Laying the foundations for a bio-economy

Biological technologies are becoming an important part of the economy. Biotechnology already contributes at least 1% of US GDP, with revenues growing as much as 20% annually. The introduction of composable biological parts will enable an engineering discipline similar to the ones that resulted in modern aviation and information technology. As the sophistication of biological engineering increases, it will provide new goods and services at lower costs and higher efficiencies. Broad access to foundational engineering technologies is seen by some as a threat to physical and economic security. However, regulation of access will serve to suppress the innovation required to produce new vaccines and other countermeasures as well as limiting general economic growth

Optimization of Ribosome Structure and Function by rRNA Base Modification

BACKGROUND: Translating mRNA sequences into functional proteins is a fundamental process necessary for the viability of organisms throughout all kingdoms of life. The ribosome carries out this process with a delicate balance between speed and accuracy. This work investigates how ribosome structure and function are affected by rRNA base modification. The prevailing view is that rRNA base modifications serve to fine tune ribosome structure and function. METHODOLOGY/PRINCIPAL FINDINGS: To test this hypothesis, yeast strains deficient in rRNA modifications in the ribosomal peptidyltransferase center were monitored for changes in and translational fidelity. These studies revealed allele-specific sensitivity to translational inhibitors, changes in reading frame maintenance, nonsense suppression and aa-tRNA selection. Ribosomes isolated from two mutants with the most pronounced phenotypic changes had increased affinities for aa-tRNA, and surprisingly, increased rates of peptidyltransfer as monitored by the puromycin assay. rRNA chemical analyses of one of these mutants identified structural changes in five specific bases associated with the ribosomal A-site. CONCLUSIONS/SIGNIFICANCE: Together, the data suggest that modification of these bases fine tune the structure of the A-site region of the large subunit so as to assure correct positioning of critical rRNA bases involved in aa-tRNA accommodation into the PTC, of the eEF-1A•aa-tRNA•GTP ternary complex with the GTPase associated center, and of the aa-tRNA in the A-site. These findings represent a direct demonstration in support of the prevailing hypothesis that rRNA modifications serve to optimize rRNA structure for production of accurate and efficient ribosomes

Synthetic biology: ethical ramifications 2009

During 2007 and 2008 synthetic biology moved from the manifesto stage to research programs. As of 2009, synthetic biology is ramifying; to ramify means to produce differentiated trajectories from previous determinations. From its inception, most of the players in synthetic biology agreed on the need for (a) rationalized design and construction of new biological parts, devices, and systems as well as (b) the re-design of natural biological systems for specified purposes, and that (c) the versatility of designed biological systems makes them suitable to address such challenges as renewable energy, the production of inexpensive drugs, and environmental remediation, as well as providing a catalyst for further growth of biotechnology. What is understood by these goals, however, is diverse. Those assorted understandings are currently contributing to different ramifications of synthetic biology. The Berkeley Human Practices Lab, led by Paul Rabinow, is currently devoting its efforts to documenting and analyzing these ramifications as they emerge

Base methylations in the double-stranded RNA by a fused methyltransferase bearing unwinding activity

Modifications of rRNAs are clustered in functional regions of the ribosome. In Helix 74 of Escherichia coli 23S rRNA, guanosines at positions 2069 and 2445 are modified to 7-methylguanosine(m7G) and N2-methylguanosine(m2G), respectively. We searched for the gene responsible for m7G2069 formation, and identified rlmL, which encodes the methyltransferase for m2G2445, as responsible for the biogenesis of m7G2069. In vitro methylation of rRNA revealed that rlmL encodes a fused methyltransferase responsible for forming both m7G2069 and m2G2445. We renamed the gene rlmKL. The N-terminal RlmL activity for m2G2445 formation was significantly enhanced by the C-terminal RlmK. Moreover, RlmKL had an unwinding activity of Helix 74, facilitating cooperative methylations of m7G2069 and m2G2445 during biogenesis of 50S subunit. In fact, we observed that RlmKL was involved in the efficient assembly of 50S subunit in a mutant strain lacking an RNA helicase deaD

A Forward-Genetic Screen and Dynamic Analysis of Lambda Phage Host-Dependencies Reveals an Extensive Interaction Network and a New Anti-Viral Strategy

Latently infecting viruses are an important class of virus that plays a key role in viral evolution and human health. Here we report a genome-scale forward-genetics screen for host-dependencies of the latently-infecting bacteriophage lambda. This screen identified 57 Escherichia coli (E. coli) genes—over half of which have not been previously associated with infection—that when knocked out inhibited lambda phage's ability to replicate. Our results demonstrate a highly integrated network between lambda and its host, in striking contrast to the results from a similar screen using the lytic-only infecting T7 virus. We then measured the growth of E. coli under normal and infected conditions, using wild-type and knockout strains deficient in one of the identified host genes, and found that genes from the same pathway often exhibited similar growth dynamics. This observation, combined with further computational and experimental analysis, led us to identify a previously unannotated gene, yneJ, as a novel regulator of lamB gene expression. A surprising result of this work was the identification of two highly conserved pathways involved in tRNA thiolation—one pathway is required for efficient lambda replication, while the other has anti-viral properties inhibiting lambda replication. Based on our data, it appears that 2-thiouridine modification of tRNAGlu, tRNAGln, and tRNALys is particularly important for the efficient production of infectious lambda phage particles

Biochemical and Structural Insights into the Mechanisms of SARS Coronavirus RNA Ribose 2′-O-Methylation by nsp16/nsp10 Protein Complex

The 5′-cap structure is a distinct feature of eukaryotic mRNAs, and eukaryotic viruses generally modify the 5′-end of viral RNAs to mimic cellular mRNA structure, which is important for RNA stability, protein translation and viral immune escape. SARS coronavirus (SARS-CoV) encodes two S-adenosyl-L-methionine (SAM)-dependent methyltransferases (MTase) which sequentially methylate the RNA cap at guanosine-N7 and ribose 2′-O positions, catalyzed by nsp14 N7-MTase and nsp16 2′-O-MTase, respectively. A unique feature for SARS-CoV is that nsp16 requires non-structural protein nsp10 as a stimulatory factor to execute its MTase activity. Here we report the biochemical characterization of SARS-CoV 2′-O-MTase and the crystal structure of nsp16/nsp10 complex bound with methyl donor SAM. We found that SARS-CoV nsp16 MTase methylated m7GpppA-RNA but not m7GpppG-RNA, which is in contrast with nsp14 MTase that functions in a sequence-independent manner. We demonstrated that nsp10 is required for nsp16 to bind both m7GpppA-RNA substrate and SAM cofactor. Structural analysis revealed that nsp16 possesses the canonical scaffold of MTase and associates with nsp10 at 1∶1 ratio. The structure of the nsp16/nsp10 interaction interface shows that nsp10 may stabilize the SAM-binding pocket and extend the substrate RNA-binding groove of nsp16, consistent with the findings in biochemical assays. These results suggest that nsp16/nsp10 interface may represent a better drug target than the viral MTase active site for developing highly specific anti-coronavirus drugs

Differential equations matrics and models

xvi, 112p. : il.; 25 cm

Learn React Hooks: build and refactor modern React.js applications using Hooks

This ultimate guide on React Hooks helps you modernize managing state and effects in React apps using Hooks. You will learn various types of Hooks and how it integrates with Context and Suspense APIs. You will create custom Hooks and learn to use Hooks with Redux and MobX. Lastly, you will learn to migrate your existing React applications to Hooks

Analyses of murine neutrophil granulocyte steady-state homeostatic regulation

Neutrophile Granulozyten werden durch einen weitgehend unverstandenen homöostatischen Feedback-Mechanismus reguliert. Diese Regulation richtet sich nach dem Bedarf in der Peripherie. Es wird sozusagen nur die Anzahl an Neutrophilen produziert bzw. freigesetzt, die wirklich benötigt wird. Es ist schon lange bekannt, dass die Knochenmarkzellularität invers mit dem G-CSF-Spiegel korreliert. Allerdings ist der Mechanismus, der die Produktion mit der Freisetzung verbindet, noch unbekannt. In dieser Arbeit wird ein positiver Feedback-Mechanismus beschrieben, der mit einem Anstieg von G-CSF im Plasma und starken Verschiebungen auf der Ebene von myeloischen Knochenmarkprogenitorzellen und hämatopoetischen Stammzellen einhergeht. Nach Antikörper-vermittelter Depletion der Neutrophilen entsteht ein Anstieg der GMP-Population (Granulozyten/Makrophagen-Progenitoren) auf Kosten der MEP-Population (Megakaryozyten/Erythrozyten Progenitoren). Desweiteren findet man eine starke Expansion an hämatopoetischen Stammzellen, die in der sogenannten LSK-Population angereichert sind. Der Mechanismus ähnelt den beobachtbaren Veränderungen nach Gabe von rekombinantem G-CSF und ist in der Tat mit einem starken Anstieg des Plasma G-CSF assoziiert. Die hier gezeigten Daten unterstreichen die Kausalität des G-CSF Anstiegs (ein blockierener anti G-CSF Antikörper unterbindet komplett den Feedback). Der Mechanismus ist unabhängig von Lymphozyten, kommensalen Bakterien und dem Adaptorprotein MyD88. Vermittelt wird dieser Feedback-Mechanismus über TLR4 in einem MyD88-unabhängigen, dafür TRIF-abhängigen Signaltransduktionsweg. Ein möglicher Sensor bei der Regulation der Neutrophilen-Homöostase für diesen regulatorischen Feedback-Mechanismus im steady-state nutzt also hoch konservierte pattern recognition Rezeptoren, die indirekt das Fehlen ausreichender Mengen von Granulozyten detektieren.Polymorphonuclear neutrophil granulocytes represent the first line of immune response against invading pathogens. Neutrophil numbers are tightly controlled by an incompletely understood homeostatic feedback loop, which adjusts the bone marrow’s supply to peripheral needs. While it has long been known that bone marrow cellularity is inversely correlated with G-CSF (granulocyte colony stimulating factor) levels, the mechanism linking peripheral clearance to production remains unknown. In this work, a positive feedback loop in response to neutropenia is described that includes an increase of G-CSF in plasma levels and shifts on hematopoietic progenitors and hematopoietic stem cells towards the granulocyte lineage in the bone marrow. Antibody-induced neutropenia in mice leads to an increase of granulocyte macrophage progenitors at the cost of megakaryocyte erythrocyte progenitors in the marrow. Additionally, the number of lin- Sca1+ c-kit+ cells (enriched with hematopoietic stem cells) expands, and plasma G-CSF goes up. In fact, the consequences of neutrophil depletion on the marrow level are comparable with the changes in mice that received recombinant human G-CSF. The positive feedback loop was found to be independent of lymphocytes, commensal bacteria and the adaptor protein MyD88. Instead, the above-mentioned phenomena are dependent on TLR4/TRIF signalling. In conclusion, a possible sensor in the regulation of neutrophil homeostasis relies on highly conserved pattern recognition receptors indirectly sensing the consequences of reduced neutrophil levels