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Caleb J Bashor, James J Collins
Engineering synthetic gene regulatory circuits proceeds through iterative cycles of design, building, and testing. Initial circuit designs must rely on often-incomplete models of regulation established by fields of reductive inquiry-biochemistry and molecular and systems biology. As differences in designed and experimentally observed circuit behavior are inevitably encountered, investigated, and resolved, each turn of the engineering cycle can force a resynthesis in understanding of natural network function...
March 16, 2018: Annual Review of Biophysics
Paween Mahinthichaichan, Robert B Gennis, Emad Tajkhorshid
Cytochrome aa3 is the terminal respiratory enzyme of all eukaryotes and many bacteria and archaea, reducing O2 to water and harnessing the free energy from the reaction to generate the transmembrane electrochemical potential. The diffusion of O2 to the heme-copper catalytic site, which is buried deep inside the enzyme, is the initiation step of the reaction chemistry. Our previous molecular dynamics (MD) study with cytochrome ba3 , a homologous enzyme of cytochrome aa3 in Thermus thermophilus, demonstrated that O2 diffuses from the lipid bilayer to its reduction site through a 25-Å long tunnel inferred by Xe-binding sites detected by X-ray crystallography$ ...
March 16, 2018: Biochemistry
Daviel Gómez, L Ázaro Hernández, Lourdes Yabor, Gerrit T S Beemster, Christoph C Tebbe, Jutta Papenbrock, José Carlos Lorenzo
Plant scientists usually record several indicators in their abiotic factor experiments. The common statistical management involves univariate analyses. Such analyses generally create a split picture of the effects of experimental treatments since each indicator is addressed independently. The Euclidean distance combined with the information of the control treatment could have potential as an integrating indicator. The Euclidean distance has demonstrated its usefulness in many scientific fields but, as far as we know, it has not yet been employed for plant experimental analyses...
March 15, 2018: Journal of Plant Research
A B Chetverin
Qβ replicase (RNA-directed RNA polymerase of bacteriophage Qβ) has an unsurpassed capacity to amplify polynucleotides in vitro. In 1986, the Group of Viral RNA Biochemistry was organized at the Institute of Protein Research in order to exploit this property for the synthesis of messenger RNAs to be used in cell-free translation systems. Although the task has not been implemented in full, this work has led to a number of unexpected important results including uncovering the nature of the "template-free" RNA synthesis by Qβ replicase, discovering the ability of RNA molecules for spontaneous recombination, revealing the unusual mechanism Qβ replicase uses to discriminate between its proper and improper templates, and discovering a new function of the largest ribosomal protein S1, that is also one of the replicase subunits...
January 2018: Biochemistry. Biokhimii︠a︡
Anish Sharda, Bruce Furie
The protein disulfide isomerase (PDI) family of thiol isomerases are intracellular enzymes known to catalyze the oxidation, reduction and isomerization of disulfide bonds during protein synthesis in the endoplasmic reticulum. PDI and related members of the thiol isomerase family are known to localize extracellularly where they possess various functions. Among these, the role of PDI in the initiation of thrombus formation is best characterized. PDI is secreted within seconds from activated platelets and endothelial cells at the site of vascular injury and accumulates in the developing platelet-fibrin thrombus...
March 15, 2018: Expert Review of Hematology
Ursula J Lemberger, Claudia D Fuchs, Christian Schöfer, Andrea Bileck, Christopher Gerner, Tatjana Stojakovic, Makoto M Taketo, Michael Trauner, Gerda Egger, Christoph H Österreicher
Background: Wnt/β-catenin signaling plays a crucial role in embryogenesis, tissue homeostasis, metabolism and malignant transformation of different organs including the liver. Continuous β-catenin signaling due to somatic mutations in exon 3 of the Ctnnb1 gene is associated with different liver diseases including cancer and cholestasis. Results: Expression of a degradation resistant form of β-catenin in hepatocytes resulted in 100% mortality within 31 days after birth...
February 16, 2018: Oncotarget
Li-Chan Yang, Jiunn-Wang Liao, Chi-Luan Wen, Wen-Chuan Lin
Dendrobium Taiseed Tosnobile is a new species of herba dendrobii (Shi-Hu) that was developed by crossbreeding D. tosaense and D. nobile . Its pharmacological activity and active component have been reported, but its subchronic toxicity and genetic safety have not yet been investigated. This study assessed the 90-day oral toxicity and genetic safety of the aqueous extracts of D. Taiseed Tosnobile (DTTE) in male and female Sprague-Dawley (SD) rats. Eighty rats were divided into four groups, each consisting of ten male and ten female rats...
2018: Evidence-based Complementary and Alternative Medicine: ECAM
Yuval Elani, Tatiana Trantidou, Douglas Wylie, Linda Dekker, Karen Polizzi, Robert V Law, Oscar Ces
There is increasing interest in constructing artificial cells by functionalising lipid vesicles with biological and synthetic machinery. Due to their reduced complexity and lack of evolved biochemical pathways, the capabilities of artificial cells are limited in comparison to their biological counterparts. We show that encapsulating living cells in vesicles provides a means for artificial cells to leverage cellular biochemistry, with the encapsulated cells serving organelle-like functions as living modules inside a larger synthetic cell assembly...
March 14, 2018: Scientific Reports
Stephen Smith, Neil Dalchau
Synthesizing a genetic network which generates stable Turing patterns is one of the great challenges of synthetic biology, but a significant obstacle is the disconnect between the mathematical theory and the biological reality. Current mathematical understanding of patterning is typically restricted to systems of two or three chemical species, for which equations are tractable. However, when models seek to combine descriptions of intercellular signal diffusion and intracellular biochemistry, plausible genetic networks can consist of dozens of interacting species...
March 2018: Journal of the Royal Society, Interface
Ronan O'Malley, Ganesh Rao, Penelope Stein, Oliver Bandmann
The diagnosis of acute intermittent porphyria (AIP) is often overlooked. We describe a patient with this condition who had all the 'bells and whistles', in whom the diagnosis was only made after considerable delay. Far from an esoteric condition haunting examination candidates, AIP is an important cause of a broad spectrum of neurological symptoms. Its early recognition allows the astute clinician to prevent potentially devastating sequelae. We provide practical guidance on the investigation and management of this complex disorder...
March 14, 2018: Practical Neurology
Julie A Reisz, Alexander S Barrett, Travis Nemkov, Kirk C Hansen, Angelo D'Alessandro
Proteins have been historically regarded as "nature's robots": Molecular machines that are essential to cellular/extracellular physical mechanical properties and catalyze key reactions for cell/system viability. However, these robots are kept in check by other protein-based machinery to preserve proteome integrity and stability. During aging, protein homeostasis is challenged by oxidation, decreased synthesis, and increasingly inefficient mechanisms responsible for repairing or degrading damaged proteins...
March 14, 2018: Expert Review of Proteomics
Melanie Li, Swetlana Sirko
Building on the seminal work by Geoffrey Harris in the 1970s, the neuroendocrinology field, having undergone spectacular growth, has endeavored to understand the mechanisms of hormonal connectivity between the brain and the rest of the body. Given the fundamental role of the brain in the orchestration of endocrine processes through interactions among neurohormones, it is thus not surprising that the structural and/or functional alterations following traumatic brain injury (TBI) can lead to endocrine changes affecting the whole organism...
March 14, 2018: Journal of Clinical Medicine
G F Metallov, E N Ponomareva, M N Sorokina, V A Grigoryev, A A Korchunov
The article reports data on the dynamics of blood parameters and parameters of protein, fat, and water-salt metabolism in female starlet × beluga hybrids kept under artificial conditions in the period of reproductive cycle. Gonad maturation in female hybrids in the artificial environment causes clear changes in the biochemistry of blood and of urine.
January 2018: Doklady Biological Sciences: Proceedings of the Academy of Sciences of the USSR, Biological Sciences Sections
Rodolfo A Kolliker Frers, Vanesa Cosentino, Julia Tau, Eduardo M Kerzberg, Adriana Urdapilleta, Monica Chiocconi, Nora Kogan, Matilde Otero-Losada, Francisco Capani
Studies on the inflammatory burden in recent-onset psoriatic arthritis (PsA) patients without conventional cardiovascular risk factors (CVRFs) are not available. This preliminary study focuses on cardiovascular risk in cutaneous psoriasis (CPs) and recent-onset PsA patients. Blood biochemistry (glucose, cholesterol, uric acid, lipid profile and apolipoprotein B) was analyzed using standard kits. Proatherogenic inflammation markers, C-reactive protein (CRP) and interleukin-6 (IL-6), and endothelial activators monocyte chemoattractant protein-1 (MCP-1) and soluble intercellular adhesion molecule-1 (sICAM-1), were determined by enzyme-linked immunosorbent assay...
2018: Frontiers in Immunology
A C Van Erp, R A Rebolledo, D Hoeksma, N R Jespersen, P J Ottens, R Nørregaard, M Pedersen, C Laustsen, J G M Burgerhof, J C Wolters, J Ciapaite, H E Bøtker, H G D Leuvenink, B Jespersen
Hepatic and renal energy status prior to transplantation correlates with graft survival. However, effects of brain death (BD) on organ-specific energy status are largely unknown. We studied metabolism, perfusion, oxygen consumption, and mitochondrial function in the liver and kidneys following BD. BD was induced in mechanically-ventilated rats, inflating an epidurally-placed Fogarty-catheter, with sham-operated rats as controls. A 9.4T-preclinical MRI system measured hourly oxygen availability (BOLD-related R2*) and perfusion (T1-weighted)...
March 13, 2018: Scientific Reports
Venkataramana Kandi, Parimala Reddy Basireddy
Introduction Medical education involves training necessary to become a physician or a surgeon. This includes various levels of training like undergraduate, internship, and postgraduate training. Medical education can be quite complex, since it involves training in pre-clinical subjects (anatomy, physiology, biochemistry), the para-clinical subjects (microbiology, pathology, pharmacology, and forensic medicine), and a discrete group of clinical subjects that include general medicine, surgery, obstetrics and gynaecology, ear, nose and throat specialization, paediatrics, cardiology, pulmonology, dermatology, ophthalmology, and orthopaedics, and many other clinical specializations and super specialities (cardio-thoracic surgery, neurosurgery, etc...
January 5, 2018: Curēus
Guosong Hong, Robert D Viveros, Theodore J Zwang, Xiao Yang, Charles M Lieber
Electrophysiology tools have contributed substantially to understanding brain function, yet the capabilities of conventional electrophysiology probes have remained limited in key ways due to large structural and mechanical mismatches with respect to neural tissue. In this Perspective, we discuss how the general goal of probe design in biochemistry - that the probe or label has a minimal impact on the properties and function of the system being studied - can be realized by minimizing structural, mechanical and topological differences between neural probes and brain tissue, thus leading to a new paradigm of tissue-like mesh electronics...
March 12, 2018: Biochemistry
Anirban Roy, Robert Seidel, Gaurav Kumar, Stephen E Bradforth
Direct measurements of the valence ionization energies and the reorganization energies of the three aromatic amino acids, L-Tyrosine, L-Tryptophan, and L-Phenylalanine in aqueous solution using the liquid microjet technique and two different photoemission methods - X-ray photoelectron spectroscopy (XPS) at 175 eV photon energy and resonant two-photon ionization (R2PI) using 2 x 267 nm (2 x 4.64 eV) UV laser light are reported. L-Tryptophan has the lowest vertical ionization energy, 7.3 eV, followed by Tyrosine (7...
March 12, 2018: Journal of Physical Chemistry. B
Dale Hancock, Nicole Hare, Paul Denny, Gareth Denyer
Disciplines such as Biochemistry and Molecular Biology, which involve concepts not included in the high-school curriculum, are very challenging for many first year university students. These subjects are particularly difficult for students accustomed to surface learning strategies involving memorization and recall of facts, as a deeper understanding of the relationship between concepts is needed for successful transfer to related areas and subsequent study. In this article, we explore an activity in a very large first year Molecular Biology course, in which students create multiple-choice questions related to targeted learning outcomes, and then answer and evaluate one another's questions...
March 12, 2018: Biochemistry and Molecular Biology Education
Julie A Roden, Susanne Jakob, Casey Roehrig, Tamara J Brenner
In the past ten years, increasing evidence has demonstrated that scientific teaching and active learning improve student retention and learning gains in the sciences. Graduate teaching assistants (GTAs), who play an important role in undergraduate education at many universities, require training in these methods to encourage implementation, long-term adoption, and advocacy. Here, we describe the design and evaluation of a two-day training workshop for first-year GTAs in the life sciences. This workshop combines instruction in current research and theory supporting teaching science through active learning as well as opportunities for participants to practice teaching and receive feedback from peers and mentors...
March 12, 2018: Biochemistry and Molecular Biology Education
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