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https://www.readbyqxmd.com/read/28938749/the-testicular-transcriptome-associated-with-spermatogonia-differentiation-initiated-by-gonadotrophin-stimulation-in-the-juvenile-rhesus-monkey-macaca-mulatta
#1
Suresh Ramaswamy, William H Walker, Paula Aliberti, Rahil Sethi, Gary R Marshall, Alyxzandria Smith, Seyedmehdi Nourashrafeddin, Alicia Belgorosky, Uma R Chandran, Mark P Hedger, Tony M Plant
STUDY QUESTION: What is the genetic landscape within the testis of the juvenile rhesus monkey (Macaca mulatta) that underlies the decision of undifferentiated spermatogonia to commit to a pathway of differentiation when puberty is induced prematurely by exogenous LH and FSH stimulation? SUMMARY ANSWER: Forty-eight hours of gonadotrophin stimulation of the juvenile monkey testis resulted in the appearance of differentiating B spermatogonia and the emergence of 1362 up-regulated and 225 down-regulated testicular mRNAs encoding a complex network of proteins ranging from enzymes regulating Leydig cell steroidogenesis to membrane receptors, and from juxtacrine and paracrine factors to transcriptional factors governing spermatogonial stem cell fate...
October 1, 2017: Human Reproduction
https://www.readbyqxmd.com/read/28938718/looking-back-forward-looking
#2
Scott C Edmunds, Nicole A Nogoy, Hans Zauner, Peter Li, Christopher I Hunter, Xiao Si Zhe, Laurie Goodman
GigaScience is now 5 years old, having been launched at the 2012 Intelligent Systems for Molecular Biology conference. Anyone who has attended what is the largest computational biology conference since then has had the opportunity to join us for each birthday celebration-and receive 1 of our fun T-shirts as a party prize. Since launching, we have pushed our agenda of openness, transparency, reproducibility, and reusability. Here, we look back at our first 5 years and what we have done to forward our open science goals in scientific publishing...
September 1, 2017: GigaScience
https://www.readbyqxmd.com/read/28938616/identification-of-potential-cancer-related-pseudogenes-in-lung-adenocarcinoma-based-on-cerna-hypothesis
#3
Yunzhen Wei, Zhiqiang Chang, Cheng Wu, Yinling Zhu, Kun Li, Yan Xu
Pseudogenes are initially regarded as non-functional genomic fossils resulted from inactivating gene mutations during evolution. Far from being silent, pseudogenes are proved to regulate the expression of protein-coding genes through function as microRNA sponge in vivo. The aim of our study was to propose an integrative systems biology approach to identify disease pseudogenes base on competitive endogenous RNA (ceRNA) hypothesis. Here, we applied our method to lung adenocarcinoma (LUAD) RNASeq data from TCGA and identified 33 candidate pseudogenes...
August 29, 2017: Oncotarget
https://www.readbyqxmd.com/read/28938599/a-pathways-based-prediction-model-for-classifying-breast-cancer-subtypes
#4
Tong Wu, Yunfeng Wang, Ronghui Jiang, Xinliang Lu, Jiawei Tian
Breast cancer is highly heterogeneous and is classified into four subtypes characterized by specific biological traits, treatment responses, and clinical prognoses. We performed a systemic analysis of 698 breast cancer patient samples from The Cancer Genome Atlas project database. We identified 136 breast cancer genes differentially expressed among the four subtypes. Based on unsupervised clustering analysis, these 136 core genes efficiently categorized breast cancer patients into the appropriate subtypes. Functional enrichment based on Kyoto Encyclopedia of Genes and Genomes analysis identified six functional pathways regulated by these genes: JAK-STAT signaling, basal cell carcinoma, inflammatory mediator regulation of TRP channels, non-small cell lung cancer, glutamatergic synapse, and amyotrophic lateral sclerosis...
August 29, 2017: Oncotarget
https://www.readbyqxmd.com/read/28938213/combination-of-aquifer-thermal-energy-storage-and-enhanced-bioremediation-biological-and-chemical-clogging
#5
Zhuobiao Ni, Pauline van Gaans, Huub Rijnaarts, Tim Grotenhuis
Interest in the combination concept of aquifer thermal energy storage (ATES) and enhanced bioremediation has recently risen due to the demand for both renewable energy technology and sustainable groundwater management in urban areas. However, the impact of enhanced bioremediation on ATES is not yet clear. Of main concern is the potential for biological clogging which might be enhanced and hamper the proper functioning of ATES. On the other hand, more reduced conditions in the subsurface by enhanced bioremediation might lower the chance of chemical clogging, which is normally caused by Fe(III) precipitate...
September 19, 2017: Science of the Total Environment
https://www.readbyqxmd.com/read/28938182/the-genetic-epidemiology-of-substance-use-disorder-a-review
#6
REVIEW
Elizabeth C Prom-Wormley, Jane Ebejer, Danielle M Dick, M Scott Bowers
BACKGROUND: Substance use disorder (SUD) remains a significant public health issue. A greater understanding of how genes and environment interact to regulate phenotypes comprising SUD will facilitate directed treatments and prevention. METHODS: The literature studying the neurobiological correlates of SUD with a focus on the genetic and environmental influences underlying these mechanisms was reviewed. Results from twin/family, human genetic association, gene-environment interaction, epigenetic literature, phenome-wide association studies are summarized for alcohol, nicotine, cannabinoids, cocaine, and opioids...
August 1, 2017: Drug and Alcohol Dependence
https://www.readbyqxmd.com/read/28938130/learning-in-the-machine-the-symmetries-of-the-deep-learning-channel
#7
Pierre Baldi, Peter Sadowski, Zhiqin Lu
In a physical neural system, learning rules must be local both in space and time. In order for learning to occur, non-local information must be communicated to the deep synapses through a communication channel, the deep learning channel. We identify several possible architectures for this learning channel (Bidirectional, Conjoined, Twin, Distinct) and six symmetry challenges: (1) symmetry of architectures; (2) symmetry of weights; (3) symmetry of neurons; (4) symmetry of derivatives; (5) symmetry of processing; and (6) symmetry of learning rules...
September 5, 2017: Neural Networks: the Official Journal of the International Neural Network Society
https://www.readbyqxmd.com/read/28938122/genome-regulation-by-polycomb-and-trithorax-70-years-and-counting
#8
REVIEW
Bernd Schuettengruber, Henri-Marc Bourbon, Luciano Di Croce, Giacomo Cavalli
Polycomb (PcG) and Trithorax (TrxG) group proteins are evolutionarily conserved chromatin-modifying factors originally identified as part of an epigenetic cellular memory system that maintains repressed or active gene expression states. Recently, they have been shown to globally control a plethora of cellular processes. This functional diversity is achieved by their ability to regulate chromatin at multiple levels, ranging from modifying local chromatin structure to orchestrating the three-dimensional organization of the genome...
September 21, 2017: Cell
https://www.readbyqxmd.com/read/28937978/a-new-discrete-dynamic-model-of-aba-induced-stomatal-closure-predicts-key-feedback-loops
#9
Réka Albert, Biswa R Acharya, Byeong Wook Jeon, Jorge G T Zañudo, Mengmeng Zhu, Karim Osman, Sarah M Assmann
Stomata, microscopic pores in leaf surfaces through which water loss and carbon dioxide uptake occur, are closed in response to drought by the phytohormone abscisic acid (ABA). This process is vital for drought tolerance and has been the topic of extensive experimental investigation in the last decades. Although a core signaling chain has been elucidated consisting of ABA binding to receptors, which alleviates negative regulation by protein phosphatases 2C (PP2Cs) of the protein kinase OPEN STOMATA 1 (OST1) and ultimately results in activation of anion channels, osmotic water loss, and stomatal closure, over 70 additional components have been identified, yet their relationships with each other and the core components are poorly elucidated...
September 22, 2017: PLoS Biology
https://www.readbyqxmd.com/read/28937947/wastewater-treatment-by-means-of-thermophilic-aerobic-membrane-reactors-respirometric-tests-and-numerical-models-for-determination-of-stoichiometric-kinetic-parameters
#10
Maria Cristina Collivignarelli, Giorgio Bertanza, Alessandro Abbà, Vincenzo Torretta, Ioannis Anastasios Katsoyiannis
The present work considers the pollution abatement of wastewaters, the efficiency of which is depending on stringent verification of the performance of wastewater treatment plants. This is very important especially given that eExisting wastewater/aqueous waste treatment plants often need to be upgraded in order to improve their performance. The satisfactory operation of biological treatment plants requires appropriate monitoring, and respirometric techniques are needed to determine the kinetic parameters that regulate biological processes...
September 22, 2017: Environmental Technology
https://www.readbyqxmd.com/read/28937916/nanoparticles-for-advanced-photodynamic-therapy-of-cancer
#11
Heidi Abrahamse, Cherie Ann Kruger, Sania Kadanyo, Ajay Mishra
The world widespread rise in cancer incidence has caused an increase in the demand for effective and safe materials for treatment. One of the most prevalent forms of treatment for cancer is photodynamic therapy (PDT), which is seen as an alternative to radiotherapy, as well as chemotherapy. In more recent years, researchers are exploring new nanotechnology-based strategies to improve the effectiveness of PDT. OBJECTIVE: The objective of this review is to explore the current trends and research findings associated with PDT and the development of nanotechnology as treatment modality for cancer...
September 21, 2017: Photomedicine and Laser Surgery
https://www.readbyqxmd.com/read/28937829/nonlinearity-coherence-and-complexity-biophysical-aspects-related-to-health-and-disease
#12
Alberto Foletti, Larissa Brizhik
Biological organisms are complex open dissipative systems whose dynamical stability is sustained due to the exchange of matter, energy and information. Dynamical stability occurs through a number of mechanisms that sustain efficient adaptive dynamics. Such properties of living matter can be the consequence of a self-consistent state of matter and electromagnetic field (EMF). Based on the soliton model of charge transport in redox processes, we describe a possible mechanism of the origin of endogenous EMF and coherence...
September 22, 2017: Electromagnetic Biology and Medicine
https://www.readbyqxmd.com/read/28937819/should-i-change-or-should-i-go-phenotypic-plasticity-and-matching-habitat-choice-in-the-adaptation-to-environmental-heterogeneity
#13
Pim Edelaar, Roger Jovani, Ivan Gomez-Mestre
It can be challenging for organisms to achieve a good match between their phenotypic characteristics and environmental requirements that vary in space and time. The evolution of adaptive phenotypes can result from genetic differentiation at the population level. Individuals, however, could also change their phenotype (adaptive plasticity) or select an environment because it matches with their phenotype (matching habitat choice). It is poorly known under which conditions these different solutions to environmental heterogeneity evolve and whether they operate together...
October 2017: American Naturalist
https://www.readbyqxmd.com/read/28937748/bio-optics-and-bio-inspired-optical-materials
#14
Sirimuvva Tadepalli, Joseph M Slocik, Maneesh K Gupta, Rajesh R Naik, Srikanth Singamaneni
Through the use of the limited materials palette, optimally designed micro- and nanostructures, and tightly regulated processes, nature demonstrates exquisite control of light-matter interactions at various length scales. In fact, control of light-matter interactions is an important element in the evolutionary arms race and has led to highly engineered optical materials and systems. In this review, we present a detailed summary of various optical effects found in nature with a particular emphasis on the materials and optical design aspects responsible for their optical functionality...
September 22, 2017: Chemical Reviews
https://www.readbyqxmd.com/read/28937734/discovery-of-oligonucleotide-signaling-mediated-by-crispr-associated-polymerases-solves-two-puzzles-but-leaves-an-enigma
#15
Eugene V Koonin, Kira S Makarova
The signature component of type III CRISPR-Cas systems is the Cas10 protein that consists of two Palm domains homologous to those of DNA and RNA polymerases, and nucleotide cyclases, and an HD nuclease domain. However, until very recently, the activity of the Palm domains and their role in CRISPR function have not been experimentally established. Most of the type III CRISPR-Cas systems and some type I systems also encompass proteins containing the CARF (CRISPR-associated Rossmann fold) domain that has been predicted to regulate CRISPR functions via nucleotide binding but its function in CRISPR-Cas remained obscure...
September 22, 2017: ACS Chemical Biology
https://www.readbyqxmd.com/read/28937692/bdnf-at-the-synapse-why-location-matters
#16
M Song, K Martinowich, F S Lee
Neurotrophic factors, a family of secreted proteins that support the growth, survival and differentiation of neurons, have been intensively studied for decades due to the powerful and diverse effects on neuronal physiology, as well as their therapeutic potential. Such efforts have led to a detailed understanding on the molecular mechanisms of neurotrophic factor signaling. One member, brain-derived neurotrophic factor (BDNF) has drawn much attention due to its pleiotropic roles in the central nervous system and implications in various brain disorders...
October 2017: Molecular Psychiatry
https://www.readbyqxmd.com/read/28937361/multiplex-detection-of-pancreatic-cancer-biomarkers-using-a-sers-based-immunoassay
#17
Nariman Banaei, Anne Foley, Jean Marie Houghton, Yubing Sun, Byung Kim
Early diagnosis of pancreatic cancer is critical to reduce the mortality rate of this disease. Current biological analysis approaches cannot robustly detect several low abundance pancreatic cancer biomarkers in sera, limiting the clinical application of these biomarkers. This study demonstrates a novel system for multiplex detection of pancreatic biomarkers CA19-9, MMP7 and MUC4 in sera samples with high sensitivity. Measuring the levels of these biomarkers in pancreatic cancer patients, pancreatitis patients, and healthy individuals reveals the unique expression pattern of these markers in pancreatic cancer patients, suggesting the great potential of using this approach for early diagnostics of pancreatic cancers...
September 22, 2017: Nanotechnology
https://www.readbyqxmd.com/read/28937298/probing-the-toxicity-of-nanoparticles-a-unified-in-silico-machine-learning-model-based-on-perturbation-theory
#18
Riccardo Concu, Valeria V Kleandrova, Alejandro Speck-Planche, M Natália D S Cordeiro
Nanoparticles (NPs) are part of our daily life, having a wide range of applications in engineering, physics, chemistry, and biomedicine. However, there are serious concerns regarding the harmful effects that NPs can cause to the different biological systems and their ecosystems. Toxicity testing is an essential step for assessing the potential risks of the NPs, but the experimental assays are often very expensive and usually too slow to flag the number of NPs that may cause adverse effects. In silico models centered on quantitative structure-activity/toxicity relationships (QSAR/QSTR) are alternative tools that have become valuable supports to risk assessment, rationalizing the search for safer NPs...
September 22, 2017: Nanotoxicology
https://www.readbyqxmd.com/read/28937214/injectable-thermoresponsive-hydrogel-formed-by-alginate-g-poly-n-isopropylacrylamide-releasing-doxorubicin-encapsulated-micelles-as-smart-drug-delivery-system
#19
Min Liu, Xia Song, Yuting Wen, Jing-Ling Zhu, Jun Li
In this work, we have synthesized a thermoresponsive copolymer, alginate-g-poly(N-isopropylacrylamide) (alginate-g-PNIPAAm), by conjugating PNIPAAm to alginate, where PNIPAAm with different molecular weight and narrow molecular weight distribution was synthesized by atomic transfer radical polymerization (ATRP). The copolymer dissolved in water or PBS buffer solution at room temperature, and formed self-assembled micelles with low critical micellization concentrations when temperature increased to above their critical micellization temperatures...
September 22, 2017: ACS Applied Materials & Interfaces
https://www.readbyqxmd.com/read/28937154/structural-basis-of-interstrand-cross-link-repair-by-o-6-alkylguanine-dna-alkyltransferase
#20
Alexey Y Denisov, Francis P McManus, Derek K O'Flaherty, Anne M Noronha, Christopher J Wilds
DNA interstrand cross-links (ICL) are among the most cytotoxic lesions found in biological systems. O(6)-Alkylguanine DNA alkyltransferases (AGTs) are capable of removing alkylation damage from the O(6)-atom of 2'-deoxyguanosine and the O(4)-atom of thymidine. Human AGT (hAGT) has demonstrated the ability to repair an interstrand cross-linked duplex where two O(6)-atoms of 2'-deoxyguanosine were tethered by a butylene (XLGG4) or heptylene (XLGG7) linkage. However, the analogous ICL between the O(4)-atoms of thymidine was found to evade repair...
September 22, 2017: Organic & Biomolecular Chemistry
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