Biotechnology

  • Article
    | Open Access

    Progressive familial intrahepatic cholestasis type 3 is a disease caused by mutations in the gene encoding the multidrug resistance protein 3, and has limited treatment options. Here they show that adeno-associated virus mediated gene therapy prevents disease progression in a mouse disease model.

    • Nicholas D. Weber
    • , Leticia Odriozola
    • , Javier Martínez-García
    • , Veronica Ferrer
    • , Anne Douar
    • , Bernard Bénichou
    • , Gloria González-Aseguinolaza
    •  & Cristian Smerdou
  • Article
    | Open Access

    The design of protein assemblies is a major thrust for biomolecular engineering and nanobiotechnology. Here the authors demonstrate a general mechanism for designing allosteric macromolecular assemblies and showcase a proof of concept for engineered allosteric protein assembly.

    • Luis A. Campos
    • , Rajendra Sharma
    • , Sara Alvira
    • , Federico M. Ruiz
    • , Beatriz Ibarra-Molero
    • , Mourad Sadqi
    • , Carlos Alfonso
    • , Germán Rivas
    • , Jose M. Sanchez-Ruiz
    • , Antonio Romero Garrido
    • , José M. Valpuesta
    •  & Victor Muñoz
  • Article
    | Open Access

    The kidney is vascularized with highly specialized and zonated endothelial cells that are essential for its filtration function. Here, Barry et al. provide a single-cell RNA sequencing analysis of the kidney vasculature that highlights its transcriptional heterogeneity and uncovers pathways important for its development and function.

    • David M. Barry
    • , Elizabeth A. McMillan
    • , Balvir Kunar
    • , Raphael Lis
    • , Tuo Zhang
    • , Tyler Lu
    • , Edward Daniel
    • , Masataka Yokoyama
    • , Jesus M. Gomez-Salinero
    • , Angara Sureshbabu
    • , Ondine Cleaver
    • , Annarita Di Lorenzo
    • , Mary E. Choi
    • , Jenny Xiang
    • , David Redmond
    • , Sina Y. Rabbany
    • , Thangamani Muthukumar
    •  & Shahin Rafii
  • Article
    | Open Access

    Graft versus host disease (GvHD) still hinders allogeneic hematopoietic stem cell transplantation. Here, the authors use metabolomics to analyze two cohorts of paired transplant recipients and donors, identifying significant differences in both host- and microbiota-derived metabolites.

    • David Michonneau
    • , Eleonora Latis
    • , Emmanuel Curis
    • , Laetitia Dubouchet
    • , Sivapriya Ramamoorthy
    • , Brian Ingram
    • , Régis Peffault de Latour
    • , Marie Robin
    • , Flore Sicre de Fontbrune
    • , Sylvie Chevret
    • , Lars Rogge
    •  & Gérard Socié
  • Article
    | Open Access

    Multiplexed detection of luciferase-based sensors in the same sample is challenging and limited by the substrates’ emission spectra. Here the authors establish a system based on three different luciferases and sequential detection to achieve measurements of up to six parameters within the same experiment.

    • Alejandro Sarrion-Perdigones
    • , Lyra Chang
    • , Yezabel Gonzalez
    • , Tatiana Gallego-Flores
    • , Damian W. Young
    •  & Koen J. T. Venken
  • Article
    | Open Access

    A Zika virus vaccine should protect the fetus during pregnancy. Here, using a live-attenuated Zika vaccine, the authors show that a higher neutralizing antibody titer is required to protect from in utero transmission than to protect non-pregnant mice and that a single maternal immunization protects the fetus from infection and disease.

    • Chao Shan
    • , Xuping Xie
    • , Huanle Luo
    • , Antonio E. Muruato
    • , Yang Liu
    • , Maki Wakamiya
    • , Jun-Ho La
    • , Jin Mo Chung
    • , Scott C. Weaver
    • , Tian Wang
    •  & Pei-Yong Shi
  • Article
    | Open Access

    Particle manipulation is still challenging even with the many tools available, especially manipulating particles on a surface. Here, the authors report a technique for nanomanipulation of various objects on solid substrates by modulating particle-substrate interactions through laser-induced opto-thermal dynamics.

    • Jingang Li
    • , Yaoran Liu
    • , Linhan Lin
    • , Mingsong Wang
    • , Taizhi Jiang
    • , Jianhe Guo
    • , Hongru Ding
    • , Pavana Siddhartha Kollipara
    • , Yuji Inoue
    • , Donglei Fan
    • , Brian A. Korgel
    •  & Yuebing Zheng
  • Article
    | Open Access

    Calcium carbonate biomineralisation has long been linked to acidic macromolecules. Here, the authors challenge this view and show that a huge number of gold nanoparticles coated with hydroxyl-rich proteins can be incorporated into a calcium carbonate crystal while maintaining single crystal character.

    • Yi-Yeoun Kim
    • , Robert Darkins
    • , Alexander Broad
    • , Alexander N. Kulak
    • , Mark A. Holden
    • , Ouassef Nahi
    • , Steven P. Armes
    • , Chiu C. Tang
    • , Rebecca F. Thompson
    • , Frederic Marin
    • , Dorothy M. Duffy
    •  & Fiona C. Meldrum
  • Article
    | Open Access

    Cell senescence involves stable arrest of cell proliferation and changes in gene expression and 3D genome reorganization. Here, the authors show that human condensin II complex participates in reorganization of the chromatin compartments, primarily through switching from heterochromatic B to euchromatic A compartments.

    • Osamu Iwasaki
    • , Hideki Tanizawa
    • , Kyoung-Dong Kim
    • , Andrew Kossenkov
    • , Timothy Nacarelli
    • , Sanki Tashiro
    • , Sonali Majumdar
    • , Louise C. Showe
    • , Rugang Zhang
    •  & Ken-ichi Noma
  • Article
    | Open Access

    Organoid cultures have been developed from multiple tissues, opening new possibilities for regenerative medicine. Here the authors demonstrate the derivation of GMP-compliant hydrogels from decellularized porcine small intestine which support formation and growth of human gastric, liver, pancreatic and small intestinal organoids.

    • Giovanni Giuseppe Giobbe
    • , Claire Crowley
    • , Camilla Luni
    • , Sara Campinoti
    • , Moustafa Khedr
    • , Kai Kretzschmar
    • , Martina Maria De Santis
    • , Elisa Zambaiti
    • , Federica Michielin
    • , Laween Meran
    • , Qianjiang Hu
    • , Gijs van Son
    • , Luca Urbani
    • , Anna Manfredi
    • , Monica Giomo
    • , Simon Eaton
    • , Davide Cacchiarelli
    • , Vivian S. W. Li
    • , Hans Clevers
    • , Paola Bonfanti
    • , Nicola Elvassore
    •  & Paolo De Coppi
  • Article
    | Open Access

    Most cases of autosomal dominant polycystic kidney disease (ADPKD) are due to mutations in PKD1. Here, Tsukiyama et al. generate monkeys with mutations in PKD1 and show that animals recapitulate key pathological features of the human disease, suggesting these may provide insights into ADPKD pathogenesis and contribute to the development of future therapeutic strategies.

    • Tomoyuki Tsukiyama
    • , Kenichi Kobayashi
    • , Masataka Nakaya
    • , Chizuru Iwatani
    • , Yasunari Seita
    • , Hideaki Tsuchiya
    • , Jun Matsushita
    • , Kahoru Kitajima
    • , Ikuo Kawamoto
    • , Takahiro Nakagawa
    • , Koji Fukuda
    • , Teppei Iwakiri
    • , Hiroyuki Izumi
    • , Iori Itagaki
    • , Shinji Kume
    • , Hiroshi Maegawa
    • , Ryuichi Nishinakamura
    • , Saori Nishio
    • , Shinichiro Nakamura
    • , Akihiro Kawauchi
    •  & Masatsugu Ema
  • Article
    | Open Access

    Engineered biological nanopores enable observation of single molecule chemistry events; however a cylindrical pore geometry can have undesired effects. The authors report a conical biological pore which was embedded with tetrachloroaurate(III) to allow for discrimination between different biothiols.

    • Jiao Cao
    • , Wendong Jia
    • , Jinyue Zhang
    • , Xiumei Xu
    • , Shuanghong Yan
    • , Yuqin Wang
    • , Panke Zhang
    • , Hong-Yuan Chen
    •  & Shuo Huang
  • Article
    | Open Access

    Artificial nanopores can perform selective gating of molecules analogous to transmembrane proteins. Here, the authors design a DNA origami pore with a controllable lid for size-selective gating and translocation of macromolecules and evaluate its biosensing properties by single particle assay.

    • Rasmus P. Thomsen
    • , Mette Galsgaard Malle
    • , Anders Hauge Okholm
    • , Swati Krishnan
    • , Søren S.-R. Bohr
    • , Rasmus Schøler Sørensen
    • , Oliver Ries
    • , Stefan Vogel
    • , Friedrich C. Simmel
    • , Nikos S. Hatzakis
    •  & Jørgen Kjems
  • Article
    | Open Access

    Multiple sequence alignments of proteins carry information about evolution, the protein’s fitness landscape and its stability in the face of mutations. Here, the authors demonstrate the utility of latent space models learned using variational autoencoders to infer these properties from sequences.

    • Xinqiang Ding
    • , Zhengting Zou
    •  & Charles L. Brooks III
  • Article
    | Open Access

    Plasmodium growth is adapted to the reproductive cycle of mosquitoes, but underlying mechanisms are unclear. Here, Lampe et al. show that the blood-meal induced miR-276 balances the termination of the mosquito amino acid catabolism and egg development, providing nutrients for Plasmodium sporozoite development.

    • Lena Lampe
    • , Marius Jentzsch
    • , Sylwia Kierszniowska
    •  & Elena A. Levashina
  • Article
    | Open Access

    Biology has often served as the inspiration for the design of body armor; one common limitation is the flexibility of the resultant armor. Here, the authors examine the armour of chiton and use the observed design principles to 3D print flexible armor.

    • Matthew Connors
    • , Ting Yang
    • , Ahmed Hosny
    • , Zhifei Deng
    • , Fatemeh Yazdandoost
    • , Hajar Massaadi
    • , Douglas Eernisse
    • , Reza Mirzaeifar
    • , Mason N. Dean
    • , James C. Weaver
    • , Christine Ortiz
    •  & Ling Li
  • Article
    | Open Access

    N6-methyladenosine (m6A) and N6,2′-O-dimethyladenosine (m6Am) are eukaryotic mRNA modifications. Here the authors develop m6A-Crosslinking-Exonuclease-sequencing to map quantitative methylome changes at single-base-resolution after individually knocking out each known methyltransferase or demethylase.

    • Casslynn W. Q. Koh
    • , Yeek Teck Goh
    •  & W. S. Sho Goh
  • Article
    | Open Access

    Although most are silenced, certain transposable elements (TEs) have been co-opted by the host. Here, the authors quantify the epigenomic status of TEs using data from the Roadmap Epigenomics Project, provide a systematic profile of TE activity across normal human tissues and development, finding that TEs encompass a quarter of the human regulatory epigenome, with 47% of TEs in regulatory states.

    • Erica C. Pehrsson
    • , Mayank N. K. Choudhary
    • , Vasavi Sundaram
    •  & Ting Wang
  • Article
    | Open Access

    Here, Bhattacharya et al. chemically mutagenize Leishmania and identify genes associated with resistance to miltefosine and paromomycin by next generation sequencing. The study shows that a protein kinase (CDPK1) can mediate resistance to paromomycin by affecting translation.

    • Arijit Bhattacharya
    • , Philippe Leprohon
    • , Sophia Bigot
    • , Prasad Kottayil Padmanabhan
    • , Angana Mukherjee
    • , Gaétan Roy
    • , Hélène Gingras
    • , Anais Mestdagh
    • , Barbara Papadopoulou
    •  & Marc Ouellette
  • Article
    | Open Access

    Glycolysis is elevated in many cancers. In this study, the authors show that lactoylglutathione, a by-product of methylglyoxal produced from increased glycolysis, is elevated in lung cancer in mouse models and humans, arguing reactive metabolite production can be a liability for cancers.

    • Alba Luengo
    • , Keene L. Abbott
    • , Shawn M. Davidson
    • , Aaron M. Hosios
    • , Brandon Faubert
    • , Sze Ham Chan
    • , Elizaveta Freinkman
    • , Lauren G. Zacharias
    • , Thomas P. Mathews
    • , Clary B. Clish
    • , Ralph J. DeBerardinis
    • , Caroline A. Lewis
    •  & Matthew G. Vander Heiden
  • Article
    | Open Access

    Class 1 CRISPR systems are not as developed for genome editing as Class 2 systems are. Here the authors show that Cas3 can be used to generate functional knockouts and knock-ins, as well as Cas3-mediated exon-skipping in DMD cells.

    • Hiroyuki Morisaka
    • , Kazuto Yoshimi
    • , Yuya Okuzaki
    • , Peter Gee
    • , Yayoi Kunihiro
    • , Ekasit Sonpho
    • , Huaigeng Xu
    • , Noriko Sasakawa
    • , Yuki Naito
    • , Shinichiro Nakada
    • , Takashi Yamamoto
    • , Shigetoshi Sano
    • , Akitsu Hotta
    • , Junji Takeda
    •  & Tomoji Mashimo
  • Article
    | Open Access

    Ni–Fe based compound are known as active electrocatalysts for oxygen evolution reaction, but not a good choice for the other half-reaction of water-splitting. Here the authors report a unique interface between Ni and γ-Fe2O3 that efficiently catalyzes the cathodic hydrogen evolution reaction.

    • Bryan H. R. Suryanto
    • , Yun Wang
    • , Rosalie K. Hocking
    • , William Adamson
    •  & Chuan Zhao
  • Article
    | Open Access

    Unlike the other domesticated maize, sweet maize and popcorn retain tillering growth habit, but the underlying mechanism is unknown. Here, the authors identify a transcription factor tin1 that maintains outgrowth of tiller independent of tb1 and show its conservation in foxtail millet and rice.

    • Xuan Zhang
    • , Zhelong Lin
    • , Jian Wang
    • , Hangqin Liu
    • , Leina Zhou
    • , Shuyang Zhong
    • , Yan Li
    • , Can Zhu
    • , Jiacheng Liu
    •  & Zhongwei Lin
  • Article
    | Open Access

    Compared to single nucleotide variants and short indels, structural variants (SVs) are often more challenging to detect using high-throughput sequencing based methods. Here, the authors develop LinkedSV, a computational tool for SV detection using linked-read exome and genome sequencing data.

    • Li Fang
    • , Charlly Kao
    • , Michael V. Gonzalez
    • , Fernanda A. Mafra
    • , Renata Pellegrino da Silva
    • , Mingyao Li
    • , Sören-Sebastian Wenzel
    • , Katharina Wimmer
    • , Hakon Hakonarson
    •  & Kai Wang
  • Article
    | Open Access

    Trypanosoma brucei relies on uptake and conversion of purines from the host, which constitutes a potential drug target. Here, Hulpia et al. combine structural elements from known trypanocidal nucleoside analogues and develop a potent trypanocide with curative activity in animal models of acute and late stage sleeping sickness.

    • Fabian Hulpia
    • , Dorien Mabille
    • , Gustavo D. Campagnaro
    • , Gabriela Schumann
    • , Louis Maes
    • , Isabel Roditi
    • , Anders Hofer
    • , Harry P. de Koning
    • , Guy Caljon
    •  & Serge Van Calenbergh
  • Article
    | Open Access

    Addition of small nanoparticles into polymer melt can lead to decrease in viscosity but the underlying mechanism for such viscosity reduction remains unclear. Here, the authors investigate the reduction in viscosity by large-scale molecular dynamics simulation and experimental rheology measurements for an all-polymer nanocomposite formed by linear polystyrene chains and PS single-chain nanoparticle.

    • Tao Chen
    • , Huan-Yu Zhao
    • , Rui Shi
    • , Wen-Feng Lin
    • , Xiang-Meng Jia
    • , Hu-Jun Qian
    • , Zhong-Yuan Lu
    • , Xing-Xing Zhang
    • , Yan-Kai Li
    •  & Zhao-Yan Sun
  • Article
    | Open Access

    Nanotechnology can bring significant advancements to hemostatic patches. Here, the authors design a superhydrophobic hemostatic surface with immobilized carbon nanofibers that can stop bleeding instantaneously upon application, seal the wound subsequently by promoting quick fibrin formation, and facilitate unforced and facile patch removal without tearing the wound.

    • Zhe Li
    • , Athanasios Milionis
    • , Yu Zheng
    • , Marcus Yee
    • , Lukas Codispoti
    • , Freddie Tan
    • , Dimos Poulikakos
    •  & Choon Hwai Yap
  • Article
    | Open Access

    The basis of sexual dimorphism in non-model species may be elusive, in part due to a lack of genomic and molecular resources. Here, Li et al. report a high-quality anuran genome and reveal candidate genes and pathways associated with shaping sexually dimorphic nuptial spines in a moustache toad.

    • Jun Li
    • , Haiyan Yu
    • , Wenxia Wang
    • , Chao Fu
    • , Wei Zhang
    • , Fengming Han
    •  & Hua Wu
  • Article
    | Open Access

    Tightly controlling cell output is challenging, which has limited development and applications of bacterial sensors. Here the authors develop tunable, fast-responding sensors to control production of metabolic pigments and use them to assess zinc deficiency in a low-cost, minimal equipment fashion.

    • Monica P. McNerney
    • , Cirstyn L. Michel
    • , Krishi Kishore
    • , Janet Standeven
    •  & Mark P. Styczynski
  • Article
    | Open Access

    DNA composite materials have potential for biomedical sciences; however, control over the materials can be an issue. Here, the authors report on a carbon-nanotube reinforced DNA-silica gel with controllable mechanical properties to steer the attachment, proliferation, migration and release of cells.

    • Yong Hu
    • , Carmen M. Domínguez
    • , Jens Bauer
    • , Simone Weigel
    • , Alessa Schipperges
    • , Claude Oelschlaeger
    • , Norbert Willenbacher
    • , Stephan Keppler
    • , Martin Bastmeyer
    • , Stefan Heißler
    • , Christof Wöll
    • , Tim Scharnweber
    • , Kersten S. Rabe
    •  & Christof M. Niemeyer
  • Article
    | Open Access

    Polymer brushes are often used to functionalise surfaces. Here, the authors report on the creation of high-density, regenerating hyaluronan brushes using hyaluronan synthase enzymes which can be patterned by photo-deactivation and demonstrate biocompatibility and resistance to biofilm formation.

    • Wenbin Wei
    • , Jessica L. Faubel
    • , Hemaa Selvakumar
    • , Daniel T. Kovari
    • , Joanna Tsao
    • , Felipe Rivas
    • , Amar T. Mohabir
    • , Michelle Krecker
    • , Elaheh Rahbar
    • , Adam R. Hall
    • , Michael A. Filler
    • , Jennifer L. Washburn
    • , Paul H. Weigel
    •  & Jennifer E. Curtis
  • Article
    | Open Access

    Urinary tract infections (UTIs) are associated with changes in the gut microbiome. Here, the authors evaluate the relationship between the gut microbiome and development of UTI in kidney transplant patients and show that uropathogenic gut abundance might represent a risk factor for development of bacteriuria and UTI.

    • Matthew Magruder
    • , Adam N. Sholi
    • , Catherine Gong
    • , Lisa Zhang
    • , Emmanuel Edusei
    • , Jennifer Huang
    • , Shady Albakry
    • , Michael J. Satlin
    • , Lars F. Westblade
    • , Carl Crawford
    • , Darshana M. Dadhania
    • , Michelle Lubetzky
    • , Ying Taur
    • , Eric Littman
    • , Lilan Ling
    • , Philip Burnham
    • , Iwijn De Vlaminck
    • , Eric Pamer
    • , Manikkam Suthanthiran
    •  & John Richard Lee
  • Article
    | Open Access

    The off-target effects and on-target mutations of CRISPR editing in higher non-human primates are complex. Here the authors perform whole genome trio sequencing of rhesus monkeys and see no unexpected mutations.

    • Xin Luo
    • , Yaoxi He
    • , Chao Zhang
    • , Xiechao He
    • , Lanzhen Yan
    • , Min Li
    • , Ting Hu
    • , Yan Hu
    • , Jin Jiang
    • , Xiaoyu Meng
    • , Weizhi Ji
    • , Xudong Zhao
    • , Ping Zheng
    • , Shuhua Xu
    •  & Bing Su
  • Article
    | Open Access

    CRISPR-Cas systems have well characterized, modular structures. Here the authors use that architecture to design a Cas12a library of 560 synthetic chimeras, with altered PAM preferences and specificities.

    • R. M. Liu
    • , L. L. Liang
    • , E. Freed
    • , H. Chang
    • , E. Oh
    • , Z. Y. Liu
    • , A. Garst
    • , C. A. Eckert
    •  & R. T. Gill
  • Article
    | Open Access

    Pre-malignant cells harbouring oncogenic mutations can populate and spread throughout a tissue. Here, using a rainbow mouse system, the authors explore how clonal expansion in the mouse intestine might explain high levels of intra-tumoural heterogeneity observed in the disease.

    • Peter G. Boone
    • , Lauren K. Rochelle
    • , Joshua D. Ginzel
    • , Veronica Lubkov
    • , Wendy L. Roberts
    • , P. J. Nicholls
    • , Cheryl Bock
    • , Mei Lang Flowers
    • , Richard J. von Furstenberg
    • , Barry R. Stripp
    • , Pankaj Agarwal
    • , Alexander D. Borowsky
    • , Robert D. Cardiff
    • , Larry S. Barak
    • , Marc G. Caron
    • , H. Kim Lyerly
    •  & Joshua C. Snyder
  • Article
    | Open Access

    Thymic epithelial cells (TEC) are essential for the maturation of functional T cells, while thymus size is proportional to the overall output efficiency. Here the authors show, using transcriptome analyses, that mouse fetal TEC maintain a Myc-dependent genetic program to ensure a rapid increase in thymus size, and thereby expedited T cell generation.

    • Jennifer E. Cowan
    • , Justin Malin
    • , Yongge Zhao
    • , Mina O. Seedhom
    • , Christelle Harly
    • , Izumi Ohigashi
    • , Michael Kelly
    • , Yousuke Takahama
    • , Jonathan W. Yewdell
    • , Maggie Cam
    •  & Avinash Bhandoola
  • Article
    | Open Access

    Crosstalk between protein oxidation and other post-translational modifications remains unexplored. Here, the authors map the phosphoproteome, cysteine redox proteome and total proteome of adipocytes under acute oxidative stress and reveal crosstalk between cysteine oxidation and phosphorylation-based signalling.

    • Zhiduan Su
    • , James G. Burchfield
    • , Pengyi Yang
    • , Sean J. Humphrey
    • , Guang Yang
    • , Deanne Francis
    • , Sabina Yasmin
    • , Sung-Young Shin
    • , Dougall M. Norris
    • , Alison L. Kearney
    • , Miro A. Astore
    • , Jonathan Scavuzzo
    • , Kelsey H. Fisher-Wellman
    • , Qiao-Ping Wang
    • , Benjamin L. Parker
    • , G. Gregory Neely
    • , Fatemeh Vafaee
    • , Joyce Chiu
    • , Reichelle Yeo
    • , Philip J. Hogg
    • , Daniel J. Fazakerley
    • , Lan K. Nguyen
    • , Serdar Kuyucak
    •  & David E. James
  • Article
    | Open Access

    Adhesives are ubiquitous in commodity products, however it it essential that their synthesis and degradation be sustainable without compromising their performance. Here, the authors report a library of adhesives based on environmentally benign building blocks that perform in both dry and wet environments.

    • Anjeza Beharaj
    • , Ethan Z. McCaslin
    • , William A. Blessing
    •  & Mark W. Grinstaff
  • Article
    | Open Access

    Liquid-liquid phase separation (LLPS) of intrinsically disordered proteins plays an important part in the formation of extracellular biological materials. Here, the authors show that repeats of the peptide motif GHGLY are necessary for the LLPS of pH-responsive histidine-rich squid beak proteins.

    • Bartosz Gabryelczyk
    • , Hao Cai
    • , Xiangyan Shi
    • , Yue Sun
    • , Piet J. M. Swinkels
    • , Stefan Salentinig
    • , Konstantin Pervushin
    •  & Ali Miserez
  • Article
    | Open Access

    The folding-dependent catalytic behavior of enzymes is of fundamental biological importance, yet mechanistically underexplored. Here, the authors show that an α-helix, commonly found in proteins, can facilitate its own growth through the self-catalyzed polymerization of N-carboxyanhydride in solvents with low polarity.

    • Ziyuan Song
    • , Hailin Fu
    • , Ryan Baumgartner
    • , Lingyang Zhu
    • , Kuo-Chih Shih
    • , Yingchun Xia
    • , Xuetao Zheng
    • , Lichen Yin
    • , Christophe Chipot
    • , Yao Lin
    •  & Jianjun Cheng
  • Article
    | Open Access

    Songbirds have extensive germline–soma genome differences due to developmental elimination of a germline-specific chromosome (GRC). Here, the authors show that the GRC contains dozens of expressed developmental genes, some of which have been on the GRC since the ancestor of all songbirds.

    • Cormac M. Kinsella
    • , Francisco J. Ruiz-Ruano
    • , Anne-Marie Dion-Côté
    • , Alexander J. Charles
    • , Toni I. Gossmann
    • , Josefa Cabrero
    • , Dennis Kappei
    • , Nicola Hemmings
    • , Mirre J. P. Simons
    • , Juan Pedro M. Camacho
    • , Wolfgang Forstmeier
    •  & Alexander Suh
  • Article
    | Open Access

    One measurement of tuberculosis vaccine efficacy in clinical trials is prevention of disease, but different mechanisms can underlie disease prevention. Here, the authors develop a mathematical model that allows to identify mechanisms of action of a vaccine preventing TB disease.

    • Mario Tovar
    • , Sergio Arregui
    • , Dessislava Marinova
    • , Carlos Martín
    • , Joaquín Sanz
    •  & Yamir Moreno
  • Article
    | Open Access

    t-SNE is widely used for dimensionality reduction and visualization of high-dimensional single-cell data. Here, the authors introduce a protocol to help avoid common shortcomings of t-SNE, for example, enabling preservation of the global structure of the data.

    • Dmitry Kobak
    •  & Philipp Berens
  • Article
    | Open Access

    Wireframe DNA origami is a powerful approach to creating 2D and 3D geometries. Here the authors introduce an automated computational design approach that programs structures with high structural fidelity.

    • Hyungmin Jun
    • , Xiao Wang
    • , William P. Bricker
    •  & Mark Bathe