulli V, Civinini C, D'Alessandro R, Fiori F, Focardi E, Latino G, Lenzi P, Lizzo M, Meschini M, Paoletti S, Seidita R, Sguazzoni G, Viliani L, Benussi L, Bianco S, Piccolo D, Ferro F, Mulargia R, Robutti E, Tosi S, Benaglia A, Beschi A, Brivio F, Cetorelli F, Ciriolo V, De Guio F, Dinardo ME, Dini P, Gennai S, Ghezzi A, Govoni P, Guzzi L, Malberti M, Malvezzi S, Menasce D, Monti F, Moroni L, Paganoni M, Pedrini D, Ragazzi S, de Fatis TT, Valsecchi D, Zuolo D, Buontempo S, Cavallo N, De Iorio A, Fabozzi F, Fienga F, Iorio AOM, Layer L, Lista L, Meola S, Paolucci P, Rossi B, Sciacca C, Voevodina E, Azzi P, Bacchetta N, Bisello D, Boletti A, Bragagnolo A, Carlin R, Checchia P, Manzano PD, Dorigo T, Gasparini F, Gasparini U, Hoh SY, Margoni M, Meneguzzo AT, Presilla M, Ronchese P, Rossin R, Simonetto F, Strong G, Tiko A, Tosi M, Zanetti M, Zotto P, Zucchetta A, Zumerle G, Braghieri A, Calzaferri S, Fiorina D, Montagna P, Ratti SP, Re V, Ressegotti M, Riccardi C, Salvini P, Vai I, Vitulo P, Biasini M, Bilei GM, Ciangottini D, Fano L, Lariccia P, Mantovani G, Mariani V, Menichelli M, Moscatelli F, Rossi A, Santocchia A, Spiga D, Tedeschi T, Androsov K, Azzurri P, Bagliesi G, Bertacchi V, Bianchini L, Boccali T, Castaldi R, Ciocci MA, Dell'Orso R, Di Domenico MR, Donato S, Giannini L, Giassi A, Grippo MT, Ligabue F, Manca E, Mandorli G, Messineo A, Palla F, Ramirez-Sanchez G, Rizzi A, Rolandi G, Chowdhury SR, Shafiei N, Spagnolo P, Tenchini R, Tonelli G, Venturi A, Verdini PG, Cavallari F, Cipriani M, Del Re D, Di Marco E, Diemoz M, Longo E, Meridiani P, Organtini G, Pandolfi F, Paramatti R, Quaranta C, Rahatlou S, Rovelli C, Santanastasio F, Soffi L, Tramontano R, Amapane N, Arcidiacono R, Argiro S, Arneodo M, Bartosik N, Bellan R, Bellora A, Biino C, Cappati A, Cartiglia N, Cometti S, Costa M, Covarelli R, Demaria N, Kiani B, Legger F, Mariotti C, Maselli S, Migliore E, Monaco V, Monteil E, Monteno M, Obertino MM, Ortona G, Pacher L, Pastrone N, Pelliccioni M, Angioni GLP, Ruspa M, Salvatico R, Siviero F, Sola V, Solano A, Soldi D, Staiano A, Trocino D, Belforte S, Candelise V, Casarsa M, Cossutti F, Da Rold A, Della Ricca G, Vazzoler F, Dogra S, Huh C, Kim B, Kim DH, Kim GN, Lee J, Lee SW, Moon CS, Oh YD, Pak SI, Sekmen S, Yang YC, Kim H, Moon DH, Francois B, Kim TJ, Park J, Cho S, Choi S, Go Y, Ha S, Hong B, Lee K, Lee KS, Lim J, Park J, Park SK, Yoo J, Goh J, Gurtu A, Kim HS, Kim Y, Almond J, Bhyun JH, Choi J, Jeon S, Kim J, Kim JS, Ko S, Kwon H, Lee H, Lee K, Lee S, Nam K, Oh BH, Oh M, Oh SB, Radburn-Smith BC, Seo H, Yang UK, Yoon I, Jeon D, Kim JH, Ko B, Lee JSH, Park IC, Roh Y, Song D, Watson IJ, Yoo HD, Choi Y, Hwang C, Jeong Y, Lee H, Lee Y, Yu I, Maghrbi Y, Veckalns V, Juodagalvis A, Rinkevicius A, Tamulaitis G, Abdullah WATW, Yusli MN, Zolkapli Z, Benitez JF, Hernandez AC, Quijada JAM, Palomo LV, Castilla-Valdez H, De La Cruz-Burelo E, Heredia-De La Cruz I, Lopez-Fernandez R, Sanchez-Hernandez A, Moreno SC, Barrera CO, Ramirez-Garcia M, Valencia FV, Eysermans J, Pedraza I, Ibarguen HAS, Estrada CU, Pineda AM, Mijuskovic J, Raicevic N, Krofcheck D, Bheesette S, Butler PH, Ahmad A, Asghar MI, Awan MIM, Hassan Q, Hoorani HR, Khan WA, Shah MA, Shoaib M, Waqas M, Bialkowska H, Bluj M, Boimska B, Frueboes T, Gorski M, Kazana M, Szleper M, Traczyk P, Zalewski P, Bunkowski K, Byszuk A, Doroba K, Kalinowski A, Konecki M, Krolikowski J, Olszewski M, Walczak M, Araujo M, Bargassa P, Bastos D, Faccioli P, Gallinaro M, Hollar J, Leonardo N, Niknejad T, Seixas J, Shchelina K, Toldaiev O, Varela J, Afanasiev S, Baginyan A, Bunin P, Golunov A, Golutvin I, Gorbunov I, Kamenev A, Karjavine V, Kashunin I, Korenkov V, Lanev A, Malakhov A, Matveev V, Moisenz P, Palichik V, Perelygin V, Savina M, Shmatov S, Shulha S, Smirnov V, Teryaev O, Voytishin N, Zarubin A, Gavrilov G, Golovtcov V, Ivanov Y, Kim V, Kuznetsova E, Murzin V, Oreshkin V, Smirnov I, Sosnov D, Sulimov V, Uvarov L, Volkov S, Vorobyev A, Andreev Y, Dermenev A, Gninenko S, Golubev N, Karneyeu A, Kirsanov M, Krasnikov N, Pashenkov A, Pivovarov G, Tlisov D, Toropin A, Epshteyn V, 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Hard color-singlet exchange in dijet events in proton-proton collisions at root s=13 TeV
PHYSICAL REVIEW D 2021 AUG 26; 104(3):? Article 032009
Events where the two leading jets are separated by a pseudorapidity interval devoid of particle activity, known as jet-gap-jet events, are studied in proton-proton collisions at root s = 13 TeV. The signature is expected from hard color-singlet exchange. Each of the highest transverse momentum (p(T)) jets must have p(T)(jet) > 40 GeV and pseudorapidity 1.4 < vertical bar eta(jet)vertical bar < 4.7, with eta(jet1)eta(jet2) < 0, where jet1 and jet2 are the leading and subleading jets in p(T), respectively. The analysis is based on data collected by the CMS and TOTEM experiments during a low luminosity, high-beta* run at the CERN LHC in 2015, with an integrated luminosity of 0.66 pb(-1). Events with a low number of charged particles with p(T) > 0.2 GeV in the interval vertical bar eta vertical bar < 1 between the jets are observed in excess of calculations that assume only color-exchange. The fraction of events produced via color-singlet exchange, f(CSE), is measured as a function of p(T)(jet2), the pseudorapidity difference between the two leading jets, and the azimuthal angular separation between the two leading jets. The fraction f(CSE) has values of 0.4-1.0%. The results are compared with previous measurements and with predictions from perturbative quantum chromodynamics. In addition, the first study of jet-gap-jet events detected in association with an intact proton using a subsample of events with an integrated luminosity of 0.40 pb(-1) is presented. The intact protons are detected with the Roman pot detectors of the TOTEM experiment. The f(CSE) in this sample is 2.91 +/- 0.70(stat)(-1.01)(+1.08)(syst) times larger than that for inclusive dijet production in dijets with similar kinematics.
West AP, Wertheim JO, Wang JC, Vasylyeva TI, Havens JL, Chowdhury MA, Gonzalez E, Fang CE, Di Lonardo SS, Hughes S, Rakeman JL, Lee HH, Barnes CO, Gnanapragasam PNP, Yang Z, Gaebler C, Caskey M, Nussenzweig MC, Keeffe JR, Bjorkman PJ
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Detection and characterization of the SARS-CoV-2 lineage B.1.526 in New York
NATURE COMMUNICATIONS 2021 AUG 9; 12(1):? Article 4886
Wide-scale SARS-CoV-2 genome sequencing is critical to tracking viral evolution during the ongoing pandemic. We develop the software tool, Variant Database (VDB), for quickly examining the changing landscape of spike mutations. Using VDB, we detect an emerging lineage of SARS-CoV-2 in the New York region that shares mutations with previously reported variants. The most common sets of spike mutations in this lineage (now designated as B.1.526) are L5F, T95I, D253G, E484K or S477N, D614G, and A701V. This lineage was first sequenced in late November 2020. Phylodynamic inference confirmed the rapid growth of the B.1.526 lineage. In concert with other variants, like B.1.1.7, the rise of B.1.526 appears to have extended the duration of the second wave of COVID-19 cases in NYC in early 2021. Pseudovirus neutralization experiments demonstrated that B.1.526 spike mutations adversely affect the neutralization titer of convalescent and vaccinee plasma, supporting the public health relevance of this lineage. West and colleagues develop the Variant Database software tool for examination of changing Spike mutations in SARS-CoV-2 genomes. The authors use this to detect emerging lineages of SARS-CoV-2 in New York and report the rapid spread of the B.1.526 lineage in the city.