Top 8 Biorxiv Papers Today in Biochemistry


2.009 Mikeys
#1. Gating Mechanism of β-Ketoacyl-ACP Synthases
Jeffrey Mindrebo, Ashay Patel, Woojoo Kim, Tony Davis, Aochiu Chen, Thomas Bartholow, James La Clair, J Andrew McCammon, Joseph Noel, Michael Burkart
Formation of carbon-carbon bonds via β-ketoacyl-acyl carrier protein (ACP) synthases (KS), are key reactions during de novo fatty acid and polyketide biosynthesis. KSs recognize multiple ACPs and choreograph ping-pong mechanisms often in an iterative fashion. Therefore, KSs must limit non-productive protein-protein interactions (PPIs) to achieve high degrees of reaction fidelity. To better understand the stereochemical features governing substrate discrimination during ACP-KS PPIs, we determined x-ray crystal structures complemented by molecular dynamic simulations of E. coli AcpP in complex with the elongating KSs, FabF and FabB. Covalently trapped substrate analogs were used to interrogate critical catalytic events accompanying carbon-carbon bond formation revealing a previously unknown gating mechanism during the binding and delivery of acyl-AcpPs. Two active site loops undergo large conformational excursions during this dynamic gating mechanism and are likely evolutionarily conserved features generally in elongating KSs.
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biorxivpreprint: Gating Mechanism of β-Ketoacyl-ACP Synthases https://t.co/9d4Jtyvauv #bioRxiv
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Authors: 10
Total Words: 0
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2.008 Mikeys
#2. A low-cost and high-precision scanning electrochemical microscope built with open source tools
Alperen Guver, Nafetalai Fifita, Peker Milas, Michael Straker, Michael Guy, Kara Green, Taha Yildirim, Ilyas Unlu, Veysel Yigit, Birol Ozturk
A low-cost Scanning Electrochemical Microscope (SECM) was built with a 0.6 pA current measurement capability potentiostat and submicron resolution motorized stage, using open source software and hardware tools. The high performance potentiostat with a Python graphical user interface was built based on an open source project. Arduino boards, stepper motors, a manual XY micromanipulator stage, 3D printed couplers and gears were used in building the motorized stage. An open source motor control software was used for moving the motorized stage with high precision. An inverted microscope was utilized for viewing a standard microelectrode while scanning. The setup was tested in the formation of a map of electrochemical signals from an array of pores on a parafilm membrane. As the setup will be used in future biosensing experiments, DNA hybridization detection experiments were also performed with the setup.
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biorxivpreprint: A low-cost and high-precision scanning electrochemical microscope built with open source tools https://t.co/3Urn85z2wf #bioRxiv
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Authors: 10
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2.007 Mikeys
#3. The TFIIH components p44/p62 act as a damage sensor during nucleotide excision repair
Jamie T Barnett, Jochen Kuper, Wolfgang Koelmel, Caroline Kisker, Neil M Kad
Nucleotide excision repair (NER) protects the genome following exposure to diverse types of DNA damage, including UV light and chemotherapeutics. Mutations in human NER genes lead to diseases such as xeroderma pigmentosum and Cockayne syndrome. In eukaryotes, the major transcription factor TFIIH is the central hub of NER. The core components of TFIIH include the helicases XPB, XPD, and the five core structural subunits. Two of these core-TFIIH proteins, p44 and p62 remain relatively unstudied; although p44 is known to regulate the helicase activity of XPD during NER. p62's role is thought to be structural; however, a recent cryo-EM structure shows p44, p62, and XPD making contacts with each other, implying a more extensive role in DNA repair beyond the structural integrity of TFIIH. Here, we show that p44 stimulates XPD's ATPase, but upon encountering DNA damage further stimulation is only observed when p62 is in the ternary complex. More significantly, we show that the p44/p62 complex binds DNA independently of XPD and diffuses...
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cryoEM_Papers: The TFIIH components p44/p62 act as a damage sensor during nucleotide excision repair https://t.co/KpLg15a1nx
leemorj: RT @cryoEM_Papers: The TFIIH components p44/p62 act as a damage sensor during nucleotide excision repair https://t.co/KpLg15a1nx
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Authors: 5
Total Words: 0
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2.005 Mikeys
#4. Categorical Assignment of Pulmonary Embolism is a Simple and More Accurate Indicator of Right Ventricular Dysfunction and Short Team Mortality
Yu Lin Chen, Colin Wright, Anthony Pietropaoli, Ayman Elbadawi, Joseph Delehanty, Bryan Barrus, Igor Gosev, David Trawick, Dhwani Patel, Scott Cameron
Several risk stratification tools are available to predict short term mortality in patients with acute pulmonary embolism (PE). Right ventricular (RV) dysfunction, which is common to intermediate and high risk PE, is an independent predictor of mortality and may be a faster and simpler way to assess patient risk in acute care settings. We evaluated 571 patients presenting with acute PE as the primary diagnosis, stratifying them by the Pulmonary Embolism Severity Index (PESI), by the BOVA score, or categorically as low risk (no RV dysfunction by imaging), intermediate risk (RV dysfunction by imaging), or high risk PE (RV dysfunction by imaging with sustained hypotension). Using imaging data to firstly define the presence of RV dysfunction, and plasma cardiac troponin T (cTnT) and NTproBNP as additional evidence for myocardial strain, we evaluated the PESI and BOVA scoring systems compared to categorical assignment of PE as low risk, submassive, and massive PE. Cardiac biomarkers poorly distinguished between PESI classes and BOVA...
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biorxivpreprint: Categorical Assignment of Pulmonary Embolism is a Simple and More Accurate Indicator of Right Ventricular Dysfunction and Short Team Mortality https://t.co/tAwb4xBTuU #bioRxiv
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Authors: 10
Total Words: 6023
Unqiue Words: 1879

2.003 Mikeys
#5. A New Minimally Invasive Technique for Repairing Achilles Tendon Rupture: A Biomechanical Study
Zhao Peng, Sun Dawei, Xiong Yarun, Zhuo Ribo
Introduction: The incidence of Achilles tendon rupture shows a gradually increasing trend, which is mainly managed by minimally invasive treatment due to its advantages, such as low wound infection rate. At present, the firmness of the commonly applied minimally invasive suture method for Achilles tendon remains controversial. Our research group has developed a novel suture method for Achilles tendon, which has achieved favorable clinical outcomes. Therefore, this experiment aimed to explore the optimal approach to repair Achilles tendon rupture through comparing the biomechanical strength of the commonly used Achilles tendon suture methods currently. Materials and methods: 6 fresh frozen human cadaveric Achilles tendon specimens were sutured by three kinds of technique, and were tested through the cyclical loading after repair. Results: Results of cyclical loading showed that, the repair using the new technique was stronger after 10 cycles, 1000 cycles, and rupture. Moreover, the new technique had displayed superior...
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biorxivpreprint: A New Minimally Invasive Technique for Repairing Achilles Tendon Rupture: A Biomechanical Study https://t.co/anTqtdHcjs #bioRxiv
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Authors: 4
Total Words: 0
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2.0 Mikeys
#6. A general LC/MS-based RNA sequencing method for direct analysis of multiple-base modifications in RNA mixtures
Ning Zhang, Shundi Shi, Tony Z Jia, Ashley Ziegler, Barney Yoo, Xiaohong Yuan, Wenjia Li, Shenglong Zhang
A complete understanding of the structural and functional potential of RNA requires understanding of chemical modifications and noncanonical bases; this in turn requires advances in current sequencing methods to be able to sequence not only canonical ribonucleotides, but at the same time directly sequence these nonstandard moieties. Here, we present the first direct and modification type-independent RNA sequencing method via integration of a hydrophobic end-labeling strategy with of 2-D mass-retention time LC/MS analysis to allow de novo sequencing of RNA mixtures and enhance sample usage efficiency. Our method can directly read out the complete sequence, while identifying, locating, and quantifying base modifications accurately in both single and mixed RNA samples containing multiple different modifications at single-base resolution. Our method can also quantify stoichiometry/percentage of modified RNA vs. its canonical counterpart RNA, simulating a real biological sample where modifications exist but may not be 100% at a...
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t_z_jia: Our collaborative work now on BioRXiv with @nyit on development of a new RNA modification sequencing technique! https://t.co/Am8pd8ofPU
razoralign: A general LC/MS-based RNA sequencing method for direct analysis of multiple-base modifications in RNA mixtures https://t.co/vINeTnCGEk
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1.997 Mikeys
#7. Simple rules govern the diversity of bacterial nicotianamine-like metallophores
Clementine Laffont, Catherine Brutesco, Christine Hajjar, Gregorio Cullia, Roberto Fanelli, Laurent Ouerdane, Florine Cavelier, Pascal Arnoux
In metal-scarce environments, some pathogenic bacteria produce opine-type metallophores mainly to face the host's nutritional immunity. This is the case of staphylopine, pseudopaline and yersinopine, identified in Staphylococcus aureus, Pseudomonas aeruginosa and Yersinia pestis respectively. These metallophores are synthesized by two (CntLM) or three enzymes (CntKLM), CntM catalyzing the last step of biosynthesis using diverse substrates (pyruvate or α-ketoglutarate), pathway intermediates (xNA or yNA) and cofactors (NADH or NADPH), depending on the species. Here, we explored substrate specificity of CntM by combining bioinformatics and structural analysis with chemical synthesis and enzymatic studies. We found that NAD(P)H selectivity was mainly due to the amino acid at position 33 (S. aureus numbering) which ensures a preferential binding to NADPH when it is an arginine. Moreover, whereas CntM from P. aeruginosa preferentially uses yNA over xNA, the staphylococcal enzyme is not stereospecific. Most importantly, selectivity...
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biorxivpreprint: Simple rules govern the diversity of bacterial nicotianamine-like metallophores https://t.co/49jXY6lHgY #bioRxiv
cristobalvega: RT @biorxivpreprint: Simple rules govern the diversity of bacterial nicotianamine-like metallophores https://t.co/49jXY6lHgY #bioRxiv
sbotlite: RT @biorxivpreprint: Simple rules govern the diversity of bacterial nicotianamine-like metallophores https://t.co/49jXY6lHgY #bioRxiv
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Authors: 8
Total Words: 8092
Unqiue Words: 2830

1.997 Mikeys
#8. UHPLC/MS based large-scale targeted metabolomics method for multiple-biological matrix assay
Xialin Luo, Aihua Zhang, Xijun Wang, Haitao Lu
We develop a simply, greatly reliable and large-scale targeted metabolomics method that is exact coverage to more than 200 key metabolites with importantly biological functions. These metabolites involve in numerous metabolic pathways underlying different biochemical processes, including disease progression, drug treatment and genetic modifications. Facing to clinical demand, this method can also determine the absolute concentration of 84 metabolites produced by various biological matrixes, which can assist in clinical diagnosis of different diseases, by providing more information-rich data than conventional clinical chemistry assay. Herein, once this metabolomics protocol is open to the scientific community, it can be broadly applied to address a diversity of biochemical questions related to diseases and drug development from metabolic perspective
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Sample Sizes : [6]
Authors: 4
Total Words: 6055
Unqiue Words: 2412

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