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Dunja Mrdjen, Anto Pavlovic, Felix J Hartmann, Bettina Schreiner, Sebastian G Utz, Brian P Leung, Iva Lelios, Frank L Heppner, Jonathan Kipnis, Doron Merkler, Melanie Greter, Burkhard Becher
No abstract text is available yet for this article.
March 20, 2018: Immunity
Haide Chen, Mengmeng Jiang, Lei Xiao, He Huang
Human pluripotent stem cells (hPSCs)/OP9 coculture system is a widely used hematopoietic differentiation approach. The limited understanding of this process leads to its low efficiency. Thus, we used single-cell qPCR to reveal the gene expression profiles of individual CD34+ cells from different stages of differentiation. According to the dynamic gene expression of hematopoietic transcription factors, we overexpressed specific hematopoietic transcription factors (Gata2, Lmo2, Etv2, ERG, and SCL) at an early stage of hematopoietic differentiation...
March 15, 2018: Brazilian Journal of Medical and Biological Research, Revista Brasileira de Pesquisas Médicas e Biológicas
Yanting Luo, Jianlin He, Xiguang Xu, Ming-An Sun, Xiaowei Wu, Xuemei Lu, Hehuang Xie
Embryonic stem cells (ESCs) consist of a population of self-renewing cells displaying extensive phenotypic and functional heterogeneity. Research towards the understanding of the epigenetic mechanisms underlying the heterogeneity among ESCs is still in its initial stage. Key issues, such as how to identify cell-subset specifically methylated loci and how to interpret the biological meanings of methylation variations remain largely unexplored. To fill in the research gap, we implemented a computational pipeline to analyze single-cell methylome and to perform an integrative analysis with single-cell transcriptome data...
March 2018: PLoS Computational Biology
Luna Jammal, Ben Whalley, Edi Barkai
Training rats in a complex olfactory discrimination task results in acquisition of 'rule learning' (learning how to learn), a term describing the capability to perform the task superbly. Such rule learning results in strengthening of both excitatory and inhibitory synaptic connections between neurons in the piriform cortex. Moreover, intrinsic excitability is also enhanced throughout the pyramidal neuron population. Surprisingly, the cortical network retains its stability under these long-term modifications...
March 21, 2018: Journal of Neurophysiology
Abha Belorkar, Rajanikanth Vadigepalli, Limsoon Wong
BACKGROUND: Transcriptomic datasets often contain undeclared heterogeneity arising from biological variation such as diversity of disease subtypes, treatment subgroups, time-series gene expression, nested experimental conditions, as well as technical variation due to batch effects, platform differences in integrated meta-analyses, etc. However, current analysis approaches are primarily designed to handle comparisons between experimental conditions represented by homogeneous samples, thus precluding the discovery of underlying subphenotypes...
March 19, 2018: BMC Systems Biology
Adam Reichenthal, Mor Ben-Tov, Ronen Segev
Many studies have yielded valuable knowledge on the early visual system but it is biased since the studies have focused on terrestrial mammals alone. Here, to better account for visual systems in different environments and animal classes, we studied the structure of early visual processing in the archerfish which harnesses its extreme visual ability to hunt by shooting water jets at prey hanging on vegetation above the water. Thus, the archerfish provides a unique opportunity to study visual processing in a vertebrate which is an expert vision-guided predator with a very different brain structure than mammals...
2018: Frontiers in Neural Circuits
Meeri Eeva-Liisa Mäkinen, Laura Ylä-Outinen, Susanna Narkilahti
The electrical activity of the brain arises from single neurons communicating with each other. However, how single neurons interact during early development to give rise to neural network activity remains poorly understood. We studied the emergence of synchronous neural activity in human pluripotent stem cell (hPSC)-derived neural networks simultaneously on a single-neuron level and network level. The contribution of gamma-aminobutyric acid (GABA) and gap junctions to the development of synchronous activity in hPSC-derived neural networks was studied with GABA agonist and antagonist and by blocking gap junctional communication, respectively...
2018: Frontiers in Cellular Neuroscience
Michael F Sweeney, Carlos Sonnenschein, Ana M Soto
Background: Three-dimensional cultures of mammary epithelial cells allow for biologically-relevant studies of the development of the mammary gland in rodents and humans under normal and pathological conditions, like carcinogenesis. Under these conditions, mammotropic hormones play significant roles in tissue morphogenesis. Therefore, a system that recreates the normal, hormonally responsive epithelium would be a valuable tool to study the normal state and its transition to carcinogenesis...
2018: Cancer Cell International
Victoria Shabardina, Tabea Kischka, Hanna Kmita, Yutaka Suzuki, Wojciech Makałowski
Amoebozoans are in many aspects interesting research objects, as they combine features of single-cell organisms with complex signaling and defense systems, comparable to multicellular organisms. Acanthamoeba castellanii is a cosmopolitan species and developed diverged feeding abilities and strong anti-bacterial resistance; Entamoeba histolytica is a parasitic amoeba, who underwent massive gene loss and its genome is almost twice smaller than that of A. castellanii . Nevertheless, both species prosper, demonstrating fitness to their specific environments...
2018: International Journal of Biological Sciences
Calvin K Lee, Jaime de Anda, Amy E Baker, Rachel R Bennett, Yun Luo, Ernest Y Lee, Joshua A Keefe, Joshua S Helali, Jie Ma, Kun Zhao, Ramin Golestanian, George A O'Toole, Gerard C L Wong
Using multigenerational, single-cell tracking we explore the earliest events of biofilm formation by Pseudomonas aeruginosa During initial stages of surface engagement (≤20 h), the surface cell population of this microbe comprises overwhelmingly cells that attach poorly (∼95% stay <30 s, well below the ∼1-h division time) with little increase in surface population. If we harvest cells previously exposed to a surface and direct them to a virgin surface, we find that these surface-exposed cells and their descendants attach strongly and then rapidly increase the surface cell population...
March 20, 2018: Proceedings of the National Academy of Sciences of the United States of America
Xin-Xin Yu, Wei-Lin Qiu, Liu Yang, Lin-Chen Li, Yu-Wei Zhang, Cheng-Ran Xu
Pancreatic endocrine lineages are derived from pancreatic progenitors that undergo a cell fate transition requiring a switch from low to high Ngn3 expression. However, the underlying chromatin regulatory mechanisms are unclear. Here, we performed epigenomic analysis of gene regulatory loci featuring histone marks in cells with low or high level of Ngn3 expression. In combination with transcriptomic analysis, we discovered that in Ngn3-high cells, the removal of H3K27me3 was associated with the activation of key transcription factors and the establishment of primed and active enhancers...
March 20, 2018: Development
Lamini Ouedraogo, C J den Otter
Action potentials from individual cells were recorded from antennae (funiculi) of living tsetse flies,Glossina p. palpalis and Glossina f. fuscipesusing a "surface-contact" recording technique. Stimuli were vapours of 1-octen-3-ol, acetone and 3-methylphenol. Of the 101 and 128 olfactory cells tested for their sensitivity to odour stimuli inG. p. palpalisandG. f. fuscipes, respectively, the majority (83 and 77%) were activated by more than one chemical. The numbers of these "generalist" cells were 20 and 15% higher in females than in males...
March 17, 2018: Journal of Insect Physiology
Vasudha C Shukla, Tai-Rong Kuang, Abirami Senthilvelan, Natalia Higuita-Castro, Silvia Duarte-Sanmiguel, Samir N Ghadiali, Daniel Gallego-Perez
Recent cancer research has more strongly emphasized the biophysical aspects of tumor development, progression, and microenvironment. In addition to genetic modifications and mutations in cancer cells, it is now well accepted that the physical properties of cancer cells such as stiffness, electrical impedance, and refractive index vary with tumor progression and can identify a malignant phenotype. Moreover, cancer heterogeneity renders population-based characterization techniques inadequate, as individual cellular features are lost in the average...
March 17, 2018: Trends in Biotechnology
Amit A Upadhyay, Robert C Kauffman, Amber N Wolabaugh, Alice Cho, Nirav B Patel, Samantha M Reiss, Colin Havenar-Daughton, Reem A Dawoud, Gregory K Tharp, Iñaki Sanz, Bali Pulendran, Shane Crotty, F Eun-Hyung Lee, Jens Wrammert, Steven E Bosinger
B cells play a critical role in the immune response by producing antibodies, which display remarkable diversity. Here we describe a bioinformatic pipeline, BALDR (BCR Assignment of Lineage using De novo Reconstruction) that accurately reconstructs the paired heavy and light chain immunoglobulin gene sequences from Illumina single-cell RNA-seq data. BALDR was accurate for clonotype identification in human and rhesus macaque influenza vaccine and simian immunodeficiency virus vaccine induced vaccine-induced plasmablasts and naïve and antigen-specific memory B cells...
March 20, 2018: Genome Medicine
Sara Cristinelli, Angela Ciuffi
Single-cell analyses allow uncovering cellular heterogeneity, not only per se, but also in response to viral infection. Similarly, single cell transcriptome analyses (scRNA-Seq) can highlight specific signatures, identifying cell subsets with particular phenotypes, which are relevant in the understanding of virus-host interactions.
March 17, 2018: Current Opinion in Virology
Nurgul Atmaca, Sevket Arikan, Dinc Essiz, Hakan Kalender, Ozkan Simsek, Fatih Sultan Bilmen, Ruhi Kabakci
Mancozeb, metalaxyl and tebucanazole are widely used pesticides in agriculture and industry to treat plant pathogenic fungi. Livestock may be exposed to such substances by consuming contaminated plants. The present study was designed to evaluate the effects of these three fungicides on bovine luteal cell steroidogenesis. Luteal slices from mid-cycle corpus luteum were dissociated into single cell suspension in aerated (O2 ) culture media (DMEM/F12) by enzymatic digestion. The cells were incubated in newborn calf serum (10%) for 18 h and then with serum-free media containing mancozeb (0...
March 13, 2018: Environmental Toxicology and Pharmacology
Li Bao, Zhaoyang Qian, Maria B Lyng, Ling Wang, Yuan Yu, Ting Wang, Xiuqing Zhang, Huanming Yang, Nils Brünner, Jun Wang, Henrik J Ditzel
Single cancer cell sequencing studies currently use randomly-selected cells, limiting correlations between genomic aberrations, morphology and spatial localization. We laser-captured microdissected single cells from morphologically-distinct areas of primary breast cancer and corresponding lymph node metastasis and performed whole-exome or deep-target sequencing of greater than 100 such cells. Two major subclones co-existed in different areas of the primary tumor, and the lymph node metastasis originated from a minor subclone in the invasive front of the primary tumor with additional copy number changes including 8q gain, but no additional point mutations in driver genes...
March 15, 2018: Journal of Clinical Investigation
Li Cui, Kai Yang, Hong-Zhe Li, Han Zhang, Jian-Qiang Su, Maria Paraskevaidi, Francis Luke Martin, Bin Ren, Yong-Guan Zhu
Nitrogen (N) fixation is the conversion of inert nitrogen gas (N2) to bioavailable N essential for all forms of life. N2-fixing microorganisms (diazotrophs), which play a key role in global N cycling, remain largely obscure because a large majority are uncultured. Direct probing of active diazotrophs in the environment is still a major challenge. Herein, a novel culture-independent single-cell approach combining resonance Raman (RR) spectroscopy with 15N2 stable isotope probing (SIP) was developed to discern N2-fixing bacteria in a complex soil community...
March 20, 2018: Analytical Chemistry
Xiaoping Su, Kuiqing Cui, Shanshan Du, Hongli Li, Fenghua Lu, Deshun Shi, Qingyou Liu
Myostatin (MSTN), a protein encoded by growth differentiation factor 8 (GDF8), is primarily expressed in skeletal muscle and negatively regulates the development and regeneration of muscle. Accordingly, myostatin-deficient animals exhibit a double-muscling phenotype. The CRISPR/Cas9 system has proven to be an efficient genome-editing tool and has been applied to gene modification in cells from many model organisms such as Drosophila melanogaster, zebrafish, mouse, rat, sheep, and human. Here, we edited the GDF8 gene in fibroblasts and embryos of Debao pig and swamp buffalo using the CRISPR/Cas9 system...
March 19, 2018: In Vitro Cellular & Developmental Biology. Animal
Keunsub Lee, Kan Wang
During the last decade, small noncoding RNAs (ncRNAs) have emerged as essential post-transcriptional regulators in bacteria. Nearly all important physiological and stress responses are modulated by ncRNA regulators, such as riboswitches, trans-acting small RNAs (sRNAs), and cis-antisense RNAs. Recently, three RNA-seq studies identified a total of 1534 candidate ncRNAs from Agrobacterium tumefaciens, a pathogen and biotechnology tool for plants. Only a few ncRNAs have been functionally characterized in A. tumefaciens, and some of them appear to be involved in virulence...
March 20, 2018: Current Topics in Microbiology and Immunology
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