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Biological complex systems

Thea S Lotz, Thomas Halbritter, Christoph Kaiser, Martin M Rudolph, Leon Kraus, Florian Groher, Sabrina Steinwand, Josef Wachtveitl, Alexander Heckel, Beatrix Suess
Regulation of complex biological networks has proven to be a key bottleneck in synthetic biology. Interactions between the structurally flexible RNA and various other molecules in the form of riboswitches have shown a high-regulation specificity and efficiency and synthetic riboswitches have filled the toolbox of devices in many synthetic biology applications. Here we report the development of a novel, small molecule binding RNA aptamer, whose binding is dependent on light-induced change of conformation of its small molecule ligand...
December 5, 2018: Nucleic Acids Research
Angela Mazzeo, Enrico Jardim Clemente Santos
The biology of stem cells is one of the most dynamic and promising fields of the biological sciences, since it is the basis for the development of organisms. Its biological complexity demands efforts from several lines of research aimed mainly at its therapeutic use. Nanotechnology has been emerging as a new field of study, which shows great potential in the treatment of various diseases. This new area of health has been called "Nanomedicine" or "Bionanotechnology", which can be applied in Medicine by transport and drug delivery systems, robotic tools to be used in diagnostic and surgical processes, nanobiomaterials, gene therapies, nanobiomedical devices, among others...
November 29, 2018: Einstein
Andrew O Finley, Patrick S Forsythe, James A Crossman, Edward A Baker, Kim T Scribner
Modeling spatially explicit data provides a powerful approach to identify the effects of exogenous features associated with biological processes, including recruitment of stream fishes. However, the complex spatial and temporal dynamics of the stream and the species' reproductive and early life stage behaviors present challenges to drawing valid inference using traditional regression models. In these settings it is often difficult to ensure the spatial independence among model residuals-a key assumption that must be met to ensure valid inference...
2018: PloS One
Chang-Chih Hsieh, Yu-Chiao Liu, Mei-Chun Tseng, Ming-Hsi Chiang, Yih-Chern Horng
Dioxygen activation by FeII thiolate complexes is relatively rare in biological and chemical systems because the sulfur site is at least as vulnerable as the iron site to oxidative modification. O2 activation by FeII-SR complexes with thiolate bound trans to the O2 binding site generally affords the FeIV[double bond, length as m-dash]O intermediate and oxidized thiolate. On the other hand, O2 activation by Fe(ii)-SR complexes with thiolate bound cis to the O2 binding site generates FeIII-O-FeIII or S-oxygenated complexes...
December 5, 2018: Dalton Transactions: An International Journal of Inorganic Chemistry
Marcos Renato de Assis, Valdair Pinto
Biological products or biopharmaceuticals are medicinal products derived from living systems and manufactured by modern biotechnological methods that differ widely from the traditional synthetic drugs. Monoclonal antibodies are the most rapidly growing type of biologic. They are much larger and more complex molecules with inherent diversity; therefore, different manufacturers cannot produce identical biological products, even with the same type of host expression system and equivalent technologies. Thus, legal follow-on biologics manufactured and marketed after patent expiration are usually referred to as biosimilars...
December 2018: Therapeutic Advances in Musculoskeletal Disease
Adugna Abdi Woldesemayat, Monde Ntwasa
Drought alone or in combination with other stresses forms the major crop production constraint worldwide. Sorghum, one of the most important cereal crops is affected by drought alone or in combination with co-occurring stresses; notwithstanding, sorghum has evolved adaptive responses to combined stresses. Furthermore, an impressive number of sorghum genes have been investigated for drought tolerance. However, the molecular mechanism underling drought response remains poorly understood. We employed a systems biology approach to elucidate regulatory and broad functional features of these genes...
2018: Frontiers in Genetics
Cang Hui, David M Richardson
Invasion science is in a state of paradox, having low predictability despite strong, identifiable covariates of invasion performance. We propose shifting the foundation metaphor of biological invasions from a linear filtering scheme to one that invokes complex adaptive networks. We link invasion performance and invasibility directly to the loss of network stability and indirectly to network topology through constraints from the emergence of the stability criterion in complex systems. We propose the wind vane of an invaded network - the major axis of its adjacency matrix - which reveals how species respond dynamically to invasions...
December 1, 2018: Trends in Ecology & Evolution
Yulin Tian, Qing Lin
Photo-cross-linkers are invaluable tools for identifying drug targets and off-targets as well as probing the binding sites in medicinal chemistry and chemical biology. In this review, we summarize recent development of the ligand-based and genetically encoded photo-cross-linkers and their use in biological system. In particular, we highlight our discovery of 2-aryl-5-carboxytetrazole (ACT) as a novel class of photo-cross-linkers and their successful applications in drug target identification as well as identifying transient protein-protein interaction complexes in mammalian cells...
November 30, 2018: Chimia
Rodolfo Sumayao, Philip Newsholme, Tara McMorrow
Cystinosin is a lysosomal transmembrane protein which facilitates transport of the disulphide amino acid cystine (CySS) from the lysosomes of the cell. This protein is encoded by the CTNS gene which is defective in the lysosomal storage disorder, cystinosis. Because of the apparent involvement of cystinosin in the intermediary thiol metabolism, its discovery has fuelled investigations into its role in modulating cellular redox homeostasis. The kidney proximal tubular cells (PTCs) have become the focus of various studies on cystinosin since the protein is highly expressed in these cells and kidney proximal tubular transport dysfunction is the foremost clinical manifestation of cystinosis...
December 3, 2018: Antioxidants (Basel, Switzerland)
Natália Noronha Ferreira, Bruno Leonardo Caetano, Fernanda Isadora Boni, Flávia Sousa, Marina Magnani, Bruno Sarmento, Beatriz Stringhetti Ferreira Cury, Maria Palmira Daflon Gremião
Alginate-based polyelectrolytes complexes (PECs) and hydrogel were engineered as platforms for local bevacizumab (BVZ) therapy. This study provides deep comprehension on the microstructures of such systems, and their correlation with drug release patterns. PECs and hydrogel were characterized using Fourier transform infrared spectroscopy (FTIR), small-angle X-ray scattering (SAXS), scanning electron microscopy (SEM), atomic force microscopy (AFM) and porosimetry. Structural investigations indicated that PECs are formed by supramolecular interactions, resulting in physically crosslinked polymer networks, while the bevacizumab-loaded hydrogel has a more compact and rigid structure, promoting better entrapment of BVZ...
December 1, 2018: Journal of Pharmaceutical Sciences
Stephen W Santoro, Susanne Jakob
Olfactory experience can alter the molecular and cellular composition of chemosensory neurons within the olfactory sensory epithelia of mice. We sought to investigate the scope of cellular and molecular changes within a mouse's olfactory system as a function of its exposure to complex and salient sets of odors: those emitted from members of the opposite sex. We housed mice either separated from members of the opposite sex (sex-separated) or together with members of the opposite sex (sex-combined) until six months of age, resulting in the generation of four cohorts of mice...
December 4, 2018: Scientific Data
Dekai Ye, Li Li, Zhenhua Li, Yueyue Zhang, Min Li, Jiye Shi, Lihua Wang, Chunhai Fan, Jinghua Yu, Xiaolei Zuo
Molecular transport controls the efficiency of complex biological network systems such as cellular signaling system and cascade biomedical reaction. However, device fabrication for molecular sensing is often restricted by low transport efficiency and complicated processing. Here, we report a molecular threading-dependent transport system using three-dimensional (3D) paper origami enables the directional transport of biomolecules. We demonstrate that framework nucleic acid-based interface engineering allows orthogonal molecular recognition and enzymatic reaction with programmed order on site...
December 4, 2018: Nano Letters
Jana L Gevertz, Joanna R Wares
Mathematical models of biological systems must strike a balance between being sufficiently complex to capture important biological features, while being simple enough that they remain tractable through analysis or simulation. In this work, we rigorously explore how to balance these competing interests when modeling murine melanoma treatment with oncolytic viruses and dendritic cell injections. Previously, we developed a system of six ordinary differential equations containing fourteen parameters that well describes experimental data on the efficacy of these treatments...
2018: Computational and Mathematical Methods in Medicine
Jibin Wu, Yansong Chua, Malu Zhang, Haizhou Li, Kay Chen Tan
Environmental sounds form part of our daily life. With the advancement of deep learning models and the abundance of training data, the performance of automatic sound classification (ASC) systems has improved significantly in recent years. However, the high computational cost, hence high power consumption, remains a major hurdle for large-scale implementation of ASC systems on mobile and wearable devices. Motivated by the observations that humans are highly effective and consume little power whilst analyzing complex audio scenes, we propose a biologically plausible ASC framework, namely SOM-SNN...
2018: Frontiers in Neuroscience
Jiahao Chen, Yun-Ruei Kao, Daqian Sun, Tihomira I Todorova, David Reynolds, Swathi-Rao Narayanagari, Cristina Montagna, Britta Will, Amit Verma, And Ulrich Steidl
Myelodysplastic syndromes (MDS) frequently progress to acute myeloid leukemia (AML); however, the cells leading to malignant transformation have not been directly elucidated. As progression of MDS to AML in humans provides a biological system to determine the cellular origins and mechanisms of neoplastic transformation, we studied highly fractionated stem cell populations in longitudinal samples of patients with MDS who progressed to AML. Targeted deep sequencing combined with single-cell sequencing of sorted cell populations revealed that stem cells at the MDS stage, including immunophenotypically and functionally defined pre-MDS stem cells (pre-MDS-SC), had a significantly higher subclonal complexity compared to blast cells and contained a large number of aging-related variants...
December 3, 2018: Nature Medicine
Emilio Jiménez-Vicente, Julia Sanchez Martin Del Campo, Zhi-Yong Yang, Valerie L Cash, Dennis R Dean, Lance C Seefeldt
Nitrogenases are complex two-component metalloenzymes that catalyze biological nitrogen fixation. Three different nitrogenase types are found in the model nitrogen-fixing microbe Azotobacter vinelandii. In the case of the Mo-dependent enzyme, the two catalytic partners are referred to as the Fe protein and MoFe protein. In addition to genes encoding the catalytic components, there are a total of 68 other gene products known to be variously involved in producing, activating, protecting, sustaining, and regulating formation of the Mo-dependent nitrogenase...
2018: Methods in Enzymology
Evgeny N Imyanitov, Grigoriy A Yanus
Neoadjuvant therapy (NAT) is widely utilized in the routine management of cancer patients and various clinical trials for the treatment of breast, ovarian, rectal, esophageal, head and neck, lung, prostate and many other cancer types. There is a number of potential benefits of applying systemic treatment before the operation. NAT may significantly reduce the tumor burden thus allowing less traumatic surgery. NAT is often considered as personalized in vivo drug sensitivity test, as it allows rapid evaluation of tumor response to a given therapy and consequent adjustment of further treatment planning...
December 2018: Chinese Clinical Oncology
Papri Chakraborty, Abhijit Nag, Amrita Chakraborty, Thalappil Pradeep
Supramolecular chemistry is a major area of chemistry that utilizes weaker non-covalent interactions between molecules, including hydrogen bonding, van der Waals, electrostatic, π···π, and C-H···π interactions. Such forces have been the basis of several molecular self-assemblies and host-guest complexes in organic, inorganic, and biological systems. Atomically precise nanoclusters (NCs) are materials of growing interest that display interesting structure-property correlations. The evolving science of such systems reaffirms their molecular behavior...
December 3, 2018: Accounts of Chemical Research
Zheng Xing, Wai Kit Ma, Elizabeth J Tran
The mammalian DEAD-box RNA helicase DDX5, its paralog DDX17, and their orthologs in Saccharomyces cerevisiae and Drosophila melanogaster, namely Dbp2 and Rm62, define a subfamily of DEAD-box proteins. Members from this subfamily share highly conserved protein sequences and cellular functions. They are involved in multiple steps of RNA metabolism including mRNA processing, microRNA processing, ribosome biogenesis, RNA decay, and regulation of long noncoding RNA activities. The DDX5/Dbp2 subfamily is also implicated in transcription regulation, cellular signaling pathways, and energy metabolism...
December 2, 2018: Wiley Interdisciplinary Reviews. RNA
Robert B Hamanaka, Gökhan M Mutlu
Air pollution is a complex mixture of gaseous and particulate components, each of which has detrimental effects on human health. While the composition of air pollution varies greatly depending on the source, studies from across the world have consistently shown that air pollution is an important modifiable risk factor for significantly increased morbidity and mortality. Moreover, clinical studies have generally shown a greater impact of particulate matter (PM) air pollution on health than the gaseous components...
2018: Frontiers in Endocrinology
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