Blog

  • Kate Middleton & King Charles’ Sweet Bond Was on Display at Royal Funeral

    Kate Middleton & King Charles’ Sweet Bond Was on Display at Royal Funeral

    Kate Middleton and King Charles have always shared a warm relationship, which was evident in their recent gathering. The royals came together to pay respect to the funeral of Katharine, the Duchess of Kent, on September 16. While leaving the Westminster Cathedral, the Princess of Wales’ gesture as she bid farewell to her father-in-law has been captured in photos.

    Kate Middleton’s sweet gesture towards father-in-law King Charles was captured in a photo

    Kate Middleton’s warm gesture towards King Charles in new photos appeared to be sweet. The two met when the royal family gathered at Westminster Cathedral on Tuesday at the funeral of the Duchess of Kent, Katharine. At the age of 92, Katharine passed away on September 4. As her coffin was shifted to a hearse after the Requiem Mass service, the family members were reportedly standing on the steps. It was time to say goodbye to the attendees.

    When the 76-year-old king was about to go towards his car, his daughter-in-law warmly bid him farewell. She planted a kiss on the monarch’s cheeks, followed by a quick curtsy. While placing her hand on his shoulder, she looked at her father-in-law with warm eyes, showcasing their bond. He seemed to have responded to the gesture in the same way.

    According to PEOPLE, their interaction gave a glimpse into the sweet relationship the two share. Last year, royal biographer Sally Bedell Smith told the outlet that Middleton has always been “like the daughter he never had.” “He shares with William an impulse to protect her,” she added. Furthermore, the king has often displayed his affection for the future queen. In October 2023, he referred to Prince William’s wife as “my beloved daughter-in-law” during his speech at a Kenya banquet.

    Earlier, a report suggested that the two even teamed up to plan a reunion between William and Prince Harry. A source claimed that the 43-year-old princess joined hands with the king to end the two brothers’ ongoing feud at a royal wedding. However, things did not seem to have gone according to plan.

    Originally reported by Suushmmita Sen on Reality Tea.

    The post Photo: Kate Middleton & King Charles’ Sweet Bond Was on Display at Royal Funeral appeared first on Mandatory.

    Continue Reading

  • This ‘megaflash’ is now the longest lightning bolt on record

    This ‘megaflash’ is now the longest lightning bolt on record

    cloud: A plume of molecules or particles, such as water droplets, that move under the action of an outside force, such as wind, radiation or water currents. (in atmospheric science) A mass of airborne water droplets and ice crystals that travel as a plume, usually high in Earth’s atmosphere. Its movement is driven by winds. 

    data: Facts and/or statistics collected together for analysis but not necessarily organized in a way that gives them meaning. For digital information (the type stored by computers), those data typically are numbers stored in a binary code, portrayed as strings of zeros and ones.

    electricity: (adj. electric) A flow of charge, usually from the movement of negatively charged particles, called electrons.

    geostationary orbit: Also known as a geosynchronous orbit. This is a term for the path certain satellites take around the Earth. They move in the same direction as Earth’s rotation. Earth turns on its axis once a day. These orbit around Earth at about the same rate, usually around 23 hours, 56 minutes and 4 seconds. Their longitude (East-to-West location) seems unchanging although their path may seem to vary a bit from North to South). The end result: The satellite appears at the same point in the sky at all times (as seen from someplace on the ground).

    infuse: (n. infusion) To cause something to enter or mix with another thing (which could be an emotion, a flavor or a liquid).

    lightning: A flash of light triggered by the discharge of electricity that occurs between clouds or between a cloud and something on Earth’s surface. The electrical current can cause a flash heating of the air, which can create a sharp crack of thunder.

    millisecond: A thousandth of a second.

    online: (n.) On the internet. (adj.) A term for what can be found or accessed on the internet.

    orbit: The curved path of a celestial object or spacecraft around a galaxy, star, planet or moon. One complete circuit around a celestial body.

    particle: A minute amount of something.

    physicist: A scientist who studies the nature and properties of matter and energy.

    satellite: A moon orbiting a planet or a vehicle or other manufactured object that orbits some celestial body in space.

    system: A network of parts that together work to achieve some function. For instance, the blood, vessels and heart are primary components of the human body’s circulatory system. Similarly, trains, platforms, tracks, roadway signals and overpasses are among the potential components of a nation’s railway system. System can even be applied to the processes or ideas that are part of some method or ordered set of procedures for getting a task done.

    troposphere: The lowest level of Earth’s atmosphere. It runs from the planet’s surface to a height of  8 to 14 kilometers (5 to 9 miles), depending on the latitude. It’s the region where the air is thickest and where most weather occurs. Air currents moving through this region often flow not only horizontally, but often vertically (up and down).

    updraft: A strong mass of air that rises quickly.

    Continue Reading

  • Structure of a functional archaellum in Bacteria of the Chloroflexota phylum

    Structure of a functional archaellum in Bacteria of the Chloroflexota phylum

  • Beeby, M., Ferreira, J. L., Tripp, P., Albers, S.-V. & Mitchell, D. R. Propulsive nanomachines: the convergent evolution of archaella, flagella and cilia. FEMS Microbiol. Rev. 44, 253–304 (2020).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Denise, R., Abby, S. S. & Rocha, E. P. C. Diversification of the type IV filament superfamily into machines for adhesion, protein secretion, DNA uptake, and motility. PLoS Biol. 17, e3000390 (2019).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Makarova, K. S., Koonin, E. V. & Albers, S.-V. Diversity and evolution of type IV pili systems in Archaea. Front. Microbiol. 7, 667 (2016).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • van Wolferen, M., Ajon, M., Driessen, A. J. M. & Albers, S.-V. Molecular analysis of the UV-inducible pili operon from Sulfolobus acidocaldarius. MicrobiologyOpen 2, 928–937 (2013).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Zolghadr, B., Klingl, A., Rachel, R., Driessen, A. J. M. & Albers, S.-V. The bindosome is a structural component of the Sulfolobus solfataricus cell envelope. Extremophiles 15, 235–244 (2011).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Albers, S.-V., Szabó, Z. & Driessen, A. J. M. Archaeal homolog of bacterial type IV prepilin signal peptidases with broad substrate specificity. J. Bacteriol. 185, 3918–3925 (2003).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Reindl, S. et al. Insights on FlaI functions in archaeal motor assembly and motility from structures, conformations and genetics. Mol. Cell 49, 1069–1082 (2013).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Nuno de Sousa Machado, J., Albers, S.-V. & Daum, B. Towards elucidating the rotary mechanism of the archaellum machinery. Front. Microbiol. 13, 848597 (2022).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Ghosh, A. & Albers, S.-V. Assembly and function of the archaeal flagellum. Biochem. Soc. Trans. 39, 64–69 (2011).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Chaudhury, P. et al. The nucleotide-dependent interaction of FlaH and FlaI is essential for assembly and function of the archaellum motor. Mol. Microbiol. 99, 674–685 (2016).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • de Sousa Machado, J. N. et al. Autophosphorylation of the KaiC-like protein ArlH inhibits oligomerization and interaction with ArlI, the motor ATPase of the archaellum. Mol. Microbiol. 116, 943–956 (2021).

    Article 
    PubMed 

    Google Scholar 

  • Tsai, C.-L. et al. The structure of the periplasmic FlaG–FlaF complex and its essential role for archaellar swimming motility. Nat. Microbiol. 5, 216–225 (2020).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Banerjee, A. et al. FlaF is a β-sandwich protein that anchors the archaellum in the archaeal cell envelope by binding the S-layer protein. Structure 23, 863–872 (2015).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Banerjee, A. et al. FlaX, a unique component of the crenarchaeal archaellum, forms oligomeric ring-shaped structures and interacts with the motor ATPase FlaI. J. Biol. Chem. 287, 43322–43330 (2012).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Li, Z., Rodriguez-Franco, M., Albers, S.-V. & Quax, T. E. F. The switch complex ArlCDE connects the chemotaxis system and the archaellum. Mol. Microbiol. 114, 468–479 (2020).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Lassak, K. et al. Molecular analysis of the crenarchaeal flagellum. Mol. Microbiol. 83, 110–124 (2012).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Desmond, E., Brochier-Armanet, C. & Gribaldo, S. Phylogenomics of the archaeal flagellum: rare horizontal gene transfer in a unique motility structure. BMC Evol. Biol. 7, 106 (2007).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Lim, Y., Seo, J.-H., Giovannoni, S. J., Kang, I. & Cho, J.-C. Cultivation of marine bacteria of the SAR202 clade. Nat. Commun. 14, 5098 (2023).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Hug, L. A. et al. Community genomic analyses constrain the distribution of metabolic traits across the Chloroflexi phylum and indicate roles in sediment carbon cycling. Microbiome 1, 22 (2013).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Abby, S. S., Denise, R. & Rocha, E. P. C. Bacterial secretion system classification and evolution. In Bacterial Secretion Systems: Methods and Protocols (eds Journet, L. & Cascales, E.) 1–25 (Springer, 2024). https://doi.org/10.1007/978-1-0716-3445-5_1

  • Sutcliffe, I. C. Cell envelope architecture in the Chloroflexi_ a shifting frontline in a phylogenetic turf war. Environ. Microbiol. 13, 279–282 (2011).

    Article 
    PubMed 

    Google Scholar 

  • Jarrell, K. F., Albers, S.-V. & de Sousa Machado, J. N. A comprehensive history of motility and archaellation in Archaea. FEMS Microbes 2, xtab002 (2021).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Tammam, S. et al. PilMNOPQ from the Pseudomonas aeruginosa type IV pilus system form a transenvelope protein interaction network that interacts with PilA. J. Bacteriol. 195, 2126–2135 (2013).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Kale, V. et al. Litorilinea aerophila gen. nov., sp. nov., an aerobic member of the class Caldilineae, phylum Chloroflexi, isolated from an intertidal hot spring. Int. J. Syst. Evol. Microbiol. 63, 1149–1154 (2013).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Gaisin, V. A. et al. Chloroflexus islandicus sp. nov., a thermophilic filamentous anoxygenic phototrophic bacterium from a geyser. Int. J. Syst. Evol. Microbiol. 67, 1381–1386 (2017).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Herzog, B. & Wirth, R. Swimming behavior of selected species of Archaea. Appl. Environ. Microbiol. 78, 1670–1674 (2012).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Shahapure, R., Driessen, R. P. C., Haurat, M. F., Albers, S.-V. & Dame, R. T. The archaellum: a rotating type IV pilus. Mol. Microbiol. 91, 716–723 (2014).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Schwarzer, S., Rodriguez-Franco, M., Oksanen, H. M. & Quax, T. E. F. Growth phase dependent cell shape of Haloarcula. Microorganisms 9, 231 (2021).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Kinosita, Y., Uchida, N., Nakane, D. & Nishizaka, T. Direct observation of rotation and steps of the archaellum in the swimming halophilic archaeon Halobacterium salinarum. Nat. Microbiol. 1, 16148–16148 (2016).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Fukushima, S., Morohoshi, S., Hanada, S., Matsuura, K. & Haruta, S. Gliding motility driven by individual cell-surface movements in a multicellular filamentous bacterium Chloroflexus aggregans. FEMS Microbiol. Lett. 363, fnw056 (2016).

    Article 
    PubMed 

    Google Scholar 

  • Gambelli, L. et al. An archaellum filament composed of two alternating subunits. Nat. Commun. 13, 710 (2022).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Punjani, A., Rubinstein, J. L., Fleet, D. J. & Brubaker, M. A. CryoSPARC: algorithms for rapid unsupervised cryo-EM structure determination. Nat. Methods 14, 290–296 (2017).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Jamali, K. et al. Automated model building and protein identification in cryo-EM maps. Nature 628, 450–457 (2024).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Teufel, F. et al. SignalP 6.0 predicts all five types of signal peptides using protein language models. Nat. Biotechnol. 40, 1023–1025 (2022).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Kreutzberger, M. A. B. et al. Convergent evolution in the supercoiling of prokaryotic flagellar filaments. Cell 185, 3487–3500.e14 (2022).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Meshcheryakov, V. A. et al. High-resolution archaellum structure reveals a conserved metal-binding site. EMBO Rep. 20, e46340 (2019).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Poweleit, N. et al. CryoEM structure of the Methanospirillum hungatei archaellum reveals structural features distinct from the bacterial flagellum and type IV pilus. Nat. Microbiol. 2, 1622 (2016).

    Google Scholar 

  • Gaines, M. C. et al. Towards a molecular picture of the archaeal cell surface. Nat. Commun. 15, 10401 (2024).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Nothaft, H. & Szymanski, C. M. Protein glycosylation in bacteria: sweeter than ever. Nat. Rev. Microbiol. 8, 765–778 (2010).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • López-Castilla, A. et al. Structure of the calcium-dependent type 2 secretion pseudopilus. Nat. Microbiol. 2, 1686–1695 (2017).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Korotkov, K. V. et al. Calcium is essential for the major pseudopilin in the type 2 secretion system. J. Biol. Chem. 284, 25466–25470 (2009).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Nelson-Sathi, S. et al. Origins of major archaeal clades correspond to gene acquisitions from bacteria. Nature 517, 77–80 (2015).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Palmer, M. et al. Thermophilic Dehalococcoidia with unusual traits shed light on an unexpected past. ISME J. https://doi.org/10.1038/s41396-023-01405-0 (2023).

  • Gaines, M. et al. Unusual cell surfaces, pili and archaella of Thermoplasmatales archaea investigated by cryoEM. Preprint at Research Square https://doi.org/10.21203/rs.3.rs-5269562/v1 (2024).

  • Beaud Benyahia, B., Taib, N., Beloin, C. & Gribaldo, S. Terrabacteria: redefining bacterial envelope diversity, biogenesis and evolution. Nat. Rev. Microbiol. https://doi.org/10.1038/s41579-024-01088-0 (2024).

  • Buist, G., Steen, A., Kok, J. & Kuipers, O. P. LysM, a widely distributed protein motif for binding to (peptido)glycans. Mol. Microbiol. 68, 838–847 (2008).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Sofer, S. et al. Perturbed N-glycosylation of Halobacterium salinarum archaellum filaments leads to filament bundling and compromised cell motility. Nat. Commun. 15, 5841 (2024).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Wilde, A. & Mullineaux, C. W. Motility in cyanobacteria: polysaccharide tracks and type IV pilus motors. Mol. Microbiol. 98, 998–1001 (2015).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Nußbaum, P. et al. An oscillating MinD protein determines the cellular positioning of the motility machinery in Archaea. Curr. Biol. 30, 4956–4972.e4 (2020).

    Article 
    PubMed 

    Google Scholar 

  • Altegoer, F. et al. Structural insights into the mechanism of archaellar rotational switching. Nat. Commun. 13, 2857 (2022).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Livak, K. J. & Schmittgen, T. D. Analysis of relative gene expression data using real-time quantitative PCR and the (2^{-{Delta}{Delta}C_{T}}) method. Methods 25, 402–408 (2001).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Sivabalasarma, S., de Sousa Machado, J. N., Albers, S.-V. & Jarrell, K. F. Archaella isolation. Methods Mol. Biol. 2646, 183–195 (2023).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Emsley, P. & Cowtan, K. Coot: model-building tools for molecular graphics. Acta Crystallogr. D 60, 2126–2132 (2004).

    Article 
    PubMed 

    Google Scholar 

  • Afonine, P. V. et al. Towards automated crystallographic structure refinement with phenix.refine. Acta Crystallogr. D 68, 352–367 (2012).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Liebschner, D. et al. Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix. Acta Crystallogr. D 75, 861–877 (2019).

    Article 
    CAS 

    Google Scholar 

  • Goddard, T. D. et al. UCSF ChimeraX: meeting modern challenges in visualization and analysis. Protein Sci. 27, 14–25 (2018).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Schindelin, J. et al. Fiji: an open-source platform for biological-image analysis. Nat. Methods 9, 676–682 (2012).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Azuaje, F. Review of “Data Mining: Practical Machine Learning Tools and Techniques” by Witten and Frank. Biomed. Eng. Online 5, 51 (2006).

    Article 
    PubMed Central 

    Google Scholar 

  • Ershov, D. et al. TrackMate 7: integrating state-of-the-art segmentation algorithms into tracking pipelines. Nat. Methods 19, 829–832 (2022).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Witwinowski, J. et al. An ancient divide in outer membrane tethering systems in bacteria suggests a mechanism for the diderm-to-monoderm transition. Nat. Microbiol. 7, 411–422 (2022).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Garcia, P. S., Gribaldo, S. & Borrel, G. Diversity and evolution of methane-related pathways in Archaea. Annu. Rev. Microbiol. 76, 727–755 (2022).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Nayfach, S. et al. A genomic catalog of Earth’s microbiomes. Nat. Biotechnol. 39, 499–509 (2021).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Seemann, T. Prokka: rapid prokaryotic genome annotation. Bioinformatics 30, 2068–2069 (2014).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Chaumeil, P.-A., Mussig, A. J., Hugenholtz, P. & Parks, D. H. GTDB-Tk v2: memory friendly classification with the genome taxonomy database. Bioinformatics 38, 5315–5316 (2022).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Price, M. N., Dehal, P. S. & Arkin, A. P. FastTree 2—approximately maximum-likelihood trees for large alignments. PLoS ONE 5, e9490 (2010).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Balaban, M., Moshiri, N., Mai, U., Jia, X. & Mirarab, S. TreeCluster: clustering biological sequences using phylogenetic trees. PLoS ONE 14, e0221068 (2019).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Parks, D. H., Imelfort, M., Skennerton, C. T., Hugenholtz, P. & Tyson, G. W. CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res. 25, 1043–1055 (2015).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Olm, M. R., Brown, C. T., Brooks, B. & Banfield, J. F. dRep: a tool for fast and accurate genomic comparisons that enables improved genome recovery from metagenomes through de-replication. ISME J. 11, 2864–2868 (2017).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Johnson, L. S., Eddy, S. R. & Portugaly, E. Hidden Markov model speed heuristic and iterative HMM search procedure. BMC Bioinformatics 11, 431 (2010).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Mistry, J. et al. Pfam: the protein families database in 2021. Nucleic Acids Res. 49, D412–D419 (2021).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Minh, B. Q. et al. IQ-TREE 2: new models and efficient methods for phylogenetic inference in the genomic era. Mol. Biol. Evol. 37, 1530–1534 (2020).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Kalyaanamoorthy, S., Minh, B. Q., Wong, T. K. F., von Haeseler, A. & Jermiin, L. S. ModelFinder: fast model selection for accurate phylogenetic estimates. Nat. Methods 14, 587–589 (2017).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Minh, B. Q., Nguyen, M. A. T. & von Haeseler, A. Ultrafast approximation for phylogenetic bootstrap. Mol. Biol. Evol. 30, 1188–1195 (2013).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Néron, B. et al. MacSyFinder v2: improved modelling and search engine to identify molecular systems in genomes. Peer Community J. 3, e28 (2023).

  • Katoh, K. & Standley, D. M. MAFFT Multiple Sequence Alignment software version 7: improvements in performance and usability. Mol. Biol. Evol. 30, 772–780 (2013).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Capella-Gutiérrez, S., Silla-Martínez, J. M. & Gabaldón, T. trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses. Bioinformatics 25, 1972–1973 (2009).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Letunic, I. & Bork, P. Interactive Tree Of Life (iTOL) v5: an online tool for phylogenetic tree display and annotation. Nucleic Acids Res. 49, W293–W296 (2021).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Abramson, J. et al. Accurate structure prediction of biomolecular interactions with AlphaFold 3. Nature 630, 493–500 (2024).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Yariv, B. et al. Using evolutionary data to make sense of macromolecules with a “face-lifted” ConSurf. Protein Sci. 32, e4582 (2023).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Harrison, K. J., Crécy-Lagard, Vde & Zallot, R. Gene Graphics: a genomic neighborhood data visualization web application. Bioinformatics 34, 1406–1408 (2018).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Crooks, G. E., Hon, G., Chandonia, J. M. & Brenner, S. E. WebLogo: a sequence logo generator. Genome Res. 14, 1188–1190 (2004).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Kanehisa, M., Sato, Y. & Kawashima, M. KEGG mapping tools for uncovering hidden features in biological data. Protein Sci. 31, 47–53 (2022).

    Article 
    CAS 
    PubMed 

    Google Scholar 

Continue Reading

  • ATC indicts 11 suspects in November 26 protest case

    ATC indicts 11 suspects in November 26 protest case

    An Anti-Terrorism Court (ATC) on Wednesday indicted 11 arrested suspects in the November 26 protest case.

    ATC Judge Tahir Abbas Sipra conducted the proceedings, during which the accused pleaded not guilty. The court adjourned the hearing until September 24.

    In the same case, leaders of the Pakistan Tehreek-e-Insaf (PTI) are on interim bail until November 13. Police have submitted a challan against the arrested suspects out of the 195 workers nominated in the Secretariat Police Station case.

    Meanwhile, 184 absconding accused have already been declared proclaimed offenders by the court.


    Continue Reading

  • At the Gates’ Tomas Lindberg’s introspective lyricism broke new ground in death metal | Music

    At the Gates’ Tomas Lindberg’s introspective lyricism broke new ground in death metal | Music

    Tomas Lindberg was not the voice of death metal – he was so much better than that. During his 35-year career fronting Swedish band At the Gates, he never toed the line, never grunted about loving violence and hating Christianity because the genre dictated that you do so. Rather, he ripped up the rulebook with both his messaging and his delivery, setting a new standard for distinctiveness in extreme music.

    Lindberg – who has passed away aged 52 after being diagnosed with adenoid cystic carcinoma, a rare oral cancer – was fascinated with suffering. Yet, unlike his peers, he was seldom concerned with the suffering caused by a chainsaw or organised religion. It was the suffering inside of us, rooted in our own expectations, trauma and follies. “Twenty-two years of pain and I can feel it closing in,” goes the bridge of 1995’s semi-autobiographical fan-favourite track Cold. “The will to rise above, tearing my insides out.” And Lindberg delivered each line not with a typical, guttural rumble, but with a wailing screech that made all that anguish feel even more real.

    Born on 16 October 1972, Lindberg co-founded At the Gates in Gothenburg in 1990. They started as a somewhat lumbering musical entity, with early albums The Red in the Sky Is Ours and With Fear I Kiss the Burning Darkness attempting to push the death metal envelope using extended run times, structure-agnostic songwriting and violin solos.

    The band tightened up after guitarist/composer Alf Svensson left in 1993 and broke into a thrash metal-inspired sprint on the 1994 EP Terminal Spirit Disease. But Lindberg’s agonised poetry remained a constant. The singer told Invisible Oranges in 2010: “The whole concept of writing lyrics for me has always been to work myself through different subjects and to try to find my own standpoint, to not be guided by already fixed ideas.”

    At the Gates: Blinded by Fear – video

    In 1995, not long after a disastrous UK tour left the band furious and near penniless (at one point the band were left stranded in a Norwich car park for several days), At the Gates recorded their magnum opus, Slaughter of the Soul. Their frustration manifested across a blisteringly quick 34 minutes, ignoring all frills and breaking extreme metal down to its bare components: two or three riffs per song, chugging rhythm guitars comparable to Metallica, and histrionic harmonies influenced by Iron Maiden. With Lindberg at his most lyrically introspective (“Sweet nauseating pain, is death the only release?” he sang on Blinded by Fear) the material was as relatable as it was high-octane, and it became a surprise international hit.

    At the Gates barely got to enjoy the fruits of their labour, breaking up in 1996 after lead guitarist and co-founder Anders Björler and his brother, bassist Jonas, stepped down. They didn’t return until 2007. “We were so young, inexperienced and unused to coping with outside, or internal, pressure,” Lindberg explained during a 2014 Guitar World interview. “There’s no real communication when you’re 20.” However, their absence lent their music a quasi-mythical quality, and it piqued the intrigue of future members of such US bands as Trivium, Killswitch Engage and Lamb of God. Openly inspired by At the Gates’ fusion of power and melody, they became some of the biggest stars in metal during the midtolate 2000s.

    Once At the Gates returned, they put out three more albums and toured frequently, while Lindberg balanced the band with other musical projects and a job as a social studies teacher, not that his pupils were fussed. “What’s interesting is that it’s usually other teachers who think you’re cool,” he told Loudwire in 2021. “They want to know about touring stories [but] I’m like, um, no. I’d rather be the nice-but-a-bit-boring teacher.”

    Lindberg was diagnosed with cancer in December 2023 but kept his condition hidden from fans until last month, when At the Gates issued a statement saying that he was “being closely monitored around the clock”. Three decades after Slaughter of the Soul made his band global idols, the singer’s cliche-breaking words and passionate screaming still feel like a benchmark that no death metal vocalist is likely to touch again.

    Continue Reading

  • The struggle in licensing video streamers is possible with flexibility

    The struggle in licensing video streamers is possible with flexibility


    L-R: Rodolfo Barreto of Licks Attorneys, Thomas Choi at Ericsson, Noel Egnatios at DivX and Priscilla Srbu at Qualcomm.

    At IAM’s Patent Transactions event, Thomas Choi of Ericsson, Noel Egnatios of DivX and Priscilla Srbu of Qualcomm stress that one-size-fits-all dealmaking will not work with streamers

    Continue Reading

  • This Giant Subterranean Neutrino Detector Is Taking On the Mysteries of Physics

    This Giant Subterranean Neutrino Detector Is Taking On the Mysteries of Physics

    Located 700 meters underground near the city of Jiangmen in southern China, a giant sphere—35 meters in diameter and filled with more than 20,000 tons of liquid—has just started a mission that will last for decades. This is Juno, the Jiangmen Underground Neutrino Observatory, a new, large-scale experiment studying some of the most mysterious and elusive particles known to science.

    Neutrinos are the most abundant particles in the universe with mass. They are fundamental particles, meaning they don’t break down into smaller constituent parts, which makes them very small and very light. They also have zero electrical charge; they are neutral—hence their name. All of this means that they very often don’t interact with other matter they come into contact with, and can pass right through it without affecting it, making them difficult to observe. It’s for this reason that they’re sometimes referred to as “ghost particles.”

    They also have the ability to shift (or “oscillate”) between three different forms, also known as “flavors”: electron, mu, and tau. (Note that electron-flavored neutrinos are different from electrons; the latter are a different type of fundamental particle, with a negative charge.)

    The fact that neutrinos oscillate was proven by the physicists Takaaki Kajita and Arthur Bruce McDonald. In two separate experiments, they observed that electron-flavored neutrinos oscillate into mu- and tau-flavored neutrinos. As a result they demonstrated that these particles have mass, and that the mass of each flavor is different. For this, they won the Nobel Prize in Physics in 2015.

    An explainer on neutrino oscillations from the Fermi National Accelerator Laboratory.

    But an important yet still unknown fact is how these masses are ordered—which of the three flavors has the greatest mass, and which the least. If physicists had a better understanding of neutrino mass, this could help better describe the behavior and evolution of the universe. This is where Juno comes in.

    A Unique Experiment

    Neutrinos can’t be seen with conventional particle detectors. Instead, scientists have to look for the rare signs of them interacting with other matter—and this is what Juno’s giant sphere is for. Called a scintillator, it’s filled with a sensitive internal liquid made up of a solvent and two fluorescent compounds. If a neutrino passing through this matter interacts with it, it will produce a flash of light. Surrounding the liquid is a massive stainless steel lattice that supports a vast array of highly sensitive light sensors, called photomultiplier tubes, capable of detecting even a single photon produced by an interaction between a neutrino and the liquid, and converting it into a measurable electrical signal.

    “The Juno experiment picks up the legacy of its predecessors, with the difference that it is much larger,” says Gioacchino Ranucci, deputy head of the experiment and the former head of Borexino, another neutrino-hunting experiment. One of the main features of Juno, Ranucci explains, is that Juno can “see” both neutrinos and their antimatter counterpart: antineutrinos. The former are typically produced in Earth’s atmosphere or by the decay of radioactive materials in Earth’s crust, or else arrive from outer space—coming from stars, black holes, supernovae, or even the Big Bang. Antineutrinos, however, are artificially produced, in this case by two nuclear power plants located near the detector.

    “As they propagate, neutrinos and antineutrinos continue to oscillate, transforming into each other,” Ranucci says. Juno will be able to capture all of these signals, he explains, showing how they oscillate, “with a precision never before achieved.”

    Continue Reading

  • Vaccines Are A Hard Business. RFK Jr.’s CDC Is Making It Even Harder

    Vaccines Are A Hard Business. RFK Jr.’s CDC Is Making It Even Harder

    Continue Reading

  • Meta Is Debuting New Smart Glasses Today. Here’s How to Watch

    Meta Is Debuting New Smart Glasses Today. Here’s How to Watch

    Meta Connect, the annual event that serves as both the company’s developer conference and a platform for its new hardware announcements, is happening this week.

    Meta CEO Mark Zuckerberg is expected to take the stage at 5 pm Pacific, 8 pm Eastern, and 1 am British Summer Time on Wednesday, September 17, to announce a fleet of new smart glasses. We also expect to hear some updates on Meta’s machine intelligence efforts, and maybe a hint or two about how things are going at the company’s fledgling AI superintelligence lab.

    You can watch the video of the Meta Connect livestream from Meta’s Horizon site or on the Meta for developers Facebook page. Unlike Apple or Google, Meta doesn’t stream its conference keynote on YouTube.

    If you’re all in on the virtual reality future, you can also watch the event on a Meta Quest headset by going into the Horizon page and selecting the VR viewing option.

    If you’re a developer and want to register for Connect, you can do that by plugging your name and email into the Meta Connect website. In the upper-right corner, look for a button that reads “Register for the livestream.” Enter your information and you’ll get information about additional presentations and developer sessions.

    What to Expect

    While there may be some surprises at the event, Meta did fumble its reveal earlier this week when it accidentally leaked images of some new glasses that seem queued up to be announced at Connect. The leaked image includes the word Display, which could hint that Meta is looking to put out a new pair of glasses with an actual display built into the lenses.

    The company showed off its ambitions for such a wearable device at its Connect event last year when it debuted its prototype Orion frames, which relied on a wristband for navigation and a wireless puck for connectivity and computing power. The design of last year’s frames used waveguide technology to create virtual displays of images, text, and videos that appear in the wearer’s vision. Developers have had access to Orion frames for a year, so the technology is likely ready for its next step.

    We’re also expecting new models of the smart glasses developed by Meta and its main brand partners, Ray-Ban and Oakley.

    Tune in at 5 pm Pacific on Wednesday for more coverage of Meta Connect 2025 as it happens live.

    Continue Reading

  • Pakistan, Palestine sign health MoU in bid to foster closer bilateral ties – Pakistan

    Pakistan, Palestine sign health MoU in bid to foster closer bilateral ties – Pakistan

    Pakistan and the State of Palestine signed a memorandum of understanding (MoU) aiming to “strengthen bilateral cooperation in the health sector”, as part of an effort to foster both nations’ brotherly ties, the Ministry of National Health Services said on Wednesday.

    The two countries share strong bilateral ties as Pakistan is one of the few countries that recognises the state of Palestine. Pakistan has reiterated its support for Palestine against Israeli occupying forces at multiple international forums. The country also routinely sends humanitarian aid to Palestine’s Gaza, where Israel continues its offensive.

    Health Minister Syed Mustafa Kamal, who signed the agreement on Pakistan’s behalf with the Ambassador of Palestine Dr Zuhair Dar Zaid, remarked during the ceremony: “The purpose of this agreement is to foster closer collaboration for improving the health and well-being of the people of both brotherly nations.”

    According to a press release by the health ministry, the ceremony was attended by Secretary of Health Hamid Yaqoob, the additional secretary of health and the director general.

    Highlighting the details of the agreement, Kamal said, “A Pakistan-Palestine Health Working Group will be established within the next 30 days to oversee the implementation of the agreement and provide guidance for practical collaboration.”

    The key areas of cooperation between the two countries under the agreement will focus on “enhancing capacity in advanced medical fields such as interventional cardiology, organ transplantation, orthopaedic surgery, endoscopic ultrasound, burn and plastic surgery”.

    “Joint efforts will also be pursued in the fields of infectious diseases, ophthalmology, and pharmaceuticals,” the press release quoted Kamal as saying, adding that “opportunities for collaborative research will be explored.”

    Underscoring Pakistan’s commitment to supporting Palestine, Kamal assured the Palestinian ambassador of continued support to “Palestinian brothers and sisters in the field of health.”

    “The hearts of the people of Pakistan beat with Palestine, and we stand ready to assist them in every possible way,” he added.

    The Palestinian ambassador, while expressing gratitude towards Pakistan for its continued support, remarked that “Palestine and Pakistan are brotherly countries.“

    “Together, we will work for the improvement of [the] health and well-being of our peoples.”

    Continue Reading