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Structural biology

Gisele Cristiane de Melo Dias, Mônica Cassel, Lázaro Wender Oliveira de Jesus, Sergio Ricardo Batlouni, Maria Inês Borella
Prochilodus lineatus is an important representative of the order Characiformes and a species that offers great advantages to fish farming. Therefore, detailed knowledge of its reproductive biology can be applied to various fields of production and biotechnology. In this study, we have identified testicular germ cells during spermatogenesis and have evaluated the volumetric proportion of the testes occupied by structures of the tubular and intertubular compartments. In addition, the individual volume of type A spermatogonia was measured and used to estimate the mean number of these cells per testis...
October 22, 2016: Anatomical Record: Advances in Integrative Anatomy and Evolutionary Biology
Katsuhiko Hirota, Hiromichi Yumoto, Bayarmagnai Sapaar, Takashi Matsuo, Tetsuo Ichikawa, Yoichiro Miyake
Candida albicans is commonly found as a member of the human microflora and a major human opportunistic fungal pathogen. A perturbation of the microbiome can lead to infectious diseases caused by various microorganisms, including C. albicans. Moreover, the interactions between C. albicans and bacteria are considered to play critical roles in human health. The major biological feature of C. albicans, which impacts human health, resides in its ability to form biofilms. In particular, the extracellular matrix (ECM) of Candida biofilm plays a multifaceted role and therefore may be considered as a highly attractive target to combat biofilm-related infectious diseases...
October 21, 2016: Journal of Applied Microbiology
Stefan Grob, Ueli Grossniklaus
Nuclear organization and higher-order chromosome structure in interphase nuclei are thought to have important effects on fundamental biological processes, including chromosome condensation, replication, and transcription. Until recently, however, nuclear organization could only be analyzed microscopically. The development of chromatin conformation capture (3C)-based techniques now allows a detailed look at chromosomal architecture from the level of individual loci to the entire genome. Here we provide a robust Hi-C protocol, allowing the analysis of nuclear organization in nuclei from different wild-type and mutant plant tissues...
2017: Methods in Molecular Biology
Jong Wha J Joo, Eun Yong Kang, Elin Org, Nick Furlotte, Brian Parks, Farhad Hormozdiari, Aldons J Lusis, Eleazar Eskin
A typical GWAS tests correlation between a single phenotype and each genotype one at a time. However, single phenotype analysis might miss unmeasured aspects of complex biological networks. Analyzing many phenotypes simultaneously may increase the power to capture these unmeasured aspects and detect more variants. Several multivariate approaches aim to detect variants related to more than one phenotype, but these current approaches do not consider the effects of population structure. As a result, these approaches may result in a significant amount of false positive identifications...
October 21, 2016: Genetics
William R Pitchers, Savvas J Constantinou, Mauricio Losilla, Jason R Gallant
Electric fish have served as a model system in biology since the 18th century, providing deep insight into the nature of bioelectrogenesis, the molecular structure of the synapse, and brain circuitry underlying complex behavior. Neuroethologists have collected extensive phenotypic data that span biological levels of analysis from molecules to ecosystems. This phenotypic data, together with genomic resources obtained over the past decades, have motivated new and exciting hypotheses that position the weakly electric fish model to address fundamental 21(st) century biological questions...
October 18, 2016: Journal of Physiology, Paris
Isaac Garrido-Benavent, Sergio Pérez-Ortega, Asunción de Los Ríos
Symbiotic associations between green algae (Chlorophyta) and fungi give rise to morphologically and eco-physiologically distinct entities, or so-called, lichens. In one of the most peculiar of these associations, the partners are species of the macroscopic genus Prasiola (Trebouxiophyceae) and the ascomycete Mastodia tessellata (Verrucariaceae). This is the only known case of a lichen symbiosis involving a foliose green alga. Despite intense research targeted at understanding the biology of this particular association, little is known about the genetic variability of its symbionts...
October 18, 2016: Molecular Phylogenetics and Evolution
V Rougeron, T De Meeûs, A-L Bañuls
One key process of the life cycle of pathogens is their mode of reproduction. Indeed, this fundamental biological process conditions the multiplication and the transmission of genes and thus the propagation of diseases in the environment. Reproductive strategies of protozoan parasites have been a subject of debate for many years, principally due to the difficulty in making direct observations of sexual reproduction (i.e. genetic recombination). Traditionally, these parasites were considered as characterized by a preeminent clonal structure...
October 18, 2016: Infection, Genetics and Evolution
Florian Graef, Branko Vukosavljevic, Jean-Philippe Michel, Marius Wirth, Oliver Ries, Chiara De Rossi, Maike Windbergs, Véronique Rosilio, Christian Ducho, Sarah Gordon, Claus-Michael Lehr
Gram-negative bacteria possess a unique and complex cell envelope, composed of an inner and outer membrane separated by an intermediate cell wall-containing periplasm. This tripartite structure acts intrinsically as a significant biological barrier, often limiting the permeation of anti-infectives, and so preventing such drugs from reaching their target. Furthermore, identification of the specific permeation-limiting envelope component proves difficult in the case of many anti-infectives, due to the challenges associated with isolation of individual cell envelope structures in bacterial culture...
October 18, 2016: Journal of Controlled Release: Official Journal of the Controlled Release Society
Jie Gao, Narasimha Midde, Jun Zhu, Alvin V Terry, Campbell McInnes, James M Chapman
Using molecular modeling and rationally designed structural modifications, the multi-target structure-activity relationship for a series of ranitidine analogs has been investigated. Incorporation of a variety of isosteric groups indicated that appropriate aromatic moieties provide optimal interactions with the hydrophobic and π-π interactions with the peripheral anionic site of the AChE active site. The SAR of a series of cyclic imides demonstrated that AChE inhibition is increased by additional aromatic rings, where 1,8-naphthalimide derivatives were the most potent analogs and other key determinants were revealed...
October 6, 2016: Bioorganic & Medicinal Chemistry Letters
Ramu Guda, Sirassu Narsimha, Ramavath Babu, Srujana Muthadi, Harikiran Lingabathula, Rambabu Palabindela, Narsimha Reddy Yellu, Girijesh Kumar, Mamatha Kasula
A series of novel substituted hydrazono indolo[2,1-b]quinazoline-6,12-dione analogues have been synthesized and screened for their in vitro cytotoxic and antimicrobial activities. Among all the target compounds, 3c exhibited the most potent inhibitory activity against three cancer cell lines MCF-7, A549, HeLa with IC50 values 07.14±1.285μM, 09.18±0.968μM and 10.57±0.581μM respectively, while maintaining low toxicity towards non-cancer originated cell line, HEK-293. The detailed studies about molecular interactions with probable target protein indoleamine 2,3-dioxygenase (IDO1) were done by using docking simulations...
October 5, 2016: Bioorganic & Medicinal Chemistry Letters
Yangyang Gan, Quanqing Zhang, Yajing Chen, Yiman Zhao, Zhichao Xiong, Lingyi Zhang, Weibing Zhang
Highly sensitive and selective enrichment of endogenous peptides or proteins from complex bio-system takes a significant important place to the proteomic. In this work, a unique Fe3O4@2SiO2@mSiO2-C nanomaterial was synthesized, contributing to the separation and enrichment of low concentration peptides from complex mixture. The highly ordered mesoporous carbon structure render the nanospheres with unique properties of strongly connected pore channels, strong hydrophobic properties, high specific surface area (254...
December 1, 2016: Talanta
Huifang Zhang, Sheng Hu, Dandan Song, Hui Xu
In this paper, a novel polydopamine modified polystyrene/graphene electrospun nanofiber membrane (PS/G@PDA) was fabricated on the surface of filter paper and used for thin film microextraction (TFME) for the first time. Benefiting from the hydrophilic polydopamine (PDA) coating and the porous fibrous structure, the PS/G@PDA membrane exhibited large surface area, high extraction efficiency, rapid extraction equilibrium, special selectivity and excellent biocompatibility. A thin film microextraction-high performance liquid chromatography method was developed and applied for the analysis of six aldehyde metabolites in human urine samples...
November 2, 2016: Analytica Chimica Acta
Jiankun Cao, Hongyuan Yan, Shigang Shen, Ligai Bai, Haiyan Liu, Fengxia Qiao
New hydrophilic molecularly imprinted melamine-urea-formaldehyde monolithic resin (MIMR) is synthesized using dopamine hydrochloride as a dummy template via in-situ polymerization directly within pipette tips and it presents special molecular recognition to plant growth regulators in aqueous matrices. Hydrophilic groups (such as hydroxyl groups, imino groups, and amino groups) can be introduced into MIMR by melamine- urea-formaldehyde resin, which make MIMR materials compatible with aqueous media and show their specific molecular recognition in aqueous sample solutions...
November 2, 2016: Analytica Chimica Acta
Emilia Fisicaro, Carlotta Compari, Franco Bacciottini, Laura Contardi, Erika Pongiluppi, Nadia Barbero, Guido Viscardi, Pierluigi Quagliotto, Gaetano Donofrio, Marie Pierre Krafft
Biological and thermodynamic properties of a new homologous series of highly fluorinated bispyridinium cationic gemini surfactants, differing in the length of the spacer bridging the pyridinium polar heads in 1,1' position, are reported for the first time. Interestingly, gene delivery ability is closely associated with the spacer length due to a structural change of the molecule in solution. This conformation change is allowed when the spacer reaches the right length, and it is suggested by the trends of the apparent and partial molar enthalpies vs molality...
October 15, 2016: Journal of Colloid and Interface Science
Bin Tang, Yanmei Huang, Hongqin Yang, Peixiao Tang, Hui Li
As a natural dietary polyphenol, 3,4,5-tri-O-caffeoylquinic acid (3,4,5-triCQA) exhibits numerous stronger pharmacological activities than that of its analogues. Studies on interaction between 3,4,5-triCQA and protein are very helpful for understanding the mechanism of these enhanced biological functions. In this study, (1)H saturation transfer difference NMR ((1)H STD-NMR) combined with multi-spectroscopy were used to probe the interaction of 3,4,5-triCQA with human serum albumin (HSA). Both qualitative and quantitative (1)H STD-NMR indicated that 3,4,5-triCQA can specifically bind to HSA at the favored Sudlow's site II with caffeoyl groups as the main recognizable moiety...
October 17, 2016: Journal of Photochemistry and Photobiology. B, Biology
Milka Kostic
Every month the editors of Cell Chemical Biology bring you highlights of the most recent chemical biology literature. Our October 2016 selection includes systematic structural, biochemical, and cellular characterization of B-RAF inhibitors; connecting bacterial transporters with their physiologically relevant ligands; and rewiring yeast metabolism for industrial scale production of isoprenoids.
October 20, 2016: Cell Chemical Biology
J J Paredes, Nelly Andarawis-Puri
Tendon injuries, known as tendinopathies, are common musculoskeletal injuries that affect a wide range of the population. Canonical tendon healing is characterized by fibrosis, scar formation, and the loss of tissue mechanical and structural properties. Understanding the regenerative tendon environment is an area of increasing interest in the field of musculoskeletal research. Previous studies have focused on utilizing individual elements from the fields of biomechanics, developmental biology, cell and growth factor therapy, and tissue engineering in an attempt to develop regenerative tendon therapeutics...
October 21, 2016: Annals of the New York Academy of Sciences
Robert J Gillespie, Derrick M Knapik, Ozan Akkus
Rotator cuff injuries are common in both young and elderly patients. Despite improvements in instrumentation and surgical techniques, the failure rates following tendon reconstruction remain unacceptably high. To improve outcomes, graft patches have been developed to provide mechanical strength and to furnish a scaffold for biologic growth across the delicate tendon-bone junction. Although no patch effectively re-creates the structured, highly organized system of prenatal tendon development, augmenting rotator cuff repair may help restore native tendon-to-bone attachment while reproducing the mechanical and biologic properties of native tendon...
October 20, 2016: Journal of the American Academy of Orthopaedic Surgeons
Nina Holland
Environmental research and public health in the 21st century face serious challenges such as increased air pollution and global warming, widespread use of potentially harmful chemicals including pesticides, plasticizers, and other endocrine disruptors, and radical changes in nutrition and lifestyle typical of modern societies. In particular, exposure to environmental and occupational toxicants may contribute to the occurrence of adverse birth outcomes, neurodevelopmental deficits, and increased risk of cancer and other multifactorial diseases such as diabetes and asthma...
October 21, 2016: Reviews on Environmental Health
Jesús Ignacio Mendieta-Moreno, Daniel G Trabada, Jesus Mendieta, James P Lewis, Paulino Gómez-Puertas, Jose Ortega
The absorption of ultraviolet radiation by DNA may result in harmful genetic lesions that affect DNA replication and transcription, ultimately causing mutations, cancer and/or cell death. We analyze the most abundant photochemical reaction in DNA, the cyclobutane thymine dimer, using hybrid quantum mechanics / molecular mechanics (QM/MM) techniques and QM/MM nonadiabatic molecular dynamics. We find that, due to its double helix structure, DNA presents a free energy barrier between non-reactive and reactive conformations leading to the photolesion...
October 21, 2016: Journal of Physical Chemistry Letters
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