79 research outputs found
Obtaining deeper insights into microbiome diversity using a simple method to block host and nontargets in amplicon sequencing
Abstract Profiling diverse microbiomes is revolutionizing our understanding of biological mechanisms and ecologically relevant problems, including metaorganism (host + microbiome) assembly, functions and adaptation. Amplicon sequencing of multiple conserved, phylogenetically informative loci has therefore become an instrumental tool for many researchers. Investigations in many systems are hindered, however, since essential sequencing depth can be lost by amplification of nontarget DNA from hosts or overabundant microorganisms. Here, we introduce “blocking oligos”, a low‐cost and flexible method using standard oligonucleotides to block amplification of diverse nontargets and software to aid their design. We apply them primarily in leaves, where exceptional challenges with host amplification prevail. A . thaliana ‐specific blocking oligos applied in eight different target loci reduce undesirable host amplification by up to 90%. To expand applicability, we designed universal 16S and 18S rRNA gene plant blocking oligos for targets that are conserved in diverse plant species and demonstrate that they efficiently block five plant species from five orders spanning monocots and dicots ( Bromus erectus , Plantago lanceolata , Lotus corniculatus , Amaranth sp., Arabidopsis thaliana ). These can increase alpha diversity discovery without biasing beta diversity patterns and do not compromise microbial load information inherent to plant‐derived 16S rRNA gene amplicon sequencing data. Finally, we designed and tested blocking oligos to avoid amplification of 18S rRNA genes of a sporulating oomycete pathogen, demonstrating their effectiveness in applications well beyond plants. Using these tools, we generated a survey of the A . thaliana leaf microbiome based on eight loci targeting bacterial, fungal, oomycete and other eukaryotic microorganisms and discuss complementarity of commonly used amplicon sequencing regions for describing leaf microbiota. This approach has potential to make questions in a variety of study systems more tractable by making amplicon sequencing more targeted, leading to deeper, systems‐based insights into microbial discovery. For fast and easy design for blocking oligos for any nontarget DNA in other study systems, we developed a publicly available R package
The long-time dynamics of two hydrodynamically-coupled swimming cells
Swimming micro-organisms such as bacteria or spermatozoa are typically found
in dense suspensions, and exhibit collective modes of locomotion qualitatively
different from that displayed by isolated cells. In the dilute limit where
fluid-mediated interactions can be treated rigorously, the long-time
hydrodynamics of a collection of cells result from interactions with many other
cells, and as such typically eludes an analytical approach. Here we consider
the only case where such problem can be treated rigorously analytically, namely
when the cells have spatially confined trajectories, such as the spermatozoa of
some marine invertebrates. We consider two spherical cells swimming, when
isolated, with arbitrary circular trajectories, and derive the long-time
kinematics of their relative locomotion. We show that in the dilute limit where
the cells are much further away than their size, and the size of their circular
motion, a separation of time scale occurs between a fast (intrinsic) swimming
time, and a slow time where hydrodynamic interactions lead to change in the
relative position and orientation of the swimmers. We perform a multiple-scale
analysis and derive the effective dynamical system - of dimension two -
describing the long-time behavior of the pair of cells. We show that the system
displays one type of equilibrium, and two types of rotational equilibrium, all
of which are found to be unstable. A detailed mathematical analysis of the
dynamical systems further allows us to show that only two cell-cell behaviors
are possible in the limit of , either the cells are attracted to
each other (possibly monotonically), or they are repelled (possibly
monotonically as well), which we confirm with numerical computations
Auroral Current and Electrodynamics Structure (ACES) Observations of Ionospheric Feedback in the Alfven Resonator
In 2009, the Auroral Current and Electrodynamics Structure (ACES) High and Low sounding rockets were launched from the Poker Flat Rocket Range (PFRR) in Alaska, with the science objective of gathering in-situ data to quantify current closure in a discrete auroral arc. As ACES High crossed through the return current of an arc (that was monitored using an all sky camera from the ground at Fort Yukon), its instruments recorded clear Alfv nic signatures both poleward and equatorward of the return current region, but not within the main region of the return current itself. These data provide an excellent opportunity to study ionospheric feedback and how it interacts with the Alfv n resonator. We compare the observations with predictions and new results from a model of ionospheric feedback in the ionospheric Alfv n resonator (IAR) and report the significance and impact of these new data for the Magnetosphere-Ionosphere Coupling in the Alfv n Resonator (MICA) rocket mission to launch from PFRR this winter. MICA s primary science objectives specifically focus on better understanding the small-scale structure that the model predicts should exist within the return current region
Therapeutic targeting of ependymoma as informed by oncogenic enhancer profiling
Genomic sequencing has driven precision-based oncology therapy; however, the genetic drivers of many malignancies remain unknown or non-targetable, so alternative approaches to the identification of therapeutic leads are necessary. Ependymomas are chemotherapy-resistant brain tumours, which, despite genomic sequencing, lack effective molecular targets. Intracranial ependymomas are segregated on the basis of anatomical location (supratentorial region or posterior fossa) and further divided into distinct molecular subgroups that reflect differences in the age of onset, gender predominance and response to therapy1,2,3. The most common and aggressive subgroup, posterior fossa ependymoma group A (PF-EPN-A), occurs in young children and appears to lack recurrent somatic mutations2. Conversely, posterior fossa ependymoma group B (PF-EPN-B) tumours display frequent large-scale copy number gains and losses but have favourable clinical outcomes1,3. More than 70% of supratentorial ependymomas are defined by highly recurrent gene fusions in the NF-κB subunit gene RELA (ST-EPN-RELA), and a smaller number involve fusion of the gene encoding the transcriptional activator YAP1 (ST-EPN-YAP1)1,3,4. Subependymomas, a distinct histologic variant, can also be found within the supratetorial and posterior fossa compartments, and account for the majority of tumours in the molecular subgroups ST-EPN-SE and PF-EPN-SE. Here we describe mapping of active chromatin landscapes in 42 primary ependymomas in two non-overlapping primary ependymoma cohorts, with the goal of identifying essential super-enhancer-associated genes on which tumour cells depend. Enhancer regions revealed putative oncogenes, molecular targets and pathways; inhibition of these targets with small molecule inhibitors or short hairpin RNA diminished the proliferation of patient-derived neurospheres and increased survival in mouse models of ependymomas. Through profiling of transcriptional enhancers, our study provides a framework for target and drug discovery in other cancers that lack known genetic drivers and are therefore difficult to treat.This work was supported by an Alex's Lemonade Stand Young Investigator Award (S.C.M.), The CIHR Banting Fellowship (S.C.M.), The Cancer Prevention Research Institute of Texas (S.C.M., RR170023), Sibylle Assmus Award for Neurooncology (K.W.P.), the DKFZ-MOST (Ministry of Science, Technology & Space, Israel) program in cancer research (H.W.), James S. McDonnell Foundation (J.N.R.) and NIH grants: CA154130 (J.N.R.), R01 CA169117 (J.N.R.), R01 CA171652 (J.N.R.), R01 NS087913 (J.N.R.) and R01 NS089272 (J.N.R.). R.C.G. is supported by NIH grants T32GM00725 and F30CA217065. M.D.T. is supported by The Garron Family Chair in Childhood Cancer Research, and grants from the Pediatric Brain Tumour Foundation, Grand Challenge Award from CureSearch for Children’s Cancer, the National Institutes of Health (R01CA148699, R01CA159859), The Terry Fox Research Institute and Brainchild. M.D.T. is also supported by a Stand Up To Cancer St. Baldrick’s Pediatric Dream Team Translational Research Grant (SU2C-AACR-DT1113)
The SPARC Toroidal Field Model Coil Program
The SPARC Toroidal Field Model Coil (TFMC) Program was a three-year effort
between 2018 and 2021 that developed novel Rare Earth Yttrium Barium Copper
Oxide (REBCO) superconductor technologies and then successfully utilized these
technologies to design, build, and test a first-in-class, high-field (~20 T),
representative-scale (~3 m) superconducting toroidal field coil. With the
principal objective of demonstrating mature, large-scale, REBCO magnets, the
project was executed jointly by the MIT Plasma Science and Fusion Center (PSFC)
and Commonwealth Fusion Systems (CFS). The TFMC achieved its programmatic goal
of experimentally demonstrating a large-scale high-field REBCO magnet,
achieving 20.1 T peak field-on-conductor with 40.5 kA of terminal current, 815
kN/m of Lorentz loading on the REBCO stacks, and almost 1 GPa of mechanical
stress accommodated by the structural case. Fifteen internal demountable
pancake-to-pancake joints operated in the 0.5 to 2.0 nOhm range at 20 K and in
magnetic fields up to 12 T. The DC and AC electromagnetic performance of the
magnet, predicted by new advances in high-fidelity computational models, was
confirmed in two test campaigns while the massively parallel, single-pass,
pressure-vessel style coolant scheme capable of large heat removal was
validated. The REBCO current lead and feeder system was experimentally
qualified up to 50 kA, and the crycooler based cryogenic system provided 600 W
of cooling power at 20 K with mass flow rates up to 70 g/s at a maximum design
pressure of 20 bar-a for the test campaigns. Finally, the feasibility of using
passive, self-protection against a quench in a fusion-scale NI TF coil was
experimentally assessed with an intentional open-circuit quench at 31.5 kA
terminal current.Comment: 17 pages 9 figures, overview paper and the first of a six-part series
of papers covering the TFMC Progra
ICT4S 2029: What Will Be The Systems Supporting Sustainability in 15 Years
Research is often inspired by visions of the future. These visions can take on various narrative forms, and can fall anywhere along the spectrum from utopian to dystopian. Even though we recognize the importance of such visions to help us shape research questions and inspire rich design spaces to be explored, the opportunity to discuss them is rarely given in a research context. Imagine how civilization will have changed in 15 years. What is your vision for systems that will be supporting sustainability in that time Which transformational changes will have occurred in the mean time that allow for these systems Is ICT even the right tool or does it contradict sustainability by making our world ever more complex How can we make systems and our societies more sustainable and resilient by ICT4S This paper presents a compilation of fictional abstracts for inspiration and discussion, and provides means to stimulate discussion on future research and contributes to ICT4S community building
- …