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Biological models

Abdelmutalab G A Azrag, Christian W W Pirk, Abdullahi A Yusuf, Fabrice Pinard, Saliou Niassy, Gladys Mosomtai, Régis Babin
The antestia bug, Antestiopsis thunbergii (Gmelin 1790) is a major pest of Arabica coffee in Africa. The bug prefers coffee at the highest elevations, contrary to other major pests. The objectives of this study were to describe the relationship between A. thunbergii populations and elevation, to elucidate this relationship using our knowledge of the pest thermal biology and to predict the pest distribution under climate warming. Antestiopsis thunbergii population density was assessed in 24 coffee farms located along a transect delimited across an elevation gradient in the range 1000-1700 m asl, on Mt...
2018: PloS One
Alex D Bird, Magnus J E Richardson
Short-term synaptic depression, caused by depletion of releasable neurotransmitter, modulates the strength of neuronal connections in a history-dependent manner. Quantifying the statistics of synaptic transmission requires stochastic models that link probabilistic neurotransmitter release with presynaptic spike-train statistics. Common approaches are to model the presynaptic spike train as either regular or a memory-less Poisson process: few analytical results are available that describe depressing synapses when the afferent spike train has more complex, temporally correlated statistics such as bursts...
June 22, 2018: PLoS Computational Biology
Nicolas Henry, Eva-Maria Krammer, Florian Stengel, Quentin Adams, François Van Liefferinge, Ellen Hubin, Rui Chaves, Rouslan Efremov, Ruedi Aebersold, Guy Vandenbussche, Martine Prévost, Vincent Raussens, Stéphanie Deroo
Apolipoprotein E (apoE) is a forefront actor in the transport of lipids and the maintenance of cholesterol homeostasis, and is also strongly implicated in Alzheimer's disease. Upon lipid-binding apoE adopts a conformational state that mediates the receptor-induced internalization of lipoproteins. Due to its inherent structural dynamics and the presence of lipids, the structure of the biologically active apoE remains so far poorly described. To address this issue, we developed an innovative hybrid method combining experimental data with molecular modeling and dynamics to generate comprehensive models of the lipidated apoE4 isoform...
June 22, 2018: PLoS Computational Biology
Jinjin Xu, Mengsen Li, Zhihong Yao, Yezi Zhang, Shishi Li, Liufang Hu, Zifei Qin, Frank J Gonzalez, Xinsheng Yao
Neobavaisoflavone (NBIF), a phenolic compound isolated from Psoralea corylifolia L., possesses several significant biological properties. However, the pharmacokinetic behaviors of NBIF have been characterized as rapid oral absorption, high clearance, and poor oral bioavailability. We found that NBIF underwent massive glucuronidation and oxidation by human liver microsomes (HLM) in this study with the intrinsic clearance (CLint ) values of 12.43, 10.04, 2.01, and 6.99 μL/min/mg for M2, M3, M4, and M5, respectively...
June 18, 2018: Journal of Pharmaceutical and Biomedical Analysis
Marco Giovannini, Huaqing Ren, Jian Cao, Kornel Ehmann
Core needle biopsies are widely adopted medical procedures that consist in the removal of biological tissue to better identify a lesion or an abnormality observed through a physical exam or a radiology scan. These procedures can provide significantly more information than most medical tests and they are usually performed on bone lesions, breast masses, lymph nodes and the prostate. The quality of the samples mainly depends on the forces exerted by the needle during the cutting process. The reduction of these forces is critical to extract high-quality tissue samples...
June 15, 2018: Journal of the Mechanical Behavior of Biomedical Materials
N de Cesare, C Trevisan, E Maghin, M Piccoli, P G Pavan
The diaphragm is a mammalian skeletal muscle that plays a fundamental role in the process of respiration. Alteration of its mechanical properties due to a diaphragmatic hernia contributes towards compromising its respiratory functions, leading to the need for surgical intervention to restore the physiological conditions by means of implants. This study aims to assess via numerical modeling biomechanical differences between a diaphragm in healthy conditions and a herniated diaphragm surgically repaired with a polymeric implant, in a mouse model...
June 15, 2018: Journal of the Mechanical Behavior of Biomedical Materials
Jimmy W Huh, Ramesh Raghupathi
Pediatric traumatic brain injury (TBI) remains one of the leading causes of morbidity and mortality in children. Experimental and clinical studies demonstrate that the developmental age, the type of injury (diffuse vs. focal) and sex may play important roles in the response of the developing brain to a traumatic injury. Advancements in acute neurosurgical interventions and neurocritical care have improved and led to a decrease in mortality rates over the past decades. However, survivors are left with life-long behavioral deficits underscoring the need to better define the cellular mechanisms underlying these functional changes...
June 19, 2018: Neuropharmacology
A von Schaewen, I S Jeong, S Rips, A Fukudome, J Tolley, Y Nagashima, K Fischer, H Kaulfuerst-Soboll, H Koiwa
Production and isolation of recombinant proteins are key steps in modern Molecular Biology. Expression vectors and platforms for various hosts, including both prokaryotic and eukaryotic systems, have been used. In basic plant research, Arabidopsis thaliana is the central model for which a wealth of genetic and genomic resources is available, and enormous knowledge has been accumulated over the past years - especially since elucidation of its genome in 2000. However, until recently an Arabidopsis platform had been lacking for preparative-scale production of homologous recombinant proteins...
June 22, 2018: Plant Signaling & Behavior
Yingcai Zhao, Changhu Xue, Tiantian Zhang, YuMing Wang
Sea cucumbers, belonging to the phylum Echinodermata, have been valued for centuries as a nutritious and functional food with various bioactivities. Sea cucumbers can produce highly active substances, notably saponins, the main secondary metabolites, which are the basis of their chemical defense. The saponins are mostly triterpene glycosides with triterpenes or steroid in aglycone, which possess multiple biological properties including anti-tumor, hypolipidemic activity, improvement of nonalcoholic fatty liver, inhibition of fat accumulation, anti-hyperuricemia, promotion of bone marrow hematopoiesis, anti-hypertension, etc...
June 22, 2018: Journal of Agricultural and Food Chemistry
Aleksandra Andreevna Ageeva, Ekaterina A Khramtsova, Ilya M Magin, Peter A Purtov, Miguel A Miranda, Tatyana V Leshina
The origin of biomolecules in the pre-biological period is still a matter of debate, as is the unclarified nature of the differences in enantiomer properties, especially the medically important activity of chiral drugs. On the first issue, significant progress has been made in the last decade of the 20th century with the experimental confirmation of Frank's popular theory on chiral catalysis in spontaneous asymmetric synthesis. Prof. Soai examined the chiral catalysis of the alkylation of achiral aldehydes by achiral reagents...
June 22, 2018: Chemistry: a European Journal
Pengxiang Yang, Huijuan Song, Yibo Qin, Pingsheng Huang, Chuangnian Zhang, Deling Kong, Weiwei Wang
Dendritic cells (DCs) are increasingly used in cancer vaccines due to their ability to regulate T-cell immunity. Major limitations associated with the present DCs adoptive transfer immunotherapy are low cell viability and transient duration of transplanted DCs at the vaccination site, and the lack of recruitment of host DCs, leading to unsatisfactory T-cell immune response. Here, we developed a novel vaccine nodule comprising a simple physical mixture of the peptide nanofibrous hydrogel, DCs and tumor antigens...
June 22, 2018: Nano Letters
Vivek Halder, Julian Oeljeklaus, Geronimo Heilmann, Jan Krahn, Yanlin Liu, Yan Xiong, Markus Schlicht, Jasmin Schillinger, Barbara Kracher, Michael Ehrmann, Erich Kombrink, Farnusch Kaschani, Markus Kaiser
Bioactive natural products are important starting points for developing chemical tools for biological research. For elucidating their bioactivity profile, biological systems with concise complexity such as cell culture systems are frequently used, while unbiased investigations in more complex multicellular systems are only rarely explored. Here, we demonstrate with the natural product Rotihibin A and the plant research model system Arabidopsis thaliana that unbiased transcriptional profiling enables a rapid, label-free and compound economic evaluation of natural products' bioactivity profile in a complex multicellular organism...
June 22, 2018: Chemistry: a European Journal
Ju-Hye Yang, Esther Lee, BoHyoung Lee, Won-Kyung Cho, Jin Yeul Ma, Kwang-Il Park
Artemisia apiacea Hance is a traditional herbal medicine used for treating eczema and jaundice in Eastern Asia including China, Korea, and Japan. However, the biological and pharmacological actions of Artemisia apiacea Hance in atopic dermatitis (AD) are not fully understood. An ethanolic extract of Artemisia apiacea Hance (EAH) was tested in vitro and in vivo to investigate its anti-inflammatory activity and anti-atopic dermatitis effects. The results showed that EAH dose-dependence inhibited production of regulated on activation, normal T-cell expressed and secreted (RANTES), interleukin (IL)-6, IL-8, and thymus and activation-regulated chemokine (TARC)...
June 22, 2018: Nutrients
Eunae Kim, Cheolhee Kim
Rational drug design is accomplished through the complementary use of structural biology and computational biology of biological macromolecules involved in disease pathology. Most of the known theoretical approaches for drug design are based on knowledge of the biological targets to which the drug binds. This approach can be used to design drug molecules that restore the balance of the signaling pathway by inhibiting or stimulating biological targets by molecular modeling procedures as well as by molecular dynamics simulations...
June 22, 2018: Current Medicinal Chemistry
Seth Madlon-Kay, Michael J Montague, Lauren J N Brent, Samuel Ellis, Brian Zhong, Noah Snyder-Mackler, Julie E Horvath, Jesse Haynes Pate Skene, Michael L Platt
The neuropeptides oxytocin (OT) and arginine vasopressin (AVP) influence pair bonding, attachment, and sociality, as well as anxiety and stress responses in humans and other mammals. The effects of these peptides are mediated by genetic variability in their associated receptors, OXTR and the AVPR gene family. However, the role of these genes in regulating social behaviors in non-human primates is not well understood. To address this question, we examined whether genetic variation in the OT receptor gene OXTR and the AVP receptor genes AVPR1A and AVPR1B influence naturally-occurring social behavior in free-ranging rhesus macaques-gregarious primates that share many features of their biology and social behavior with humans...
June 21, 2018: American Journal of Primatology
Isabel M Smallegange, Hedwig M Ens
Predictions on population responses to perturbations are often derived from trait-based approaches like integral projection models (IPMs), but are rarely tested. IPMs are constructed from functions that describe survival, growth and reproduction in relation to the traits of individuals and their environment. Although these functions comprise biologically non-informative statistical coefficients within standard IPMs, model parameters of the recently developed dynamic energy budget IPM (DEB-IPM) are life-history traits like "length at maturation" and "maximum reproduction rate"...
July 2018: Journal of Animal Ecology
Jian Hu, Hui-Fang Liu, Jun Sun, Jia Wang, Rong Liu
It remains challenging to accurately discriminate between biological and crystal interfaces. Most existing analyses and algorithms focused on the features derived from a single side of the interface. However, less attention has been paid to the properties of residue pairs across protein interfaces. To address this problem, we defined a novel co-evolutionary feature for homodimers through integrating direct coupling analysis and image processing techniques. The residue pairs across biological homodimeric interfaces were significantly enriched in co-evolving residues compared to those across crystal contacts, resulting in a promising classification accuracy with area under the curves (AUCs) of more than 0...
June 22, 2018: Protein Science: a Publication of the Protein Society
Chen Tu, Ying Liu, Jing Wei, Lianzhen Li, Kirk G Scheckel, Yongming Luo
In this paper, a highly copper-resistant fungal strain NT-1 was characterized by morphological, physiological, biochemical, and molecular biological techniques. Physiological response to Cu(II) stress, effects of environmental factors on Cu(II) biosorption, as well as mechanisms of Cu(II) biosorption by strain NT-1 were also investigated in this study. The results showed that NT-1 belonged to the genus Gibberella, which exhibited high tolerance to both acidic conditions and Cu(II) contamination in the environment...
June 22, 2018: Environmental Science and Pollution Research International
Sylvain Bart, Joël Amossé, Christopher N Lowe, Christian Mougin, Alexandre R R Péry, Céline Pelosi
Ecotoxicological tests with earthworms are widely used and are mandatory for the risk assessment of pesticides prior to registration and commercial use. The current model species for standardized tests is Eisenia fetida or Eisenia andrei. However, these species are absent from agricultural soils and often less sensitive to pesticides than other earthworm species found in mineral soils. To move towards a better assessment of pesticide effects on non-target organisms, there is a need to perform a posteriori tests using relevant species...
June 21, 2018: Environmental Science and Pollution Research International
Nancy Retzlaff, Peter F Stadler
Evolutionary processes have been described not only in biology but also for a wide range of human cultural activities including languages and law. In contrast to the evolution of DNA or protein sequences, the detailed mechanisms giving rise to the observed evolution-like processes are not or only partially known. The absence of a mechanistic model of evolution implies that it remains unknown how the distances between different taxa have to be quantified. Considering distortions of metric distances, we first show that poor choices of the distance measure can lead to incorrect phylogenetic trees...
June 21, 2018: Theory in Biosciences, Theorie in Den Biowissenschaften
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